Papers that used NIH HPC Systems resources

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Papers that used Biowulf or Helix resources

If you have published research that has made significant use of these systems, please let us know by sending email to staff@hpc.nih.gov

2018 to date (66 papers)

Molecular dynamics simulations of lipid nanodiscs Pourmousa, M; Pastor, RW; Biochim. Biophys. Acta, DOI://10.1016/j.bbamem.2018.04.015 (2018)
Whole-Exome Sequencing to Identify Rare Variants and Gene Networks that Increase Susceptibility to Scleroderma in African Americans Gourh, P; Remmers, EF; Boyden, SE et al. , DOI://10.1002/art.40541 (2018)
A draft genome sequence for the Ixodes scapularis cell line, ISE6 Miller, JR; Koren, S; Dilley, KA et al. F1000Res, DOI://10.12688/f1000research.13635.1 (2018)
Insulin promoter in human pancreatic β cells contacts diabetes susceptibility loci and regulates genes affecting insulin metabolism Jian, X; Felsenfeld, G; Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1803146115 (2018)

Organization of the core respiratory network: Insights from optogenetic and modeling studies Ausborn, J; Koizumi, H; Barnett, WH et al. PLoS Comput. Biol., DOI://10.1371/journal.pcbi.1006148 (2018)
Interrogating the Functions of PRDM9 Domains in Meiosis Thibault-Sennett, S; Yu, Q; Smagulova, F et al. Genetics, DOI://10.1534/genetics.118.300565 (2018)
Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation Maziarz, M; Pfeiffer, RM; Wan, Y; Gail, MH; Bioinformatics, DOI://10.1093/bioinformatics/bty297 (2018)
ICE1 promotes the link between splicing and nonsense-mediated mRNA decay Baird, TD; Cheng, KC; Chen, YC et al. Elife, DOI://10.7554/eLife.33178 (2018)
Statistical power comparisons at 3T and 7T with a GO / NOGO task Torrisi, S; Chen, G; Glen, D et al. Neuroimage, DOI://10.1016/j.neuroimage.2018.03.071 (2018)
Gcn4 Binding in Coding Regions Can Activate Internal and Canonical 5' Promoters in Yeast Rawal, Y; Chereji, RV; Valabhoju, V et al. Mol. Cell, DOI://10.1016/j.molcel.2018.03.007 (2018)
A Latent Variable Approach to Differentiating Neural Mechanisms of Irritability and Anxiety in Youth Kircanski, K; White, LK; Tseng, WL et al. JAMA Psychiatry, DOI://10.1001/jamapsychiatry.2018.0468 (2018)
A method for determining haploid and triploid genotypes and their association with vascular phenotypes in Williams syndrome and 7q11.23 duplication syndrome Gregory, MD; Kolachana, B; Yao, Y et al. BMC Med. Genet., DOI://10.1186/s12881-018-0563-3 (2018)
A Novel Method to Extend a Partial-Body CT for the Reconstruction of Dose to Organs beyond the Scan Range Kuzmin, GA; Mille, MM; Jung, JW et al. Radiat. Res., DOI://10.1667/RR14999.1 (2018)
Association of Methylation Signals With Incident Coronary Heart Disease in an Epigenome-Wide Assessment of Circulating Tumor Necrosis Factor α Aslibekyan, S; Agha, G; Colicino, E et al. JAMA Cardiol, DOI://10.1001/jamacardio.2018.0510 (2018)
Inferring properties of disordered chains from FRET transfer efficiencies Zheng, W; Zerze, GH; Borgia, A; Mittal, J; Schuler, B; Best, RB; J Chem Phys, DOI://10.1063/1.5006954 (2018)
Genome-wide Analyses Identify KIF5A as a Novel ALS Gene Nicolas, A; Kenna, KP; Renton, AE et al. Neuron, DOI://10.1016/j.neuron.2018.02.027 (2018)

Quantification of Human Microbiome Stability Over Six Months: Implications for Epidemiologic Studies Sinha, R; Goedert, JJ; Vogtmann, E et al. Am. J. Epidemiol., DOI://10.1093/aje/kwy064 (2018)
IL1RN Variation Influences both Disease Susceptibility and Response to Human Recombinant IL-1RA Therapy in Systemic Juvenile Idiopathic Arthritis Arthur, VL; Shuldiner, E; Remmers, EF et al. , DOI://10.1002/art.40498 (2018)
A trapped human PPM1A-phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity Debnath, S; Kosek, D; Tagad, HD et al. J. Biol. Chem., DOI://10.1074/jbc.RA117.001213 (2018)
Default Mode Connectivity in Major Depressive Disorder Measured Up to 10 Days After Ketamine Administration Evans, JW; Szczepanik, J; Brutsché, N; Park, LT; Nugent, AC; Zarate, CA; Biol. Psychiatry, DOI://10.1016/j.biopsych.2018.01.027 (2018)
An Extended Guinier Analysis for Intrinsically Disordered Proteins Zheng, W; Best, RB; J. Mol. Biol., DOI://10.1016/j.jmb.2018.03.007 (2018)
ZFR coordinates crosstalk between RNA decay and transcription in innate immunity Haque, N; Ouda, R; Chen, C; Ozato, K; Hogg, JR; Nat Commun, DOI://10.1038/s41467-018-03326-5 (2018)

Shep regulates Drosophila neuronal remodeling by controlling transcription of its chromatin targets Chen, D; Dale, RK; Lei, EP; Development, DOI://10.1242/dev.154047 (2018)
Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association Domanski, J; Sansom, MSP; Stansfeld, PJ; Best, RB; J Chem Theory Comput, DOI://10.1021/acs.jctc.7b00983 (2018)
LMTK3 confers chemo-resistance in breast cancer Stebbing, J; Shah, K; Lit, LC et al. Oncogene, DOI://10.1038/s41388-018-0197-0 (2018)
A deep insight into the male and female sialotranscriptome of adult Culex tarsalis mosquitoes Ribeiro, JMC; Martin-Martin, I; Moreira, FR; Bernard, KA; Calvo, E; Insect Biochem. Mol. Biol., DOI://10.1016/j.ibmb.2018.03.001 (2018)
Argonaute2 and LaminB modulate gene expression by controlling chromatin topology Nazer, E; Dale, RK; Chinen, M; Radmanesh, B; Lei, EP; PLoS Genet., DOI://10.1371/journal.pgen.1007276 (2018)
Mechanism of Darunavir (DRV)'s High Genetic Barrier to HIV-1 Resistance: A Key V32I Substitution in Protease Rarely Occurs, but Once It Occurs, It Predisposes HIV-1 To Develop DRV Resistance Aoki, M; Das, D; Hayashi, H et al. MBio, DOI://10.1128/mBio.02425-17 (2018)

Co-evolutionary fitness landscapes for sequence design Tian, P; Louis, JM; Baber, JL; Aniana, A; Best, R; Angew. Chem. Int. Ed. Engl., DOI://10.1002/anie.201713220 (2018)
Nanopore sequencing and assembly of a human genome with ultra-long reads Jain, M; Koren, S; Miga, KH et al. Nat. Biotechnol., DOI://10.1038/nbt.4060 (2018)
Impact of time-of-day on diffusivity measures of brain tissue derived from diffusion tensor imaging Thomas, C; Sadeghi, N; Nayak, A et al. Neuroimage, DOI://10.1016/j.neuroimage.2018.02.026 (2018)
Verdazyl-ribose: A new radical for solid-state dynamic nuclear polarization at high magnetic field Thurber, KR; Le, TN; Changcoco, V; Brook, DJR; J. Magn. Reson., DOI://10.1016/j.jmr.2018.02.016 (2018)
An insight into the salivary gland and fat body transcriptome of Panstrongylus lignarius (Hemiptera: Heteroptera), the main vector of Chagas disease in Peru Nevoa, JC; Mendes, MT; da Silva, MV; Soares, SC; Oliveira, CJF; Ribeiro, JMC; PLoS Negl Trop Dis, DOI://10.1371/journal.pntd.0006243 (2018)
Minoxidil improves vascular compliance, restores cerebral blood flow and alters extracellular matrix gene expression in a model of chronic vascular stiffness Knutsen, R; Beeman, SC; Broekelmann, TJ et al. Am. J. Physiol. Heart Circ. Physiol., DOI://10.1152/ajpheart.00683.2017 (2018)

Highly Disordered Amyloid-β Monomer Probed by Single-Molecule FRET and MD Simulation Meng, F; Bellaiche, MMJ; Kim, JY; Zerze, GH; Best, RB; Chung, HS; Biophys. J., DOI://10.1016/j.bpj.2017.12.025 (2018)
Ketamine has distinct electrophysiological and behavioral effects in depressed and healthy subjects Nugent, AC; Ballard, ED; Gould, TD et al. Mol. Psychiatry, DOI://10.1038/s41380-018-0028-2 (2018)
GRL-079, a novel P2-Tp-THF-C5-alkylamine- and P2' -Abt-containing HIV-1 protease inhibitor, is extremely potent against multi-drug-resistant HIV-1 variants including HIVDRVRp51 and has a high genetic barrier against the emergence of resistant variants Delino NS, Aoki M, Hayashi H, Hattori SI, Chang SB, Takamatsu Y, Martyr CD, Das D, Ghosh AK, Mitsuya H Antimicrob Agents Chemother. , doi: 10.1128/AAC.02060-17 (2018)
Design and statistical considerations for studies evaluating the efficacy of a single dose of the human papillomavirus (HPV) vaccine Sampson, JN; Hildesheim, A; Herrero, R; Gonzalez, P; Kreimer, A; Gail, MH; Contemp Clin Trials, DOI://10.1016/j.cct.2018.02.010 (2018)
Estimating recurrence and incidence of preterm birth subject to measurement error in gestational age: A hidden Markov modeling approach Albert, PS Stat Med, DOI://10.1002/sim.7624 (2018)
Transcriptional regulation by NR5A2 links differentiation and inflammation in the pancreas Cobo, I; Martinelli, P; Flández, M et al. Nature, DOI://10.1038/nature25751 (2018)

Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells Hu, G; Cui, K; Fang, D et al. Immunity, DOI://10.1016/j.immuni.2018.01.013 (2018)
Extreme disorder in an ultrahigh-affinity protein complex Borgia, A; Borgia, MB; Bugge, K et al. Nature, DOI://10.1038/nature25762 (2018)
Assessment of PCXMC for patients with different body size in chest and abdominal x ray examinations: a Monte Carlo simulation study Borrego, D; Lowe, EM; Kitahara, CM; Lee, C; Phys Med Biol, DOI://10.1088/1361-6560/aab13e (2018)
Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology Howard, BH; Hirai, TH; Russanova, VR; PLoS ONE, DOI://10.1371/journal.pone.0191033 (2018)
Dose coefficients for children and young adolescents exposed to external neutron fields Griffin, KT; Mille, M; Lee, C; J Radiol Prot, DOI://10.1088/1361-6498/aab126 (2018)
Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations Tofoleanu, F; Yuan, Y; Pickard, FC; Tywoniuk, B; Brooks, BR; Buchete, NV; J Phys Chem B, DOI://10.1021/acs.jpcb.7b12083 (2018)

Ridding fMRI data of motion-related influences: Removal of signals with distinct spatial and physical bases in multiecho data Power, JD; Plitt, M; Gotts, SJ et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1720985115 (2018)
The Antimicrobial Peptide CRAMP Is Essential for Colon Homeostasis by Maintaining Microbiota Balance Yoshimura, T; McLean, MH; Dzutsev, AK et al. J. Immunol., DOI://10.4049/jimmunol.1602073 (2018)
Transient Receptor Potential Channels TRPM4 and TRPC3 Critically Contribute to Respiratory Motor Pattern Formation but not Rhythmogenesis in Rodent Brainstem Circuits Koizumi, H; John, TT; Chia, JX et al. eNeuro, DOI://10.1523/ENEURO.0332-17.2018 (2018)
Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance Weingarten, RA; Johnson, RC; Conlan, S et al. MBio, DOI://10.1128/mBio.02011-17 (2018)
Raf-1 Cysteine-Rich Domain Increases the Affinity of K-Ras/Raf at the Membrane, Promoting MAPK Signaling Li, S; Jang, H; Zhang, J; Nussinov, R; Structure, DOI://10.1016/j.str.2018.01.011 (2018)
5-Azacytidine prevents relapse and produces long-term complete remissions in leukemia xenografts treated with Moxetumomab pasudotox Müller, F; Cunningham, T; Stookey, S et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1714512115 (2018)

Global changes of H3K27me3 domains and Polycomb group protein distribution in the absence of recruiters Spps or Pho Brown, JL; Sun, MA; Kassis, JA; Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1716299115 (2018)
Precise genome-wide mapping of single nucleosomes and linkers in vivo Chereji, RV; Ramachandran, S; Bryson, TD; Henikoff, S; Genome Biol., DOI://10.1186/s13059-018-1398-0 (2018)
The klotho-related protein KLPH (lctl) has preferred expression in lens and is essential for expression of clic5 and normal lens suture formation Fan, J; Lerner, J; Wyatt, MK et al. Exp. Eye Res., DOI://10.1016/j.exer.2018.02.001 (2018)
Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer Klein, AP; Wolpin, BM; Risch, HA et al. Nat Commun, DOI://10.1038/s41467-018-02942-5 (2018)
Sequence determinants of protein phase behavior from a coarse-grained model Dignon, GL; Zheng, W; Kim, YC; Best, RB; Mittal, J; PLoS Comput. Biol., DOI://10.1371/journal.pcbi.1005941 (2018)
Genomic Heterogeneity Within Individual Prostate Cancer Foci Impacts Predictive Biomarkers of Targeted Therapy VanderWeele, DJ; Finney, R; Katayama, K et al. Eur Urol Focus, DOI://10.1016/j.euf.2018.01.006 (2018)

Extended amygdala connectivity changes during sustained shock anticipation Torrisi, S; Gorka, AX; Gonzalez-Castillo, J et al. Transl Psychiatry, DOI://10.1038/s41398-017-0074-6 (2018)
Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2 Ozdemir, ES; Jang, H; Gursoy, A et al. J. Biol. Chem., DOI://10.1074/jbc.RA117.001596 (2018)
Binding kinetics of ultrasmall gold nanoparticles with proteins André Lira, Rodrigo Ferreira, Ricardo Torquato, Huaying Zhao, Maria Luiza Oliva, Sergio A. Hassan, Peter Schuck and Alioscka A Sousa Nanoscale, DOI: 10.1039/C7NR06810G (2018)
SpotLearn: Convolutional Neural Network for Detection of Fluorescence In Situ Hybridization (FISH) Signals in High-Throughput Imaging Approaches Prabhakar Gudla, Koh Nakayama, Gianluca Pegoraro, Tom Misteli Cold Spring Harb Symp Quant Biol, 10.1101/sqb.2017.82.033761 (2018)
Cleavage of TL1A Differentially Regulates Its Effects on Innate and Adaptive Immune Cells Ferdinand, JR; Richard, AC; Meylan, F; Al-Shamkhani, A; Siegel, RM; J. Immunol., DOI://10.4049/jimmunol.1700891 (2018)
De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads Eccles, D; Chandler, J; Camberis, M et al. BMC Biol., DOI://10.1186/s12915-017-0473-4 (2018)

Altered avalanche dynamics in a developmental NMDAR hypofunction model of cognitive impairment Seshadri, S; Klaus, A; Winkowski, DE; Kanold, PO; Plenz, D; Transl Psychiatry, DOI://10.1038/s41398-017-0060-z (2018)
Single cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma Zheng, H; Pomyen, Y; Hernandez, MO et al. Hepatology, DOI://10.1002/hep.29778 (2018)

2017 (307 papers)

The Interplay between Long- and Short-Range Temporal Correlations Shapes Cortex Dynamics across Vigilance States Meisel, C; Klaus, A; Vyazovskiy, VV; Plenz, D; J. Neurosci., DOI://10.1523/JNEUROSCI.0448-17.2017 (2017)
Loci associated with skin pigmentation identified in African populations Crawford, NG; Kelly, DE; Hansen, MEB et al. Science, DOI://10.1126/science.aan8433 (2017)
Progressive and Multi-path Holistically Nested Neural Networks for Pathological Lung Segmentation from CT Images Harrison A.P., Xu Z., George K., Lu L., Summers R.M., Mollura D.J. In: Descoteaux M., Maier-Hein L., Franz A., Jannin P., Colli, 10.1007/978-3-319-66179-7-71 (2017)
Extending electrostatics of dielectric spheres to arbitrary charge distributions with applications to biosystems T. P. Doerr, O. I. Obolensky, and Yi-Kuo Yu Phys. Rev. E , doi://10.1103/PhysRevE.96.062414 (2017)

Reduced Local and Increased Long-Range Functional Connectivity of the Thalamus in Autism Spectrum Disorder Tomasi, D; Volkow, ND; Cereb. Cortex, DOI://10.1093/cercor/bhx340 (2017)
CDC14A Phosphatase is Essential for Hearing and Male Fertility in Mouse and Human Imtiaz, A; Belyantseva, IA; Beirl, AJ et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddx440 (2017)
Identifying subgroups of enhanced predictive accuracy from longitudinal biomarker data using tree-based approaches: applications to fetal growth Foster, JC; Liu, D; Albert, PS; Liu, A; J R Stat Soc Ser A Stat Soc, DOI://10.1111/rssa.12182 (2017)
Effects of HLA-B27 on Gut Microbiota in Experimental Spondyloarthritis Implicate an Ecological Model of Dysbiosis Gill, T; Asquith, M; Brooks, SR; Rosenbaum, JT; Colbert, RA; Arthritis Rheumatol., DOI://10.1002/art.40405 (2017)
Selection for long and short sleep duration in Drosophila melanogaster reveals the complex genetic network underlying natural variation in sleep Harbison, ST; Serrano Negron, YL; Hansen, NF; Lobell, AS; PLoS Genet., DOI://10.1371/journal.pgen.1007098 (2017)
Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N Chittori, S; Hong, J; Saunders, H et al. Science, DOI://10.1126/science.aar2781 (2017)

Identity-by-Descent Mapping Identifies Major Locus for Serum Triglycerides in Amerindians Largely Explained by an APOC3 Founder Mutation Hsueh, WC; Nair, AK; Kobes, S et al. Circ Cardiovasc Genet, DOI://10.1161/CIRCGENETICS.117.001809 (2017)
Detecting treatment differences in group sequential longitudinal studies with covariate adjustment Jeffries, NO; Troendle, JF; Geller, NL; Biometrics, DOI://10.1111/biom.12837 (2017)
Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions using Alkane Simulations Leonard, AN; Simmonett, AC; Pickard, FC et al. J Chem Theory Comput, DOI://10.1021/acs.jctc.7b00948 (2017)
Molecular Anatomy of the Developing Human Retina Hoshino, A; Ratnapriya, R; Brooks, MJ et al. Dev. Cell, DOI://10.1016/j.devcel.2017.10.029 (2017)
Arginine Kinases from the Precious Corals Corallium rubrum and Paracorallium japonicum: Presence of Two Distinct Arginine Kinase Gene Lineages in Cnidarians Matsuo, T; Yano, D; Uda, K; Iwasaki, N; Suzuki, T; Protein J., DOI://10.1007/s10930-017-9745-7 (2017)
The emergence and evolution of influenza A (H1α) viruses in swine in Canada and the United States Nelson, MI; Culhane, MR; Trovão, NS et al. J. Gen. Virol., DOI://10.1099/jgv.0.000924 (2017)
Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq Chen, L; Lee, JW; Chou, CL et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1710964114 (2017)
Replication Stress Shapes a Protective Chromatin Environment across Fragile Genomic Regions Kim, J; Sturgill, D; Sebastian, R et al. Mol. Cell, DOI://10.1016/j.molcel.2017.11.021 (2017)
Dosage-Dependent Expression Variation Suppressed on the Drosophila Male X Chromosome Lee, H; Cho, DY; Wojtowicz, D et al. G3 (Bethesda), DOI://10.1534/g3.117.300400 (2017)
Integrative Genomic Analysis of Coincident Cancer Foci Implicates CTNNB1 and PTEN Alterations in Ductal Prostate Cancer Gillard, M; Lack, J; Pontier, A et al. Eur Urol Focus, DOI://10.1016/j.euf.2017.12.003 (2017)
Holistic segmentation of the lung in cine MRI Kovacs, W; Hsieh, N; Roth, H et al. J Med Imaging (Bellingham), DOI://10.1117/1.JMI.4.4.041310 (2017)
Transcriptomic profiling of the human brain reveals that altered synaptic gene expression is associated with chronological aging Dillman, AA; Majounie, E; Ding, J et al. Sci Rep, DOI://10.1038/s41598-017-17322-0 (2017)

Identification of essential genes for cancer immunotherapy Patel, SJ; Sanjana, NE; Kishton, RJ et al. Nature, DOI://10.1038/nature23477 (2017)
In vivo tropism of Salmonella Typhi toxin to cells expressing a multiantennal glycan receptor Yang, YA; Lee, S; Zhao, J et al. Nat Microbiol, DOI://10.1038/s41564-017-0076-4 (2017)
Local and global anatomy of antibody-protein antigen recognition Wang, M; Zhu, D; Zhu, J; Nussinov, R; Ma, B; J. Mol. Recognit., DOI://10.1002/jmr.2693 (2017)
A digital 3D atlas of the marmoset brain based on multi-modal MRI Liu, C; Ye, FQ; Chern-Chyi Yen, C et al. Neuroimage, DOI://10.1016/j.neuroimage.2017.12.004 (2017)
Automated quality assessment of structural magnetic resonance images in children: Comparison with visual inspection and surface-based reconstruction White, T; Jansen, PR; Muetzel, RL et al. Hum Brain Mapp, DOI://10.1002/hbm.23911 (2017)
OCT4 supports extended LIF-independent self-renewal and maintenance of transcriptional and epigenetic networks in embryonic stem cells He, R; Xhabija, B; Al-Qanber, B; Kidder, BL; Sci Rep, DOI://10.1038/s41598-017-16611-y (2017)
Power Analysis for Genetic Association Test (PAGEANT) provides insights to challenges for rare variant association studies Derkach, A; Zhang, H; Chatterjee, N; Bioinformatics, DOI://10.1093/bioinformatics/btx770 (2017)
Demystifying P2Y1 Receptor Ligand Recognition through Docking and Molecular Dynamics Analyses Ciancetta, A; O'Connor, RD; Paoletta, S; Jacobson, KA; J Chem Inf Model, DOI://10.1021/acs.jcim.7b00528 (2017)
A STAT3-dependent transcriptional circuitry inhibits cytotoxic gene expression in T cells Ciucci, T; Vacchio, MS; Bosselut, R; Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1711160114 (2017)
Natural Language Processing for Large-Scale Medical Image Analysis Using Deep Learning Hoo-Chang Shin, Le Lu, Ronald M. Summers in Deep Learning for Medical Image Analysis, Elsevier , (p405-421) (2017)
Excessive burden of lysosomal storage disorder gene variants in Parkinson's disease Robak, LA; Jansen, IE; van Rooij, J et al. Brain, DOI://10.1093/brain/awx285 (2017)
Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations Sharma, V; Jambrina, PG; Kaukonen, M; Rosta, E; Rich, PR; Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1708628114 (2017)

Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo Johnson, TA; Chereji, RV; Stavreva, DA; Morris, SA; Hager, GL; Clark, DJ; Nucleic Acids Res., DOI://10.1093/nar/gkx1044 (2017)
A joint model for multivariate hierarchical semicontinuous data with replications Kassahun-Yimer, W; Albert, PS; Lipsky, LM; Nansel, TR; Liu, A; Stat Methods Med Res, DOI://10.1177/0962280217738141 (2017)
Phosphorylated Calmodulin Promotes PI3K Activation by Binding to the SH2 Domains Zhang, M; Jang, H; Gaponenko, V; Nussinov, R; Biophys. J., DOI://10.1016/j.bpj.2017.09.008 (2017)
Prediction of Host-Pathogen Interactions for Helicobacter pylori by Interface Mimicry and Implications to Gastric Cancer Guven-Maiorov, E; Tsai, CJ; Ma, B; Nussinov, R; J. Mol. Biol., DOI://10.1016/j.jmb.2017.10.023 (2017)
Physiological and pathophysiological implications of PGE2 and the PGE2 synthases in the kidney Wang, J; Liu, M; Zhang, X; Yang, G; Chen, L; Prostaglandins Other Lipid Mediat., DOI://10.1016/j.prostaglandins.2017.10.006 (2017)
Genetic Analysis of Inherited Retinal Diseases in Indigenous Southern African Populations Lisa Jane Roberts (R. Ramesar & A. Swaroop, thesis advisors) PhD thesis, University of Cape Town (2017)

Independence between pre-mRNA splicing and DNA methylation in an isogenic minigene resource Kyster K. Nanan, Cody Ocheltree, David Sturgill, Mariana D. Mandler, Maria Prigge, Garima Varma, Shalini Oberdoerffer Nucleic Acids Res., doi://10.1093/nar/gkx900 (2017)
Multimodal mapping of the brain's functional connectivity and the adult outcome of attention deficit hyperactivity disorder Sudre, G; Szekely, E; Sharp, W; Kasparek, S; Shaw, P; Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1705229114 (2017)
The Kölliker-Fuse nucleus orchestrates the timing of expiratory abdominal nerve bursting Barnett, WH; Jenkin, SEM; Milsom, WK et al. J. Neurophysiol., DOI://10.1152/jn.00499.2017 (2017)
PaRSnIP: Sequence-Based Protein Solubility Prediction using Gradient Boosting Machine Rawi, R; Mall, R; Kunji, K; Shen, CH; Kwong, PD; Chuang, GY; Bioinformatics, DOI://10.1093/bioinformatics/btx662 (2017)
Unpicking the determinants of amide NHO[double bond, length as m-dash]C hydrogen bond strength with diphenylacetylene molecular balances Luccarelli, J; Jones, IM; Thompson, S; Hamilton, AD; Org. Biomol. Chem., DOI://10.1039/c7ob02026k (2017)
Peptide dimerization-dissociation rates from replica exchange molecular dynamics Leahy, CT; Kells, A; Hummer, G; Buchete, NV; Rosta, E; J Chem Phys, DOI://10.1063/1.5004774 (2017)

Identification of UT-A1-and AQP2 interacting proteins in rat inner medullary collecting duct Chou, CL; Hwang, G; Hageman, DJ et al. Am. J. Physiol., Cell Physiol., DOI://10.1152/ajpcell.00082.2017 (2017)
Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex Guo, TW; Bartesaghi, A; Yang, H et al. Cell, DOI://10.1016/j.cell.2017.09.006 (2017)
How Many Protein Sequences Fold to a Given Structure? A Coevolutionary Analysis Tian, P; Best, RB; Biophys. J., DOI://10.1016/j.bpj.2017.08.039 (2017)
The FUT2 secretor variant p.Trp154Ter influences serum vitamin B12 concentration via holo-haptocorrin, but not holo-transcobalamin, and is associated with haptocorrin glycosylation Velkova, A; Diaz, JEL; Pangilinan, F et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddx369 (2017)
A novel central nervous system-penetrating protease inhibitor overcomes human immunodeficiency virus 1 resistance with unprecedented aM to pM potency Aoki, M; Hayashi, H; Rao, KV et al. Elife, DOI://10.7554/eLife.28020 (2017)
A functional connectivity-based neuromarker of sustained attention generalizes to predict recall in a reading task Jangraw, DC; Gonzalez-Castillo, J; Handwerker, DA et al. Neuroimage, DOI://10.1016/j.neuroimage.2017.10.019 (2017)

MicroRNA Signature of Cigarette Smoking and Evidence for a Putative Causal Role of MicroRNAs in Smoking-Related Inflammation and Target Organ Damage Willinger, CM; Rong, J; Tanriverdi, K et al. Circ Cardiovasc Genet, DOI://10.1161/CIRCGENETICS.116.001678 (2017)
De novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing Schmidt, MH; Vogel, A; Denton, AK et al. Plant Cell, DOI://10.1105/tpc.17.00521 (2017)
Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates Lemon, JK; Khil, PP; Frank, KM; Dekker, JP; J. Clin. Microbiol., DOI://10.1128/JCM.01069-17 (2017)
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Assessing variation across 8 established East Asian loci for type 2 diabetes mellitus in American Indians: Suggestive evidence for new sex-specific diabetes signals in GLIS3 and ZFAND3 Muller, YL; Piaggi, P; Chen, P et al. Diabetes Metab. Res. Rev., DOI://10.1002/dmrr.2869 (2017)
Estimating the Heritability of Structural and Functional Brain Connectivity in Families Affected by Attention-Deficit/Hyperactivity Disorder Sudre, G; Choudhuri, S; Szekely, E et al. JAMA Psychiatry, DOI://10.1001/jamapsychiatry.2016.3072 (2017)

Oculocutaneous albinism type 1: link between mutations, tyrosinase conformational stability, and enzymatic activity Dolinska, MB; Kus, NJ; Farney, SK; Wingfield, PT; Brooks, BP; Sergeev, YV; Pigment Cell Melanoma Res, DOI://10.1111/pcmr.12546 (2017)
DLX3-Dependent Regulation of Ion Transporters and Carbonic Anhydrases is Crucial for Enamel Mineralization Duverger, O; Ohara, T; Bible, PW; Zah, A; Morasso, MI; J. Bone Miner. Res., DOI://10.1002/jbmr.3022 (2017)
Untangling the relatedness among correlations, Part II: Inter-subject correlation group analysis through linear mixed-effects modeling Chen, G; Taylor, PA; Shin, YW; Reynolds, RC; Cox, RW; Neuroimage, DOI://10.1016/j.neuroimage.2016.08.029 (2017)
Topographical and physiological differences of the skin mycobiome in health and disease Jo, JH; Kennedy, EA; Kong, HH; Virulence, DOI://10.1080/21505594.2016.1249093 (2017)
Empirically derived patterns of psychiatric symptoms in youth: A latent profile analysis Kircanski, K; Zhang, S; Stringaris, A et al. J Affect Disord, DOI://10.1016/j.jad.2016.09.016 (2017)
Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge Lee, J; Tofoleanu, F; Pickard, FC et al. J. Comput. Aided Mol. Des., DOI://10.1007/s10822-016-9968-2 (2017)
Immobilized MutS-Mediated Error Removal of Microchip-Synthesized DNA Wan, W; Wang, D; Gao, X; Hong, J; Methods Mol. Biol., DOI://10.1007/978-1-4939-6343-0_17 (2017)
Perfluoroalkyl Chemicals, Menstrual Cycle Length, and Fecundity: Findings from a Prospective Pregnancy Study Lum, KJ; Sundaram, R; Barr, DB; Louis, TA; Buck Louis, GM; Epidemiology, DOI://10.1097/EDE.0000000000000552 (2017)
Anxiety Patients Show Reduced Working Memory Related dlPFC Activation During Safety and Threat Balderston, NL; Vytal, KE; O'Connell, K et al. Depress Anxiety, DOI://10.1002/da.22518 (2017)

2016 (385 papers)

Toward elucidating the heat activation mechanism of the TRPV1 channel gating by molecular dynamics simulation Wen, H; Qin, F; Zheng, W; Proteins, DOI://10.1002/prot.25177 (2016)
Hydrogen Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III Esser, L; Zhou, F; Zhou, Y et al. J. Biol. Chem., DOI://10.1074/jbc.M116.744391 (2016)
Estimation of FST and the Impact of de novo Mutation Shriner, D; Chen, G; Adeyemo, A; Rotimi, CN; Hum. Hered., DOI://10.1159/000477782 (2016)
Robust spike sorting of retinal ganglion cells tuned to spot stimuli Ghahari, A; Badea, TC; Conf Proc IEEE Eng Med Biol Soc, DOI://10.1109/EMBC.2016.7591054 (2016)
Identifying Host Genetic Variants Associated with Microbiome Composition by Testing Multiple Beta Diversity Matrices Hua, X; Goedert, JJ; Landi, MT; Shi, J; Hum. Hered., DOI://10.1159/000448733 (2016)
Winner's Curse Correction and Variable Thresholding Improve Performance of Polygenic Risk Modeling Based on Genome-Wide Association Study Summary-Level Data Shi, J; Park, JH; Duan, J et al. PLoS Genet., DOI://10.1371/journal.pgen.1006493 (2016)
Lineage-Specific and Non-specific Cytokine-Sensing Genes Respond Differentially to the Master Regulator STAT5 Zeng, X; Willi, M; Shin, HY; Hennighausen, L; Wang, C; Cell Rep, DOI://10.1016/j.celrep.2016.11.079 (2016)
Block network mapping approach to quantitative trait locus analysis Shreif, ZZ; Gatti, DM; Periwal, V; BMC Bioinformatics, DOI://10.1186/s12859-016-1351-8 (2016)
Meta-analysis of quantitative pleiotropic traits for next-generation sequencing with multivariate functional linear models Chiu, CY; Jung, J; Chen, W et al. Eur. J. Hum. Genet., DOI://10.1038/ejhg.2016.170 (2016)

Towards understanding the structural basis of partial agonism at the dopamine D3 receptor Michino, M; Boateng, CA; Donthamsetti, P et al. J. Med. Chem., DOI://10.1021/acs.jmedchem.6b01148 (2016)
Comparison of parametric and machine methods for variable selection in simulated Genetic Analysis Workshop 19 data Holzinger, ER; Szymczak, S; Malley, J et al. BMC Proc, DOI://10.1186/s12919-016-0021-1 (2016)
From 20th Century Metabolic Wall Charts to 21st Century Systems Biology: Database of Mammalian Metabolic Enzymes Corcoran, CC; Grady, CR; Pisitkun, T; Parulekar, J; Knepper, MA; Am. J. Physiol. Renal Physiol., DOI://10.1152/ajprenal.00601.2016 (2016)
Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions Venable, RM; Ingólfsson, HI; Lerner, MG et al. J Phys Chem B, DOI://10.1021/acs.jpcb.6b09111 (2016)
DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases Ligthart, S; Marzi, C; Aslibekyan, S et al. Genome Biol., DOI://10.1186/s13059-016-1119-5 (2016)
Structure-Based Scaffold Repurposing for G Protein-Coupled Receptors: Transformation of Adenosine Derivatives into 5HT2B/5HT2C Serotonin Receptor Antagonists Tosh, DK; Ciancetta, A; Warnick, E; Crane, S; Gao, ZG; Jacobson, KA; J. Med. Chem., DOI://10.1021/acs.jmedchem.6b01183 (2016)

Genetic architecture distinguishes systemic juvenile idiopathic arthritis from other forms of juvenile idiopathic arthritis: clinical and therapeutic implications Ombrello, MJ; Arthur, VL; Remmers, EF et al. Ann. Rheum. Dis., DOI://10.1136/annrheumdis-2016-210324 (2016)
Mechanisms of Evolution in High-Consequence Drug Resistance Plasmids He, S; Chandler, M; Varani, AM; Hickman, AB; Dekker, JP; Dyda, F; MBio, DOI://10.1128/mBio.01987-16 (2016)
Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study Shi, J; Hua, X; Zhu, B et al. PLoS Med., DOI://10.1371/journal.pmed.1002162 (2016)
Mapping Complex Traits in a Diversity Outbred F1 Mouse Population Identifies Germline Modifiers of Metastasis in Human Prostate Cancer Winter, JM; Gildea, DE; Andreas, JP et al. Cell Syst, DOI://10.1016/j.cels.2016.10.018 (2016)
Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data Ying, J; Delaglio, F; Torchia, DA; Bax, A; J. Biomol. NMR, DOI://10.1007/s10858-016-0072-7 (2016)
A comparison study of multivariate fixed models and Gene Association with Multiple Traits (GAMuT) for next-generation sequencing Chiu, CY; Jung, J; Wang, Y et al. Genet. Epidemiol., DOI://10.1002/gepi.22014 (2016)

Robust skull stripping using multiple MR image contrasts insensitive to pathology Roy, S; Butman, JA; Pham, DL; Neuroimage, DOI://10.1016/j.neuroimage.2016.11.017 (2016)
Association of Irritability and Anxiety With the Neural Mechanisms of Implicit Face Emotion Processing in Youths With Psychopathology Stoddard, J; Tseng, WL; Kim, P et al. JAMA Psychiatry, DOI://10.1001/jamapsychiatry.2016.3282 (2016)
Allosteric control of antibody-prion recognition through oxidation of a disulfide bond between the CH and CL chains Zhao, J; Nussinov, R; Ma, B; Protein Eng. Des. Sel., DOI://10.1093/protein/gzw065 (2016)
Early generated B1 B cells with restricted BCRs become chronic lymphocytic leukemia with continued c-Myc and low Bmf expression Hayakawa, K; Formica, AM; Brill-Dashoff, J et al. J. Exp. Med., DOI://10.1084/jem.20160712 (2016)
Molecular Diagnosis of Inherited Retinal Diseases in Indigenous African Populations by Whole-Exome Sequencing Roberts, L; Ratnapriya, R; du Plessis, M; Chaitankar, V; Ramesar, RS; Swaroop, A; Invest. Ophthalmol. Vis. Sci., DOI://10.1167/iovs.16-19785 (2016)
High-level expression of improved thermo-stable alkaline xylanase variant in Pichia Pastoris through codon optimization, multiple gene insertion and high-density fermentation Lu, Y; Fang, C; Wang, Q; Zhou, Y; Zhang, G; Ma, Y; Sci Rep, DOI://10.1038/srep37869 (2016)
Stage-Specific Transcriptome and Proteome Analyses of the Filarial Parasite Onchocerca volvulus and Its Wolbachia Endosymbiont Bennuru, S; Cotton, JA; Ribeiro, JM et al. MBio, DOI://10.1128/mBio.02028-16 (2016)
NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors Kim, JW; Yang, HJ; Brooks, MJ et al. Cell Rep, DOI://10.1016/j.celrep.2016.10.074 (2016)
Integrative network analysis reveals molecular mechanisms of blood pressure regulation Tianxiao Huan, Qingying Meng et al. Mol Syst Biol., doi: 10.15252/msb.20145399 (2016)
C. elegans DAF-2 as a Model for Human Insulin Receptoropathies David A. Bulger, Tetsunari Fukushige, Sijung Yun, Robert K. Semple, John A. Hanover, and Michael W. Krause Genes|Genomes|Genetics, doi:10.1534/g3.116.03718 (2016)
Generation and differentiation of induced pluripotent stem cells reveal ankylosing spondylitis risk gene expression in bone progenitors Gerlinde Layh-Schmitt, Shajia Lum Fatemehm Navid, Stephen R. Brooks, Emily Lazowick, Kathryn M. Davis, Cristina Montagna, Massimo Gadina, Robert A. Colbert Clinical Rheumatology, doi:10.1007/s10067-016-3469-5 (2016)
Whole-genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic-trait mapping Dreger, DL; Rimbault, M; Davis, BW; Bhatnagar, A; Parker, HG; Ostrander, EA; Dis Model Mech, DOI://10.1242/dmm.027037 (2016)

Two Na+ Sites Control Conformational Change in a Neurotransmitter Transporter Homolog Sotiria Tavoulari, Eleonora Margheritis, Anu Nagarajan, David C. DeWitt, Yuan -Wei Zhang, Edwin Rosado, Silvia Ravera, Elizabeth Rhoades, Lucy R. Forrest and Gary Rudnick J Biol Chem. , doi: 10.1074/jbc.M115.692012. (2016)
Techniques for blood volume fMRI with VASO: From low-resolution mapping towards sub-millimeter layer-dependent applications Huber, L; Ivanov, D; Handwerker, DA et al. Neuroimage, DOI://10.1016/j.neuroimage.2016.11.039 (2016)
The genome of Onchocerca volvulus, agent of river blindness Cotton, JA; Bennuru, S; Grote, A et al. Nat Microbiol, DOI://10.1038/nmicrobiol.2016.216 (2016)
Structures of the Multidrug Transporter P-glycoprotein Reveal Asymmetric ATP Binding and the Mechanism of Polyspecificity Esser, L; Zhou, F; Pluchino, KM et al. J. Biol. Chem., DOI://10.1074/jbc.M116.755884 (2016)
Physiological basis of vascular autocalibration (VasA): Comparison to hypercapnia calibration methods Kazan, SM; Huber, L; Flandin, G; Ivanov, D; Bandettini, P; Weiskopf, N; Magn Reson Med, DOI://10.1002/mrm.26494 (2016)
Serine/Threonine Phosphatases and Aquaporin-2 Regulation in Renal Collecting Duct Sophia LeMaire, Viswanathan Raghuram, Cameron R. Grady, Christina M. Pickering, Chung-Lin Chou, Ezigbobiara N Umejiego, Mark A. Knepper Am. J. Physiol. - Renal Physiol. , DOI: 10.1152/ajprenal.00455.2016 (2016)

Identification of a novel lipid binding motif in apolipoprotein B by the analysis of hydrophobic cluster domains Scott M. Gordon, Mohsen Pourmousa, Maureen Sampson, Denis Sviridov, Rafique Islam, B. Scott Perrin Jr., Georgina Kemeh, Richard W. Pastor, Alan T. Remaley Biochimica et Biophysica Acta - Membranes, doi://10.1016/j.bbamem.2016.10.019 (2016)
Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association Jan Domanski, George Hedger, Robert B. Best, Phillip James Stansfeld, and Mark S. P. Sansom J. Phys. Chem. B, doi://10.1021/acs.jpcb.6b08445 (2016)
Transcriptome Profiling of NIH3T3 Cell Lines Expressing Opsin and the P23H Opsin Mutant Identifies Candidate Drugs for the Treatment of Retinitis Pigmentosa Yuanyuan Chen, Matthew J. Brooks, Linn Gieser, Anand Swaroop, Krzysztof Palczewski Pharmacological Research, doi://10.1016/j.phrs.2016.10.031 (2016)
RNA-seq analyses of the midgut from blood- and serum-fed Ixodes ricinus ticks Perner, J; Provazník, J; Schrenková, J; Urbanová, V; Ribeiro, JM; Kopáček, P; Sci Rep, DOI://10.1038/srep36695 (2016)
Transgenic mouse model of IgM(+) lymphoproliferative disease mimicking Waldenström macroglobulinemia Tompkins, VS; Sompallae, R; Rosean, TR et al. Blood Cancer J, DOI://10.1038/bcj.2016.95 (2016)
Mechanism of O2 diffusion and reduction in FeFe hydrogenases Adam Kubas, Christophe Orain et al. Nature Chemistry, doi:10.1038/nchem.2592 (2016)

Variance Decomposition for Single-Subject task-based fMRI activity estimates across many sessions Javier Gonzalez-Castillo, Gang Chen, Thomas E. Nichols, Peter A. Bandettini NeuroImage, doi://10.1016/j.neuroimage.2016.10.024 (2016)
Explicit Incorporation of Hard and Soft Protein-Protein Interactions Into Models for Crowding Effects in Binary and Ternary Protein Mixtures I. Comparison of Approximate Analytical Solutions With Numerical Simulation Travis Hoppe, and Allen P. Minton J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.6b07736 (2016)
Resting State Connectivity of the Human Habenula at Ultra-High Field Salvatore Torrisi, Camilla L. Nord, Nicholas L. Balderston, Jonathan P. Roiser, Christian Grillon, Monique Ernst NeuroImage, 10.1016/j.neuroimage.2016.10.034 (2016)
The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts Saini, N; Roberts, SA; Klimczak, LJ et al. PLoS Genet., DOI://10.1371/journal.pgen.1006385 (2016)
Deriving frequency-dependent spatial patterns in MEG-derived resting state sensorimotor network: A novel multiband ICA technique Nugent, A. C., Luber, B., Carver, F. W., Robinson, S. E., Coppola, R. and Zarate, C. A. Hum. Brain Mapp., doi:10.1002/hbm.23417 (2016)
Additional Rare Variant Analysis in Parkinson's Disease Cases with and Without Known Pathogenic Mutations: Evidence for Oligogenic Inheritance Steven J. Lubbe, Valentina Escott-Price et al. Human Molecular Genetics, doi://10.1093/hmg/ddw348 (2016)

Longitudinal imaging in C9orf72 mutation carriers: Relationship to phenotype Mary Kay Floeter, Devin Bageac, Laura E. Danielian, Laura E. Braun, Bryan J. Traynor, , Justin Kwan NeuroImage: Clinical, doi://10.1016/j.nicl.2016.10.014 (2016)
Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells Juan, AH; Wang, S; Ko, KD et al. Cell Rep, DOI://10.1016/j.celrep.2016.09.087 (2016)
Light induced structural changes of the photoprotein mnemiopsin: Characterization and contribution in photoinactivation Pashandi, Z; Molakarimi, M; Sajedi, RH; Taghdir, M; Naderi-Manesh, H; J. Photochem. Photobiol. B, Biol., DOI://10.1016/j.jphotobiol.2016.10.018 (2016)
Racial differences in microRNA and gene expression in hypertensive women Dluzen, DF; Noren Hooten, N; Zhang, Y et al. Sci Rep, DOI://10.1038/srep35815 (2016)
Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases Gergely N Nagy, Reynier Suardiaz, Anna Lopata, Oliver Ozohanics, Karoly Vekey, Bernard R. Brooks, Ibolya Leveles, Judit Toth, Beata G Vertessy, and Edina Rost JACS, doi://10.1021/jacs.6b09012 (2016)
Molecular lock regulates binding of glycine to a primitive NMDA receptor Alvin Yu, Robert Alberstein, Alecia Thomas, Austin Zimmet, Richard Grey, Mark L. Mayer, and Albert Y. Lau PNAS, doi: 10.1073/pnas.1607010113 (2016)

Sources and implications of whole-brain fMRI signals in humans Jonathan D Power, Mark Plitt, Timothy O Laumann, Alex Martin Neuroimage, doi://10.1016/j.neuroimage.2016.09.038 (2016)
Diagnosis of Parkinson's disease on the basis of clinical-genetic classification: a population-based modelling study Mike A. Nalls, Cory Y. McLean et al. Lancet Neurol., doi: 10.1016/S1474-4422(15)00178-7 (2016)
Microenvironmental Gene Expression Plasticity Among Individual Drosophila melanogaster Lin, Y; Chen, ZX; Oliver, B; Harbison, ST; G3 (Bethesda), DOI://10.1534/g3.116.035444 (2016)
Elevated basal serum tryptase identifies a multisystem disorder associated with increased TPSAB1 copy number Lyons, JJ; Yu, X; Hughes, JD et al. Nat. Genet., DOI://10.1038/ng.3696 (2016)
Hydrogen Bonding to the substrate is not required for Rieske iron-sulfur protein docking to the quinol oxidation site of complex III Lothar Esser, Fei Zhou, Yihui Zhou, Yumei Xiao, Wai-kwan Tang, Chang-An Yu, Zhaohai Qin and Di Xia J. Biol. Chem., doi: 10.1074/jbc.M116.744391 (2016)
SARAH Domain-Mediated MST2-RASSF Dimeric Interactions Goar Sànchez-Sanz , Bartomiej Tywoniuk , David Matallanas, David Romano, Lan K. Nguyen, Boris N. Kholodenko, Edina Rosta , Walter Kolch , Nicolae-Viorel Buchete PLoS Computational Biology, doi://10.1371/journal.pcbi.1005051 (2016)

Systems-level analysis reveals selective regulation of Aqp2 gene expression by vasopressin Sandoval, PC; Claxton, JS; Lee, JW; Saeed, F; Hoffert, JD; Knepper, MA; Sci Rep, DOI://10.1038/srep34863 (2016)
Evaluation of KIR3DL1/KIR3DS1 polymorphism in Behçet's disease Erer, B; Takeuchi, M; Ustek, D et al. Genes Immun., DOI://10.1038/gene.2016.36 (2016)
Rapid development of a DNA vaccine for Zika virus Dowd, KA; Ko, SY; Morabito, KM et al. Science, DOI://10.1126/science.aai9137 (2016)
Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pKa corrections Frank C. Pickard IV, Gerhard König, Florentina Tofoleanu, Juyong Lee, Andrew C. Simmonett, Yihan Shao, Jay W. Ponder, Bernard R. Brooks J. Computer-Aided Molecular Design, DOI: 10.1007/s10822-016-9955-7 (2016)
A Modified P1 Moiety Enhances in vitro Antiviral Activity against Various Multi-Drug-Resistant HIV-1 Variants and in vitro CNS Penetration Properties of a Novel Nonpeptidic Protease Inhibitor, GRL-10413 Masayuki Amano, Pedro Miguel Salcedo-Gomez, Rui Zhao, Ravikiran S. Yedidi, Debananda Das, Haydar Bulut, Nicole S. Delino, Sheri Venkata Reddy, Arun K. Ghosh and Hiroaki Mitsuya Antimicrobial Agents and Chemotherapy, doi: 10.1128/AAC.01428-16 (2016)
Peripheral Blood Transcriptomic Signatures of Fasting Glucose and Insulin Concentrations BH Chen, M-F Hivert et al. Diabetes, doi://10.2337/db16-0470 (2016)

On the Selective Packaging of Genomic RNA by HIV-1 Mauricio Comas-Garcia, Sean R. Davis and Alan Rein Viruses, doi://10.3390/v8090246 (2016)
Behavioral and Neural Sustained Attention Deficits in Bipolar Disorder and Familial Risk for Bipolar Disorder David Pagliaccio, Jillian Lee Wiggins, et al. Biological Psychiatry, doi://10.1016/j.biopsych.2016.09.006 (2016)
Mutations of SGO2 and CLDN14 collectively cause coincidental Perrault syndrome R Faridi, AR Rehman et al. Clinical Genetics, DOI: 10.1111/cge.12867 (2016)
CYP2A6 genetic variation alters striatal-cingulate circuits, network hubs, and executive processing in smokers Sufang Li, Yihong Yang, Ewa Hoffmann, Rachel F. Tyndale, Elliot A. Stein Biological Psychiatry, doi://10.1016/j.biopsych.2016.09.013 (2016)
Absolute binding free energies for octa-acids and guests in SAMPL5 Florentina Tofoleanu, Juyong Lee, Frank C. Pickard IV, Gerhard Kzönig, Jing Huang, Minkyung Baek, Chaok Seok, Bernard R. Brooks J. Computer-Aided Molecular Design, DOI: 10.1007/s10822-016-9965-5 (2016)
Introduction, evolution, and dissemination of influenza A viruses in exhibition swine, USA, 2009-2013 Martha I. Nelson, Karla M. Stucker, et al. J. Virology, doi: 10.1128/JVI.01457-16 (2016)
Differential cytokine sensitivities of STAT5-dependent enhancers rely on Stat5 autoregulation Willi, M; Yoo, KH; Wang, C; Trajanoski, Z; Hennighausen, L; Nucleic Acids Res., DOI://10.1093/nar/gkw844 (2016)
Novel genetic loci underlying human intracranial volume identified through genome-wide association Adams, HH; Hibar, DP; Chouraki, V et al. Nat. Neurosci., DOI://10.1038/nn.4398 (2016)
DNA methylation-based measures of biological age: meta-analysis predicting time to death Chen, BH; Marioni, RE; Colicino, E et al. Aging (Albany NY), DOI://10.18632/aging.101020 (2016)
The genetics of blood pressure regulation and its target organs from association studies in 342,415 individuals Ehret, GB; Ferreira, T; Chasman, DI et al. Nat. Genet., DOI://10.1038/ng.3667 (2016)
Characterization and phosphoproteomic analysis of a human immortalized podocyte model of Fabry disease generated using CRISPR/Cas9 technology Pereira, EM; Labilloy, A; Eshbach, ML et al. Am. J. Physiol. Renal Physiol., DOI://10.1152/ajprenal.00283.2016 (2016)
Alternative Isoform Analysis of Ttc8 Expression in the Rat Pineal Gland Using a Multi-Platform Sequencing Approach Reveals Neural Regulation Hartley, SW; Mullikin, JC; Klein, DC; Park, M; , ; Coon, SL; PLoS ONE, DOI://10.1371/journal.pone.0163590 (2016)

Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane Mingzhen Zhang, Jie Zheng, Ruth Nussinov, Buyong Ma Scientific Reports, 10.1038/srep33340 (2016)
Integrative Transcriptome Analyses of Metabolic Responses in Mice Define Pivotal LncRNA Metabolic Regulators Yang, L; Li, P; Yang, W et al. Cell Metab., DOI://10.1016/j.cmet.2016.08.019 (2016)
REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants Ioannidis, NM; Rothstein, JH; Pejaver, V et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2016.08.016 (2016)
Daily physical activity patterns from hip- and wrist-worn accelerometers Shiroma, EJ; Schepps, MA; Harezlak, J et al. Physiol Meas, DOI://10.1088/0967-3334/37/10/1852 (2016)
Association of Superoxide Dismutase 2 (SOD2) Genotype with Gray Matter Volume Shrinkage in Chronic Alcohol Users: Replication and Further Evaluation of an Addiction Gene Panel Gitik M, Srivastava V, Hodgkinson CA, Shen PH, Goldman D, Meyerhoff DJ Int. J. Neuropsychopharmacol., DOI://10.1093/ijnp/pyw033 (2016)
DNA Transposition at Work Hickman, AB; Dyda, F; Chem. Rev., DOI://10.1021/acs.chemrev.6b00003 (2016)
Expression, purification and identification of a thermolysin-like protease, neutral protease I, from Aspergillus oryzae with the Pichia pastoris expression system Ma, X; Liu, Y; Li, Q et al. Protein Expr. Purif., DOI://10.1016/j.pep.2016.08.008 (2016)
The African diaspora: history, adaptation and health Rotimi CN, Tekola-Ayele F, Baker JL, Shriner D Curr. Opin. Genet. Dev., DOI://10.1016/j.gde.2016.08.005 (2016)
3D-printed head models for navigated non-invasive brain stimulation Dayan, E; Thompson, RM; Buch, ER; Cohen, LG; Clin Neurophysiol, DOI://10.1016/j.clinph.2016.08.011 (2016)
Genome-wide association study of 40,000 individuals identifies two novel loci associated with bipolar disorder Hou, L; Bergen, SE; Akula, N et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddw181 (2016)
Distinct fMRI Responses to Self-Induced versus Stimulus Motion during Free Viewing in the Macaque Russ, BE; Kaneko, T; Saleem, KS; Berman, RA; Leopold, DA; J. Neurosci., DOI://10.1523/JNEUROSCI.1152-16.2016 (2016)
A genome-wide association study in multiple system atrophy Sailer, A; Scholz, SW; Nalls, MA et al. Neurology, DOI://10.1212/WNL.0000000000003221 (2016)

An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations Frank C. Pickard, Gerhard Koenig, Andrew C. Simmonett, Yihan Shao, Bernard R. Brooks Bioorganic & Medicinal Chemistry, doi://10.1016/j.bmc.2016.08.031 (2016)
Skin microbiome before development of atopic dermatitis: Early colonization with commensal staphylococci at 2 months is associated with a lower risk of atopic dermatitis at 1 year s: Kennedy EA, Connolly J, O'B Hourihane J, Fallon PG, McLean WI, Murray D, Jo J-H, Segre JA, Kong HH, Irvine AD J. Allergy and Clinical Immunology , doi: 10.1016/j.jaci.2016.07.029 (2016)
Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster Hangnoh Lee, Dong-Yeon Cho, Cale Whitworth, Robert Eisman, Melissa Phelps, John Roote, Thomas Kaufman, Kevin Cook, Steven Russell, Teresa Przytycka, Brian Oliver PLoS Genetics, doi://10.1371/journal.pgen.1006295 (2016)
Diverse Human Skin Fungal Communities in Children Converge in Adulthood Jo, JH; Deming, C; Kennedy, EA et al. J. Invest. Dermatol., DOI://10.1016/j.jid.2016.05.130 (2016)
A Model for Transposition of the Colistin Resistance Gene mcr-1 by ISApl1 Snesrud, E; He, S; Chandler, M et al. Antimicrob. Agents Chemother., DOI://10.1128/AAC.01457-16 (2016)
Transferability of genome-wide associated loci for asthma in African Americans Faruque, MU; Chen, G; Doumatey, AP et al. J Asthma, DOI://10.1080/02770903.2016.1188941 (2016)

Biallelic hypomorphic mutations in a linear deubiquitinase define otulipenia, an early-onset autoinflammatory disease Zhou, Q; Yu, X; Demirkaya, E et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1612594113 (2016)
GWAS analysis of handgrip and lower body strength in older adults in the CHARGE consortium Matteini, AM; Tanaka, T; Karasik, D et al. Aging Cell, DOI://10.1111/acel.12468 (2016)
Quantifying antiepileptic drug effects using intrinsic excitability measures Christian Meisel, Dietmar Plenz, Andreas Schulze-Bonhage, Heinz Reichmann Epilepsia, DOI: 10.1111/epi.13517 (2016)
Genetic causes of moderate to severe hearing loss point to modifiers S. Naz, A. Imtiaz et al. Clinical Genetics, DOI: 10.1111/cge.12856 (2016)
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The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities Afonin, KA; Viard, M; Tedbury, P et al. Nano Lett., DOI://10.1021/acs.nanolett.5b04676 (2016)
Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning Hoo-Chang Shin Holger R. Roth ; Mingchen Gao ; Le Lu ; Ziyue Xu ; Isabella Nogues ; Jianhua Yao ; Daniel Mollura ; Ronald M. Summers IEEE Transactions on Medical Imaging, OI 10.1109/TMI.2016.2528162 (2016)
Preterm birth and air pollution: Critical windows of exposure for women with asthma Pauline Mendola, Maeve Wallace, Beom Seuk Hwang, Danping Liu, Candace Robledo, Tuija Mӓnnistö, Rajeshwari Sundaram, Seth Sherman, Qi Ying, Katherine L. Grantz J. Allergy Clin. Immunology, doi:10.1016/j.jaci.2015.12.1309 (2016)
Necdin is a breast cancer metastasis suppressor that regulates the transcription of c-Myc Minnkyong Lee, Sarah M. Beggs, Derek Gildea, Sujata Bupp, Jens Lichtenberg, Niraj S. Trivedi, NISC Comparative Sequencing Program, Ying Hu, David M. Bodine, and Nigel P.S. Crawford1 Oncotarget, doi: 10.18632/oncotarget.5230 (2016)

Genome-wide footprinting: ready for prime time? Myong-Hee Sung, Songjoon Baek & Gordon L Hager Nature Methods, doi:10.1038/nmeth.3766 (2016)
A Comparison of Methods to Reweight from Classical Molecular Simulations to QM/MM Potentials Eric Christopher Dybeck, Gerhard König, Bernard R. Brooks, and Michael R. Shirts J. Chem. Theory. Comput, DOI: 10.1021/acs.jctc.5b01188 (2016)
Multistrand Structure Prediction of Nucleic Acid Assemblies and Design of RNA Switches Eckart Bindewald, Kirill A. Afonin, Mathias Viard, Paul Zakrevsky, Taejin Kim, and Bruce A. Shapiro Nano Letters, DOI: 10.1021/acs.nanolett.5b04651 (2016)
Understanding the Mechanism of the Hydrogen Abstraction from Arachidonic Acid Catalyzed by the Human Enzyme 15-Lipoxygenase-2. A Quantum Mechanics/Molecular Mechanics Free Energy Simulation Reynier Suardiaz, Pablo Garcia Jambrina, Laura Masgrau, Ángels Gonzàlez-Lafont, Edina Rosta, and Josè M. Lluch J. Chem. Theory. Comput, DOI: 10.1021/acs.jctc.5b01236 (2016)
Impact of time-of-day on brain morphometric measures derived from T₁-weighted magnetic resonance imaging Aaron Trefler, Neda Sadeghi, Adam G. Thomas, Carlo Pierpaoli, Chris I. Baker, Cibu Thomas Neuroimage, doi:10.1016/j.neuroimage.2016.02.034 (2016)
Production of small cysteine-rich effector proteins in Escherichia coli for structural and functional studies Xiaoxiao Zhang, Neal Nguyen, Susan Breen, Megan A. Outram, Peter N. Dodds, Bostjan Kobe, Peter S. Solomon and Simon J. Williams Molecular Plant Pathology, DOI: 10.1111/mpp.12385 (2016)

Deubiquitylation of protein cargo is not an essential step in exosome formation Alyssa R. Huebner, Lei Cheng, Poorichaya Somparn, Mark A. Knepper, Robert A. Fenton and Trairak Pisitkun Molecular and Cellular Proteomics, doi: 10.1074/mcp.M115.054965 (2016)
Enhancer of Rudimentary Cooperates with Conserved RNA-Processing Factors to Promote Meiotic mRNA Decay and Facultative Heterochromatin Assembly Sugiyama, T; Thillainadesan, G; Chalamcharla, VR et al. Mol. Cell, DOI://10.1016/j.molcel.2016.01.029 (2016)
Mechanism of Protein Molecule Isolation by IR Laser Ablation of Droplet Beam Kensuke Komatsu, Takuya Nirasawa, Mariko Hoshino-Nagasaka, and Jun-ya Kohno J. Phys. Chem. A, DOI: 10.1021/acs.jpca.5b10873 (2016)
A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes Grabundzija, I; Messing, SA; Thomas, J et al. Nat Commun, DOI://10.1038/ncomms10716 (2016)
A genome landscape of SRSF3-regulated splicing events and gene expression in human osteosarcoma U2OS cells Ajiro M, Jia R, Yang Y, Zhu J, Zheng ZM Nucleic Acids Res., DOI://10.1093/nar/gkv1500 (2016)
Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients Alena Gros, Maria R Parkhurst, Eric Tran, Anna Pasetto, Paul F Robbins, Sadia Ilyas, Todd D Prickett, Jared J Gartner, Jessica S Crystal, Ilana M Roberts, Kasia Trebska-McGowan, John R Wunderlich, James C Yang & Steven A Rosenberg Nature Medicine, doi:10.1038/nm.4051 (2016)

Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts Liang Ma, Zehua Chen, Da Wei Huang et. al. Nature Communications, doi:10.1038/ncomms10740 (2016)
Gene-Based Association Analysis for Censored Traits Via Fixed Effect Functional Regressions. Fan R, Wang Y, Yan Q, Ding Y, Weeks DE, Lu Z, Ren H, Cook RJ, Xiong M, Swaroop A, Chew EY, Chen W Genet Epidemiol. , doi: 10.1002/gepi.21947 (2016)
Finite sample pointwise confidence intervals for a survival distribution with right-censored data Michael P. Fay and Erica H. Brittain Statistics in Medicine, DOI: 10.1002/sim.6905 (2016)
Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept Franke, B; Stein, JL; Ripke, S et al. Nat. Neurosci., DOI://10.1038/nn.4228 (2016)
High-throughput single-molecule screen for small-molecule perturbation of splicing and transcription kinetics Day CR, Chen H, Coulon A, Meier JL, Larson DR, Methods, DOI://10.1016/j.ymeth.2015.11.025 (2016)
Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing Yu-Chih Tsai, Sean Conlan, Clayton Deming, NISC Comparative Sequencing Program, Julia A. Segre, Heidi H. Kong Jonas Korlach, and Julia Oh mBio, doi: 10.1128/mBio.01948-15 (2016)

Recessive mutations of TMC1 associated with moderate to severe hearing loss Ayesha Imtiaz , Azra Maqsood , Atteeq U. Rehman, Robert J. Morell, Jeffrey R. Holt, Thomas B. Friedman, Sadaf Naz Neurogenetics, DOI 10.1007/s10048-016-0477-1 (2016)
Light-regulated Molecular Trafficking in a Synthetic Water-soluble Host Jesús del Barrio, Sean T. J. Ryan, Pablo G. Jambrina, Edina Rosta, and Oren A Scherman JACS, DOI: 10.1021/jacs.5b11642 (2016)
Cryo-EM Structures of the Magnesium Channel CorA Reveal Symmetry Break upon Gating Doreen Matthies, Olivier Dalmas, Mario J. Borgnia, Pawel K. Dominik, Alan Merk, Prashant Rao, Bharat G. Reddy, Shahidul Islam, Alberto Bartesaghi, Eduardo Perozo, Sriram Subramaniam Cell, doi:10.1016/j.cell.2015.12.055 (2016)
Structural insights into the mechanism of activation of the TRPV1 channel by a membrane-bound tarantula toxin Chanhyung Bae, Claudio Anselmi, Jeet Kalia, Andres Jara-Oseguera, Charles D Schwieters, Dmitriy Krepkiy ,Chul Won Lee, Eun-Hee Kim, Jae Il Kim, Josè D Faraldo-Gòmez and Kenton J Swartz eLife, DOI: http://dx.doi.org/10.7554/eLife.11273 (2016)
Self-aggregation and coaggregation of the p53 core fragment with its aggregation gatekeeper variant Jiangtao Lei , Ruxi Qi , Guanghong Wei , Ruth Nussinov and Buyong Ma Phys. Chem. Chem. Phys., DOI: 10.1039/C5CP06538K (2016)
Cutting Edge: Expression of IRF8 in Gastric Epithelial Cells Confers Protective Innate Immunity against Helicobacter pylori Infection Yan, M; Wang, H; Sun, J et al. J. Immunol., DOI://10.4049/jimmunol.1500766 (2016)

Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation Thompson B, Varticovski L, Baek S, Hager GL PLoS ONE, DOI://10.1371/journal.pone.0148619 (2016)
Vibratory Urticaria Associated with a Missense Variant in ADGRE2 Boyden, SE; Desai, A; Cruse, G et al. N. Engl. J. Med., DOI://10.1056/NEJMoa1500611 (2016)
Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology Zhao Z, Martin C, Fan R, Bourne PE, Xie L BMC Bioinformatics, DOI://10.1186/s12859-016-0941-9 (2016)
Identifying subgroups of enhanced predictive accuracy from longitudinal biomarker data by using tree-based approaches: applications to fetal growth Jared C. Foster, Danping Liu, Paul S. Albert and Aiyi Liu Journal of the Royal Statistical Society: Series A (Statisti, 10.1111/rssa.12182 (2016)
How Does Hyperphopsphorylation Promote Tau Aggregation and Modulate Filament Structure and Stability? Liang Xu, Jie Zheng, Martin Margittai, Ruth Nussinov, and Buyong Ma ACS Chemical Neuroscience, 10.1021/acschemneuro.5b00294 (2016)
In vivo tissue has non-linear rheological behavior distinct from 3D biomimetic hydrogels, as determined by AMOTIV microscopy Blehm BH, Devine A, Staunton JR, Tanner K Biomaterials, DOI://10.1016/j.biomaterials.2015.12.019 (2016)

Meta-analysis of Genome-Wide Association Studies for Extraversion: Findings from the Genetics of Personality Consortium van den Berg, SM; de Moor, MH; Verweij, KJ et al. Behav. Genet., DOI://10.1007/s10519-015-9735-5 (2016)
Draft Genome Sequence of a Klebsiella pneumoniae Carbapenemase-Positive Sequence Type 111 Pseudomonas aeruginosa Strain Dotson GA, , Dekker JP, Palmore TN, Segre JA, Conlan S Genome Announc, DOI://10.1128/genomeA.01663-15 (2016)
The Histone Variant MacroH2A1.2 Is Necessary for the Activation of Muscle Enhancers and Recruitment of the Transcription Factor Pbx1 Dell'Orso, S; Wang, AH; Shih, HY et al. Cell Rep, 2211-1247 (2016)
Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice Davies, B; Hatton, E; Altemose, N et al. Nature, DOI://10.1038/nature16931 (2016)
r2VIM: A new variable selection method for random forests in genome-wide association studies Silke Szymczak, Emily Holzinger, Abhijit Dasgupta, James D. Malley, Anne M. Molloy, James L. Mills, Lawrence C. Brody, Dwight Stambolian and Joan E. Bailey-Wilson BioData Mining, 10.1186/s13040-016-0087-3 (2016)
Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance Gelio Alves, Guanghui Wang, Aleksey Y. Ogurtsov, Steven K. Drake, Marjan Gucek, Anthony F. Suffredini, David B. Sacks, Yi-Kuo Yu J Am Soc Mass Spectrom 27:194-210, 10.1007/s13361-015-1271-2 (2016)
CircInteractome: A web tool for exploring circular RNAs and their interacting proteins and microRNAs Dudekula, DB; Panda, AC; Grammatikakis, I; De, S; Abdelmohsen, K; Gorospe, M; RNA Biol, DOI://10.1080/15476286.2015.1128065 (2016)
Somatic mutational landscape of AML with inv(16) or t(8;21) identifies patterns of clonal evolution in relapse leukemia Sood, R; Hansen, NF; Donovan, FX et al. Leukemia, DOI://10.1038/leu.2015.141 (2016)
Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function Pattaro, C; Teumer, A; Gorski, M et al. Nat Commun, DOI://10.1038/ncomms10023 (2016)
Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels Kilpeläinen, TO; Carli, JF; Skowronski, AA et al. Nat Commun, DOI://10.1038/ncomms10494 (2016)
New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk Lu, Y; Day, FR; Gustafsson, S et al. Nat Commun, DOI://10.1038/ncomms10495 (2016)
Interaction of methylation-related genetic variants with circulating fatty acids on plasma lipids: a meta-analysis of 7 studies and methylation analysis of 3 studies in the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium Ma, Y; Follis, JL; Smith, CE et al. Am. J. Clin. Nutr., DOI://10.3945/ajcn.115.112987 (2016)

Is the MC1R variant p. R160W associated with Parkinson's? Lubbe, SJ; Escott-Price, V; Brice, A et al. Ann. Neurol., DOI://10.1002/ana.24527 (2016)
Comparison of the Conformations of KRAS Isoforms, K-Ras4A and K-Ras4B, Points to Similarities and Significant Differences Mayukh Chakrabarti, Hyunbum Jang, and Ruth Nussinov J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.5b11110 (2016)
Risk of End-stage Renal Disease in Patients with Lupus Nephritis, 1970 to 2015 A systematic review and Bayesian meta-analysis Maria G. Tektonidou, Abhijit Dasgupta and Michael M. Ward Arthritis and Rheumatology, DOI: 10.1002/art.39594 (2016)
Coupling of the Non-Amyloid-Component (NAC) Domain and the KTK(E/Q)GV Repeats Stabilize the α-Synuclein Fibrils Liang Xu, Ruth Nussinov, Buyong Ma Eur. J. Med. Chem. , doi:10.1016/j.ejmech.2016.01.044 (2016)
Novel nucleosomal particles containing core histones and linker DNA but no histone H1 Cole, HA; Cui, F; Ocampo, J et al. Nucleic Acids Res., DOI://10.1093/nar/gkv943 (2016)
The TRAIL receptor agonist drozitumab targets basal B triple-negative breast cancer cells that express vimentin and Axl Dine, JL; O'Sullivan, CC; Voeller, D et al. Breast Cancer Res. Treat., DOI://10.1007/s10549-015-3673-z (2016)

Epigenetic regulation of hematopoiesis by DNA methylation Gore, AV; Athans, B; Iben, JR et al. Elife, DOI://10.7554/eLife.11813 (2016)
Role of the D1-D2 Linker of Human VCP/p97 in the Asymmetry and ATPase Activity of the D1-domain Tang WK, Xia D Sci Rep, DOI://10.1038/srep20037 (2016)
Genetic variants associated with response to lithium treatment in bipolar disorder: a genome-wide association study Liping Hou, Urs Heilbronner et al. Lancet, doi:10.1016/S0140-6736(16)00143-4 (2016)
Autosomal-Recessive Hearing Impairment due to Rare Missense Variants within S1PR2 Regie Lyn P. Santos-Cortez, Rabia Faridi, Atteeq U. Rehman et al. American Journal of Human Genetics, doi://10.1016/j.ajhg.2015.12.004 (2016)
Post-transcriptional Control of Tumor Cell Autonomous Metastatic Potential by CCR4-NOT Deadenylase CNOT7 Faraji, F; Hu, Y; Yang, HH et al. PLoS Genet., DOI://10.1371/journal.pgen.1005820 (2016)
Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool Thomas Hoenen, Allison Groseth, Kyle Rosenke et al. Emerging Infectious Diseases, doi: 10.3201/eid2202.151796. (2016)

Group 3 innate lymphoid cells continuously require the transcription factor GATA-3 after commitment Zhong, C; Cui, K; Wilhelm, C et al. Nat. Immunol., DOI://10.1038/ni.3318 (2016)
Mitochondrial Membrane Potential Identifies Cells with Enhanced Stemness for Cellular Therapy Sukumar, M; Liu, J; Mehta, GU et al. Cell Metab., DOI://10.1016/j.cmet.2015.11.002 (2016)
Reliability of 7T (1) H-MRS measured human prefrontal cortex glutamate, glutamine, and glutathione signals using an adapted echo time optimized PRESS sequence: A between- and within-sessions investigation Lally, N; An, L; Banerjee, D et al. J Magn Reson Imaging, DOI://10.1002/jmri.24970 (2016)
A meta-analysis of 120 246 individuals identifies 18 new loci for fibrinogen concentration de Vries, PS; Chasman, DI; Sabater-Lleal, M et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddv454 (2016)
Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes Lorenzi, H; Khan, A; Behnke, MS et al. Nat Commun, DOI://10.1038/ncomms10147 (2016)
PubChem Substance and Compound databases Kim, S; Thiessen, PA; Bolton, EE et al. Nucleic Acids Res., DOI://10.1093/nar/gkv951 (2016)
SBR-Blood: systems biology repository for hematopoietic cells Lichtenberg, J; Heuston, EF; Mishra, T; Keller, CA; Hardison, RC; Bodine, DM; Nucleic Acids Res., DOI://10.1093/nar/gkv1263 (2016)
GABBR1 and SLC6A1, Two Genes Involved in Modulation of GABA Synaptic Transmission, Influence Risk for Alcoholism: Results from Three Ethnically Diverse Populations Enoch, MA; Hodgkinson, CA; Shen, PH et al. Alcohol. Clin. Exp. Res., DOI://10.1111/acer.12929 (2016)
SDHB-Deficient Cancers: The Role of Mutations That Impair Iron Sulfur Cluster Delivery Saxena, N; Maio, N; Crooks, DR et al. J. Natl. Cancer Inst., DOI://10.1093/jnci/djv287 (2016)
Evolutionary Dynamics of Influenza A Viruses in US Exhibition Swine Nelson, MI; Wentworth, DE; Das, SR et al. J. Infect. Dis., DOI://10.1093/infdis/jiv399 (2016)

2015 (340 papers)

Bayesian dose-response analysis for epidemiological studies with complex uncertainty in dose estimation Deukwoo Kwon, F. Owen Hoffman, Brian E. Moroz, Steven L. Simon Statistics in Medicine, DOI: 10.1002/sim.6635 (2015)
Augmented trial designs for evaluation of principal surrogates Erin E. Gabriel and Dean Follmann Biostatistics, 10.1093/biostatistics/kxv055 (2015)

Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly Datta, SA; Clark, PK; Fan, L et al. J. Virol., DOI://10.1128/JVI.02061-15 (2015)
Multivariate classification of smokers and nonsmokers using SVM-RFE on structural MRI images Ding X, Yang Y, Stein EA, Ross TJ Hum Brain Mapp, DOI://10.1002/hbm.22956 (2015)
The higher level of complexity of K-Ras4B activation at the membrane Hyunbum Jang, Avik Banerjee, Tanmay S. Chavan, Shaoyong Lu, Jian Zhang, Vadim Gaponenko and Ruth Nussinov FASEB J. , doi: 10.1096/fj.15-279091 (2015)
Mixed group of Rhizobiales microbes in lung and blood of a patient with fatal pulmonary illness Shyh-Ching Lo, Guo-Chiuan Hung, Bing jie Li, Haiyan Lei, Tianwei Li, Kenjiro Nagamine, Shien Tsai, Mark J Zucker, Ludmilla Olesnicky Int J Clin Exp Patho, 8(11), 13834-13852. (2015)
Meta-analysis of Complex Diseases at Gene Level by Generalized Functional Linear Models Ruzong Fan, Yifan Wang, Chi-yang Chiu, Wei Chen, Haobo Ren, Yun Li, Michael Boehnke, Christopher I. Amos, Jason H. Moore, Momiao Xiong Genetics, DOI: 10.1534/genetics.115.180869 (2015)
TET-catalyzed oxidation of intragenic 5-methylcytosine regulates CTCF-dependent alternative splicing Ryan J Marina, David Sturgill, Marc A Bailly, Morgan Thenoz, Garima Varma, Maria F Prigge, Kyster K Nanan, Sanjeev Shukla, Nazmul Haque, Shalini Oberdoerffer EMBO J., DOI 10.15252/embj.201593235 (2015)

RNA Polymerase III Output Is Functionally Linked to tRNA Dimethyl-G26 Modification Arimbasseri, AG; Blewett, NH; Iben, JR et al. PLoS Genet., DOI://10.1371/journal.pgen.1005671 (2015)
Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design Jason Gorman, Cinque Soto, Max M Yang, et al. Nature Structural and Molecular Biology, doi:10.1038/nsmb.3144 (2015)
ADAR2 affects mRNA coding sequence edits with only modest effects on gene expression or splicing in vivo Allissa A. Dillman, Mark R. Cookson & Dagmar Galter RNA Biology, DOI://10.1080/15476286.2015.1110675 (2015)
Controlled DNA double-strand break induction in mice reveals post-damage transcriptome stability Jeongkyu Kim, David Sturgill, Andy D. Tran, David A. Sinclair and Philipp Oberdoerffer Nucleic Acids Research, doi: 10.1093/nar/gkv1482 (2015)
Distributed acoustic cues for caller identity in macaque vocalization Makoto Fukushima, Alex M. Doyle, Matthew P. Mullarkey, Mortimer Mishkin, Bruno B. Averbeck Royal Society Open Science, DOI: 10.1098/rsos.150432 (2015)
Socioeconomic disadvantage and neural development from infancy through early childhood Chin-Lun Hung, G; Hahn, J; Alamiri, B et al. Int J Epidemiol, DOI://10.1093/ije/dyv303 (2015)

Directed and persistent movement arises from mechanochemistry of the ParA/ParB system Hu L, Vecchiarelli AG, Mizuuchi K, Neuman KC, Liu J Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1505147112 (2015)
Assessment of established HDL-C loci for association with HDL-C levels and type 2 diabetes in Pima Indians Anup K. Nair, Paolo Piaggi, Nellie A. McLean, Manmeet Kaur, Sayuko Kobes, William C. Knowler, Clifton Bogardus, Robert L. Hanson, Leslie J. Baier Diabetologia, doi://10.1007/s00125-015-3835-x (2015)
Genome-wide association study identifies African-ancestry specific variants for metabolic syndrome Tekola-Ayele, F; Doumatey, AP; Shriner, D et al. Mol. Genet. Metab., DOI://10.1016/j.ymgme.2015.10.008 (2015)
High-Affinity Interaction of the K-Ras4B Hypervariable Region with the Ras Active Site Tanmay S. Chavan, Hyunbum Jang, Lyuba Khavrutskii, Sherwin J. Abraham, Avik Banerjee, Benjamin C. Freed, Liv Johannessen, Sergey G. Tarasov, Vadim Gaponenko, Ruth Nussinov4, Nadya I. Tarasova Biophys. J. , doi:10.1016/j.bpj.2015.09.034 (2015)
Coupling between histone conformations and DNA geometry in nucleosomes on a microsecond timescale: atomistic insights into nucleosome functions Alexey K. Shaytan, Grigoriy A. Armeev, Alexander Goncearenco, Victor B. Zhurkin, David Landsman, Anna R. Panchenko J. Mol. Biol., doi:10.1016/j.jmb.2015.12.004 (2015)
Evolutionary context for the association of γ-globin, serum uric acid, and hypertension in African Americans Shriner, D; Kumkhaek, C; Doumatey, AP et al. BMC Med. Genet., DOI://10.1186/s12881-015-0249-z (2015)

Drug-Protein Hydrogen Bonds Govern the Inhibition of the ATP Hydrolysis of the Multidrug Transporter P-glycoprotein Eduardo E. Chufan, Khyati Kapoor, Suresh V. Ambudkar Biochemical Pharmacology, doi:10.1016/j.bcp.2015.12.007 (2015)
MYCN controls an alternative RNA splicing program in high-risk metastatic neuroblastoma Shile Zhang, Jun S. Wei1 , Samuel Q. Li , Tom C. Badgett , Young K. Song , Saurabh Agarwal , Cristian Coarfa , Catherine Tolman , Laura Hurd , Hongling Liao , Jianbin He , Xinyu Wen , Zhihui Liu , Carol J. Thiele , Frank Westermann , Shahab Asgharzadeh , Robert C. Seeger , John M. Maris , Jamie M. Guidry Auvil , Malcolm A. Smith , Eric D. Kolaczyk , Jason Shohet , Javed Khan Cancer Letters, doi://10.1016/j.canlet.2015.11.045 (2015)
Multi-modal characterization of rapid anterior hippocampal volume increase associated with aerobic exercise Adam G. Thomas, Andrea Dennis, Nancy B. Rawlings, Charlotte J. Stagg, Lucy Matthews, Martyn Morris, Shannon H. Kolind, Sean Foxley, Mark Jenkinson, Thomas E. Nichols, Helen Dawes, Peter A. Bandettini, Heidi Johansen-Berg NeuroImage, doi:10.1016/j.neuroimage.2015.10.090 (2015)
Allosteric stabilization of the amyloid-β peptide hairpin by the fluctuating N-terminal Liang Xu , Ruth Nussinov and Buyong Ma Chem. Commun., DOI: 10.1039/C5CC08107F (2015)
Intrinsic excitability measures track antiepileptic drug action and uncover increasing/decreasing excitability over the wake/sleep cycle Christian Meisel, Andreas Schulze-Bonhage, Dean Freestone, Mark James Cook, Peter Achermann, Dietmar Plenz PNAS, doi: 10.1073/pnas.1513716112 (2015)
Transcriptional and Chromatin Regulation during Fasting - The Genomic Era Goldstein I, Hager GL Trends Endocrinol. Metab., DOI://10.1016/j.tem.2015.09.005 (2015)
Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Bacillus amyloliquefaciens BS006 Rocío M. Gamez, Fernando Rodríguez, Johan F. Bernal, Richa Agarwala, David Landsman, Leonardo Mariño-Ramírez Genome Announc., doi: 10.1128/genomeA.01391-15 (2015)
Evaluation of Genome Wide Association Study Associated Type 2 Diabetes Susceptibility Loci in Sub Saharan Africans Adeyemo, AA; Tekola-Ayele, F; Doumatey, AP et al. Front Genet, DOI://10.3389/fgene.2015.00335 (2015)
HIV Therapeutics and Methods of Making and Using Same Paolo Lusso and Raffaelo Cimbro Patent, United States Patent Application 20150313990 (2015)
NCICT: a computational solution to estimate organ doses for pediatric and adult patients undergoing CT scans Choonsik Lee, Kwang Pyo Kim, Wesley E Bolch, Brian E Moroz and Les Folio J. Radiological Protection, doi:10.1088/0952-4746/35/4/891 (2015)
Reduction of All-Atom Protein Folding Dynamics to One-Dimensional Diffusion Wenwei Zheng and Robert B. Best J. Phys. Chem. , DOI: 10.1021/acs.jpcb.5b09741 (2015)
Transient misfolding dominates multidomain protein folding Alessandro Borgia, Katherine R. Kemplen, Madeleine B. Borgia, Andrea Soranno, Sarah Shammas, Bengt Wunderlich, Daniel Nettels, Robert B. Best, Jane Clarke & Benjamin Schuler Nature Communications, doi:10.1038/ncomms9861 (2015)

Replicate exome-sequencing in a multiple-generation family: improved interpretation of next-generation sequencing data Praveen F. Cherukuri, Valerie Maduro, Karin V. Fuentes-Fajardo, Kevin Lam, David R. Adams, Cynthia J. Tifft, James C. Mullikin, William A. Gahl, Cornelius F. Boerkoel and NISC Comparative Sequencing Program BMC Genomics, doi:10.1186/s12864-015-2107-y (2015)
HLA-DRB1*11 and variants of the MHC class II locus are strong risk factors for systemic juvenile idiopathic arthritis Michael J. Ombrello, Elaine F. Remmers, Ioanna Tachmazidou et al and the International Childhood Arthritis Genetics (INCHARGE) Consortium PNAS, doi: 10.1073/pnas.1520779112 (2015)
Estimation of interaction effects using pooled biospecimens in a case-control study Michelle R. Danaher, Paul S. Albert, Aninyda Roy and Enrique F. Schisterman Statistics in Medicine, DOI: 10.1002/sim.6798 (2015)
Epstein-Barr virus from Burkitt Lymphoma biopsies from Africa and South America share novel LMP-1 promoter and gene variations Lei H, Li T, Li B, Tsai S, Biggar RJ, Nkrumah F, Neequaye J, Gutierrez M, Epelman S, Mbulaiteye SM, Bhatia K, Lo SC Sci Rep., doi: 10.1038/srep16706 (2015)
A 3D Searchable Database of Transgenic Zebrafish Gal4 and Cre Lines for Functional Neuroanatomy Studies Gregory D. Marquart, Kathryn M. Tabor, Mary Brown, Jennifer L. Strykowski, Gaurav K. Varshney, Matthew C. LaFave, Thomas Mueller, Shawn M. Burgess, Shin-ichi Higashijima and Harold A. Burgess Frontiers in Neural Circuits, doi://10.3389/fncir.2015.00078 (2015)
A Novel MHC-I Surface Targeted for Binding by the MCMV m06 Immunoevasin Revealed by Solution NMR Sgourakis NG, May NA, Boyd LF, Ying J, Bax A, Margulies DH J. Biol. Chem., DOI://10.1074/jbc.M115.689661 (2015)

GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site Lu S, Banerjee A, Jang H, Zhang J, Gaponenko V, Nussinov R J. Biol. Chem., DOI://10.1074/jbc.M115.664755 (2015)
Epidermal devices for noninvasive, precise, and continuous mapping of macrovascular and microvascular blood flow Webb, RC; Ma, Y; Krishnan, S et al. Sci Adv, DOI://10.1126/sciadv.1500701 (2015)
Clinical feasibility of using mean apparent propagator (MAP) MRI to characterize brain tissue microstructure Alexandru V. Avram, Joelle E. Sarlls, Alan S. Barnett, Evren Özarslan, Cibu Thomas, M. Okan Irfanoglu, Elizabeth Hutchinson, Carlo Pierpaoli, Peter J. Basser NeuroImage, doi:10.1016/j.neuroimage.2015.11.027 (2015)
Aurora B kinase is a potent and selective target in MYCN-driven neuroblastoma Bogen, D; Wei, JS; Azorsa, DO et al. Oncotarget, DOI://10.18632/oncotarget.6208 (2015)
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Molecular profiling and targeted therapy for advanced thoracic malignancies: a biomarker-derived, multiarm, multihistology phase II basket trial Lopez-Chavez A, Thomas A, Rajan A, Raffeld M, Morrow B, Kelly R, Carter CA, Guha U, Killian K, Lau CC, Abdullaev Z, Xi L, Pack S, Meltzer PS, Corless CL, Sandler A, Beadling C, Warrick A, Liewehr DJ, Steinberg SM, Berman A, Doyle A, Szabo E, Wang Y, Giaccone G J Clin Oncol. , doi: 10.1200/JCO.2014.58.2007 (2015)
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Commensal-dendritic-cell interaction specifies a unique protective skin immune signature Naik S, Bouladoux N, Linehan JL, Han SJ, Harrison OJ, Wilhelm C, Conlan S, Himmelfarb S, Byrd AL, Deming C, Quinones M, Brenchley JM, Kong HH, Tussiwand R, Murphy KM, Merad M, Segre JA, Belkaid Y Nature, doi: 10.1038/nature14052 (2015)
Automated prostate cancer detection using T2-weighted and high-b-value diffusion-weighted magnetic resonance imaging Jin Tae Kwak, Sheng Xu, Bradford J. Wood, Baris Turkbey, Peter L. Choyke, Peter A. Pinto, Shijun Wang and Ronald M. Summers Medical Physics, doi://10.1118/1.4918318 (2015)
SNPfisher: tools for probing genetic variation in laboratory-reared zebrafish Matthew G. Butler, James R. Iben, Kurt C. Marsden, Jonathan A. Epstein, Michael Granato and Brant M. Weinstein Development, doi: 10.1242/dev.118786 (2015)
X Chromosome and Autosome Dosage Responses in Drosophila melanogaster Heads Zhen-Xia Chen and Brian Oliver Genes | Genomes | Genetics, doi://10.1534/g3.115.017632 (2015)
Dissecting the Roles of MicroRNAs in Coronary Heart Disease via Integrative Genomic Analyses Tianxiao Huan, Jian Rong, Kahraman Tanriverdi, Qingying Meng, Anindya Bhattacharya, David D. McManus, Roby Joehanes, Themistocles L. Assimes, Ruth McPherson, Nilesh J. Samani, Jeanette Erdmann, Heribert Schunkert, Coronary ARteryDIsease Genome wide Replication and Meta-analysis (CARDIoGRAM) Consortium, Paul Courchesne, Peter J. Munson, Andrew D. Johnson, Christopher J. O'Donnell, Bin Zhang, Martin G. Larson, Jane E. Freedman, Daniel Levy, Xia Yang Arteriosclerosis, Thrombosis, and Vascular Biology, doi: 10.1161/ATVBAHA.114.305176 (2015)
Mutations decouple proton transfer from phosphate cleavage in the dUTPase catalytic reaction Anna Lopata, Pablo G. Jambrina, Pankaz K. Sharma, Bernard R. Brooks, Judit Toth, Beata G. Vertessy, and Edina Rosta ACS Catalysis, DOI: 10.1021/cs502087f (2015)

Pleiotropy Analysis of Quantitative Traits at Gene Level by Multivariate Functional Linear Models Wang Y, Liu A, Mills JL, Boehnke M, Wilson AF, Bailey-Wilson JE, Xiong M, Wu CO, Fan R Genet Epidemiol., doi: 10.1002/gepi.21895 (2015)
Modeling the effect of codon translation rates on co-translational protein folding mechanisms of arbitrary complexity Luca Caniparoli and Edward P. O'Brien J. Chem. Phys., doi://10.1063/1.4916914 (2015)
A Functional Data Analysis Approach for Circadian Patterns of Activity of Teenage Girls Ruzong Fan, Victoria Chen, Yunlong Xie, Lanlan Yin, Sungduk Kim, Paul S Albert, Bruce Simons-Morton J. Circadian Rhythms, DOI: 10.5334/jcr.ac (2015)
Continual Reintroduction of Human Pandemic H1N1 Influenza A Viruses into Swine in the United States, 2009 to 2014 Martha I. Nelson, Jered Stratton, Mary Lea Killian, Alicia Janas-Martindale and Amy L. Vincent J. Virology, doi: 10.1128/JVI.00459-15 (2015)
Global migration of influenza A viruses in swine Martha I. Nelson, Cècile Viboud, Amy L. Vincent, Marie R. Culhane, Susan E. Detmer, David E. Wentworth, Andrew Rambaut, Marc A. Suchard, Edward C. Holmes & Philippe Lemey Nature Communications, doi:10.1038/ncomms7696 (2015)
Towards predicting metastatic progression of melanoma based on gene expression data Yuanyuan Li, Juno M. Krahn, Gordon P. Flake, David M. Umbach andLeping Li Pigment Cell and Melanoma Research, DOI: 10.1111/pcmr.12374 (2015)

An Integrated Bayesian Nonparametric Approach for Stochastic and Variability Orders in ROC Curve Estimation: An Application to Endometriosis Diagnosis Beom Seuk Hwang & Zhen Chena* J. Am. Stat. Assoc., DOI:10.1080/01621459.2015.1023806 (2015)
Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin David De Sancho, Adam Kubas, Po-Hung Wang, Jochen Blumberger, and Robert B. Best J. Chem. Theory Comput. , DOI: 10.1021/ct5011455 (2015)
Genome-wide identification of microRNA expression quantitative trait loci Tianxiao Huan, Jian Rong, Chunyu Liu, Xiaoling Zhang, Kahraman Tanriverdi, Roby Joehanes, Brian H. Chen, Joanne M. Murabito, Chen Yao, Paul Courchesne, Peter J. Munson, Christopher J. O'Donnell, Nancy Cox, Andrew D. Johnson, Martin G. Larson, Daniel Levy & Jane E. Freedman Nature Communications, doi:10.1038/ncomms7601 (2015)
Molecular modeling of the human P2Y14 receptor: A template for structure-based design of selective agonist ligands Kevin Trujillo, Silvia Paoletta, Evgeny Kiselev, Kenneth A. Jacobson Bioorganic & Medicinal Chemistry, doi:10.1016/j.bmc.2015.03.042 (2015)
Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation Antonio Cardone, Aaron Bornstein, Harish C. Pant, Mary Brady, Ram Sriram and Sergio A. Hassan J. Computational Chemistry, DOI: 10.1002/jcc.23883 (2015)
An Apela RNA-Containing Negative Feedback Loop Regulates p53-Mediated Apoptosis in Embryonic Stem Cells Li M, Gou H, Tripathi BK, Huang J, Jiang S, Dubois W, Waybright T, Lei M, Shi J, Zhou M, Huang J Cell Stem Cell , doi: 10.1016/j.stem.2015.04.002 (2015)

Single-unit activity during natural vision: diversity, consistency, and spatial sensitivity among AF face patch neurons McMahon DB, Russ BE, Elnaiem HD, Kurnikova AI, Leopold DA J. Neurosci., DOI://10.1523/JNEUROSCI.3825-14.2015 (2015)
Expression, Activation and Characterization of Porcine Trypsin in Pichia pastoris GS115 Min Shu, Wei Shen, Xiaojuan Wang, Fei Wang, Lixin Ma, , Chao Zhai Protein Expression and Purification, Protein Expression and Purification (2015)
The Structure of an Oxalate Oxidoreductase Provides Insight into Microbial 2-Oxoacid Metabolism Marcus I. Gibson, Edward J. Brignole, Elizabeth Pierce, Mehmet Can Stephen W. Ragsdale, and Catherine L. Drennan Biochemistry, DOI: 10.1021/acs.biochem.5b00521 (2015)
Mutation rate and genotype variation of Ebola virus from Mali case sequences T. Hoenen, D. Safronetz, A. Groseth, K. R. Wollenberg, O. A. Koita, B. Diarra, I. S. Fall, F. C. Haidara, F. Diallo, M. Sanogo, Y. S. Sarro, A. Kone, A. C. G. Togo, A. Traore, M. Kodio, A. Dosseh, K. Rosenke, E. de Wit, F. Feldmann, H. Ebihara, V. J. Munster, K. C. Zoon, H. Feldmann, S. Sow Science, DOI: 10.1126/science.aaa5646 (2015)
Deep Sequencing in Microdissected Renal Tubules Identifies Nephron Segment-Specific Transcriptomes Jae Wook Lee, Chung-Lin Chou and Mark A. Knepper J. Am. Soc. Nephrology, doi: 10.1681/ASN.2014111067 (2015)
S Values for 131I based on the ICRP Adult Voxel Phantoms Stephanie Lamart, Steven L. Simon, Andre Bouville, Brian E. Moroz and Choonsik Lee Radiation Protection Dosimetry, doi: 10.1093/rpd/ncv016 (2015)
Engineering of customized meganucleases via in vitro compartmentalization and in cellulo optimization Ryo Takeuchi, Michael Choi, Barry L. Stoddard Methods Mol Biol., doi: 10.1007/978-1-4939-1862-1_6 (2015)
The relationship between glucose metabolism, resting-state fMRI BOLD signal, and GABAA-binding potential: a preliminary study in healthy subjects and those with temporal lobe epilepsy Nugent AC, Martinez A, D'Alfonso A, Zarate CA, Theodore WH J. Cereb. Blood Flow Metab., DOI://10.1038/jcbfm.2014.228 (2015)
Is visual registration equivalent to semiautomated registration in prostate biopsy Kwak, JT; Hong, CW; Pinto, PA et al. Biomed Res Int, DOI://10.1155/2015/394742 (2015)
Rare variants in neuronal excitability genes influence risk for bipolar disorder Ament SA, Szelinger S, Glusman G, Ashworth J, Hou L, Akula N, Shekhtman T, Badner JA, Brunkow ME, Mauldin DE, Stittrich AB, Rouleau K, Detera-Wadleigh SD, Nurnberger JI Jr, Edenberg HJ, Gershon ES, Schork N; Bipolar Genome Study, Price ND, Gelinas R, Hood L, Craig D, McMahon FJ, Kelsoe JR, Roach JC PNAS, doi: 10.1073/pnas.1424958112 (2015)
Computational and experimental studies of reassociating RNA/DNA hybrids containing split functionalities Afonin KA, Bindewald E, Kireeva M, Shapiro BA Methods Enzymol. , doi: 10.1016/bs.mie.2014.10.058 (2015)
Common genetic variants influence human subcortical brain structures Hibar DP, Stein JL, Renteria ME et al. Nature, doi: 10.1038/nature14101 (2015)

Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium Li Q, Wojciechowski R, Simpson CL et al. Human Genetics, doi: 10.1007/s00439-014-1500-y. (2015)
The bigger they are, the harder they fall: A topical review on sedimented solutes for solid-state NMR Enrico Ravera Concepts in Magnetic Resonance, DOI: 10.1002/cmr.a.21318 (2015)
Renal Type A Intercalated Cells Contain Albumin in Organelles with Aldosterone-Regulated Abundance Thomas Buus Jensen, Muhammad Umar Cheema, Agata Szymiczek, Helle Hasager Damkier, and Jeppe Praetorius PLoS One, doi: 10.1371/journal.pone.0124902 (2015)
A Meta-analysis of Gene Expression Signatures of Blood Pressure and Hypertension Tianxiao Huan , Tõnu Esko , Marjolein J. Peters et al. PLoS Genetics, DOI: 10.1371/journal.pgen.1005035 (2015)
Nucleus detection using gradient orientation information and linear least squares regression Jin Tae Kwak ; Stephen M. Hewitt ; Sheng Xu ; Peter A. Pinto ; Bradford J. Wood Proc. SPIE Medical Imaging 2015, doi:10.1117/12.2081413 (2015)
Characterization of the p300 Taz2-p53 TAD2 complex and comparison with the p300 Taz2-p53 TAD1 complex Miller Jenkins, LM; Feng, H; Durell, SR et al. Biochemistry, DOI://10.1021/acs.biochem.5b00044 (2015)

Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility Jennifer Wessel, Audrey Y Chu, Sara M Willems et al. Nature Communications, doi: 10.1038/ncomms6897 (2015)
A Rapid and Simple Screening Method to Identify Conditions for Enhanced Stability of Modular Vaccine Candidates Alemu Tekewe, Natalie K. Connorsa , Frank Sainsbury, Nani Wibowo, Linda H.L. Lua, Anton P.J. Middelberg Biochemical Engg. Journal, doi:10.1016/j.bej.2015.04.004 (2015)
Computational Structural Analysis of C-Terminal Residues of Proteins Containing Transmembrane Regions M.C. Rishyakulya, K.M. Saravanan Int. J. Comp. Biol. 4(1):44-54 (2015)
Clonality and Evolutionary History of Rhabdomyosarcoma Li Chen , Jack F. Shern , Jun S. Wei, Marielle E. Yohe, Young K. Song, Laura Hurd, Hongling Liao, Daniel Catchpoole, Stephen X. Skapek, Frederic G. Barr, Douglas S. Hawkins, Javed Khan PLos Genetics, DOI: 10.1371/journal.pgen.1005075 (2015)
Practice Structure Improves Unconscious Transitional Memories by Increasing Synchrony in a Premotor Network. Song S, Gotts SJ, Dayan E, Cohen LG. J. Cognitive Neuroscience, doi:10.1162/jocna00796 (2015)
Tissue- and time-dependent transcription in Ixodes ricinus salivary glands and midguts when blood feeding on the vertebrate host Kotsyfakis M, Schwarz A, Erhart J, Ribeiro JM Sci Rep, DOI://10.1038/srep09103 (2015)
Permutation Testing for Treatment-Covariate Interactions and Subgroup Identification Jared C. Foster, Bin Nan, Lei Shen, Niko Kaciroti, Jeremy M. G. Taylor Statistics in Bioscience, DOI 10.1007/s12561-015-9125-9 (2015)
Burden of Serious Infections in Adults With Systemic Lupus Erythematosus: A National Population-Based Study, 1996-2011 Maria G. Tektonidou, Zhong Wang, Abhijit Dasgupta and Michael M. Ward Arthritis Care and Research, DOI: 10.1002/acr.22575 (2015)
Synthesis and cell-selective antitumor properties of amino acid conjugated tumor-associated carbohydrate antigen-coated gold nanoparticles Biswas S, Medina SH, Barchi JJ Carbohydr. Res., DOI://10.1016/j.carres.2014.11.002 (2015)
Chromatin Architecture Reorganization during Stem Cell Differentiation Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanenkov VV, Ecker JR, Thomson JA, Ren B Nature, doi: 10.1038/nature14222 (2015)
Dependence of Internal Friction on Folding Mechanism Wenwei Zheng, David De Sancho, Travis Hoppe, and Robert B. Best JACS, DOI: 10.1021/ja511609u (2015)
Mechanisms of Membrane Binding of Small GTPase K-Ras4B Farnesylated Hypervariable Region Hyunbum Jang, Sherwin J. Abraham, Tanmay S. Chavan, Ben Hitchinson, Lyuba Khavrutskii, Nadya I. Tarasova, Ruth Nussinov and Vadim Gaponenko J. Biol. Chem. , doi: 10.1074/jbc.M114.620724 (2015)

Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity Minghui Li, Marharyta Petukh, Emil Alexov, and Anna R. Panchenko J Chem Theory Comput., doi: 10.1021/ct401022c (2015)
Quantitative residue-specific protein backbone torsion angle dynamics from concerted measurement of 3J couplings Lee JH, Li F, Grishaev A, Bax A. J Am Chem Soc. , doi: 10.1021/ja512593s (2015)
Genome accessibility is widely preserved and locally modulated during mitosis Hsiung CC, Morrissey CS, Udugama M, Frank CL, Keller CA, Baek S, Giardine B, Crawford GE, Sung MH, Hardison RC, Blobel GA Genome Res. , doi: 10.1101/gr.180646 (2015)
Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules Catherine M. Kelly , Julien Muzard , Bernard R. Brooks , Gil Lee and Nicolae-Viorel Buchete Phys. Chem. Chem. Phys., DOI: 10.1039/C4CP05307A (2015)
A Novel Tricyclic Ligand-Containing Nonpeptidic HIV-1 Protease Inhibitor, GRL-0739, Effectively Inhibits the Replication of Multidrug-Resistant HIV-1 Variants and Has a Desirable Central Nervous System Penetration Property In Vitro Masayuki Amano, Yasushi Tojo, Pedro Miguel Salcedo-Gòmez, Garth L. Parham, Prasanth R. Nyalapatla, Debananda Das, Arun K. Ghosh and Hiroaki Mitsuya Antimicrob Agents Chemother., doi: 10.1128/AAC.04757-14 (2015)
Identification of common genetic variants controlling transcript isoform variation in human whole blood Xiaoling Zhang, Roby Joehanes, Brian H Chen, Tianxiao Huan, Saixia Ying, Peter J Munson, Andrew D Johnson, Daniel Levy & Christopher J O'Donnell Nature Genetics, doi:10.1038/ng.3220 (2015)

Whole-genome sequencing to understand the genetic architecture of common gene expression and biomarker phenotypes Andrew R. Wood, Marcus A. Tuke, Mike Nalls et al. Hum Mol Genet., doi: 10.1093/hmg/ddu560 (2015)
Visualizing transient dark states by NMR spectroscopy Anthis NJ, Clore GM Q. Rev. Biophys., DOI://10.1017/S0033583514000122 (2015)
Functional MRI mapping of dynamic visual features during natural viewing in the macaque Russ BE, Leopold DA Neuroimage, DOI://10.1016/j.neuroimage.2015.01.012 (2015)
Analysis of the contribution of experimental bias, experimental noise, and inter-subject biological variability on the assessment of developmental trajectories in diffusion MRI studies of the brain Sadeghi, N; Nayak, A; Walker, L et al. Neuroimage, DOI://10.1016/j.neuroimage.2014.12.084 (2015)
Systems biology of polycystic kidney disease: a critical review Menezes LF, Germino GG Wiley Interdiscip Rev Syst Biol Med, DOI://10.1002/wsbm.1289 (2015)
High-Level Expression of Endo-β-N-Acetylglucosaminidase H from Streptomyces plicatus in Pichia pastoris and Its Application for the Deglycosylation of Glycoproteins Fei Wang, Xiaojuan Wang, Xiaolan Yu, Lin Fu, Yunyun Liu, Lixin Ma , Chao Zhai PLoS One, DOI: 10.1371/journal.pone.0120458 (2015)

A Genome-wide Association Study of Myasthenia Gravis Alan E. Renton, Hannah A. Pliner, Carlo Provenzano et al. JAMA Neurology, doi:10.1001/jamaneurol.2014.4103 (2015)
An Equilibrium Model for the Combined Effect of Macromolecular Crowding and Surface Adsorption on the Formation of Linear Protein Fibrils Travis Hoppe1, Allen P. Minton Biophys. J. , doi:10.1016/j.bpj.2014.12.033 (2015)
DNA methylation age of blood predicts all-cause mortality in later life Marioni, RE, Shah, S, McRae, AF, Chen, BH, Colicino, E, Harris, SE, Gibson, J, Henders, AK, Redmond, P, Cox, SR, Pattie, A, Corley, J, Murphy, L, Martin, NG, Montgomery, GW, Feinberg, AP, Fallin, M, Multhaup, ML, Jaffe, AE, Joehanes, R, Schwartz, J, Just, AC, Lunetta, KL, Murabito, JM, Starr, JM, Horvath, S, Baccarelli, AA, Levy, D, Visscher, PM, Wray, NR & Deary, IJ Genome Biology, doi://10.1186/s13059-015-0584-6 (2015)
Addressing population-specific multiple testing burdens in genetic association studies Sobota, RS; Shriner, D; Kodaman, N et al. Ann. Hum. Genet., DOI://10.1111/ahg.12095 (2015)
Stretch-Enhancers Delineate Disease-Associated Regulatory Nodes in T Cells Golnaz Vahedi, Yuka Kanno, Yasuko Furumoto, Kan Jiang, Stephen C. J. Parker, Michael R. Erdos, Sean R. Davis, Rahul Roychoudhuri, Nicholas P. Restifo, Massimo Gadina, Zhonghui Tang, Yijun Ruan, Francis S. Collins, Vittorio Sartorelli & John J. O'Shea Nature, doi:10.1038/nature14154 (2015)
Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD. Fetics SK, Guterres H, Kearney BM, Buhrman G, Ma B, Nussinov R, Mattos C Structure, doi: 10.1016/j.str.2014.12.017 (2015)

Dynamics of chromatin accessibility and long-range interactions in response to glucocorticoid pulsing Stavreva DA, Coulon A, Baek S, Sung MH, John S, Stixova L, Tesikova M, Hakim O, Miranda T, Hawkins M, Stamatoyannopoulos JA, Chow CC, Hager GL Genome Res. , doi: 10.1101/gr.184168.114 (2015)
Role of contingency in striatal response to incentive in adolescents with anxiety Benson BE, Guyer AE, Nelson EE, Pine DS, Ernst M Cogn Affect Behav Neurosci, DOI://10.3758/s13415-014-0307-6 (2015)
The NAD(+)-dependent SIRT1 deacetylase translates a metabolic switch into regulatory epigenetics in skeletal muscle stem cells Ryall, JG; Dell'Orso, S; Derfoul, A et al. Cell Stem Cell, DOI://10.1016/j.stem.2014.12.004 (2015)
Efficient Data Mining for Local Binary Pattern in Texture Image Analysis Jin Tae Kwak, , Sheng Xu , Bradford J. Wood Expert Systems with Applications, doi:10.1016/j.eswa.2015.01.055 (2015)
What's Next for Next-Gen Sequencing? MaryAnn Labant Genetic Engineering and Biotechnology News, doi:10.1089/gen.35.03.02. (2015)
Vasopressin-responsive miRNAs and AQP2-targeting miRNAs in kidney collecting duct cells Jae-Eun Kim , Hyun Jun Jung , Yu-Jung Lee , Tae-Hwan Kwon Am. J. Physiol. - Renal Physiol., DOI: 10.1152/ajprenal.00334.2014 (2015)
A highly potent human antibody neutralizes dengue virus serotype 3 by binding across three surface proteins Guntur Fibriansah, Joanne L. Tan et al. Nature Communications, doi:10.1038/ncomms7341 (2015)
Design, Synthesis, and Application of Spinach Molecular Beacons Triggered by Strand Displacement Sanchita Bhadra, Andrew D. Ellington Methods in Enzymology, doi:10.1016/bs.mie.2014.10.049 (2015)
Transcriptional profiles reveal a stepwise developmental program of memory CD8(+) T cell differentiation Roychoudhuri, R; Lefebvre, F; Honda, M et al. Vaccine, DOI://10.1016/j.vaccine.2014.10.007 (2015)
Optimizing the order of hypotheses in serial testing of multiple endpoints in clinical trials. Zhang Z, Wang C, Troendle JF. Stat. Med., doi: 10.1002/sim.6425. (2015)
CENP-A nucleosomes localize to transcription factor hotspots and subtelomeric sites in human cancer cells Rajbir K Athwal, Marcin P Walkiewicz, Songjoon Baek, Song Fu, Minh Bui, Jordi Camps, Thomas Ried, Myong-Hee Sung and Yamini Dalal Epigenetics and Chromatin, doi:10.1186/1756-8935-8-2 (2015)
Coupled-Cluster Studies of Extensive Green Fluorescent Protein Models Using the Reduced Virtual Space Approach Robert Send , Carl-Mikael Suomivuori , Ville R. I. Kaila , and Dage Sundholm J. Phys. Chem. B, DOI: 10.1021/jp5120898 (2015)

Myosin II controls cellular branching morphogenesis and migration in three dimensions by minimizing cell-surface curvature Elliott, H; Fischer, RS; Myers, KA et al. Nat. Cell Biol., DOI://10.1038/ncb3092 (2015)
Withdrawal from long-term methamphetamine self-administration 'normalizes' neurometabolites in rhesus monkeys: a (1) H MR spectroscopy study Yang S, Belcher AM, Chefer S, Vaupel DB, Schindler CW, Stein EA, Yang Y. Addict Biol., doi: 10.1111/adb.12078. (2015)
Antagonistic cross-regulation between Sox9 and Sox10 controls an anti-tumorigenic program in melanoma Shakhova, O; Cheng, P; Mishra, PJ et al. PLoS Genet., DOI://10.1371/journal.pgen.1004877 (2015)
Molecular basis of the polyspecificity of P-glycoprotein (ABCB1): recent biochemical and structural studies Chufan EE, Sim HM, Ambudkar SV Adv Cancer Res, doi: 10.1016/bs.acr.2014.10.003 (2015)
fMRI functional connectivity applied to adolescent neurodevelopment Ernst M, Torrisi S, Balderston N, Grillon C, Hale EA. Annu Rev Clin Psychol., doi: 10.1146/annurev-clinpsy-032814-112753 (2015)
A systematic heritability analysis of the human whole blood transcriptome. Huan T, Liu C, Joehanes R, Zhang X, Chen BH, Johnson AD, Yao C, Courchesne P, O'Donnell CJ, Munson PJ, Levy D. Human Genetics (2015)
Detecting Functional Connectivity during Audiovisual Integration with MEG: a Comparison of Connectivity Metrics. Ard TD, Carver F, Holroyd T, Horwitz B, Coppola R. Brain Connect. (2015)
Cerebro-cerebellar connectivity is increased in primary lateral sclerosis Meoded A, Morrissette AE, Katipally R, Schanz O, Gotts SJ, Floeter MK Neuroimage Clin, DOI://10.1016/j.nicl.2014.12.009 (2015)
Functional mapping of face-selective regions in the extrastriate visual cortex of the marmoset Hung, CC; Yen, CC; Ciuchta, JL et al. J. Neurosci., DOI://10.1523/JNEUROSCI.2659-14.2015 (2015)
Modulation of Alzheimer's Aβ protofilament-membrane interactions by lipid headgroups. Tofoleanu F, Brooks BR, Buchete NV. ACS Chem Neurosci., doi://abs/10.1021/cn500277f (2015)
Insights into the Mechanism of Inhibition of CXCR4: Identification of Piperidinylethanamine Analogs as Anti-HIV-1 Inhibitors Das D, Maeda K, Hayashi Y, Gavande N, Desai DV, Chang SB, Ghosh AK, Mitsuya H Antimicrob Agents Chemother., pii: AAC.04654-14. (2015)
Variable selection method for the identification of epistatic models Holzinger ER, Szymczak S, Dasgupta A, Malley J, Li Q, Bailey-Wilson JE Pac Symp Biocomput, 2335-6936 (2015)

CDD: NCBI's conserved domain database Marchler-Bauer, A; Derbyshire, MK; Gonzales, NR et al. Nucleic Acids Res., DOI://10.1093/nar/gku1221 (2015)
Analysis of soluble protein entry into primary cilia using semipermeabilized cells David K. Breslow, Maxence V. Nachury Methods in Cell Biology, doi:10.1016/bs.mcb.2014.12.006 (2015)
NRG1, ERBB4 and AKT1 Epistasis Increases Schizophrenia Risk and is Biologically Validated via Functional Neuroimaging in Healthy Controls Nicodemus KK, Law AJ, Radulescu E, Luna A, Kolachana B, Vakkalanka R, Rujescu D, Giegling I, Straub RE, McGee K, Gold B, Dean M, Muglia P, Callicott JH, Tan HY, Weinberger DR. Arch Gen Psychiatry, doi: 10.1001/archgenpsychiatry.2010.117 (2015)
Maturation of the HIV-1 core by a non-diffusional phase transition Frank GA, Narayan K, Bess JW Jr, Del Prete GQ, Wu X, Moran A, Hartnell LM, Earl LA, Lifson JD, Subramaniam S Nature Communications, doi: 10.1038/ncomms6854 (2015)
Meta-analysis of Correlated Traits via Summary Statistics from GWASs with an Application in Hypertension Xiaofeng Zhu, Tao Feng, Bamidele O. Tayo et al. Am J Hum Genet., doi: 10.1016/j.ajhg.2014.11.011. (2015)
Protein structural information derived from NMR chemical shift with the neural network program TALOS-N Shen Y, Bax A Methods Mol. Biol., DOI://10.1007/978-1-4939-2239-0_2 (2015)

BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones Kanno T, Kanno Y, LeRoy G, Campos E, Sun HW, Brooks SR, Vahedi G, Heightman TD, Garcia BA, Reinberg D, Siebenlist U, O'Shea JJ, Ozato K Nat Struct Mol Biol., doi: 10.1038/nsmb.2912 (2015)
Structures of oxalate oxidoreductase : C₂ activation by a microbial TPP-dependent ferredoxin oxidoreductase Gibson, Marcus Ian PhD Thesis, MIT Dept of Chemistry (2015)

2014 (191 papers)

Telomere attrition and candidate gene mutations preceding monosomy 7 in aplastic anemia. Dumitriu B, Feng X, Townsley DM, Ueda Y, Yoshizato T, Calado RT, Yang Y, Wakabayashi Y, Kajigaya S, Ogawa S, Zhu J, Young NS Blood, doi://10.1182/blood-2014-10-607572 (2014)
Polymorphism in Self-Assembly of Peptide-Based β-Hairpin Contributes to Network Morphology and Hydrogel Mechanical Rigidity Yifat Miller, Buyong Ma, and Ruth Nussinov J. Phys. Chem. B, DOI: 10.1021/jp511485n (2014)
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The Genomic Landscape of the Ewing Sarcoma Family of Tumors Reveals Recurrent STAG2 Mutation Andrew S. Brohl, David A. Solomon, Wendy Chang et al. PLoS Genetics, DOI: 10.1371/journal.pgen.1004475 (2014)
Spatial Localization of the Ebola Virus Glycoprotein Mucin-Like Domain Determined by Cryo-Electron Tomography Erin E. H. Tran, James A. Simmons, Alberto Bartesaghi, Charles J. Shoemaker, Elizabeth Nelson, Judith M. White and Sriram Subramaniam J. Virology, doi: 10.1128/JVI.00870-14 (2014)

Integrated Design of Antibodies for Systems Biology Using AbDesigner Trairak Pisitkun, Patrick Dummer, Poorichaya Somparn, Nattiya Hirankarn, Jeffrey B Kopp and Mark A Knepper Proteomics and Bioinformatics, doi://10.4172/jpb.1000307 (2014)
Parkinson's disease in GTP cyclohydrolase 1 mutation carriers Niccoló E. Mencacci, Ioannis U. Isaias, Martin M. Reich et al. Brain, doi: 10.1093/brain/awu179 (2014)
Brain Network Informed Subject Community Detection In Early-Onset Schizophrenia Zhi Yang, Yong Xu, Ting Xu, Colin W. Hoy, Daniel A. Handwerker, Gang Chen, Georg Northoff, Xi-Nian Zuo & Peter A. Bandettini Scientific Reports, doi:10.1038/srep05549 (2014)
Role of Albumin in the Formation and Stabilization of Nanoparticle Aggregates in Serum Studied by Continuous Photon Correlation Spectroscopy and Multiscale Computer Simulations Ashwinkumar A. Bhirde , Sergio A Hassan , Erick Harr , and Xiaoyuan Chen J. Phys. Chem. C, DOI: 10.1021/jp5034068 (2014)
Comparative validation of the D. melanogaster modENCODE transcriptome annotation ZX Chen, D Sturgill, J Qu, H Jiang et al. Genome Research, doi://10.1101/gr.159384.113 (2014)
Phosphoproteomic Analysis Reveals Regulatory Mechanisms at the Kidney Filtration Barrier Markus M. Rinschen, Xiongwu Wu, Tim K�nig, Trairak Pisitkun, Henning Hagmann, Caroline Pahmeyer, Tobias Lamkemeyer, Priyanka Kohli, Nicole Schnell, Bernhard Schermer, Stuart Dryer, Bernard R. Brooks, Pedro Beltrao, Marcus Krueger, Paul T. Brinkkoetter, Thomas Benzing J Am Soc Nephrol., doi: 10.1681/ASN.2013070760 (2014)

Common genetic variation in the glucokinase gene (GCK) is associated with type 2 diabetes and rates of carbohydrate oxidation and energy expenditure Muller YL, Piaggi P, Hoffman D, Huang K, Gene B, Kobes S, Thearle MS, Knowler WC, Hanson RL, Baier LJ, Bogardus C Diabetologia, doi: 10.1007/s00125-014-3234-8 (2014)
Task Dependence, Tissue Specificity, and Spatial Distribution of Widespread Activations in Large Single-Subject Functional MRI Datasets at 7T Javier Gonzalez-Castillo, Colin W. Hoy, Daniel A. Handwerker, Vinai Roopchansingh, Souheil J. Inati, Ziad S. Saad, Robert W. Cox and Peter A. Bandettini Cerebral Cortex, doi://10.1093/cercor/bhu148 (2014)
Corpus Callosum Size Is Highly Heritable in Humans, and May Reflect Distinct Genetic Influences on Ventral and Rostral Regions Girma Woldehawariat, Pedro E. Martinez, Peter Hauser, David M. Hoover, Wayne W. C. Drevets, Francis J. McMahon PLoS One, DOI: 10.1371/journal.pone.0099980 (2014)
Thermodynamic, Dynamic and Solvational Properties of PDEδ Binding to Farnesylated Cystein: A Model Study for Uncovering the Molecular Mechanism of PDEδ Interaction with Prenylated Proteins S. Suladze, S. Ismail, and R. Winter J. Phys. Chem. B, DOI: 10.1021/jp411466r (2014)
Inhibition of Paracoccidioides lutzii Pb01 Isocitrate Lyase by the Natural Compound Argentilactone and Its Semi-Synthetic Derivatives Renata Silva do Prado, Ricardo Justino Alves et al PLoS One, DOI: 10.1371/journal.pone.0094832 (2014)
Genome-wide association analysis identifies six new loci associated with forced vital capacity Loth DW, Artigas MS, Gharib SA et al. Nat Genet., doi: 10.1038/ng.3011. (2014)

Introductions and evolution of human-origin seasonal influenza A viruses in multinational swine populations Martha I. Nelson, David E. Wentworth, Marie R. Culhane, Amy L. Vincent, Cecile Viboud, Matthew P. LaPointe, Xudong Lin, Edward C. Holmes and Susan E. Detmer J. Virology, doi: 10.1128/JVI.01080-14 (2014)
The evolutionary dynamics of influenza A and B viruses in the tropical city of Managua, Nicaragua Martha I. Nelson, Angel Balmaseda, Guillermina Kuan, Saira Saborio, Xudong Lin, Rebecca A. Halpin, Timothy B. Stockwell, David E. Wentworth, Eva Harris, Aubree Gordon Virology, DOI: 10.1016/j.virol.2014.05.025 (2014)
Highly efficient production of peptides: N-glycosidase F for N-glycomics analysis Ling Hua, b, Xin Gao, Xiaopan Yang, Deyou Wan, Chunpeng He, Jiyue Cao, Haifeng Song Protein Expression and Purification, DOI: 10.1016/j.pep.2014.02.004 (2014)
Approaches to retrospective sampling for longitudinal transition regression models Sally Hunsberger, Paul S. Albert, and Marie Thoma Statistics and Its Interface 7:75-85, doi://10.4310/SII.2014.v7.n1.a9 (2014)
Identification and Characterization of Seminal Fluid Proteins in the Asian Tiger Mosquito, Aedes albopictus Kathryn E. Boes, José M. C. Ribeiro, Alex Wong, Laura C. Harrington, Mariana F. Wolfner, and Laura K. Sirot PLoS Neglected Tropical Diseases, doi: 10.1371/journal.pntd.0002946 (2014)
Marginal analysis of measurement agreement among multiple raters with non-ignorable missing ratings Zhen Chen and Yunlong Xie Statistics and Its Interface 7:113-120, doiL//10.4310/SII.2014.v7.n1.a12 (2014)

Linear mixed models for multiple outcomes using extended multivariate skew-t distributions Binbing Yu, A. James O'Malley, and Pulak Ghosh Statistics and Its Interface 7:101-111, doi://10.4310/SII.2014.v7.n1.a11 (2014)
Matched longitudinal analysis of biomarkers associated with survival Lori E. Dodd, Reed F. Johnson, Joseph E. Blaney and Dean Follmann Clinical & Vaccine Immunology, doi: 10.1128/CVI.00252-14 (2014)
Frontotemporal dementia and its subtypes: a genome-wide association study Ferrari R, Hernandez D, Nalls M et al. The Lancet Neurology, DOI: 10.1016/S1474-4422(14)70065-1 (2014)
Activity and Architecture of Pyroglutamate Modified Amyloid-β (AβpE3-42) Pores Alan L Gillman , Hyunbum Jang , Joon Lee , Srinivasan Ramachandran , Bruce L. Kagan , Ruth Nussinov , and Fernando Teran Arce J. Phys. Chem. B, DOI: 10.1021/jp5040954 (2014)
Computational Tools and Algorithms for Designing Customized Synthetic Genes Nathan Gould, Oliver Hendy, and Dimitris Papamichail Front Bioeng Biotechnol, doi: 10.3389/fbioe.2014.00041 (2014)
Role of LDB1 in the transition from chromatin looping to transcription activation. Krivega I, Dale RK, Dean A. Genes Dev., doi: 10.1101/gad.239749.114 (2014)

Implicit treatment of solvent dispersion forces in protein simulations Sergio A Hassan Journal of Computational Chemistry, DOI: 10.1002/jcc.23655 (2014)
Conscious recall of different aspects of skill memory Sunbin Song & Leonardo G Cohen Frontiers in Behavioural Neuroscience, doi:10.3389/fnbeh.2014.00233 (2014)
A novel role of CDX1 in embryonic epicardial development Chu M, Wang L, Wang H, Shen T, Yang Y, Sun Y, Tang N, Ni T, Zhu J, Mailman RB, Wang Y PLoS One, doi: 10.1371/journal.pone.0103271 (2014)
Pre-fusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy Alberto Bartesaghi, Alan Merk, Mario J. Borgnia, Jacqueline L. S. Milne, and Sriram Subramaniam Nat Struct Mol Biol., doi: 10.1038/nsmb.2711 (2014)
The spatial structure of resting state connectivity stability on the scale of minutes Javier Gonzalez-Castillo, Daniel A Handwerker, Meghan E. Robinson, Colin Wier Hoy, Laura Cathleen Buchanan, Ziad S Saad and Peter A Bandettini Frontiers in Neuroscience, DOI://10.3389/fnins.2014.00138 (2014)
The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner. King MR, Matzat LH, Dale RK, Lim SJ, Lei EP J. Cell. Sci., doi: 10.1242/jcs.151126 (2014)

Use of LC-MS/MS and Bayes' Theorem to Identify Protein Kinases That Phosphorylate Aquaporin-2 at Ser256 Davis Bradford, Viswanathan Raghuram, Justin L.L. Wilson, Chung-Lin Chou, Jason D. Hoffert, Mark A. Knepper, Trairak Pisitkun Am. J. Physiol. - Cell Physiol. , DOI: 10.1152/ajpcell.00377.2012 (2014)
miR-155 Activates Cytokine Gene Expression in Th17 Cells by Regulating the DNA-Binding Protein Jarid2 to Relieve Polycomb-Mediated Repression Thelma M. Escobar, Chrysi Kanellopoulou, David G. Kugler et al Immunity, doi://10.1016/j.immuni.2014.03.014 (2014)
Nill-Schiff base complex as an enzyme inhibitor of hen egg white lysozyme: a crystallographic and spectroscopic study Banabithi Koley Seth, Aurkie Ray, Sampa Biswas and Samita Basu Metallomics, DOI: 10.1039/C4MT00098F (2014)
Identification of the Genomic Insertion Site of Pmel-1 TCR α and β Transgenes by Next-Generation Sequencing Yun Ji, Natalie Abrams, Wei Zhu, Eddie Salinas, Zhiya Yu, Douglas C. Palmer, Parthav Jailwala, Zulmarie Franco, Rahul Roychoudhuri, Eric Stahlberg, Luca Gattinoni, Nicholas P. Restifo PLoS One, DOI: 10.1371/journal.pone.0096650 (2014)
Combination of longitudinal biomarkers in predicting binary events Danping Liu and Paul S Albert Biostatistics, doi: 10.1093/biostatistics/kxu020 (2014)
Rare missense variants in POT1 predispose to familial cutaneous malignant melanoma Shi J, Yang XR, Ballew B Nature Genetics, doi: 10.1038/ng.2941 (2014)

Pleiotropic genes for metabolic syndrome and inflammation Kraja AT, Chasman DI, North KE et al. Molecular Genetics & Metabolism, doi://10.1016/j.ymgme.2014.04.007 (2014)
Perturbation of nuclear spin polarizations in solid state NMR of nitroxide-doped samples by magic-angle spinning without microwaves Kent R. Thurber and Robert Tycko J. Chem. Phys. , DOI: 10.1063/1.4874341 (2014)
Rhythmic Bursting in the Pre-Bötzinger Complex: Mechanisms and Models Ilya A. Rybak, Yaroslav I. Molkov, Patrick E. Jasinski, Natalia A. Shevtsova, Jeffrey C. Smith Progress in Brain Research, doi://10.1016/B978-0-444-63274-6.00001-1 (2014)
Early targets of lithium in rat kidney inner medullary collecting duct include p38 and ERK1/2 Francesco Trepiccione, Trairak Pisitkun, Jason D Hoffert, Søren B Poulsen, Giovambattista Capasso, Søren Nielsen, Mark A Knepper, Robert A Fenton and Birgitte M Christensen Kidney International, doi: 10.1038/ki.2014.107 (2014)
Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I Ville R. I. Kaila, Mârten Wikström and Gerhard Hummer PNAS, doi: 10.1073/pnas.1319156111 (2014)
Hierarchical clustering of ryanodine receptors enables emergence of a calcium clock in sinoatrial node cells Michael D. Stern, Larissa A. Maltseva, Magdalena Juhaszova, Steven J. Sollott, Edward G. Lakatta, and Victor A. Maltsev J. Gen. Physiol. , doi: 10.1085/jgp.201311123 (2014)
Progress in the search for histidine acid phosphatase inhibitors in Francisella tularensis Ruoyi Pu DS Thesis, U. Texas (2014)
Conserved hydrogen-bonding network of P2 bis-tetrahydrofuran containing HIV-1 protease inhibitors (PI) with protease active site amino acid-backbone aid in their activity against PI-resistant HIV Ravikiran S. Yedidi, Harisha Garimella, Manabu Aoki, Hiromi Aoki, Darshan V. Desai, Simon B. Chang, David A. Davis, W. Sean Fyvie, Joshua D. Kaufman, David W. Smith, Debananda Das, Paul T. Wingfield, Kenji Maeda, Arun K. Ghosh and Hiroaki Mitsuya Antimicrob Agents Chemother., doi://10.1128/AAC.00107-14 (2014)
Non-invasive urinary metabolomic profiling identifies diagnostic and prognostic markers in lung cancer Ewy A Mathe, Andrew D Patterson, Majda Haznadar, Soumen K Manna, Kristopher W. Krausz, Elise D Bowman, Peter G. Shields, Jeffrey R. Idle, Philip B Smith, Katsuhiro Anami, Dickran Kazandjian, Emmanuel Hatzakis, Frank J Gonzalez, and Curtis C. Harris Cancer Res., doi:10.1158/0008-5472.CAN-14-0109 (2014)
Impact of subdomain D1 of the short form S1b of the human prolactin receptor on its inhibitory action on the function of the long form of the receptor induced by prolactin J.-H. Kang, S.A. Hassan, 1, P. Zhao, C.H. Tsai-Morris, M.L. Dufau Biochim. et Biophys. Acta, doi://10.1016/j.bbagen.2014.04.006 (2014)
A Fast and Powerful Tree-Based Association Test for Detecting Complex Joint Effects in Case-Control Studies Han Zhang, William Wheeler, Zhaoming Wang, Philip R. Taylor and Kai Yu Bioinformatics, doi://10.1093/bioinformatics/btu186 (2014)
Post-Translational Decrease in Respiratory Chain Proteins in the Polg Mutator Mouse Brain David N. Hauser, Allissa A. Dillman, Jinhui Ding, Yan Li, Mark R. Cookson PLoS One, DOI: 10.1371/journal.pone.0094646 (2014)

Studies on Inhibition of Respiratory Cytochrome bc1 Complex by the Fungicide Pyrimorph Suggest a Novel Inhibitory Mechanism Yu-Mei Xiao, Lothar Esser, Fei Zhou, Chang Li, Yi-Hui Zhou, Chang-An Yu, Zhao-Hai Qin, Di Xia PLoS One, DOI: 10.1371/journal.pone.0093765 (2014)
Regulation of a novel isoform of Receptor Expression Enhancing Protein REEP6 in rod photoreceptors by bZIP transcription factor NRL Hong Hao, Shobi Veleri, Bo Sun, Douglas S. Kim, Patrick W. Keeley, Jung-Woong Kim, Hyun-Jin Yang, Sharda P. Yadav, Souparnika H. Manjunath, Raman Sood, Paul Liu, Benjamin E. Reese and Anand Swaroop Human Molecular Genetics, doi: 10.1093/hmg/ddu143 (2014)
Distributed MRI reconstruction using gadgetron-based cloud computing Hui Xue, Souheil Inati, Thomas Sangild Sørensen, Peter Kellman and Michael S. Hansen Magnetic Resonance in Medicine, DOI: 10.1002/mrm.25213 (2014)
Hemoglobinopathic erythrocytes affect the intraerythrocytic multiplication of Plasmodium falciparum in vitro Svetlana Glushakova, Amanda Balaban, Philip G. McQueen, Rosane Coutinho, Jeffery L. Miller, Ralph Nossal, Rick M. Fairhurst, Joshua Zimmerberg J. Infectious Diseases, doi:10.1093/infdis/jiu203 (2014)
A potent anti-dengue human antibody preferentially recognizes the conformation of E protein monomers assembled on the virus surface Guntur Fibriansah, Joanne L Tan,Scott A Smith, Adamberage R Alwis, Thiam-Seng Ng, Victor A Kostyuchenko, Kristie D Ibarra, Jiaqi Wang, Eva Harris, Aravinda Silva, James E Crowe, and Shee-Mei Lok EMBO Molecular Medicine, doi: 10.1002/emmm.201303404 (2014)
A mixture of transition models for heterogeneous longitudinal ordinal data: with applications to longitudinal bacterial vaginosis data Kyeongmi Cheon, Marie E. Thoma, Xiangrong Kong and Paul S. Albert Statistics in Medicine, DOI: 10.1002/sim.6151 (2014)
Abdominal lymphadenopathy detection using random forest Kevin M. Cherry, Shijun Wang, Evrim B. Turkbey, Ronald M. Summers SPIE Proceedings, Volume 9035, Lung, Chest, and Abdomen II, doi:10.1117/12.2043837 (2014)
VTET: a variable threshold exact test for identifying disease-associated copy number variations enriched in short genomic regions Jianxin Shi, Xiaohong R. Yang, Neil E. Caporaso, Maria T. Landi, and Peng Li Frontiers in Genetics, doi://10.3389/fgene.2014.00053 (2014)
Accuracy Evaluation of the Unified P-Value from Combining Correlated P-Values Gelio Alves and Yi-Kuo Yu PLoS One, doi: 10.1371/journal.pone.0091225 (2014)
Differential Coding of Conspecific Vocalizations in the Ventral Auditory Cortical Stream Makoto Fukushima, Richard C. Saunders, David A. Leopold, Mortimer Mishkin, and Bruno B. Averbeck J. Neuroscience, doi: 10.1523/JNEUROSCI.3969-13.2014 (2014)
Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein Ville R. I. Kaila, Friedrich Schotte, Hyun Sun Cho, Gerhard Hummer & Philip A. Anfinrud Nature Chemistry, doi:10.1038/nchem.1898 (2014)
Practice and sleep form different aspects of skill Sunbin Song & Leonardo G. Cohen Nature Communications, doi:10.1038/ncomms4407 (2014)

Temperature-dependent solvation modulates the dimensions of disordered proteins René Wuttke, Hagen Hofmann, Daniel Nettels, Madeleine B. Borgia, Jeetain Mittal, Robert B. Best, and Benjamin Schuler PNAS, doi: 10.1073/pnas.1313006111 (2014)
Hypoosmotic Expression of Dunaliella bardawil ζ-Carotene Desaturase Is Attributed to a Hypoosmolarity-Responsive Element Different from Other Key Carotenogenic Genes Yong-Min Lao, Lan Xiao, Li-Xin Luo and Jian-Guo Jiang Plant Physiology, doi://10.1104/pp.114.235390 (2014)
Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue Jianxin Shi, Crystal N. Marconett, Jubao Duan et al. Nature Communications, doi:10.1038/ncomms4365 (2014)
Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs Hyunbum Jang, Fernando Teran Arce, Srinivasan Ramachandran, Bruce L. Kagan, Ratnesh Lal and Ruth Nussinov Chem. Soc. Rev., doi://10.1039/C3CS60459D (2014)
Abnormal cortical growth in schizophrenia targets normative modules of synchronized development Aaron F. Alexander-Bloch, Philip T. Reiss, Judith Rapoport, Harry McAdams, Jay N. Giedd, Ed T. Bullmore, Nitin Gogtay Biological Psychiatry, doi://10.1016/j.biopsych.2014.02.010 (2014)
Calcium Inhibition of Ribonuclease H1 Two-Metal Ion Catalysis Edina Rosta, Wei Yang, and Gerhard Hummer JACS, DOI: 10.1021/ja411408x (2014)

Multiscale free energy simulations: An efficient method for connecting classical MD simulations to QM or QM/MM free energies using Non-Boltzmann Bennett reweighting schemes Gerhard König, Phillip Stephen Hudson, Stefan Boresch, and H. Lee Woodcock J. Chem. Theory & Computation, DOI: 10.1021/ct401118k (2014)
A Network Characteristic That Correlates Environmental and Genetic Robustness Zeina Shreif, Vipul Periwal PLoS Computational Biology, DOI: 10.1371/journal.pcbi.1003474 (2014)
A GCH1 haplotype confers sex-specific susceptibility to pain crises and altered endothelial function in adults with sickle cell anemia Inna Belfer, Victoria Youngblood et al. Am. J. Hematology, DOI: 10.1002/ajh.23613 (2014)
Meta-analysis of Loci Associated with Age at Natural Menopause in African-American Women CTL Chen, C-T Liu, GK Chen, et al Human Molecular Genetics, doi: 10.1093/hmg/ddu041 (2014)
Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4 Gerhard König, Frank C. Pickard IV, Ye Mei, Bernard R. Brooks J. Computer-Aided Molecular Design, doi://10.1007/s10822-014-9708-4 (2014)
Predicting Stroke Through Genetic Risk Functions CA Ibrahim-Verbaas,M Fornage, JC Bis, et al Stroke, doi: 10.1161/STROKEAHA.113.003044 (2014)

Multilocus Genetic Risk Score Associates With Ischemic Stroke in Case-Control and Prospective Cohort Studies R Malik, S Bevan, M Nalls et al Stroke, doi: 10.1161/STROKEAHA.113.002938 (2014)
Reverse regression: A method for joint analysis of multiple endpoints in randomized clinical trials Zhiwei Zhang Statistica Sinica, doi://10.5705/ss.2010.111 (2014)
Using single cell sequencing data to model the evolutionary history of a tumor Kyung In Kim and Richard Simon BMC Bioinformatics :27, doi: 10.1186/1471-2105-15-27 (2014)
Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors Jack F. Shern, Li Chen, Juliann Chmielecki, et al. Cancer Discovery, doi:10.1158/2159-8290.CD-13-0639 (2014)
Fluorescence excitation and ultraviolet absorption spectra and theoretical calculations for benzocyclobutane: Vibrations and structure of its excited S1(π,π*) electronic state Hee Won Shin, Esther J. Ocola, Sunghwan Kim and Jaan Laane J. Chem. Phys., doi://10.1063/1.4858412 (2014)
Spectral Tuning of Rhodopsin and Visual Cone Pigments Xiuwen Zhou , Dage Sundholm , Tomasz Adam Wesolowski , and Ville R. I. Kaila J.Am.Chem.Soc., DOI: 10.1021/ja411864m (2014)

RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder N Akula, J Barb, X Jiang, J R Wendland, K H Choi, S K Sen, L Hou, D T W Chen, G Laje, K Johnson, B K Lipska, J E Kleinman, H Corrada-Bravo, S Detera-Wadleigh, P J Munson and F J McMahon Molecular Psychiatry, doi: 10.1038/mp.2013.170 (2014)

2013 (141 papers)

PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data Fahad Saeed, Trairak Pisitkun, Jason D Hoffert, Sara Rashidian, Guanghui Wang, Marjan Gucek and Mark A Knepper Proteome Sci. , doi: 10.1186/1477-5956-11-S1-S14 (2013)
Molecular insights into the reversible formation of tau protein fibrils Yin Luo, Paul Dinkel, Xiang Yu, Martin Margittai, Jie Zheng, Ruth Nussinov, Guanghong Wei and Buyong Ma Chem. Commun., DOI: 10.1039/C3CC00241A (2013)
Developing a library of recognition proteins using FimH as a protein scaffold Rochelle Nguyen Master's Thesis, U. Washington (2013)
Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation Kyong-Rim Kieffer-Kwon, Zhonghui Tang, Ewy Mathe et al. Cell, doi://10.1016/j.cell.2013.11.039 (2013)
Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki) David Sturgill, John H Malone, Xia Sun, Harold E Smith, Leonard Rabinow, Marie-Laure Samson and Brian Oliver BMC Bioinformatics, doi:10.1186/1471-2105-14-320 (2013)

Theta band activity in response to emotional expressions and its relationship with gamma band activity as revealed by MEG and advanced beamformer source imaging Qian Luo, Xi Cheng, Tom Holroyd, Duo Xu, Frederick W. Carver and James Blair Frontiers in Human Neuroscience, doi: 10.3389/fnhum.2013.00940 (2013)
Overfitting, generalization, and MSE in class probability estimation with high-dimensional data Kyung In Kim, Richard Simon Biometric Journal, DOI: 10.1002/bimj.201300083 (2013)
Radionuclide labeling and evaluation of candidate radioligands for PET imaging of histone deacetylase in the brain Young Jun Seo, Lisa Muench, Alicia Reid, Jinzhu Chen, Yeona Kang, Jacob M. Hooker, Nora D. Volkow, Joanna S. Fowler, Sung Won Kim Bioorganic and Medicinal Chemistry Letters 23:6700-6705 (2013)
An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease Farhoud Faraji, Ying Hu, Gang Wu, Natalie E. Goldberger, Renard C. Walker, Jinghui Zhang and Kent W. Hunter Genome Research, doi: 10.1101/gr.166223.113 (2013)
Efficacy of Cyclin Dependent Kinase 4 Inhibitors as Potent Neuroprotective Agents against Insults Relevant to Alzheimer's Disease Priyankar Sanphui, Sumit Kumar Pramanik, Nandini Chatterjee, Ponnusamy Moorthi, Biswadip Banerji, Subhas Chandra Biswas PLoS One, doi: 10.1371/journal.pone.0078842 (2013)
Multiple Transport-Active Binding Sites Are Available for a Single Substrate on Human P-Glycoprotein (ABCB1) Eduardo E. Chufan, Khyati Kapoor, Hong-May Sim, Satyakam Singh, Tanaji T. Talele, Stewart R. Durell, Suresh V. Ambudkar PLoS One, DOI: 10.1371/journal.pone.0082463 (2013)

Prediction of the location and size of the stomach using patient characteristics for retrospective radiation dose estimation following radiotherapy Stephanie Lamart, Rebecca Imran, Steven L Simon, Kazutaka Doi, Lindsay M Morton, Rochelle E Curtis, Choonik Lee, Vladimir Drozdovitch, Roberto Maass-Moreno, Clara C Chen, Millie Whatley, Donald L Miller, Karel Pacak and Choonsik Lee Physics in Medicine and Biology, doi:10.1088/0031-9155/58/24/8739 (2013)
Optimization of virus detection in cells using massively parallel sequencing Shasta D. McClenahan, Christine Uhlenhaut, Philip R. Krause Biologicals, DOI://10.1016/j.biologicals.2013.11.002 (2013)
Whole exome sequencing identifies variation in CYB5A and RNF10 associated with adiposity and type 2 diabetes. Huang K, Nair AK, Muller YL, Piaggi P, Bian L, Del Rosario M, Knowler WC, Kobes S, Hanson RL, Bogardus C, Baier LJ. Obesity, doi: 10.1002/oby.20647 (2013)
Antimicrobial activity of eugenol and cinnamaldehyde against extended spectrum beta lactamase producing enterobacteriaceae by in vitro and molecular docking analysis Lena Dhara, Anusri Tripathi Eur.J.Integrative Med., 10.1016/j.eujim.2013.08.005 (2013)
Efficient logistic regression designs under an imperfect population identifier Paul S. Albert, Aiyi Liu, Tonja Nansel Biometrics, DOI: 10.1111/biom.12106 (2013)
Molecular Isotopic Distribution Analysis (MIDAs) with Adjustable Mass Accuracy Gelio Alves, Aleksey Y. Ogurtsov, Yi-Kuo Yu J. Am. Soc. for Mass Spectrometry, doi://10.1007/s13361-013-0733-7 (2013)

Vitamin D-Binding Protein and Vitamin D Status of Black Americans and White Americans Camille E. Powe, , Michele K. Evans, Julia Wenger, Alan B. Zonderman, Anders H. Berg, Michael Nalls, Hector Tamez, Dongsheng Zhang, Ishir Bhan, S. Ananth Karumanchi, Neil R. Powe, and Ravi Thadhani New England J. Medicine, DOI: 10.1056/NEJMoa1306357 (2013)
PW02-001 - Exome sequencing for autoinflammatory disorders SE Boyden, Q Zhou, I Aksentijevich and DL Kastner Pediatric Rheumatology, doi:10.1186/1546-0096-11-S1-A141 (2013)
Endogenous Carbamylation of Renal Medullary Proteins J'Neka S. Claxton, Pablo C. Sandoval, Gary Liu, Chung-Lin Chou, Jason D. Hoffert, and Mark A. Knepper PLoS One, doi: 10.1371/journal.pone.0082655 (2013)
Interpreting the effects of altered brain anatomical connectivity on fMRI functional connectivity: a role for computational neural modeling Barry Horwitz, Chuhern Hwang, and Jeff Alstott Frontiers in Human Neuroscience, doi: 10.3389/fnhum.2013.00649 (2013)
Shared Genetic Susceptibility to Ischemic Stroke and Coronary Artery Disease Dichgans, Malik et al. Stroke, doi: 10.1161/STROKEAHA.113.002707 (2013)
Mtr4-like Protein Coordinates Nuclear RNA Processing for Heterochromatin Assembly and for Telomere Maintenance Nathan N. Lee, Venkata R. Chalamcharla, Francisca Reyes-Turcu, Sameet Mehta, Martin Zofall, Vanivilasini Balachandran, Jothy Dhakshnamoorthy, Nitika Taneja, Soichiro Yamanaka, 5, Ming Zhou, Shiv I.S. Grewal Cell, doi://10.1016/j.cell.2013.10.027 (2013)

Testing multiple biological mediators simultaneously Simina M. Boca, Rashmi Sinha, Amanda J. Cross, Steven C. Moore and Joshua N. Sampson Bioinformatics, doi: 10.1093/bioinformatics/btt633 (2013)
Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data Sandro Bottaro, Kresten Lindorff-Larsen, and Robert B. Best J. Chem. Theory and Computation, DOI: 10.1021/ct400730n (2013)
Mechanism of Membrane Permeation Induced by Synthetic β-Hairpin Peptides Kshitij Gupta, Hyunbum Jang, Kevin Harlen, Anu Puri, Ruth Nussinov, Joel P. Schneider, Robert Blumenthal Biophys. J. , doi: 10.1016/j.bpj.2013.09.040 (2013)
Ebola Virus RNA Editing Depends on the Primary Editing Site Sequence and an Upstream Secondary Structure Masfique Mehedi, Thomas Hoenen, Shelly Robertson, Stacy Ricklefs, Michael A. Dolan, Travis Taylor, Darryl Falzarano, Hideki Ebihara, Stephen F. Porcella, Heinz Feldmann PLoS Pathogens, doi:10.1371/journal.ppat.1003677 (2013)
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Ischemic stroke is associated with the ABO locus: The EuroCLOT study FMK Williams, AM Carter, PG Hysi et al and EuroCLOT Investigators, the Wellcome Trust Case Control Consortium 2, MORGAM, MetaStroke and the International Stroke Genetics Consortium Annals of Neurology, DOI: 10.1002/ana.23838 (2013)
Initial Assessment of the Pathogenic Mechanisms of the Recently Identified Alzheimer Risk Loci P Holton, M Ryten, MA Nalls et al. Annals of Human Genetics, DOI: 10.1111/ahg.12000 (2013)
Alternative Complex III from phototrophic bacteria and its electron acceptor auracyanin Erica L.W. Majumder, Jeremy D. King, Robert E. Blankenship Biochim. et Biophys. Acta - Bioenergetics, doi://10.1016/j.bbabio.2013.01.008 (2013)
Identification of Early Replicating Fragile Sites that Contribute to Genome Instability JH Barlow, RB Faryabi, E Callen, N Wong, A Malhowski, H Tang Chen, G Gutierrez-Cruz, H-W Sun, P McKinnon, G Wright, R Casellas, DF Robbiani, L Staudt, O Fernandez-Capetillo, A Nussenzweig Cell, doi://10.1016/j.cell.2013.01.006 (2013)
Genetic variation associated with circulating monocyte count in the eMERGE Network DR Crosslin, A McDavid, N Weston et al Hum. Mol. Genetics, doi: 10.1093/hmg/ddt010 (2013)
PI(4,5)P2-Mediated Cell Signaling: Emerging Principles and PTEN as a Paradigm for Regulatory Mechanism Arne Gericke, Nicholas R. Leslie, Mathias Lösche, Alonzo H. Ross Adv Exp Med Biol, doi: 10.1007/978-94-007-6331-9_6 (2013)

2012 (146 papers)

An efficient algorithm for clustering of large-scale mass spectrometry data Saeed F, Pisitkun T, Knepper MA, Hoffert JD Proceedings (IEEE Int Conf Bioinformatics Biomed), doi://10.1109/BIBM.2012.6392738 (2012)
A Dual Polybasic Motif Determines Phosphoinositide Binding and Regulation in the P2X Channel Family Louis-Philippe Bernier, Dominique Blais, É ́ric Boué-Grabot, Philippe Séguéla PLoS One 7:1-9, doi: 10.1371/journal.pone.0040595 (2012)

Estimating Diagnostic Accuracy of Raters Without a Gold Standard by Exploiting a Group of Experts Zhang B, Chen Z, Albert PS. Biometrics, doi: 10.1111/j.1541-0420.2012.01789.x (2012)
Entropy of single-file water in (6,6) carbon nanotubes Aparna Waghe, Jayendran C. Rasaiah, and Gerhard Hummer J. Chem. Phys. , doi://10.1063/1.4737842 (2012)
Assessment of the Effect of 24-Hour Aldosterone Administration on Protein Abundance in Fluorescence-Sorted Mouse Distal Renal Tubules by Mass Spectrometry Jensen T.B., Pisitkun T., Hoffert J.D., Jensen U.B., Fenton R.A, Praetorius H.A, Knepper M.A, Praetorius J. Nephron Physiology, DOI:10.1159/000346832 (2012)
On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in SN2 Reactions Edina Rosta and Arieh Warshal J Chem Theory Comput. , doi: 10.1021/ct2009329 (2012)
An efficient dynamic programming algorithm for phosphorylation site assignment of large-scale mass spectrometry data Fahad Saeed, Trairak Pisitkun, Jason D. Hoffert, Guanghui Wang, Marjan Gucek, and Mark A. Knepper Proceedings of IEEE Int Conf Bioinformatics Biomed, doi://10.1109/BIBMW.2012.6470210 (2012)
Cell population-specific expression analysis of human cerebellum A Kuhn, A Kumar, A Beilina, A Dillman, MR Cookson, AB Singleton BMC Genomics, doi:10.1186/1471-2164-13-610 (2012)

Both Genome Segments Contribute to the Pathogenicity of Very Virulent Infectious Bursal Disease Virus Olivier Escaffre, Cyril Le Nouën, Michel Amelot, Xavier Ambroggio, Kristen M. Ogden, Olivier Guionie, Didier Toquin, Hermann Müller, Mohammed R. Islam and Nicolas Eterradossi J. Virology, doi: 10.1128/JVI.02360-12 (2012)
Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. II. Results for hexapeptides with non-polar side chains O. I. Obolensky, Wells W. Wu, Rong-Fong Shen, Yi-Kuo Yu Rapid Comm. in Mass. Spec., DOI: 10.1002/rcm.6451 (2012)
Melatonin inhibits matrix metalloproteinase-9 activity by binding to its active site Deep Sankar Rudra, Uttam Pal, Nakul Chandra Maiti, Russel J. Reiter, Snehasikta Swarnakar J. Pineal Research, DOI: 10.1111/jpi.12034 (2012)
RPA Accumulation during Class Switch Recombination Represents 5'-3' DNA-End Resection during the S-G2/M Phase of the Cell Cycle Arito Yamane, Davide F. Robbiani, Wolfgang Resch, Anne Bothmer, Hirotaka Nakahashi, Thiago Oliveira, Philipp C. Rommel, Eric J. Brown, Andre Nussenzweig, Michel C. Nussenzweig, Rafael Casellas Cell Reports, doi://10.1016/j.celrep.2012.12.006, (2012)
Molecular structures of trimeric HIV-1 Env in complex with small antibody derivatives Joel R. Meyerson, Erin E. H. Tran, Oleg Kuybeda, Weizao Chen, Dimiter S. Dimitrov, Andrea Gorlani, Theo Verrips, Jeffrey D. Lifson, and Sriram Subramaniam PNAS, doi:10.1073/pnas.1214810110 (2012)
Effect of compatible and noncompatible osmolytes on the enzymatic activity and thermal stability of bovine liver catalase H. Sepasi Tehrani, A.A. Moosavi-Movahedia, H. Ghourchian, F. Ahmad, A. Kiany, M.S. Atri, Sh Ariaeenejad, K. Kavousi & A.A. Sabourya J. Biomol. Struct. Dynamics, DOI:10.1080/07391102.2012.742460 (2012)
RNA Interference Mediated Inhibition of Dengue Virus Multiplication and Entry in HepG2 Cells MA Alhoot, SM Wang, SD Sekaran PLoS One, RNA Interference Mediated Inhibition of Dengue Virus Multiplication and Entry in HepG2 Cells (2012)
On the edge of web-based multiple sequence alignment services Nguyen, Ken D. Tsinghua Science and Technology 17(6):629-637 (2012)
Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. O. I. Obolensky, Wells W. Wu, Rong-Fong Shen, Yi-Kuo Yu Rapid Comm. in Mass. Spec., DOI: 10.1002/rcm.6451 (2012)
Mechanisms for the Insertion of Toxic, Fibril-like β-Amyloid Oligomers into the Membrane Hyunbum Jang , Laura Connelly , Fernando Teran Arce , Srinivasan Ramachandran , Bruce L. Kagan , Ratnesh Lal , and Ruth Nussinov J. Chem. Theory Compt. , DOI: 10.1021/ct300916f (2012)
Structural Ensemble of an Intrinsically Disordered Polypeptide Jeetain Mittal , Tae Hyeon Yoo , George Georgiou , and Thomas Michael Truskett J. Phys. Chem. B, DOI: 10.1021/jp308984e (2012)
STATs Shape the Active Enhancer Landscape of T Cell Populations Golnaz Vahedi, Hayato Takahashi, Shingo Nakayamada, Hong-wei Sun, Vittorio Sartorelli, Yuka Kanno, John J. O'Shea Cell, doi://10.1016/j.cell.2012.09.044, (2012)
Screening system for orthogonal suppressor tRNAs based on the species-specific toxicity of suppressor tRNAs Hong Tian, Danni Deng, Jie Huang, Dongning Yao, Xiaowei Xu, Xiangdong Gao Biochimie, doi://10.1016/j.biochi.2012.12.010 (2012)
Structural and Mechanistic Investigations of Phosphothreonine Lyase Class of Enzymes Alok Gopalkrishna Shenoy Graduate Thesis, Utah State University (2012)
Evaluation of Gene Association Methods for Coexpression Network Construction and Biological Knowledge Discovery Sapna Kumari, Jeff Nie, Huann-Sheng Chen, Hao Ma, Ron Stewart, Xiang Li, Meng-Zhu Lu, William M. Taylor, Hairong Wei PLoS One, doi:10.1371/journal.pone.0050411 (2012)
Common genetic variation near the Connexin-43 gene is associated with resting heart rate in African Americans: A Genome-wide Association Study of 13,372 participants R Deo, MA Nalls, CL Avery, JG Smith et al. Heart Rhythm, doi://10.1016/j.hrthm.2012.11.014 (2012)
Protein Secondary Structure Determination by Constrained Single-Particle Cryo-Electron Tomography Alberto Bartesaghi, Federico Lecumberry, Guillermo Sapiro, Sriram Subramaniam Structure 20(12):2003-2013 (2012)
A Systematic Approach for Development of an OPLS-Like Force Field and Its Application to Hydrofluorocarbons Eugene Paulechka , Kenneth Kroenlein , Andrei Kazakov , and Michael Frenkel J. Phys. Chem. B, DOI: 10.1021/jp309119h (2012)

The Impact of Ancestry and Common Genetic Variants on QT Interval in African Americans JG Smith, CL Avery, DS Evans, MA Nalls et al. Circulation: Cardiovascular Genetics, doi: 10.1161/CIRCGENETICS.112.962787 (2012)
The effect of spatial smoothing on fMRI decoding of columnar-level organization with linear support vector machine Masaya Misaki, Wen-Ming Luh, Peter A. Bandettini J. Neuroscience Methods, doi://10.1016/j.jneumeth.2012.11.004 (2012)
Candidate Gene Association Study of BMI-Related Loci, Weight, and Adiposity in Old Age Rachel A. Murphy, Michael A. Nalls, Margaux Keller, Melissa Garcia, Stephen B. Kritchevsky, Frances A. Tylavsky, Anne B. Newman, Gregory J. Tranah, Gudny Eiriksdottir, Vilmundur Gudnason and Tamara B. Harris J. Gerontology A, doi: 10.1093/gerona/gls227 (2012)
Conformational Exploration of Two Peptides and Their Hybrid Polymer Conjugates: Potentialities as Self-Aggregating Materials Nurit Haspel, Adéle D. Laurent, David Zanuy , Ruth Nussinov, Carlos Aleman, Jordi Puiggali, and Guillermo Revilla-López J. Phys. Chem. B, DOI: 10.1021/jp3043363 (2012)
Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography F Schotte, HS Cho, VRI Kaila, H Kamikubo, N Dashdorj, ER Henry, TJ Graber, R Henning, M Wulff, G Hummer, M Kataoka, and PA Anfinrud PNAS, doi: 10.1073/pnas.1210938109 (2012)
Effects of the BDNF Val66Met Polymorphism on White Matter Microstructure in Healthy Adults H Tost, T Alam, M Geramita, C Rebsch, B Kolachana, D Dickinson, BA Verchinski, H Lemaitre, AS Barnett, JW Trampush, DR Weinberger and S Marenco Neuropsychopharmacology , doi: 10.1038/npp.2012.214 (2012)

Sodium and calcium mechanisms of rhythmic bursting in excitatory neural networks of the pre-Bötzinger complex: a computational modelling study Patrick E. Jasinski, Yaroslav I. Molkov, Natalia A. Shevtsova, Jeffrey C. Smith, Ilya A. Rybak Eur. J. Neuroscience, DOI: 10.1111/ejn.12042 (2012)
Effects of image contrast on functional MRI image registration Javier Gonzalez-Castillo, Kristen N. Duthie, Ziad S. Saad, Carlton Chu, Peter A. Bandettini, Wen-Ming Luh NeuroImage, doi://10.1016/j.neuroimage.2012.10.076 (2012)
Accurate decoding of sub-TR timing differences in stimulations of sub-voxel regions from multi-voxel response patterns Masaya Misaki, Wen-Ming Luh, Peter A. Bandettini NeuroImage, doi://10.1016/j.neuroimage.2012.10.069, (2012)
Novel Loci Associated with PR Interval in a Genome-Wide Association Study of Ten African American Cohorts AM Butler, X Yin, DS Evans, MA Nalls et al. Circulation: Cardiovascular Genetics, doi: 10.1161/CIRCGENETICS.112.963991 (2012)
Response of the Mitochondrial Proteome of Rat Renal Proximal Convoluted Tubules to Chronic Metabolic Acidosis D Freund, JE Prenni, NP Curthoys Renal Physiology, ,doi: 10.1152/ajprenal.00526.2012 (2012)
PTEN: An Intercellular Peacekeeper? Nick R. Leslie Science Signaling, DOI: 10.1126/scisignal.2003685 (2012)
Gene Silencing Mediated by siRNA-binding Fusion Proteins Is Attenuated by Double-stranded RNA-binding Domain Structure James C Geoghegan, Brian L Gilmore and Beverly L Davidson Molecular Therapy Nucleic Acids, doi:10.1038/mtna.2012.43 (2012)
A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography Oleg Kuybeda, Gabriel A. Frank, Alberto Bartesaghi, Mario Borgnia, Sriram Subramaniam , Guillermo Sapiro J. Struct. Biol. , doi://10.1016/j.jsb.2012.10.010 (2012)
Novel inhibitors of a Grb2 SH3C domain interaction identified by a virtual screen Philip C. Simister, James Luccarelli, Sam Thompson, Daniel H. Appella, Stephan M. Feller , Andrew D. Hamilton Bioorganic & Medicinal Chemistry, doi://10.1016/j.bmc.2012.10.023 (2012)
Statistical tests for detecting associations with groups of genetic variants: generalization, evaluation, and implementation John Ferguson, William Wheeler, YiPing Fu, Ludmila Prokunina-Olsson, Hongyu Zhao and Joshua Sampson Eur. J. Hum. Genetics, doi: 10.1038/ejhg.2012.220 (2012)
Imputation of Exome Sequence Variants into Population- Based Samples and Blood-Cell-Trait-Associated Loci in African Americans: NHLBI GO Exome Sequencing Project Paul L. Auer, Jill M. Johnsen, Andrew D. Johnson et al. Am. J. Hum. Genet., doi://10.1016/j.ajhg.2012.08.031 (2012)
SHAVE: shrinkage estimator measured for multiple visits increases power in GWAS of quantitative traits Osorio D Meirelles, Jun Ding, Toshiko Tanaka, Serena Sanna, Hsih-Te Yang, Dawood B Dudekula, Francesco Cucca, Luigi Ferrucci, Goncalo Abecasis and David Schlessinger European J. Hum. Genetics, doi: 10.1038/ejhg.2012.215 (2012)

Membrane Association of the PTEN Tumor Suppressor: Electrostatic Interaction with Phosphatidylserine-Containing Bilayers and Regulatory Role of the C-Terminal Tail Siddharth S. Shenoy, Hirsh Nanda, c, Mathias Lösche J. Struct. Biol. , doi://10.1016/j.jsb.2012.10.003, (2012)
Characterization of synonymous codon usage bias in the pseudorabies virus US1 gene Meili Li, Zhiyao Zhao, Jianhong Chen, Bingyun Wang, Zi Li, Jian Li and Mingsheng Cai Virologica Sinica, DOI: 10.1007/s12250-012-3270-9 (2012)
Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins Raghunath Chatterjee, Jianfei Zhao, Ximiao He, Andrey Shlyakhtenko, Ishminder Mann, Joshua J. Waterfall, Paul Meltzer, B. K. Sathyanarayana, Peter C. FitzGerald, Charles Vinson Genes | Genomes | Genetics, doi://10.1534/g3.112.004002 (2012)
Genetic risk factors for ischaemic stroke and its subtypes (the METASTROKE Collaboration): a meta-analysis of genome-wide association studies M Traylor, M Farrall, EG Holliday et al & International Stroke Genetics Consortium The Lancet Neurology, doi://10.1016/S1474-4422(12)70234-X, (2012)
Siblings with Ischemic Stroke Study (SWISS): Results of a Genome-wide Scan for Stroke Loci JF. Meschia, M Nalls, M Matarin, TG. Brott, RD. Brown, Jr., J Hardy, B Kissela, SS. Rich, A Singleton, D Hernandez, L Ferrucci, K Pearce, M Keller, BB. Worrall, for the Siblings with Ischemic Stroke Study (SWISS) Investigators Stroke, doi: 10.1161/STROKEAHA.111.620484 (2012)
Effect of Complement CR1 on Brain Amyloid Burden During Aging and Its Modification byAPOEGenotype M Thambisetty, Y An, M Nalls et al for the Baltimore Longitudinal Study of Aging and the Alzheimer's Disease Neuroimaging Initiative Biological Psychiatry, doi://10.1016/j.biopsych.2012.08.015 (2012)

CPhos: a program to calculate and visualize evolutionarily conserved functional phosphorylation sites Boyang Zhao, Trairak Pisitkun, Jason D. Hoffert, Mark A. Knepper, Fahad Saeed Proteomics, DOI: 10.1002/pmic.201200189 (2012)
Quantitative Phosphoproteomics in Nuclei of Vasopressin-Sensitive Renal Collecting Duct Cells Steven J. Bolger, Patricia A. Gonzales Hurtado, Jason D. Hoffert, Fahad Saeed, Trairak Pisitkun, and Mark A. Knepper Am J Physiol Cell Physiol, doi:10.1152/ajpcell.00260.2012 (2012)
Are Myocardial Infarction-Associated Single-Nucleotide Polymorphisms Associated With Ischemic Stroke? Cheng YC, Anderson CD, Bione S et al Stroke, doi: 10.1161/STROKEAHA.111.632075 (2012)
Lin28b Reprograms Adult Bone Marrow Hematopoietic Progenitors to Mediate Fetal-Like Lymphopoiesis Joan Yuan, Cuong K. Nguyen, Xiuhuai Liu, Chrysi Kanellopoulou, Stefan A. Muljo Science 335 (6073):1195-1200 (2012)
The development and application of transposon mutagenesis and unnatural amino acid mutagenesis technologies Jia Liu Ph.D Thesis, U. Maryland (2012)
Mouse model of endemic Burkitt translocations reveals the long-range boundaries of Ig-mediated oncogene deregulation AL Kovalchuk, C Ansarah-Sobrinho, O Hakim, W Resch, Helena Tolarová, W Dubois, A Yamane, M Takizawa, IKlein, GL Hager, HC Morse III, M Potter, MC Nussenzweig, and R Casellas PNAS, doi: 10.1073/pnas.1200106109 (2012)

Testing associations of copy number variations in genome-wide association studies Jianxin Shi and Peng Li Statistica Sinica, doi://10.5705/ss.2012.071s (2012)
Systems Biology in Physiology: The Vasopressin Signaling Network in Kidney Mark A. Knepper Am. J. Physiol. - Cell Physiol. , doi: 10.1152/ajpcell.00270.2012 (2012)
Comparing the Expected Misclassification Cost for Two Classifiers Based on Estimates From the Same Sample James F. Troendle, Kai F. Yu, Peter H. Westfall, Gene Pennello & Enrique F. Schisterman Statistics in Biopharmaceutical Research, DOI:10.1080/19466315.2012.695263 (2012)
Theory for cross effect dynamic nuclear polarization under magic-angle spinning in solid state nuclear magnetic resonance: The importance of level crossings Kent Thurber and Robert Tycko J. Chem. Phys. , doi://10.1063/1.4747449 (2012)
Prediction of variable translation rate effects on cotranslational protein folding Edward P. O'Brien, Michele Vendruscolo & Christopher M. Dobson Nature Communications, doi:10.1038/ncomms1850 (2012)
Directed evolution reveals requisite sequence elements in the functional expression of P450 2F1 in Escherichia coli JBYH Behrendorff, CD Moore, K-H Kim, D-H Kim, CA Smith, WA Johnston, C-H Yun, GS Yost, and EMJ Gillam Chemical Research in Toxicology, DOI: 10.1021/tx300281g (2012)

Using Genome-wide Complex Trait Analysis to quantify 'missing heritability' in Parkinson's disease MF Keller, M Saad, et al and International Parkinson's Disease Genomics Consortium and the Wellcome Trust Case Control Consortium 2 Human Molecular Genetics, doi: 10.1093/hmg/dds335 (2012)
Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics R Schmitz, RM Young et al Nature, doi:10.1038/nature11378 (2012)
Automated subcortical segmentation using FIRST: Test-retest reliability, interscanner reliability, and comparison to manual segmentation Allison C. Nugent, David A. Luckenbaugh, Suzanne E. Wood, Wendy Bogers, Carlos A. Zarate Jr., Wayne C Drevets Human Brain Mapping, DOI: 10.1002/hbm.22068 (2012)
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone φ, ψ and Side-Chain χ1 and χ2 Dihedral Angles Robert B. Best, Xiao Zhu, Jihyun Shim, Pedro E. M. Lopes, Jeetain Mittal, Michael Feig, and Alexander D. MacKerell, Jr. J. Chem. Theory Comput., DOI: 10.1021/ct300400x (2012)
Profibrogenic chemokines and viral evolution predict rapid progression of hepatitis C to cirrhosis Patrizia Farci, Kurt Wollenberg, Giacomo Diaz, Ronald E. Engle, Maria Eliana Lai, Paul Klenerman, Robert H. Purcell, Oliver G. Pybus, and Harvey J. Alter PNAS, doi: 10.1073/pnas.1210592109 (2012)
Multiple Testing of Composite Null Hypotheses in Heteroscedastic Models Wenguang Sun & Alexander C. McLain Journal of the American Statistical Association 107(498):637-687 (2012)

Use of support vector machines for disease risk prediction in genome-wide association studies: Concerns and opportunities F Mittag, F Büchel, M Saad, A Jahn, C Schulte, Z Bochdanovits, J Simón-Sánchez, MA Nalls, M Keller, DG Hernandez, JR Gibbs, S Lesage, A Brice, P Heutink, M Martinez, NW Wood, J Hardy, AB Singleton, A Zell, T Gasser, M Sharma for the International Parkinson's Disease Genomics Consortium (IPDGC) Human Mutation, DOI: 10.1002/humu.22161 (2012)
Drying Transition in the Hydrophobic Gate of the GLIC Channel Blocks Ion Conduction Fangqiang Zhu and Gerhard Hummer Biophys. J. 103(2):219-227, doi://10.1016/j.bpj.2012.06.003 (2012)
Structural Mechanism of Trimeric HIV-1 Envelope Glycoprotein Activation Erin E. H. Tran, Mario J. Borgnia, Oleg Kuybeda, David M. Schauder, Alberto Bartesaghi, Gabriel A. Frank, Guillermo Sapiro, Jacqueline L. S. Milne, Sriram Subramaniam PLoS Pathogens, doi:10.1371/journal.ppat.1002797 (2012)
The impact of random-effect misspecification on percentile estimation for longitudinal growth data Kyeongmi Cheon, Paul S. Albert, Zhiwei Zhang Statistics in Medicine, DOI: 10.1002/sim.5437 (2012)
Mitochondrial DNA Sequence Variation Associated with Dementia and Cognitive Function in the Elderly Tranah GJ, Nalls MA, Katzman SM, Yokoyama JS, Lam ET, Zhao Y, Mooney S, Thomas F, Newman AB, Liu Y, Cummings SR, Harris TB, Yaffe K J. Alzheimer's Disease, doi://10.3233/JAD-2012-120466 (2012)
Weighted logrank tests for interval censored data when assessment times depend on treatment Michael P. Fay, Joanna H. Shih Statistics in Medicine, DOI: 10.1002/sim.5447 (2012)
Genetic Contributions to Individual Differences in Vulnerability to Addiction and Abilities to Quit George R. Uhl and Tomas Drgon in Drug Abuse and Addiction in Mental Illness, DOI: 10.1007/978-1-4614-3375-0-7 (2012)
Understanding Neuroplastic Effects of Transcranial Direct Current Stimulation through Analysis of Dynamics of Large-Scale Brain Networks Anusha Venkatakrishnan Ph.D. Thesis, University of Maryland (2012)
Design and Assembly of Large Synthetic DNA Constructs Aleksandr E. Miklos, Randall A. Hughes, Andrew D. Ellington Current Protocols in Molecular Biology, DOI: 10.1002/0471142727.mb0323s99 (2012)
Leptin regulates dopamine responses to sustained stress in humans Paul R Burghardt, Tiffany M Love, Christian S. Stohler, Colin Hodgkinson, Pei-Hong Shen, Mary Ann Enoch, David Goldman, Jon-Kar Zubieta J. Neurosci. , doi: 10.1523/JNEUROSCI.2521-12.2012 (2012)
Estimating ancestral proportions in a multi-ethnic US sample: implications for studies of admixed populations Orna Levran, Olaoluwakitan Awolesi, Pei-Hong Shen, Miriam Adelson, and Mary Jeanne Kreek Human Genomics, doi: 10.1186/1479-7364-6-2 (2012)
The Peptide-Receptive Transition State of MHC Class I Molecules: Insight from Structure and Molecular Dynamics Michael G. Mage, Michael A. Dolan, Rui Wang, Lisa F. Boyd, Maria Jamela Revilleza, Howard Robinson, Kannan Natarajan, Nancy B. Myers, Ted H. Hansen and David H. Margulies J. Immunol. , doi: 10.4049/jimmunol.1200831 (2012)

The Folliculin-FNIP1 pathway deleted in human Birt-Hogg-Dubé syndrome is required for B cell development Baba M, Keller JR, Sun HW, Resch W, Kuchen S, Suh HC, Hasumi H, Hasumi Y, Kieffer-Kwon KR, Gonzalez CG, Hughes RM, Klein ME, Oh HF, Bible P, Southon E, Tessarollo L, Schmidt LS, Linehan WM, Casellas R. Blood, DOI 10.1182/blood-2012-02-410407 (2012)
Identifying Protein Kinase Target Preferences Using Mass Spectrometry Jacqueline Douglass, Ruwan Gunaratne, Davis Bradford, Fahad Saeed, Jason D. Hoffert, Peter J. Steinbach, Mark A. Knepper, and Trairak Pisitkun Cell Physiol., doi: 10.1152/ajpcell.00166.2012 (2012)
Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains Jeffery B. Klauda, Viviana Monje, Taehoon Kim, and Wonpil Im J. Phys. Chem. B, DOI: 10.1021/jp304056p (2012)
Crystal structure of a plectonemic RNA supercoil Jason R. Stagno, Buyong Ma, Jess Li, Amanda S. Altieri, R. Andrew Byrd & Xinhua Ji Nature Communications, doi:10.1038/ncomms1903 (2012)
Codon optimization for high level expression of human bone morphogenetic protein-2 in Escherichia coli Debbie S. Retnoningruma, H.T. Pramestia, P.Y. Santikaa, O. Valeriusb, S. Asjariea, T. Suciatia Prot. Expr. and Pur., doi://10.1016/j.pep.2012.05.010 (2012)
Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases Sarah Baxter, Abigail R. Lambert, Ryan Kuhar, Jordan Jarjour, Nadia Kulshina, Fabio Parmeggiani, Patrick Danaher, Jacob Gano, David Baker, Barry L. Stoddard and Andrew M. Scharenberg Nucleic Acids Research, doi: 10.1093/nar/gks502 (2012)

Trigger factor slows co-translational folding through kinetic trapping while sterically protecting the nascent chain from aberrant cytosolic interactions Edward P O'Brien, John Christodoulou, Michele Vendruscolo, and Christopher M. Dobson J. Am. Chem. Soc. , DOI: 10.1021/ja302305u (2012)
Genomic Analysis of Immune Response against Vibrio cholerae Hemolysin in Caenorhabditis elegans Surasri N. Sahu, Jada Lewis, Isha Patel, Serdar Bozdag, Jeong H. Lee, Joseph E. LeClerc, and Hediye Nese Cinar PLoS One, doi: 10.1371/journal.pone.0038200 (2012)
Spontaneous High-Gamma Band Activity Reflects Functional Organization of Auditory Cortex in the Awake Macaque Makoto Fukushima, Richard C. Saunders, David A. Leopold, Mortimer Mishkin, and Bruno B. Averbeck Neuron, DOI 10.1016/j.neuron.2012.04.014 (2012)
Mitochondrial DNA sequence variation is associated with free-living activity energy expenditure in the elderly Gregory J. Tranah, Ernest T. Lam, Shana M. Katzman, Michael A. Nalls, Yiqiang Zhao, Daniel S. Evans, Jennifer S. Yokoyama, Ludmila Pawlikowska, Pui-Yan Kwok, Sean Mooney, Stephen Kritchevsky, Bret H. Goodpaster, Anne B. Newman, Tamara B. Harris, Todd M. Manini, Steven R. Cummings, For the Health, Aging and Body Composition Study Biochim. et Biophys. Acta - Bioenergetics, doi://10.1016/j.bbabio.2012.05.012 (2012)
An online tool for calculation of free-energy balance for the renal inner medulla Ryan L. Vilbig, Abhijit Sarkar, Joseph Zischkau, Mark A. Knepper, and Trairak Pisitkun Am. J. Physiol. , doi: 10.1152/ajprenal.00147.2012 (2012)
Application of systems biology principles to protein biomarker discovery: Urinary exosomal proteome in renal transplantation Trairak Pisitkun, Maria T. Gandolfo, Samarjit Das, Mark A. Knepper, Serena M. Bagnasco Proteomics -- Clinical Applications, doi://10.1002/prca.201100108 (2012)

Methods of adjusted comparison of medians James F. Troendle, Zhiwei Zhang, Megan E. Mathews, Junchi Guo Biometrical Journal, DOI: 10.1002/bimj.201100220 (2012)
Characterization of a Dynamic String Method for the Construction of Transition Pathways in Molecular Reactions Margaret E. Johnson and Gerhard Hummer J. Phys. Chem. B, DOI: 10.1021/jp212611k (2012)
Tissue-Specific Regulation of Chromatin Insulator Function Leah H. Matzat, Ryan K. Dale, Nellie Moshkovich, and Elissa P. Lei PLoS Genetics, doi: 10.1371/journal.pgen.1003069 (2012)
A Subset-Based Approach Improves Power and Interpretation for the Combined Analysis of Genetic Association Studies of Heterogeneous Traits Samsiddhi Bhattacharjee, Preetha Rajaraman, Kevin B. Jacobs, William A. Wheeler, Beatrice S. Melin, Patricia Hartge, GliomaScan Consortium, Meredith Yeager, Charles C. Chung, Stephen J. Chanock, Nilanjan Chatterjee Am. J. Hum. Genet., doi:/10.1016/j.ajhg.2012.03.015 (2012)
Seeing is believing: video classification for computed tomographic colonography using multiple-instance learning. Shijun Wang, Matthew T McKenna, Tan B Nguyen, Joseph E Burns, Nicholas Petrick, Berkman Sahiner, Ronald M Summers IEEE Transactions on Medical Imaging 31 (5):1141 (2012)
Cross-seeding and Conformational Selection between Three- and Four-repeat Human Tau Proteins Xiang Yu, Yin Luo, Paul Dinkel, Jie Zheng, Guanghong Wei, Martin Margittai, Ruth Nussinov, Buyong Ma J. Biol. Chem., doi: 10.1074/jbc.M112.340794 (2012)

An Integrative Segmentation Method for Detecting Germline Copy Number Variations in SNP Arrays Jianxin Shi, Peng Li Genetic Epidemiology 36(4):373-383, DOI: 10.1002/gepi.21631 (2012)
Structural and Functional Consequences of Phosphate-Arsenate Substitutions in Selected Nucleotides: DNA, RNA, and ATP Yu Xu, Buyong Ma, and Ruth Nussinov J. Phys. Chem. B, doi: 10.1021/jp300307u (2012)
Imino Hydrogen Positions in Nucleic Acids from Density Functional Theory Validated by NMR Residual Dipolar Couplings Alexander Grishaev, Jinfa Ying, Ad Bax J. Am. Chem. Soc., doi: 10.1021/ja301775j (2012)
The transcriptome of Spodoptera exigua larvae exposed to different types of microbes Laura Pascual, Agata K. Jakubowska, Jose M. Blanca, Joaquin Cañizares, Juan Ferré, Gernot Gloeckner, Heiko Vogel, Salvador Herrero Insect Biochem. Mol. Bio. , doi://10.1016/j.ibmb.2012.04.003 (2012)
A Two-Platform Design for Next Generation Genome-Wide Association Studies Joshua N. Sampson, Kevin Jacobs, Zhaoming Wang, Meredith Yeager, Stephen Chanock, Nilanjan Chatterjee Genetic Epidemiology, doi: 10.1002/gepi.21634 (2012)
Postnatal development-and age-related changes in DNA-methylation patterns in the human genome Paraskevi Salpea, Valya R. Russanova, Tazuko H. Hirai, Thomae G. Sourlingas, Kalliope E. Sekeri-Pataryas, Roberto Romero, Jonathan Epstein and Bruce H. Howard Nucleic Acids Research, doi: 10.1093/nar/gks312 (2012)

Restraints on backbone conformations in solid state NMR studies of uniformly labeled proteins from quantitative amide¹⁵N-¹⁵N and carbonyl ¹³C-¹³C dipolar recoupling data Kan-Nian Hua, Wei Qiang, Guillermo A. Bermejo, Charles D. Schwieters, Robert Tycko J. Magnetic Resonance, doi:10.1016/j.jmr.2012.03.001 (2012)
The interleukin-6 receptor as a target for prevention of coronary heart disease: a mendelian randomisation analysis The Interleukin-6 Receptor Mendelian Randomisation Analysis (IL6R MR) Consortium Lancet, doi: 10.1016/S0140-6736(12)60110-X (2012)
Distinct contributions of human hippocampal theta to spatial cognition and anxiety Brian R. Cornwell, Nicole Arkin, Cassie Overstreet, Frederick W. Carver, Christian Grillon Hippocampus, doi: 10.1002/hipo.22019 (2012)
Simple models of human brain functional networks Petra E. Vértes, Aaron F. Alexander-Bloch, Nitin Gogtay, Jay N. Giedd, Judith L. Rapoport, and Edward T. Bullmore PNAS, doi: 10.1073/pnas.1111738109 (2012)
Computational tools for metabolic engineering Wilbert B. Copeland, Bryan A. Bartley, Deepak Chandran, Michal Galdzicki, Kyung H. Kim, Sean C. Sleight, Costas D. Maranas, Herbert M. Sauro Metabolic Engineering, doi:10.1016/j.ymben.2012.03.001 (2012)
Nickel (II)-Schiff base complex recognizing domain II of bovine and human serum albumin: Spectroscopic and docking studies Aurkie Ray, Banabithi Koley Seth, Uttam Pal, Samita Basu Spectrochimica Acta Part A: Molecular and Biomolecular Spect, doi:10.1016/j.saa.2012.02.060 (2012)
Modular engineering of a microbially-produced viral capsomere vaccine for influenza Nani Wibowo, Yap P. Chuan, Linda H.L. Lua, Anton P.J. Middelberg Chemical Engineering Science, doi:10.1016/j.ces.2012.04.001 (2012)
Predicting kinase-substrate interactions in the era of proteomics. Focus on “Identifying protein kinase target preferences using mass spectrometry” Ewout J. Hoorn and Marcel E. Meima Am J. Phyiol. Cell Physiol., 10.1152/ajpcell.00232.2012 (2012)
Search and Analysis of Identical Reverse Octapeptides in Unrelated Proteins Konda Mani Saravanan, Samuel Selvaraj Genomics, Proteomics & Bioinformatics, doi://10.1016/j.gpb.2012.11.005 (2012)
Self-consistent treatment of the local dielectric permittivity and electrostatic potential in solution for polarizable macromolecular force fields Sergio A Hassan J. Chem. Phys. , doi://10.1063/1.4742910 (2012)
Effects of Point Substitutions on the Structure of Toxic Alzheimer's β-Amyloid Channels: Atomic Force Microscopy and Molecular Dynamics Simulations Connelly L, Jang H, Arce FT, Ramachandran S, Kagan BL, Nussinov R, Lal R. Biochemistry, doi: 10.1021/bi300257e (2012)
Quantitative Proteomics Identifies Vasopressin-Responsive Nuclear Proteins in Collecting Duct Cells. Laura K. Schenk, Steven J. Bolger, Kelli Luginbuhl, Patricia A. Gonzales, Markus M. Rinschen, Ming-Jiun Yu, Jason D. Hoffert, Trairak Pisitkun and Mark A. Knepper J. Am. Soc. Nephrology, doi: 10.1681/ASN.2011070738 (2012)

Whole-brain, time-locked activation with simple tasks revealed using massive averaging and model-free analysis Javier Gonzalez-Castillo, Ziad S. Saad, Daniel A. Handwerker, Souheil J. Inati, Noah Brenowitz, and Peter A. Bandettini PNAS, doi: 10.1073/pnas.1121049109 (2012)
Comprehensive Research Synopsis and Systematic Meta-Analyses in Parkinson's Disease Genetics: The PDGene Database Lill CM , Roehr JT , McQueen MB , Kavvoura FK , Bagade S , et al. PLoS Genetics, doi:10.1371/journal.pgen.1002548 (2012)
Unraveling the ORE1 Regulon in Arabidopsis thaliana: Molecular and Functional Characterization of Up- and Down-stream Components von Lilian Paola Matallana-Ramírez PhD Thesis, University of Potsdam (2012)
SRC Homology 2 Domain Binding Sites in Insulin, IGF-1 and FGF receptor mediated signaling networks reveal an extensive potential interactome BA Liu, BW Engelmann, K Jablonowski, K Higginbotham, AB Stergachis and PD Nash Cell Communication and Signaling 10:27 (2012)
Optimization and Modeling of Protein Refolding Conditions Bernd Rainer Kurt Anselment PhD Thesis, Institute of Biochemical Engineering of the Technische Universit�t M�nchen (2012)
Cooperative Genome-Wide Analysis Shows Increased Homozygosity in Early Onset Parkinson's Disease Simón-Sánchez J , Kilarski LL , Nalls MA , Martinez M , Schulte C , et al. PLoS One, doi:10.1371/journal.pone.0028787 (2012)

Stochastic Modeling for the Expression of a Gene Regulated by Competing Transcription Factors Hsih-Te Yang, Minoru S. H. Ko PLoS One, doi:10.1371/journal.pone.0032376 (2012)
Marginal analysis of longitudinal count data in long sequences: Methods and applications to a driving study Zhiwei Zhang, Paul S. Albert, and Bruce Simons-Morton Ann.Appl.Stat. 6(1):27-54 (2012)
Theory and simulation of ion conduction in the pentameric GLIC channel Fangqiang Zhu and Gerhard Hummer J. Chem. Theory and Computation, doi: 10.1021/ct2009279 (2012)
A Meta-Analysis and Genome-Wide Association Study of Platelet Count and Mean Platelet Volume in African Americans Qayyum R , Snively BM , Ziv E , Nalls MA , Liu Y , et al. PLoS Genetics, doi:10.1371/journal.pgen.1002491 (2012)
Distinct Regulatory Mechanisms and Functions for p53-Activated and p53-Repressed DNA Damage Response Genes in Embryonic Stem Cells Mangmang Li, Yunlong He, Wendy Dubois, Xiaolin Wu, Jianxin Shi, Jing Huang Molecular Cell, doi:10.1016/j.molcel.2012.01.020 (2012)
Modeling fecundity in the presence of a sterile fraction using a semi-parametric transformation model for grouped survival data Alexander McLain, Rajeshwari Sundaram, Germaine Buck Louis Stat. Meth. in Med. Res. , doi: 10.1177/0962280212438646 (2012)

Pair diffusion, hydrodynamic interactions, and available volume in dense fluids Jeetain Mittal, Gerhard Hummer arXiv preprint, arXiv:1202.6039 (2012)
Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA Pavel P Khil, Fatima Smagulova, Kevin M Brick, R. Daniel Camerini-Otero and Galina V Petukhova Genome Res., doi:10.1101/gr.130583.111 (2012)
A Bayesian approach to mixture cure models with spatial frailties for population-based cancer relative survival data Binbing Yu, Ram C. Tiwari Canadian Journal of Statistics, doi: 10.1002/cjs.10135 (2012)
Using DNAWorks in Designing Oligonucleotides for PCR-Based Gene Synthesis. David Hoover Methods in Molecular Biology 852(3):215-223 (2012)
Comparison of Common Homology Modeling Algorithms: Application of User-Defined Alignments. Michael A. Dolan, James W. Noah and Darrell Hurt Methods in Molecular Biology 857:399-414 (2012)
The elusive phosphotyrosine: pinning down a rare species. Focus on “Large-scale phosphotyrosine proteomic profiling of rat renal collecting duct epithelium reveals predominance of proteins involved in cell polarity determination Carolyn M. Ecelbarger Am J Physiol Cell Physiol January 302:C16-C17 (2012)

Computational separation of conformational heterogeneity using cryo-electron tomography and 3D sub-volume averaging Gabriel A. Frank, Alberto Bartesaghi, Oleg Kuybeda, Mario J. Borgnia, Tommi A. White, Guillermo Sapiro, Sriram Subramaniam J. Struct. Biol. , doi:/10.1016/j.jsb.2012.01.004 (2012)
A Joint Mixed Effects Dispersion Model for Menstrual Cycle Length and Time-to-Pregnancy Alexander C. McLain, Kirsten J. Lum, Rajeshwari Sundaram Biometrics, doi: 10.1111/j.1541-0420.2011.01711.x (2012)
PDB Ligand Conformational Energies Calculated Quantum-Mechanically Markus Sitzmann, Iwona Wedlich, Igor V Filippov, Chenzhong Liao, Megan L. Peach, Wolf-Dietrich Ihlenfeldt, Rajeshri G Karki, Yulia V Borodina, Raul E Cachau, and Marc C Nicklaus J. Chem. Inf. Model. , doi: 10.1021/ci200595n (2012)
Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke The International Stroke Genetics Consortium (ISGC), the Wellcome Trust Case Control Consortium et al. Nature Genetics, doi:10.1038/ng.1081 (2012)
A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs Alexander Zawaira and Youtaro Shibayama J. Struct. Funct. Genomics, doi://10.1007/s10969-012-9141-7 (2012)
DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes Ofir Hakim, Wolfgang Resch, Arito Yamane, Isaac Klein, Kyong-Rim Kieffer-Kwon, Mila Jankovic, Thiago Oliveira, Anne Bothmer, Ty C. Voss, Camilo Ansarah-Sobrinho, Ewy Mathe, Genqing Liang, Jesse Cobell, Hirotaka Nakahashi, Davide F. Robbiani, Andre Nussenzweig, Gordon L. Hager, Michel C. Nussenzweig & Rafael Casellas Nature, doi:10.1038/nature10909 (2012)

Bubblegrams Reveal the Inner Body of Bacteriophage φKZ Weimin Wu, Julie A. Thomas, Naiqian Cheng, Lindsay W. Black, Alasdair C. Steven Science 335 (6065):182 (2012)
Integrated cross-species transcriptional network analysis of metastatic susceptibility Ying Hu, Gang Wu, Michael Rusch, Luanne Lukes, Kenneth H. Buetow, Jinghui Zhang, and Kent W. Hunter PNAS, doi: 10.1073/pnas.1117872109 (2012)
All-D-Enantiomer of β-Amyloid Peptide Forms Ion Channels in Lipid Bilayers Ricardo Capone, Hyunbum Jang, Samuel A Kotler, Laura S Connelly, Fernando Teran Arce, Srinivasan Ramachandran, Bruce L. Kagan, Ruth Nussinov, and Ratnesh Lal J. Chem. Theory and Computation, doi: 10.1021/ct200885r (2012)
Inositol phosphate-induced stabilization of inositol 1, 3, 4, 5, 6-pentakisphosphate 2-kinase and its role in substrate specificity Varin Gosein, Ting-Fung Leung, Oren Krajden, Gregory J. Miller Protein Science, doi: 10.1002/pro.2049 (2012)
Probing Structural Features of Alzheimer's β-Amyloid Pores in Bilayers Using Site-Specific Amino Acid Substitutions Ricardo Capone, Hyunbum Jang, Samuel A Kotler, Bruce L. Kagan, Ruth Nussinov, and Ratnesh Lal J. Phys. Chem. B, doi: 10.1021/bi2017427 (2012)
Atomic Force Microscopy and MD Simulations Reveal Pore-Like Structures of All-D-Enantiomer of Alzheimer's β-Amyloid Peptide: Relevance to the Ion Channel Laura S Connelly, Fernando Teran Arce, Hyunbum Jang, Ricardo Capone, Samuel A Kotler, Srinivasan Ramachandran, Bruce L. Kagan, Ruth Nussinov, and Ratnesh Lal J. Phys. Chem. B, doi: 10.1021/jp2108126 (2012)

2011 (131 papers)

Imputation of sequence variants for identification of genetic risks for Parkinson's disease: a meta-analysis of genome-wide association studies International Parkinson Disease Genomics Consortium Lancet, doi: 10.1016/S0140-6736(10)62345-8 (2011)
Comparing statistical methods for removing seasonal variation from vitamin D measurements in case-control studies Hong Zhang, Jiyoung Ahn, and Kai Yu Statistics and its Interface 3:85-93 (2011)
Antimicrobial Protegrin-1 Forms Amyloid-Like Fibrils with Rapid Kinetics Suggesting a Functional Link Hyunbum Jang, Fernando Teran Arce, Mirela Mustata, Srinivasan Ramachandran, Ricardo Capone, Ruth Nussinov, Ratnesh Lal Biophys. J., doi: 10.1016/j.bpj.2011.01.072 (2011)
Quantifying Protein-Protein Interactions Within Noncovalent Complexes Using Electrospray Ionization Mass Spectrometry Elisabetta Boeri Erba, Konstantin Barylyuk, Yang Yang, and Renato Zenobi Anal. Chem. 83(24):9251-9259 (2011)
Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes Klein IA, Resch W, Jankovic M, Oliveira T, Yamane A, Nakahashi H, Di Virgilio M, Bothmer A, Nussenzweig A, Robbiani DF, Casellas R, Nussenzweig MC. Cell 147(1):95-106 (2011)
Recombination mapping using Boolean logic and high-density SNP genotyping for exome sequence filtering Thomas C. Markello, Ted Han, Hannah Carlson-Donohoe, Chidi Ahaghotu, Ursula Harper, MaryPat Jones, Settara Chandrasekharappa, Yair Anikster, David R. Adams, NISC Comparative Sequencing Program, William A. Gahl, Cornelius F. Boerkoel Mol. Genetics & Metabolism, doi:10.1016/j.ymgme.2011.12.014 (2011)
Independent component analysis of resting brain activity reveals transient modulation of local cortical processing by transcranial direct current stimulation. Venkatakrishnan A, Contreras-Vidal JL, Sandrini M, Cohen LG. Conf Proc IEEE Eng Med Biol Soc. Aug:8102-5 (2011)
The Anatomical Distance of Functional Connections Predicts Brain Network Topology in Health and Schizophrenia Aaron F. Alexander-Bloch, Petra E. Vértes, Reva Stidd, François Lalonde, Liv Clasen, Judith Rapoport, Jay Giedd, Edward T. Bullmore and Nitin Gogtay Cerebral Cortex, doi:10.1093/cercor/bhr388 (2011)
Parietofrontal integrity determines neural modulation associated with grasping imagery after stroke Ethan R. Buch, Amirali Modir Shanechi, Alissa D. Fourkas, Cornelia Weber, Niels Birbaumer and Leonardo G. Cohen Brain, doi:10.1093/brain/awr331 (2011)
Analysis of Biological Features Associated with Meiotic Recombination Hot and Cold Spots in Saccharomyces cerevisiae Loren Hansen, Nak-Kyeong Kim, Leonardo Mariño-Ramírez, David Landsman PLoS One, doi:10.1371/journal.pone.0029711 (2011)
Tryptic y++ Fragment Ion Distributions Are Guided by Coulombic Repulsion Karl K. Irikura, John K. Merle and Yamil Sim´n-Manso J. Am. Soc. Mass Spec., doi:10.1007/s13361-011-0293-7 (2011)
Structural models of TREK channels and their gating mechanism Adina L Milac, Andriy Anishkin, Sarosh N Fatakia, Carson C Chow, Sergei Sukharev, and H Robert Guy Channels, doi: 10.4161/chan.5.1.13905 (2011)
Expression, purification and characterization of recombinant human serine proteinase inhibitor Kazal-type 6 (SPINK6) in Pichia pastoris Hairong Lu, Jinjiang Huang, Guodong Li, Kuikui Ge, Hongyu Wu, Qingshan Huang Protein Expression and Purification, doi:10.1016/j.pep.2011.12.004 (2011)
Overproduction of recombinant proteins in plants Erin Egelkrout, Vidya Rajan, John A. Howard Plant Science, doi:10.1016/j.plantsci.2011.12.005 (2011)
Condensin dysfunction in human cells induces nonrandom chromosomal breaks in anaphase, with distinct patterns for both unique and repeated genomic regions Alexander Samoshkin, Stanimir Dulev, Dmitry Loukinov, Jeffrey A. Rosenfeld and Alexander V. Strunnikov Chromosoma Biology of the Nucleus, doi: 10.1007/s00412-011-0353-6 (2011)
Effects of pH on proteins: Predictions for ensemble and single molecule pulling experiments Edward P O'Brien , Bernard R. Brooks , and Devarajan Thirumalai JACS, doi: 10.1021/ja206557y (2011)
Inherited Variation at Chromosome 12p13. 33, Including RAD52, Influences the Risk of Squamous Cell Lung Carcinoma Jianxin Shi, Nilanjan Chatterjee, Melissa Rotunno, Yufei Wang, Angela C. Pesatori, Dario Consonni, Peng Li, William Wheeler, Peter Broderick, Marc Henrion, Timothy Eisen, Zhaoming Wang, Wei Chen, Qiong Dong, Demetrius Albanes, Michael Thun, Margaret R. Spitz, Pier Alberto Bertazzi, Neil E. Caporaso, Stephen J. Chanock, Christopher I. Amos, Richard S. Houlston and Maria Teresa Landi Cancer Discovery, doi: 10.1158/2159-8290.CD-11-024 (2011)
Causal Inference on Quantiles with an Obstetric Application Zhiwei Zhang, Zhen Chen, James F. Troendle, and Jun Zhang Biometrics, doi: 10.1111/j.1541-0420.2011.01712.x (2011)

Does feature selection improve classification accuracy? Impact of sample size and feature selection on classification using anatomical magnetic resonance images Carlton Chu, Ai-Ling Hsu, Kun-Hsien Chou, Peter Bandettini, Ching-Po Lin, , and the Alzheimer's Disease Neuroimaging Initiative NeuroImage, doi:10.1016/j.neuroimage.2011.11.066 (2011)
Structural basis of anthrax edema factor neutralization by a neutralizing antibody Michelle Makiya, Michael Dolan, Liane Agulto, Robert Purcell, Zhaochun Chen Biochem. Biophys. Res. Comm., doi:10.1016/j.bbrc.2011.11.108 (2011)
High-level expression and characterization of a highly thermostable chitosanase from Aspergillus fumigatus in Pichia pastoris Xiaomei Chen, Chao Zhai, Lixin Kang, Chunhua Li, Hong Yan, Yuling Zhou, Xiaolan Yu and Lixin Ma Biotech. Letters, doi: 10.1007/s10529-011-0816-0 (2011)
Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging. Joel R. Meyerson, Tommi A. White et al J. Visualized Experiments, doi: 10.3791/2770 (2011)
Interaction of Merocyanine 540 with Serum Albumins: Photophysical and Binding Studies Mousumi Banerjee, Uttam Pal, Arijita Subudhhi, Abhijit Chakrabarti, Samita Basu J. Photochemistry and Photobiology B, doi:10.1016/j.jphotobiol.2011.12.005 (2011)
Gene Expression Databases for Kidney Epithelial Cells Jennifer C. Huling, Trairak Pisitkun, Jae H. Song, Ming-Jiun Yu, Jason D. Hoffert, and Mark A. Knepper Am. J. Physiol. - Renal Physiol., doi: 10.?1152/?ajprenal.?00457.?2011 doi: 10.?1152/?ajprenal.?00457.?2011 (2011)

Dynamics of the G protein-coupled vasopressin V2 receptor signaling network revealed by quantitative phosphoproteomics Jason D. Hoffert, Trairak Pisitkun, Fahad Saeed, Jae V. Song, Chung-Lin Chou and Mark A. Knepper Mol. Cell Proteomics, doi: 10.1074/mcp.M111.014613 (2011)
Standard reactions for comparative rate studies: Experiments on the dehydrochlorination reactions of 2-chloropropane, chlorocyclopentane, and chlorocyclohexane Iftikhar A. Awan, Donald R. Burgess Jr., Wing Tsang, Jeffrey A. Manion Int. J. Chem. Kinetics, doi: 10.1002/kin.20566 (2011)
Convergence and error estimation in free energy calculations using the weighted histogram analysis method Fangqiang Zhu, Gerhard Hummer J. Comp. Chem. , doi: 10.1002/jcc.21989 (2011)
The discovery of population differences in network community structure: New methods and applications to brain functional networks in schizophrenia Aaron Alexander-Bloch, Renaud Lambiotte, Ben Roberts, Jay Giedd, Nitin Gogtay, Ed Bullmore NeuroImage, doi:10.1016/j.neuroimage.2011.11.035 (2011)
A linear mixed model for predicting a binary event from longitudinal data under random effects misspecification Paul S. Albert Stat. Med., doi: 10.1002/sim.4405 (2011)
Antimicrobial Properties of Amyloid Peptides Bruce Kagan , Hyunbum Jang , Ricardo Capone , Fernando Teran Arce , Srinivasan Ramachandran , Ratnesh Lal , and Ruth Nussinov Molecular Pharmaceutics, doi: 10.1021/mp200419b (2011)

Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis Rasmus Siersbæk, Ronni Nielsen, Sam John, Myong-Hee Sung, Songjoon Baek, Anne Loft, Gordon L Hager and Susanne Mandrup Embo J. , doi:10.1038/emboj.2011.65 (2011)
Material Properties of Matrix Lipids Determine Conformation and Intermolecular Reactivity of a Diacetylenic Phosphatidylcholine in the Lipid Bilayer Anu Puri , Hyunbum Jang , Amichai Yavlovich , Athar M Masood , Timothy D. Veenstra , Carlos Luna , Helim Aranda-Espinoza , Ruth Nussinov , and Robert Blumenthal Langmuir, doi: 10.1021/la203453x (2011)
Expressão e caracterização de fragmentos de anticorpos recominanes Anti-CD3 humano em Pichia pastoris Sousa, Victor Edgard Tavares Master's thesis, University of Brasilia (2011)
Genome-Wide Association Analysis of Ischemic Stroke in Young Adults Yu-Ching Cheng, Jeffrey R. O'Connel et al Genes | Genomes | Genetics, doi: 10.1534/g3.111.001164 (2011)
Three-Dimensional Structures of Soluble CD4-Bound States of Trimeric Simian Immunodeficiency Virus Envelope Glycoproteins Determined by Using Cryo-Electron Tomography Tommi A. White, Alberto Bartesaghi, Mario J. Borgnia, M. Jason V. de la Cruz, Rachna Nandwani, James A. Hoxie, Julian W. Bess, Jeffrey D. Lifson, Jacqueline L. S. Milne and Sriram Subramaniam J. Virol., doi: 10.1128/?JVI.05297-11 (2011)
Dehydratase Mediated 1-Propanol Production in Metabolically Engineered Escherichia coli. Rachit Jain, Yajun Yan Microbial Cell Factories, doi:10.1186/1475-2859-10-97 (2011)
The Histone Database: an integrated resource for histones and histone fold-containing proteins Leonardo Mariño-Ramírez, Kevin M. Levine, Mario Morales, Suiyuan Zhang, R. Travis Moreland, Andreas D. Baxevanis and David Landsman J. Biol. Databases and Curation, doi: 10.1093/database/bar048 (2011)
Water-Exclusion Effects and Liquid-Structure Forces in Implicit Solvation Sergio A Hassan and Peter J Steinbach J. Phys. Chem. B, doi: 10.1021/jp208184e (2011)
Impact of surface roughness on diffusion of confined fluids William P. Krekelberg, Vincent K. Shen, Jeffrey R. Errington, and Thomas M. Truskett J. Chem. Phys. , doi:10.1063/1.3651478 (2011)
An electrostatic switch controls palmitoylation of the large conductance voltage-and calcium-activated potassium (BK) channel Owen Jeffries, Lijun Tian, Heather McClafferty & Michael J. Shipston. J. Biol. Chem. , doi: 10.1074/jbc.M111.224840 (2011)
Energetics of direct and water-mediated proton-coupled electron transfer. Ville R. I. Kaila and Gerhard Hummer JACS, doi: 10.1021/ja2082262 (2011)
Resting and Active States of the ERK2: HePTP Complex Dana M. Francis, Bartosz Rózycki, Antoni Tortajada, Gerhard Hummer, Wolfgang Peti, and Rebecca Page JACS, doi: 10.1021/ja2075136 (2011)

Dynamic water networks in cytochrome cbb3 oxidase Vivek Sharma, Mårten Wikströma, Ville R.I. Kaila Biochim. et Biophys. Acta, doi:10.1016/j.bbabio.2011.09.010 (2011)
Identification, Replication, and Fine-Mapping of Loci Associated with Adult Height in Individuals of African Ancestry N'Diaye A, Chen GK et al. PLoS Genetics, doi:10.1371/journal.pgen.1002298 (2011)
Synthesis and bio-evaluation of human macrophage migration inhibitory factor inhibitor to develop anti-inflammatory agent Athar Alama, Chinmay Pala, Manish Goyala, Milan Kumar Kundub, Rahul Kumara, Mohd Shameel Iqbala, Sumanta Deya, Samik Bindua, Souvik Sarkara, Uttam Palc, Nakul C. Maitic, Susanta Adhikarid, Uday Bandyopadhyay Bioorganic and Medicinal Chemistry, doi:10.1016/j.bmc.2011.10.056 (2011)
Investigation of Anatomical Thalamo-Cortical Connectivity and fMRI Activation in Schizophrenia Stefano Marenco, Jason L Stein, Antonina A Savostyanova, Fabio Sambataro, Hao-Yang Tan, Aaron L Goldman, Beth A Verchinski, Alan S Barnett, Dwight Dickinson, José A Apud, Joseph H Callicott, Andreas Meyer-Lindenberg and Daniel R Weinberger Neuropsychopharmacology, doi: 10.1038/npp.2011.215 (2011)
NHLBI-AbDesigner: An online tool for design of peptide-directed antibodies Trairak Pisitkun, Jason D. Hoffert, Fahad Saeed, and Mark A. Knepper Am. J. Cell. Physiol. , doi: 10.1152/ajpcell.00325.201 (2011)
A coarse-grained model for PEGylated lipids: the effect of PEGylation on size and shape of self-assembled structures Hwankyu Lee, Richard W. Pastor J. Phys. Chem. B, doi: 10.1021/jp2020148 (2011)

Oncogenically active MYD88 mutations in human lymphoma V.N. Ngo, R.M. Young, R. Schmitz et al Nature, doi:10.1038/nature09671 (2011)
Overexpression of synthesized cephalosporin C acylase containing mutations in the substrate transport tunnel Ying Wang, Huimin Yu, Wensi Song, Ming An, Jing Zhang, Hui Luo, Zhongyao Shen J. Biosci. Bioeng., doi:10.1016/j.jbiosc.2011.08.027 (2011)
Capsomer Vaccines Protect Mice from Vaginal Challenge with Human Papillomavirus Wai-Hong Wu, Elizabeth Gersch, Kihyuck Kwak, Subhashini Jagu, Balasubramanyam Karanam, Warner K. Huh, Robert L. Garcea, Richard B. S. Roden PLoS One, doi:10.1371/journal.pone.0027141 (2011)
N-Protonated Isomers as Gateways to Peptide Ion Fragmentation Fredrik Haeffner, John K. Merle and Karl K. Irikura J. Am. Soc. Mass Spec., doi: 10.1007/s13361-011-0241-6 (2011)
PubChem3D: Biologically relevant 3-D similarity Sunghwan Kim , Evan E Bolton and Stephen H Bryant J. Cheminform., doi:10.1186/1758-2946-3-26 (2011)
Genomic Risk Profiling of Ischemic Stroke: Results of an International Genome-Wide Association Meta-Analysis James F. Meschia, Andrew Singleton, Michael A. Nalls, Stephen S. Rich, Pankaj Sharma, Luigi Ferrucci, Mar Matarin, Dena G. Hernandez, Kerra Pearce, Thomas G. Brott, Robert D. Brown Jr., John Hardy, Bradford B. Worrall PLoS One, doi:10.1371/journal.pone.0023161 (2011)

Large-Scale Phosphotyrosine Proteomic Profiling of Rat Renal Collecting Duct Epithelium Reveals Predominance of Proteins Involved in Cell Polarity Determination Boyang Zhao, Mark A. Knepper, Chung-Lin Chou, and Trairak Pisitkun Cell Physiol. , doi: 10.?1152/ajpcell.00300.2011 (2011)
Logistic regression analysis of biomarker data subject to pooling and dichotomization Z. Zhang, A. Liu, R.H., Lyles, B. Mukherjee Statistics in Medicine, doi: 10.1002/sim.4367 (2011)
Generalized degrees of freedom and adaptive model selection in linear mixed-effects models Bo Zhang, Xiaotong Shen, Sunni L. Mumford Comp. Stats & Data Anal., doi:10.1016/j.csda.2011.09.001 (2011)
Flexible cullins in cullin-ring E3 ligases allosterically regulate ubiquitination Jin Liu and Ruth Nussinov J. Biol. Chem. , doi: 10.1074/jbc.M111.277236 (2011)
Application of a yeast two-hybrid based screening system in the identification of amyloid-beta aggregation inhibitors in pharmaceutical plants Li-Wei Wang, Yan-Fang Yang, Ying-Tao Zhang J. Chinese Pharm. Sciences 20(5):510-517 (2011)
Arl2-GTP and Arl3-GTP regulate a GDI-like transport system for farnesylated cargo Shehab A Ismail, Yong-Xiang Chen, Alexandra Rusinova, Anchal Chandra, Martin Bierbaum, Lothar Gremer, Gemma Triola, Herbert Waldmann, Philippe I H Bastiaens & Alfred Wittinghofer Nature Chem. Bio. , doi:10.1038/nchembio.686 (2011)
In silico implementation of synthetic gene networks. Mario Andrea Marchisio Methods in Mol. Bio. , doi: 10.1007/978-1-61779-412-4_1 (2011)
Selective cell-surface labeling of the molecular motor protein prestin Ryan M. McGuire, Jonathan J. Silberg, Fred A. Pereira, c, Robert M. Raphael Biochem. Biophys. Res. Comm., doi://10.1016/j.bbrc.2011.05.121 (2011)
The Core of Ure2p Prion Fibrils Is Formed by the N-Terminal Segment in a Parallel Cross-? Structure: Evidence from Solid-State NMR Dmitry S. Kryndushkin, Reed B. Wickner, Robert Tycko J. Mol. Biol. , doi://10.1016/j.jmb.2011.03.067 (2011)
Latent class models for joint analysis of disease prevalence and high-dimensional semicontinuous biomarker data Bo Zhang, Zhen Chen and Paul S. Albert Biostatistics, doi: 10.1093/biostatistics/kxr024 (2011)
White Matter Microstructural Correlates of Superior Long-term Skill Gained Implicitly under Randomized Practice Sunbin Song, Nikhil Sharma, Ethan R. Buch and Leonardo G. Cohen Cerebral Cortex, doi: 10.1093/cercor/bhr247 (2011)
Genetic Association for Renal Traits among Participants of African Ancestry Reveals New Loci for Renal Function C-T Liu, MK Garnaas et al. PLoS Genetics, doi:10.1371/journal.pgen.1002264 (2011)

A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies N. Akula, A. Baranova, D Seto, J Solka, MA Nalls, A Singleton, L Ferrucci, T Tanaka, S Bandinelli, YS Cho, YJ Kim, J-Y Lee, B-G Han, Bipolar Disorder Genome Study (BiGS) Consortium, The Wellcome Trust Case-Control Consortium, FJ McMahon PLoS One, doi:10.1371/journal.pone.0024220 (2011)
Conditional Allele Mouse Planner (CAMP): software to facilitate the planning and design of breeding strategies involving mice with conditional alleles Jason D. Hoffert, Trairak Pisitkun, R. Lance Miller. Transgenic Research, doi: 10.1007/s11248-011-9545-3 (2011)
Tackling Force-Field Bias in Protein Folding Simulations: Folding of Villin HP35 and Pin WW Domains in Explicit Water Jeetain MIttal and Robert B. Best Biophys. J. , doi: 10.1016/j.bpj.2010.05.005 (2011)
Rbx1 Flexible Linker Facilitates Cullin-RING Ligase Function Before Neddylation and After Deneddylation Jin Liu and Ruth Nussinov Biophys. J. , doi: 10.1016/j.bpj.2010.05.021 (2011)
Polymorphic Triple β-Sheet Structures Contribute to Amide Hydrogen/Deuterium (H/D) Exchange Protection in the Alzheimer Amyloid β42 Peptide Buyong Ma and Ruth Nussinov J. Biol. Chem. , doi: 10.1074/jbc.M111.241141 (2011)
Effect modification by population dietary folate on the association between MTHFR genotype, homocysteine, and stroke risk: a meta-analysis of genetic studies and randomised trials Holmes MV, Newcombe, P, Hubacek JA et a. The Lancet, doi:10.1016/S0140-6736 (2011)

Genome-wide Association Study for Serum Urate Concentrations and Gout among African Americans Identifies Genomic Risk Loci and a Novel URAT1 Loss-of-Function Allele Tin, A, Woordward OM et al. Hum. Mol. Genet., doi: 10.1093/hmg/ddr307 (2011)
Structural variants of IFNα preferentially promote antiviral functions Nancy Vázquez, Hana Schmeisser, Michael A. Dolan, Joseph Bekisz, Kathryn C. Zoon and Sharon M. Wahl Blood, doi:10.1182/blood-2010-12-325027 (2011)
Enhanced translation by Nucleolin via G-rich elements in coding and non-coding regions of target mRNAs Kotb Abdelmohsen, Kumiko Tominaga, Eun Kyung Lee, Subramanya Srikantan, Min-Ju Kang, Mihee M. Kim, Roza Selimyan, Jennifer L. Martindale, Xiaoling Yang, France Carrier, Ming Zhan, Kevin G. Becker and Myriam Gorospe Nucleic Acids Research, doi: 10.1093/nar/gkr488 (2011)
A Two-Stage Meta-Analysis Identifies Several New Loci for Parkinson's Disease. International Parkinson's Disease Genomics Consortium (IPDGC) and Wellcome Trust Case Control Consortium 2 (WTCCC2) PLoS Genetics, doi: 10.1371/journal.pgen.1002142 (2011)
A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers Kan-Nian Hu, Wei Qiang and Robert Tycko J. Biomol. NMR, doi: 10.1007/s10858-011-9517-1 (2011)
Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures Audray Harris, Mario J. Borgnia, Dan Shi, Alberto Bartesaghi, Haifeng He, Robert Pejchal, Yun (Kenneth) Kang, Rafael Depetris, Andre J. Marozsan, Rogier W. Sanders, Per Johan Klasse, Jacqueline L. S. Milne, Ian A. Wilson, William C. Olson, John P. Moore, and Sriram Subramaniam PNAS, doi: 10.1073/pnas.1101414108 (2011)

Genome-Wide Association Study of White Blood Cell Count in 16,388 African Americans: the Continental Origins and Genetic Epidemiology Network (COGENT) Reiner AP, Lettre G, Nalls MA, Ganesh SK, Mathias R, et al. PLoS Genetics, doi:10.1371/journal.pgen.1002108 (2011)
Multiple Loci Are Associated with White Blood Cell Phenotypes Nalls MA, Couper DJ, Tanaka T, van Rooij FJA, Chen M-H, et al. PLoS Genetics, doi:10.1371/journal.pgen.1002113 (2011)
Phage display of tissue inhibitor of metalloproteinases-2 (TIMP-2): Identification of selective inhibitors of collagenase-1 (MMP-1) Harinath Bahudhanapati, Yingnan Zhang, Sachdev S. Sidhu and Keith Brew J. Biol. Chem. , doi: 10.1074/jbc.M111.253328 (2011)
Energetics and dynamics of proton transfer reactions along short water wires Ville R. I. Kaila and Gerhard Hummer Phys. Chem. Chem. Phys. , doi:10.1039/C1CP21112A (2011)
A survival analysis approach to modeling human fecundity Rajeshwari Sundaram, Alexander C. Mclain and Germaine M. Buck Louis Biostatistics, doi: 10.1093/biostatistics/kxr015 doi: 10.1093/biostatistics/kxr015 doi: 10.1093/biostatistics/kxr01 (2011)
Simulated Self-Assembly of the HIV-1 Capsid: Protein Shape and Native Contacts Are Sufficient for Two-Dimensional Lattice Formation Bo Chen and Robert Tycko Biophys. J. , doi: 10.1016/j.bpj.2011.05.025 (2011)

PubChem3D: Similar conformers Evan Bolton, Sunghwan Kim and Stephen H Bryant J. Cheminform. , doi: 10.1186/1758-2946-3-13. (2011)
Microscopic events in β-hairpin folding from alternative unfolded ensembles Robert Best & Jeetain Mittal PNAS, doi: 10.1073/pnas.1016685108 (2011)
The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-β Enhanceosome Example Yongping Pan, Ruth Nussinov PLoS Computational Biology, doi:10.1371/journal.pcbi.1002077 (2011)
Thermodynamics of Boroxine Formation from the Aliphatic Boronic Acid Monomers R-B (OH) 2 (R= H, H3C, H2N, HO, and F): A Computational Investigation Krishna L. Bhat, George D. Markham, Joseph D. Larkin, and Charles W. Bock J. Phys. Chem. A, doi: 10.1021/jp202409m (2011)
Agricultural intensification, priming for persistence and the emergence of Nipah virus: a lethal bat-borne zoonosis Juliet R. C. Pulliam, Jonathan H. Epstein, Jonathan Dushoff, Sohayati A. Rahman, Michel Bunning, Aziz A. Jamaluddin, Alex D. Hyatt, Hume E. Field, Andrew P. Dobson and Peter Daszak, the Henipavirus Ecology Research Group (HERG) Journal of the Royal Society Interface, doi: 10.1098/?rsif.2011.0223 (2011)
Tools for Vaccine Design: Prediction and Validation of Highly Immunogenic and Conserved Class II Epitopes and Development of Epitope-Driven Vaccines Manmohan Singh, Indresh K. Srivastava Anne S. De Groot, Matthew Ardito, Ryan Tassone, Paul Knopf, Leonard Moise, William Martin Development of Vaccines: From Discovery to Clinical Testing, John Wiley & Sons, doi: 10.1002/9781118023648.ch3 (2011)

Improved genetic association tests for an ordinal outcome representing the disease progression process Hong Zhang, Sholom Wacholder, Jing Qin, Allan Hildesheim, Kai Yu Genetic Epidemiology, doi: 10.1002/gepi.20599 (2011)
Roles of the four DNA polymerases of the crenarchaeon Sulfolobus solfataricus and accessory proteins in DNA replication Jeong-Yun Choi, Robert L. Eoff, Matthew G. Pence, Jian Wang, Martha V. Martin, Eun-Jin Kim, Lindsay M. Folkmann and F. Peter Guengerich J. Biol. Chem. , doi: 10.1074/jbc.M111.258038 (2011)
RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function Moshkovich N, Nisha P, Boyle PJ, Thompson BA, Dale RK, Lei EP Genes Dev., doi: 10.1101/gad.16651211 (2011)
Polymorphism of amyloid β peptide in different environments: implications for membrane insertion and pore formation Fernando Terán Arce, Hyunbum Jang, Srinivasan Ramachandran, Preston B. Landon, Ruth Nussinov and Ratnesh Lal Soft Matter, doi: 10.1039/C1SM05162H (2011)
Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from QM/MM Simulations Edina Rosta , Marcin Nowotny , Wei Yang , and Gerhard Hummer JACS, doi: 10.1021/ja200173a (2011)
Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements Ofir Hakim, Myong-Hee Sung, Ty C. Voss, Erik Splinter, Sam John, Peter J. Sabo, Robert E. Thurman, John A. Stamatoyannopoulos, Wouter de Laat, and Gordon L. Hager Genome Research, doi:10.1101/gr.111153.110 (2011)

The association between inflammation-related genes and serum androgen levels in men: The prostate, lung, colorectal, and ovarian study Tamra E. Meyer, Lisa W. Chu, Qizhai Li, Kai Yu, Philip S. Rosenberg, Idan Menashe, Anand P. Chokkalingam, Sabah M. Quraishi, Wen-Yi Huang, Jocelyn M. Weiss, Rudolf Kaaks, Richard B. Hayes, Stephen J. Chanock, Ann W. Hsing The Prostate, doi: 10.1002/pros.21407 (2011)
Cystine knot peptides binding to Alpha IIb Beta 3 integrins and methods of use Cochran, J, Silverman, AP, Kariolis, Mihalis S. US Patent application 20110136740 (2011)
Protein Tertiary Structure Prediction based on main chain angle using a hybrid Bees Colony Optimization Algorithm ZN Mahmood, M. Mahmuddin, M.N. Mahmood International Journal of Modern Physics: Conference Series, DOI: 10.1142/S201019451200520X (2011)
Cloning and overexpression of influenza a H1N1 NS1 protein in escherichia coli Ong, Lih Lih Masters thesis, Universiti Teknologi Malaysia (2011)
Synergistic interactions between repeats in tau protein and Aβ amyloids may be responsible for accelerated aggregation via polymorphic states Yifat Miller, Buyong Ma, and Ruth Nussinov Biochemistry, doi: 10.1021/bi200400u (2011)
Driving Forces Enable High-Titer Anaerobic 1-Butanol Synthesis in Escherichia coli Claire R. Shen, Ethan I. Lan, Yasumasa Dekishima, Antonino Baez, Kwang Myung Cho, and James C. Liao App. Env. Microbiology, doi:10.1128/AEM.03034-10 (2011)

A joint modeling approach to data with informative cluster size: Robustness to the cluster size model Zhen Chen, Bo Zhang, Paul S. Albert Statistics in Medicine, doi: 10.1002/sim.4239 (2011)
On the stability and ranking of predictors from random forest variable importance measures Kristin K Nicodemus Brief. Bioinfo., doi: 10.1093/bib/bbr016 (2011)
Human Insulin production in E.Coli: Gene optimization, Assembly, Cloning and Protein Expression Gamal Abd El-Aziz, Metwali M.Reda, S.H.Abdel-Aziz, EL-Rashdy M. Redwan J. Biotech. Res. 11:37 (2011)
Thermochemistry of imidazolium-based ionic liquids: experiment and first-principles calculations Sergey P. Verevkin, Vladimir N. Emel'yanenko, Dzmitry H. Zaitsau, Andreas Heintz, Chris D. Muzny and Michael Frenkel Phys. Chem. Chem. Phys., doi:10.1039/C0CP00747A (2011)
Intermittent Hypoxia-Induced Sensitization of Central Chemoreceptors Contributes to Sympathetic Nerve Activity during Late Expiration in Rats Yaroslav I. Molkov, Daniel B Zoccal, Davi J.A. Moraes, Julian F.R. Paton, Benedito H. Machado, and Ilya A Rybak J. Neurophysiol., doi: 10.?1152/jn.00070.2011 (2011)
Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide Guillem Revilla-López, Juan Torras, Ruth Nussinov, Carlos Alemán and David Zanuy Physical Chemistry Chemical Physics, doi: 10.1039/C0CP02572K (2011)

PubChem3D: Diversity of shape Evan Bolton, Sunghwan Kim, and Stephen Bryant J. Cheminform. , doi: 10.1186/1758-2946-3-9 (2011)
Crystal structure of basic 7S globulin, a xyloglucan-specific endo-β-1, 4-glucanase inhibitor protein-like protein from soybean lacking inhibitory activity against endo-β-glucanase Takuya Yoshizawa, Toshiyuki Shimizu, Mayuki Yamabe, Misako Taichi, Yuji Nishiuchi, Naoki Shichijo, Satoru Unzai, Hisashi Hirano, Mamoru Sato, Hiroshi Hashimoto FEBS Journal, doi: 10.1111/j.1742-4658.2011.08111.x (2011)
Conformational Relaxation and Water Penetration Coupled to Ionization of Internal Groups in Proteins Ana Damjanovic, Bernard R. Brooks, and Bertrand García-Moreno E J. Phys. Chem. , published online 23 Mar (2011)
Efficient Adaptively Weighted Analysis of Secondary Phenotypes in Case-Control Genome-Wide Association Studies Huilin Li and Mitchell Gail Human Heredity, DOI: 10.1159/000338943 (2011)
Structural basis of p38α regulation by hematopoietic tyrosine phosphatase Dana M Francis, Bartosz Rózycki, Dorothy Koveal, Gerhard Hummer, Rebecca Page & Wolfgang Peti Nature Chem. Bio. , doi:10.1038/nchembio.707 (2011)
Microscopic mechanism of nanocrystal formation from solution by cluster aggregation and coalescence Sergio A. Hassan J. Chem. Phys. 134:114508 (2011)

PubChem3D: a new resource for scientists Evan E Bolton, Jie Chen, Sunghwan Kim, Lianyi Han, Siqian He, Wenyao Shi, Vahan Simonyan, Yan Sun, Paul A Thiessen and Jiyao Wang, et al. J. Cheminform. 3:32 (2011)
Water Transport through Nanotubes with Varying Interaction Strength between Tube Wall and Water Matthew Melillo, Fangqiang Zhu, Mark A. Snyder, and Jeetain Mittal J. Phys. Chem. Letters (2011)
Large-scale Exploration of Gene-Gene Interactions in Prostate Cancer Using a Multistage Genome-wide Association Study Julia Ciampa, Meredith Yeager, Laufey Amundadottir, Kevin Jacobs, Peter Kraft, Charles Chung, Sholom Wacholder, Kai Yu, William Wheeler, Michael J Thun, W Ryan Divers, Susan Gapstur, Demetrius Albanes, Jarmo Virtamo, Stephanie Weinstein, Edward Giovannucci, Walter C Willet, Geraldine Cancel-Tassin, Olivier Cussenot, Antoine Valeri, David Hunter, Robert Hoover, Gilles Thomas, Stephen Chanock, and Nilanjan Chatterjee Cancer Res., doi: 10.1158/0008-5472.CAN-10-2646 (2011)
PubChem3D: Conformer generation. Evan E Bolton, Sunghwan Kim, and Stephen H Bryant J. Cheminform., doi: 10.1186/1758-2946-3-4 (2011)
Molecular-Level Examination of Cu2+ Binding Structure for Amyloid Fibrils of 40-Residue Alzheimer's β by Solid-State NMR Spectroscopy Sudhakar Parthasarathy, Fei Long, Yifat Miller, Yiling Xiao, Dan McElheny, Kent Thurber, Buyong Ma, Ruth Nussinov, and Yoshitaka Ishii JACS, published online 22 Feb (2011)
Symmetry-Based Self-Assembled Nanotubes Constructed Using Native Protein Structures: The Key Role of Flexible Linkers Buch, Idit; Tsai, Chung-Jung; J. Wolfson, Haim; Nussinov, Ruth Protein & Peptide Letters 18(4):362-372 (2011)

Genome-Wide Association Studies of the PR Interval in African Americans JG Smith, JW. Magnani, C Palmer, YA Meng, EZ Soliman, SK Musani, KF Kerr, RB Schnabel, SA Lubitz, N Sotoodehnia, S Redline, A Pfeufer, M Müller, DS Evans, MA Nalls, Y Liu, AB Newman, AB Zonderman, MK Evans, R Deo, PT Ellinor, DN Paltoo, C Newton-Cheh, E J Benjamin, R Mehra, A Alonso, SR Heckbert, ER Fox, Candidate-gene Association Resource (CARe) Consortium PLoS Genetics, doi:10.1371/journal.pgen.1001304 (2011)
Modelling batched Gaussian longitudinal weight data in mice subject to informative dropout Paul S. Albert, Joanna H Shih Stat. Meth. in Med. Res., doi: 10.1177/0962280210397886 (2011)
The Unique Alzheimer's β-Amyloid Triangular Fibril Has a Cavity along the Fibril Axis under Physiological Conditions Yifat Miller, Buyong Ma, and Ruth Nussinov J. Am. Chem. Soc., doi: 10.1021/ja1100273 (2011)
Novel HIV-1 protease inhibitors (PIs) containing a bicyclic P2 functional moiety, tetrahydropyrano-tetrahydrofuran, that are potent against multi-PI-resistant HIV-1 variants Kazuhiko Ide, Manabu Aoki, Masayuki Amano, Yasuhiro Koh, Ravikiran S. Yedidi, Debananda Das, Sofiya Leschenko, Bruno Chapsal, Arun K. Ghosh, and Hiroaki Mitsuya Antimicrob Agents Chemother., doi:10.1128/AAC.01540-10 (2011)
Binding of a C-end rule peptide to neuropilin-1 receptor: A molecular modeling approach Nurit Haspel , David Zanuy , Ruth Nussinov , Tambet Teesalu , Erkki Ruoslahti , and Carlos Aleman Biochemistry, doi: 10.1021/bi101662j (2011)
SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions Bartosz Rózycki, Young C. Kim and Gerhard Hummer Structure, doi:10.1016/j.str.2010.10.006 (2011)

Distinct DNA methylation changes highly correlated with chronological age in the human brain Dena G Hernandez, Michael A Nalls, J Raphael Gibbs, Sampath Arepalli, Marcel van der Brug, Sean Chong, Matthew Moore, Dan L Longo, Mark Cookson, Bryan J Traynor and Andrew Singleton Human Molecular Genetics, published online 7 Jan (2011)
An Audit Strategy for Progression-Free Survival Lori E. Dodd, Edward L. Korn, Boris Freidlin, Robert Gray, Suman Bhattacharya Biometrics, doi: 10.1111/j.1541-0420.2010.01539.x (2011)
Atomistic modeling of peptides bound to a chemically active surface: conformational implications David Curcó, Guillem Revilla-López, Carlos Alemán, David Zanuy J. Peptide Science, doi: 10.1002/psc.1321 (2011)
Genome-wide association study implicates PARD3B-based AIDS restriction Troyer, J.L., Nelson, G.W., Lautenberger, J.A., Chinn, L., McIntosh, C., Johnson, R.C., Sezgin, E., Kessing, B., Malasky, M., Hendrickson, S.L., Li, G., Pontius, J., Tang, M., An, P., Winkler, C.A., Limou, S., Le Clerc, S., Delaneau, O., Zagury, J.-F., Schuitemaker, H., van Manen, D., Bream, J.H., Gomperts, E.D., Buchbinder, S., Goedert, J.J., Kirk, G.D., O'Brien, S.J. J. Infect. Dis 203(10):1491-502 (2011)
De novo Synthesis and Expression of a Thermostable Xylanase from Geobacillus stearothermophilus in Escherichia coli Zhang Zhigang, Pei Xiaoqiong & Wu Zhongliu Chin. J. Appl. Environ. Biol., doi: 10.3724/SP.J.1145.2009.00271 (2011)

2010 (96 papers)

Polymorphic C-terminal β-sheet interactions determine the formation of fibril or ADDL-like globulomer for the Alzheimer Aβ42 dodecamer Buyong Ma and Ruth Nussinov J. Biol. Chem. , doi: 10.1074/jbc.M110.133488 (2010)
Patterns and Complexity in Biological Systems: A Study of Sequence Structure and Ontology-based Networks Kimberley Glass PhD thesis, University of Maryland. (2010)
Dependence of Protein Folding Stability and Dynamics on the Density and Composition of Macromolecular Crowders Jeetain Mittal and Robert B Best BIophys. J. 98(2):315-320 (2010)
Predicting In Vitro Drug Sensitivity using Random Forests Gregory Riddick, Hua Song, Susie Ahn, Jennifer Walling, Diego Borges-Rivera, Wei Zhang, and Howard A. Fine Bioinformatics, published online 5 Dec (2010)
Large-Scale Phosphoproteomic Analysis of Membrane Proteins in Renal Proximal and Distal Tubule Marina Feric, Boyang Zhao, Jason D. Hoffert, Trairak Pisitkun, and Mark A. Knepper Am. J. Physiol. - Cell Physiol. , doi: 10.1152/ajpcell.00360.2010 (2010)
Microarray Meta-Miner (MMM): An integrated method and a web tool to identify genes with similar expression profile Nagarajan, V.; Varma, S.; Hurt, D.; Yongjian Guo; Huyen, Y Computer Technology and Development, doi:10.1109/ICCTD.2010.5646068 (2010)
Atomic-Scale Simulations Confirm that Soluble β-Sheet-Rich Peptide Self-Assemblies Provide Amyloid Mimics Presenting Similar Conformational Properties Xiang Yu, Jingdai Wang, Jui-Chen Yang, Qiuming Wang, Stephen Z.D. Cheng, Ruth Nussinov, and Jie Zheng Biophys. J. 98(1):27-36 (2010)

Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks Margaret E. Johnson and Gerhard Hummer PNAS, doi: 10.1073/pnas.1010954108 (2010)
Molecular Architectures of Trimeric SIV and HIV-1 Envelope Glycoproteins on Intact Viruses: Strain-Dependent Variation in Quaternary Structure Tommi A. White, Alberto Bartesaghi, Mario J. Borgnia, Joel R. Meyerson, M. Jason V. de la Cruz, Julian W. Bess, Rachna Nandwani, James A. Hoxie, Jeffrey D. Lifson, Jacqueline L. S. Milne, Sriram Subramaniam PLoS Pathogens, doi:10.1371/journal.ppat.1001249 (2010)
Nanoscale architecture of integrin-based cell adhesions Kanchanawong P, Shtengel G, Pasapera AM, Ramko EB, Davidson MW, Hess HF, Waterman CM. Nature 468(7323):580-4 (2010)
Accounting for multiple comparisons in a genome-wide association study (GWAS) Randall C Johnson, George W Nelson, Jennifer L Troyer, James A Lautenberger, Bailey D Kessing, Cheryl A Winkler, Stephen J O'Brien BMC Genomics 11:724 (2010)
Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations Sijung Yun and Robert H Guy J. Mol. Graph. and Modeling, doi:10.1016/j.jmgm.2010.12.002 (2010)
Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences Robert B Best, Jeetain Mittal Proteins: Structure, Function and Bioinf, doi: 10.1002/prot.22972 (2010)
The Human Glucocorticoid Receptor as an RNA-Binding Protein: Global Analysis of Glucocorticoid Receptor-Associated Transcripts and Identification of a Target RNA Motif Ishmael FT, Fang X, Houser KR, Pearce K, Abdelmohsen K, Zhan M, Gorospe M, Stellato C. J. Immunol. , doi:10.4049/jimmunol.1001794 (2010)
Comprehensive engineering of Escherichia coli for enhanced expression of IgG antibodies Tomohiro Makinoa, Georgios Skretas, Tae Hyun Kang and George Georgiou Metabolic Engg. , doi:10.1016/j.ymben.2010.11.002 (2010)
Analysis of progression-free survival data using a discrete time survival model that incorporates measurements with and without diagnostic error Sally Hunsberger, Paul S Albert, Lori Dodd Clinical Trials, doi: 10.1177/1740774510384887 (2010)
Microscopic properties of nanopore water from its time-dependent dielectric response Jürgen Köfinger and Christoph Dellago Phy. Rev. B 82:205416 (2010)
Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome Jie Zheng, Pavel P Khil, R Daniel Camerini-Otero and Teresa M Przytycka Genome Biology 11:R103, doi:10.1186/gb-2010-11-10-r103 (2010)
Expression of Recombinant Cytochromes c in E. coli. Yuri Londer Methods in Molecular Biology 705:123-150 (2010)

Analysis of the stabilities of hexameric amyloid-β (1-42) models using discrete molecular dynamics simulations Sijung Yun, Sajung Yun and H. Robert Guy J. Mol. Graphics and Modelling, doi:10.1016/j.jmgm.2010.11.008 (2010)
Crystal Structures Exploring the Origins of the Broader Specificity of Escherichia coli Heat-Labile Enterotoxin Compared to Cholera Toxin Holmner A, Mackenzie A, Okvist M, Jansson L, Lebens M, Teneberg S, Krengel U. J. Mol. Biol. , doi:10.1016/j.jmb.2010.11.060 (2010)
RAId_aPS: MS/MS Analysis with Multiple Scoring Functions and Spectrum-Specific Statistics Gelio Alves, Aleksey Y. Ogurtsov, and Yi-Kuo Yu PLoS One 5(11):e15438 (2010)
Origin of Twist-Bend Coupling in Actin Filaments Enrique M. De La Cruz, Jeremy Roland, Brannon R. McCullough, Laurent Blanchoin, Jean-Louis Martiel Biophys. J. , doi:10.1016/j.bpj.2010.07.009 (2010)
Approximating probabilities of correlated events Li QiZhai, Zheng Gang, Liu AiYi, Li ZhaoHai & Yu Kai Science China Mathematics 53(11):2937-2948 (2010)
Dockomatic-automated ligand creation and docking Casey W Bullock , Reed B Jacob , Owen M McDougal, Greg Hampikian and Tim Andersen BMC Research Notes, doi:10.1186/1756-0500-3-289 (2010)

Water in the Polar and Nonpolar Cavities of the Protein Interleukin-1β Hao Yin, Guogang Feng, G. Marius Clore, Gerhard Hummer, and Jayendran C. Rasaiah J. Phy. Chem. B, doi: 10.1021/jp108731r (2010)
Assigning statistical significance to proteotypic peptides via database searches Gelio Alves, Aleksey Ogurtsov, Yi-Kuo Yu J. Proteomics, doi:10.1016/j.jprot.2010.10.005 (2010)
A Computational Investigation of the Nitrogen-Boron Interaction in o-(N, N-Dialkylaminomethyl) arylboronate Systems Joseph D. Larkin, John S. Fossey, Tony D. James, Bernard R. Brooks, and Charles W. Bock J. Phys. Chem. A, doi: 10.1021/jp1087674 (2010)
Multiple imputation for estimating the risk of developing dementia and its impact on survival Binbing Yu, Jane S. Saczynski, Lenore Launer Biometrical Journal 52(5) :616-627 (2010)
Pore opening and closing of a pentameric ligand-gated ion channel Fangqiang Zhu and Gerhard Hummer PNAS, doi: 10.1073/pnas.1009313107 (2010)
Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse Robert B Best and Jeetain Mittal J. Phys. Chem. B, doi: 10.1021/jp108618d (2010)

Nematic Order in Small Systems: Measuring the Elastic and Wall-Anchoring Constants in Vibrofluidized Granular Rods Jennifer Galanis, Ralph Nossal, Wolfgang Losert, and Daniel Harries Phys. Rev. Let. 105:168001 (2010)
β-Barrel Topology of Alzheimer's β-Amyloid Ion Channels Hyunbum Jang, Fernando Teran Arce, Srinivasan Ramachandran, Ricardo Capone, Ratnesh Lal, and Ruth Nussinov J. Mol. Biol. , doi:10.1016/j.jmb.2010.10.025 (2010)
Quantitative protein and mRNA profiling shows selective post-transcriptional control of protein expression by vasopressin in kidney cells Sookkasem Khositseth, Trairak Pisitkun, Dane H. Slentz, Guanghui Wang, Jason D. Hoffert, Mark A. Knepper* and Ming-Jiun Yu Molecular & Cellular Proteomics, doi: 10.1074/mcp.M110.004036 (2010)
An approach for jointly modeling multivariate longitudinal measurements and discrete time-to-event data Paul S. Albert and Joanna H. Shih Ann. Appl. Stat. 4(3):1517-1532 (2010)
Electrostatic Interactions and Binding Orientation of HIV-1 Matrix Studied by Neutron Reflectivity Hirsh Nanda, Siddhartha A.K. Datta, Frank Heinrich, Mathias L�sche, Alan Rein, Susan Krueger, Joseph E. Curtis Biophys. J. , doi: 10.1016/j.bpj.2010.07.062 (2010)
Biological Validation of Increased Schizophrenia Risk With NRG1, ERBB4, and AKT1 Epistasis via Functional Neuroimaging in Healthy Controls Kristin K. Nicodemus, Amanda J. Law, Eugenia Radulescu, Augustin Luna, Bhaskar Kolachana, Radhakrishna Vakkalanka, Dan Rujescu, Ina Giegling, Richard E. Straub, Kate McGee, Bert Gold, Michael Dean, Pierandrea Muglia, Joseph H. Callicott, Hao-Yang Tan, Daniel R. Weinberger Arch. Gen. Psych. 67(10):991-1001 (2010)

Conformational Profile of a Proline-Arginine Hybrid Guillermo Revilla-López, Ana I. Jiménez, Carlos Cativiela, Ruth Nussinov, Carlos Alemán, and David Zanuy J. Chem. Inf. and Modeling, doi: 10.1021/ci100135f (2010)
Mapping mouse IL-13 binding regions using structure modeling, molecular docking, and high-density peptide microarray analysis Satish K Madala, Michael A. Dolan, Deepak Sharma, Thirumalai R. Ramalingam, Mark S. Wilson, Margaret M. Mentink-Kane, Daniel C. Masison, Thomas A. Wynn Proteins: Structure, Function and Bioinf, doi: 10.1002/prot.22881 (2010)
Robust and accurate data enrichment statistics via distribution function of sum of weights. Stojmirovic A, Yu YK Bioinformatics, doi: 10.1093/bioinformatics/btq511 (2010)
Using Principal Components of Genetic Variation for Robust and Powerful Detection of Gene-Gene Interactions in Case-Control and Case-Only Studies Samsiddhi Bhattacharjee, Zhaoming Wang, Julia Ciampa, Peter Kraft, Stephen Chanock, Kai Yu and Nilanjan Chatterjee Am. J. Hum. Genet. 86(3):331-342 (2010)
Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber Sun-Shin Cha1, Young Jun An, Chang Ro Lee, Hyun Sook Lee, Yeon-Gil Kim, Sang Jin Kim, Kae Kyoung Kwon, Gian Marco De Donatis, Jung-Hyun Lee, Michael R Maurizi and Sung Gyun Kang Embo J. , doi:10.1038/emboj.2010.226 (2010)
Models of membrane-bound Alzheimer's abeta peptide assemblies Yinon Shafrir, Stewart Durell, Nelson Arispe, H. Robert Guy Proteins, doi: 10.1002/prot.22853 (2010)

In Vitro Selection of Highly Darunavir-Resistant and Replication-Competent HIV-1 Variants by Using a Mixture of Clinical HIV-1 Isolates Resistant to Multiple Conventional Protease Inhibitors Yasuhiro Koh, Masayuki Amano, Tomomi Towata, Matthew Danish, Sofiya Leshchenko-Yashchuk, Debananda Das, Maki Nakayama, Yasushi Tojo, Arun K. Ghosh, and Hiroaki Mitsuya J. Virol. , doi:10.1128/JVI.00967-10 (2010)
Structural and Dynamic Determinants of Ligand Binding and Regulation of Cyclin-Dependent Kinase 5 by Pathological Activator p25 and Inhibitory Peptide CIP A. Cardone, S.A. Hassan, R.W. Albers, R.D. Sriram and H.C. Pant J. Mol. Biol., doi:10.1016/j.jmb.2010.06.040 (2010)
Hollow core of Alzheimer's Aβ42 amyloid observed by cryoEM is relevant at physiological pH Yifat Miller, Buyong Ma, Chung-Jung Tsai, Ruth Nussinov PNAS, 10.1073/pnas.1004704107 (2010)
Population dynamics of a pathogen: the conundrum of vivax malaria Philip G. McQueen Biophys. Revs. 2(3):111-120 (2010)
Scaling Factors and Uncertainties for ab Initio Anharmonic Vibrational Frequencies Russell D. Johnson, III, Karl K. Irikura, Raghu N. Kacker and Rdiger Kessel J. Chem. Theory. Comp., doi: 10.1021/ct100244d (2010)
Molecular Basis for the Structural Stability of an Enclosed β Barrel Loop Pu Tian and Harris D. Bernstein J. Mol. Biol. , doi:10.1016/j.jmb.2010.07.035 (2010)

Predictive Correlations Based on Large Experimental Datasets: Critical Constants for Pure Compounds Andrei Kazakov, Chris D. Muzny, Vladimir Diky, Robert D. Chirico and Michael Frenkel Fluid Phase Equilibria 298(1):131-142 (2010)
Using Cases to Strengthen Inference on the Association between Single Nucleotide Polymorphisms and a Secondary Phenotype in Genome-Wide Association Studies Huilin Li, Mitchell H. Gail, Sonja Berndt, and Nilanjan Chatterjee Genet. Epidemiol. 34(5):427-433 (2010)
Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization Yongping Pan and Ruth Nussinov PLoS Computational Biology, doi: 10.1371/journal.pcbi.1000878. (2010)
Release of genotype 1 hepatitis E virus from cultured hepatoma and polarized intestinal cells depends on ORF3 protein and requires an intact PXXP motif Suzanne U. Emerson, Hanh T. Nguyen, Udana Torian, Danielle Burke, Ronald Engle and Robert H. Purcell J. Virol. , doi:10.1128/JVI.00593-10 (2010)
Structural Convergence Among Diverse, Toxic β-Sheet Ion Channels Hyunbum Jang, Fernando Teran Arce, Srinivasan Ramachandran, Ricardo Capone, Ratnesh Lal and Ruth Nussinov J. Phys. Chem. B, doi: 10.1021/jp104073k (2010)
The Influence of GABRA2, Childhood Trauma and their Interaction on Alcohol, Heroin and Cocaine Dependence Mary-Anne Enoch, Colin A Hodgkinson, Qiaoping Yuan, Pei-Hong Shen, David Goldman, Alec Roy Biol Psychiatry., doi: 10.1016/j.biopsych.2009.08.019 (2010)

Genome-wide association identifies candidate genes that influence the human electroencephalogram Colin A. Hodgkinson, Mary-Anne Enoch, Vibhuti Srivastava et al. PNAS, doi: 10.1073/pnas.0908134107 (2010)
Multiple chronic pain states are associated with a common amino acid�changing allele in KCNS1 Michael Costigan, Inna Belfer, Robert S. Griffin et al. Brain, doi: 10.1093/brain/awq195 (2010)
Haplotype-Based Study of the Association of Alcohol Metabolizing Genes with Alcohol Dependence in Four Independent Populations Jixia Liu, Zhifeng Zhou, Colin A. Hodgkinson, Qiaoping Yuan, Pei-Hong Shen, Connie J. Mulligan, Alex Wang, Rebecca R. Gray, Alec Roy, Matti Virkkunen, David Goldman, Mary-Anne Enoch Alcohol Clin Exp Res., doi: 10.1111/j.1530-0277.2010.01346.x (2010)
Mutations from a family-shuffling-library reveal amino acid residues responsible for the thermostability of endoglucanase CelA from Clostridium thermocellum Zhuo-Lin Yi and Zhong-Liu Wu Biotech. Letters, 10.1007/s10529-010-0363-0 (2010)
Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA Randall A. Hughes and Andrew D. Ellington Nucleic Acids Research, doi:10.1093/nar/gkq521 (2010)
Phosphoproteomic profiling reveals vasopressin-regulated phosphorylation sites in collecting duct Bansal AD, Hoffert JD, Pisitkun T, Hwang S, Chou CL, Boja ES, Wang G, Knepper MA. J. Am. Soc. Nephrol. 21(2):303-15 (2010)
De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds Shen Y, Bryan PN, He Y, Orban J, Baker D, Bax A. Protein Science 19(2):349-56 (2010)
Balance between α and β Structures in Ab Initio Protein Folding Robert B. Best and Jeetain Mittal J. Phys. Chem. B , doi: 10.1021/jp102575b (2010)
Tautomerism and Magnesium Chelation of HIV-1 Integrase Inhibitors: A Theoretical Study Chenzhong Liao and Marc C. Nicklaus Chem Med Chem, published online 8 Jun (2010)
FastMEDUSA: A parallelized tool to infer gene regulatory networks Serdar Bozdag, Aiguo Li, Stefan Wuchty, Howard A. Fine Bioinformatics, doi:10.1093/bioinformatics/btq275 (2010)
Structural basis of G protein-coupled receptor-G protein interactions Jianxin Hu, Yan Wang, Xiaohong Zhang, John R Lloyd, Jian Hua Li, Joel Karpiak, Stefano Costanzi, J¨rgen Wess Nature Chem. Biol., doi:10.1038/nchembio.385 (2010)
Antimicrobial Protegrin-1 Forms Ion Channels: Molecular Dynamic Simulation, Atomic Force Microscopy, and Electrical Conductance Studies Ricardo Capone, Mirela Mustata, Hyunbum Jang, Fernando Teran Arce, Ruth Nussinov, and Ratnesh Lal Biophys. J., doi: 10.1016/j.bpj.2010.02.024 (2010)

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor J. Phys. Chem. B, published online 24 May (2010)
Comparison of multivariate classifiers and response normalizations for pattern-information fMRI Masaya Misaki, Youn Kima, Peter A. Bandettini and Nikolaus Kriegeskorte Neuroimage, doi:10.1016/j.neuroimage.2010.05.051 (2010)
Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain J. Raphael Gibbs, Marcel P. van der Brug, Dena G. Hernandez, Bryan J. Traynor, Michael A. Nalls, Shiao-Lin Lai, Sampath Arepalli, Allissa Dillman, Ian P. Rafferty, Juan Troncoso, Robert Johnson, H. Ronald Zielke, Luigi Ferrucci, Dan L. Longo, Mark R. Cookson, Andrew B. Singleton PLoS Genetics 6(5):e1000952, doi:10.1371/journal.pgen.1000952 (2010)
Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic states Yifat Miller, Buyong Ma, and Ruth Nussinov PNAS, published online 6 May (2010)
Efficient expression and purification of human aglycosylated Fcγ receptors in Escherichia coli Sang Taek Jung, Tae Hyun Kang, George Georgiou Biotech. and Bioengg., published online 7 May (2010)
Emotional Automaticity Is a Matter of Timing Qian Luo, Tom Holroyd, Catherine Majestic, Xi Cheng, Julia Schechter, and R. James Blair J. Neuroscience 30(17):5825-5829 (2010)

How Does the Reductase Help To Regulate the Catalytic Cycle of Cytochrome P450 3A4 Using the Conserved Water Channel? Dan Fishelovitch, Sason Shaik, Haim J. Wolfson and Ruth Nussinov J. Phys. Chem. B 114(17):5964-5970 (2010)
Improving polyp detection algorithms for CT colonography: Pareto front approach Adam Huang, Jiang Li, Ronald M. Summers, Nicholas Petrick, Amy K. Hara Pattern Recognition Letters, doi:10.1016/j.patrec.2010.03.013 (2010)
Solution conformation and dynamics of the HIV-1 integrase core domain Nicholas C. Fitzkee, James E. Masse, Yang Shen, David R. Davies, and Ad Bax J. Biol. Chem. , doi/10.1074/jbc.M110.113407 (2010)
Use of Multiple Assays Subject to Detection Limits With Regression Modeling in Assessing the Relationship Between Exposure and Outcome Albert, Paul S, Harel, Ofer, Perkins, Neil, Browne, Richard Epidemiology, doi: 10.1097/EDE.0b013e3181ce9eed (2010)
Low-Temperature Dynamic Nuclear Polarization at 9.4 Tesla With a 30 Milliwatt microwave source Kent R. Thurber, Wai-Ming Yau and Robert Tycko J. Magnetic Resonance :doi:10.1016/j.jmr.20 (2010)
Neural substrates of graphomotor sequence learning: A combined fMRI and kinematic study Bruce A. Swett, Jose L. Contreras-Vidal, Rasmus Birn and Allen R. Braun J. Neurophysiol., doi:10.1152/jn.00449.2009 (2010)

Extensive and Modular Intrinsically Disordered Segments in C. elegans TTN-1 and Implications in Filament Binding, Elasticity and Oblique Striation Jeffrey G. Forbes, Denise B. Flaherty, Kan Ma, Hiroshi Qadota, Guy M. Benian, and Kuan Wang J. Mol. Biol. , doi:10.1016 (2010)
A Novel Point Mutation in Helix 10 of the Human Glucocorticoid Receptor Causes Generalized Glucocorticoid Resistance by Disrupting the Structure of the Ligand-Binding Domain Nancy Nader, Bert E. Bachrach, Darrell E. Hurt, Sonia Gajula, Amy Pittman, Rachel Lescher, and Tomoshige Kino J. Clin. Endocrin. & Metab., published online 24 March (2010)
Engineering anti-VEGF disulfide-stabilized single chain antibody variable fragments (sc-dsFv) with phage displayed sc-dsFv libraries Yi-Jen Huang, Ing-Chien Chen, Chung-Ming Yu, Yu-Ching Lee, Hung-Ju Hsu, Anna Ching-Ching Tung, Hung-Ju Chang and An-Suei Yang J. Biol. Chem. , published online 12 Jan (2010)
Engineering Anti-vascular Endothelial Growth Factor Single Chain Disulfide-stabilized Antibody Variable Fragments (sc-dsFv) with Phage-displayed sc-dsFv Libraries Yi-Jen Huang, Ing-Chien Chen, Chung-Ming Yu, Yu-Ching Lee, Hung-Ju Hsu, Anna Tung Ching Ching, Hung-Ju Chang, An-Suei Yang J. Biol. Chem. 285:7880-7891 (2010)
Depletion forces drive polymer-like self-assembly in vibrofluidized granular materials Jennifer Galanis, Ralph Nossal, and Daniel Harries Soft Matter 6:1026-1034 (2010)
The behaviour of random forest permutation-based variable importance measures under predictor correlation Kristin Nicodemus, James Malley, Carolin Srobl, Andreas Ziegler BMC Bioinformatics 11:110 (2010)

Molecular Dynamics Reveal the Essential Role of Linker Motions in the Function of Cullin-RING E3 Ligases Jin Liu and Ruth Nussinov J. Mol. Biol. 396(5):1508-1523 (2010)
Quantitative phosphoproteomic analysis reveals vasopressin V2-receptor-dependent signaling pathways in renal collecting duct cells Markus M. Rinschen, Ming-Jiun Yu, Guanghui Wang, Emily S. Boja, Jason D. Hoffert, Trairak Pisitkun, and Mark A. Knepper PNAS, doi/10.1073/pnas.0910646107 (2010)
Noncoding RNA Gas5 Is a Growth Arrest-and Starvation-Associated Repressor of the Glucocorticoid Receptor Tomoshige Kino, Darrell E. Hurt, Takamasa Ichijo, Nancy Nader, and George P. Chrousos Sci. Signal. 3(107):ra8 (2010)
Functional Significance for an Heterogenous Ribonucleoprotein A18 (hnRNP A18) Signature RNA Motif in the 3'UTR of Ataxia Telengiectasia Mutated and RAD3 Related (ATR) Transcript Ruiqing Yang, Ming Zhan, Narasimha Rao Nalabothula, Qingyuan Yang, Fred E. Indig and France Carrier J. Biol. Chem., published online 26 Jan (2010)
Evidence of statistical epistasis between DISC1, CIT and NDEL1 impacting risk for schizophrenia: biological validation with functional neuroimaging Kristin K. Nicodemus, Joseph H. Callicott, Rachel G. Higier, Augustin Luna, Devon C. Nixon, Barbara K. Lipska, Radhakrishna Vakkalanka, Ina Giegling, Dan Rujescu, David St. Clair, Pierandrea Muglia, Yin Yao Shugart and Daniel R. Weinberger Human Genetics 10.1007:s00439-009-0782-y (2010)
Meta-analysis of genome-wide association data detects a risk locus for major mood disorders on chromosome 3p21. 1 Francis J McMahon, Nirmala Akula, Thomas G Schulze, Pierandrea Muglia, Federica Tozzi, Sevilla D Detera-Wadleigh, C J M Steele, René Breuer, Jana Strohmaier, Jens R Wendland, Manuel Mattheisen, Thomas W Mühleisen, Wolfgang Maier, Markus M Nöthen, Sven Cichon, Anne Farmer, John B Vincent, Florian Holsboer, Martin Preisig & Marcella Rietschel for the Bipolar Disorder Genome Study (BiGS) Consortium Nature Genetics 42:128-131 (2010)
Interfacial thermodynamics of confined water near molecularly rough surfaces Jeetain Mittal and Gerhard Hummer Faraday Discussions: Wetting Dynamics of Hydrophobic and Str (2010)
Genetic Crossovers Are Predicted Accurately by the Computed Human Recombination Map Pavel P. Khil and R. Daniel Camerini-Otero PLoS Genetics 6(1):e1000831 (2010)
Genome Wide Association for Addiction: Replicated Results and Comparisons of Two Analytic Approaches Tomas Drgon, Ping-Wu Zhang, Catherine Johnson, Donna Walther, Judith Hess, Michelle Nino, and George R. Uhl PLoS One 5(1):e8832 (2010)
Construction of synthetic open reading frame encoding human interferon alpha 2b for high expression in Escherichia coli and characterization of its gene product Debbie S. Retnoningrum, Ratih A. Ningruma, Yohanes N. Kurniawana, Ana Indrayatia and Heni Rachmawati J. Biotechnol. 145(2):193-198 (2010)
JAGS Version 2.2.0 user manual Martyn Plummer Testing of JAGS was carried out on Helix. (2010)

2009 (86 papers)

Preferred drifting along the DNA major groove and cooperative anchoring of the p53 core domain: mechanisms and scenarios Yongpin Pan and Ruth Nussinov J. Mol. Recognit. 23(2):232-40 (2009)
Computational Investigation of the Oxidative Deboronation of Boroglycine, H2N-CH2-B (OH) 2, Using H2O and H2O2 Larkin JD, Markham GD, Milkevitch M, Brooks BR, Bock CW. J. Phys. Chem. A 113(41):11028-34 (2009)
Modeling Familial Association of Ages at Onset of Disease in the Presence of Competing Risk Joanna Shih and Paul S Albert Biometrics, published online 9 Dec (2009)
JAGS v2.0 Martyn Plummer (2009)
Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts Yang Shen and Ad Bax J. Biomolec. NMR 10.1007:s10858-009-9395-y (2009)
Homology modeling and molecular dynamics simulations of HgiDII methyltransferase in complex with DNA and S-adenosyl-methionine: Catalytic mechanism and interactions with DNA Juan A. Castelán-Vega, Alicia Jiménez-Alberto and Rosa M. Ribas-Aparicio J. Molecular Modeling 10.1007:s00894-009-0632-9 (2009)
An experimentally based computer search identifies unstructured membrane-binding sites in proteins: Application to class-I myosins, PAKs and CARMIL Hanna Brzeska, Jake Guag, Kirsten Remmert, Susan Chacko and Edward D. Korn J. Biol. Chem. 285:5738-5747 (2009)

Using Compressibility Factor as a Predictor of Confined Hard-Sphere Fluid Dynamics Jeetain Mittal J. Phys. Chem. B 113(42):13800-13804 (2009)
Prediction of Potency of Protease Inhibitors Using Free Energy Simulations with Polarizable Quantum Mechanics-Based Ligand Charges and a Hybrid Water Model Debananda Das, Yasuhiro Koh, Yasushi Tojo, Arun K. Ghosh and Hiroaki Mitsuya J. Chem. Inf. Mod. 49(12):2851-2862 (2009)
Misfolded Amyloid Ion Channels Present Mobile β-Sheet Subunits in Contrast to Conventional Ion Channels Hyunbum Jang, Fernando Teran Arce, Ricardo Capone, Srinivasan Ramachandran, Ratnesh Lal, and Ruth Nussinov Biophys. J. 97(11):3029-3037 (2009)
Effectiveness of Hair Bundle Motility as the Cochlear Amplifier Bora Sul and Kuni H. Iwasa Biophys. J. 97(10):2653-2663 (2009)
Oligonucleotide Design and Codon Optimization for PCR-based Gene Synthesis Paul Jamesen Steiner Master's Thesis, MIT (2009)
Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels. Anishkin A, Milac AL, Guy HR. Proteins 78(4):932-949 (2009)
Electrophysiological investigation of prestin function: Impact of cysteine replacement and characterization of self-association during voltage stimulation Ryan M. McGuire PhD Thesis, Rice University (2009)
NF90 selectively represses the translation of target mRNAs bearing an AU-rich signature motif Yuki Kuwano, Rudolf Pullmann, Jr., Bernard S. Marasa, Kotb Abdelmohsen, Eun Kyung Lee, Xiaoling Yang, Jennifer L. Martindale, Ming Zhan and Myriam Gorospe Nucleic Acids Research 38(1):225-38 (2009)
Thermodynamic Perspective on the Dock-Lock Growth Mechanism of Amyloid Fibrils ? Edward P. O'Brien, Yuko Okamoto, John E. Straub, Bernard R. Brooks and D. Thirumalai J. Phys. Chem. B 113(43):14421-14430 (2009)
MicroRNA Expression in Squamous Cell Carcinoma and Adenocarcinoma of the Esophagus: Associations with Survival Ewy A. Mathé, Giang Huong Nguyen, Elise D. Bowman, Yiqiang Zhao, Anuradha Budhu, Aaron J. Schetter, Rosemary Braun, Mark Reimers, Kensuke Kumamoto, Duncan Hughes, Nasser K. Altorki, Alan G. Casson, Chang-Gong Liu, Xin Wei Wang, Nozomu Yanaihara, Nobutoshi Hagiwara, Andrew J. Dannenberg, Masao Miyashita, Carlo M. Croce and Curtis C. Harris Clin. Cancer. Res. 15:6192 (2009)
K3 Fragment of Amyloidogenic β2-Microglobulin Forms Ion Channels: Implication for Dialysis Related Amyloidosis Mirela Mustata, Ricardo Capone, Hyunbum Jang, Fernando Teran Arce, Srinivasan Ramachandran, Ratnesh Lal and Ruth Nussinov J. Am. Chem. Soc. 131(41):14938-14945 (2009)
Modeling Aqueous Solvent Effects through Local Properties of Water S.A. Hassan and E.L. Mehler , in Modeling Solvent Environments, Ed. M. Feig, Wiley-VCH (2009)
Evidence for a Partially Structured State of the Amylin Monomer Sara M. Vaiana, Robert B. Best, Wai-Ming Yau, William A. Eaton, and James Hofrichter Biophys. J. 97(11):2948-2957 (2009)
The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation Jin Lui and Ruth Nussinov PLoS Computational Biology 5(10):e1000527 (2009)
Generalized Rosenfeld scalings for tracer diffusivities in not-so-simple fluids: Mixtures and soft particles William P. Krekelberg, Mark J. Pond, Gaurav Goel, Vincent K. Shen, Jeffrey R. Errington, Thomas M. Truskett Phys. Rev. E 80:061205 (2009)
Enhanced bacterial expression of several mammalian cytochrome P450s by codon optimization and chaperone coexpression Zhong-Liu Wu, Jing Qiao, Zhi-Gang Zhang, F. Peter Guengerich, Yan Liu and Xiao-Qiong Pei Biotechnology Letters 31(10):1589-1593 (2009)
Theoretical Characterization of Substrate Access/Exit Channels in the Human Cytochrome P450 3A4 Enzyme: Involvement of Phenylalanine Residues in the Gating Mechanism Dan Fishelovitch, Sason Shaik, Haim J. Wolfson, and Ruth Nussinov J. Phys. Chem B 113(39):13018-13025 (2009)
A simple and efficient algorithm for genome-wide homozygosity analysis in disease Wei Liu, Jinhui Ding, Jesse Raphael Gibbs, Sue Jane Wang, John Hardy & Andrew Singleton Molecular Systems Biology 5:304 (2009)
A fast mean-field method for large-scale high-dimensional data and its application in colonic polyp detection at CT colonography Shijun Wang, Ronald M Summers, Changshui Zhang IEEE International Joint Conference on Neural Networks ijcnn:32511-3258 (2009)
Polymorphism of Alzheimer's A β 17-42(p3) Oligomers: The Importance of the Turn Location and Its Conformation Yifat Miller, Buyong Ma, and Ruth Nussinov Biophys. J. 97(4):1168-1177 (2009)
RAId_deNovo: using de novo based spectrum-specific statistics to combine search results from multiple scoring functions and more Gelio Alves, Aleksey Y. Ogurtsov, Yi-Kuo Yu arXiv.org (2009)
Quantitative Mitochondrial Phosphoproteomics Using iTRAQ on an LTQ-Orbitrap with High Energy Collision Dissociation Emily Boja, Darci Phillips, Stephanie A French, Robert A. Harris, and Robert Stephen Balaban J. Proteome Research 8(10):4665-4675 (2009)
Molecular Dynamics Simulations of PIP 2 and PIP 3 in Lipid Bilayers: Determination of Ring Orientation, and the Effects of Surface Zheng Li, Richard M. Venable, Laura A. Rogers, Diana Murray, and Richard W. Pastor Biophys. J. 97(1):155-163 (2009)
Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View Yongpin Pan and Ruth Nussinov PLoS Computational Biology :e1000448. (2009)

Functional but not structural changes associated with learning: An exploration of longitudinal Voxel-Based Morphometry (VBM) Thomas AG, Marrett S, Saad ZS, Ruff DA, Martin A, Bandettini PA. Neuroimage 48(1):117-25 (2009)
Phosphine Polymerization by Nitric Oxide: Experimental Characterization and Theoretical Predictions of Mechanism Yi-Lei Zhao, Jason W. Flora, William David Thweatt, Stephen L. Garrison, Carlos Gonzalez, K. N. Houk and Manuel Marquez Inorg. Chem. 48(3):1223-1231 (2009)
Protein Segments with Conformationally Restricted Amino Acids Can Control Supramolecular Organization at the Nanoscale David Zanuy, Gema Ballano, Ana I. Jimnez, Jordi Casanovas, Nurit Haspel, Carlos Cativiela, David Curc, Ruth Nussinov and Carlos Alemán J. Chem. Info. and Modeling 49(7):1623=9 (2009)
Amygdala function and 5-HTT gene variants in adolescent anxiety and major depressive disorder Lau JY, Goldman D, Buzas B, Fromm SJ, Guyer AE, Hodgkinson C, Monk CS, Nelson EE, Shen PH, Pine DS, Ernst M. Biol. Psychiatry , doi: 10.1016/j.biopsych.2008.08.037 (2009)
HTR3B is associated with alcoholism with antisocial behavior and alpha EEG power�an intermediate phenotype for alcoholism and co-morbid behaviors Ducci F, Enoch MA, Yuan Q, Shen PH, White KV, Hodgkinson C, Albaugh B, Virkkunen M, Goldman D. Alcohol, doi: 10.1016/j.alcohol.2008.09.005 (2009)
Association of Substance Use Disorders With Childhood Trauma but not African Genetic Heritage in an African American Cohort Ducci F, Roy A, Shen PH, Yuan Q, Yuan NP, Hodgkinson CA, Goldman LR, Goldman D. Am. J. Psychiatry, doi: 10.1176/appi.ajp.2009.08071068 (2009)

Kinetic Barriers of H-Atom Transfer Reactions in Alkyl, Allylic, and Oxoallylic Radicals as Calculated by Composite Ab Initio Methods Carrigan J. Hayes and Donald R. Burgess, Jr. J. Phys. Chem. A 113(11):2473-2482 (2009)
On the Mechanism of Nitrosoarene-Alkyne Cycloaddition Andrea Penoni, Giovanni Palmisano, Yi-Lei Zhao, Kendall N. Houk, Jerome Volkman and Kenneth M. Nicholas J. Am. Chem. Soc. 131(2):653-661 (2009)
Artificial reaction coordinate “tunneling” in free-energy calculations: The catalytic reaction of RNase H Edina Rosta, H. Lee Woodcock, Bernard R. Brooks, Gerhard Hummer J. Comput. Chem. 30(11):1634-41 (2009)
Building and assessing atomic models of proteins from structural templates: Learning and benchmarks Brinda Kizhakke Vallat, Jaroslaw Pillardy, Peter M�jek, Jaroslaw Meller, Thomas Blom, BaoQiang Cao, Ron Elber Proteins 76(4):930-945 (2009)
Imaging incorporation of circulating docosahexaenoic acid into the human brain using positron emission tomography John C. Umhau, Weiyin Zhou, Richard E. Carson, Stanley I. Rapoport, Alla Polozova, James Demar, Nahed Hussein, Abesh K. Bhattacharjee, Kaizong Ma, Giuseppe Esposito, Sharon Majchrzak, Peter Herscovitch, William C. Eckelman, Karen A. Kurdziel, and Norman Salem . Jr J. Lipid Res. 50(7):1259-68 (2009)
Error and efficiency of replica exchange molecular dynamics simulations Edina Rosta and Gerhard Hummer J. Chem. Phys. 131:165102 (2009)

Insights Into Crowding Effects on Protein Stability From a Coarse-Grained Model VK Shen, J Cheung, JR Errington, TM Truskett J. Biomech. Engg. 131(7):0710002 (2009)
The bis-Electrophile Diepoxybutane Cross-Links DNA to Human Histones but Does Not Result in Enhanced Mutagenesis in Recombinant Systems Elisabeth M. Loecken, Surendra Dasari, Salisha Hill, David L. Tabb and F. Peter Guengerich Chem. Res. Toxicol. 22(6):1069-1076 (2009)
Revealing the dimer dissociation and existence of a folded monomer of the mature HIV-2 protease Louis JM, Ishima R, Aniana A, Sayer JM. Protein Science 18(12):2442-53 (2009)
Molecular dynamics study of the structure and interparticle interactions of polyethylene glycol-conjugated PAMAM dendrimers Hwankyu Lee and Ronald G. Larson J. Phys. Chem. B 113(40):13202-13207 (2009)
Computer Assisted Analysis of Genes MV Fachal, M Furlan Reproductive Endocrinology Part 2:113-117 (2009)
Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides Robert B Best, Gerhard Hummer J. Phys. Chem B 113(26):9004-9015 (2009)

Predictor Correlation Impacts Machine Learning Algorithms: Implications for Genomic Studies Kristin K. Nicodemus and James D. Malley Bioinformatics 25:1884-1889 (2009)
A Partially Linear Tree-based Regression Model for Multivariate Outcomes Kai Yu, William Wheeler, Qizhai Li, Andrew W. Bergen, Neil Caporaso, Nilanjan Chatterjee, and Jinbo Chen Biometrics, published online 10 May (2009)
A finite mixture survival model to characterize risk groups of neuroblastoma Sally Hunsberger, Paul S. Albert and Wendy B. London Stat. Med. 28:1301-1314 (2009)
Post-rituximab Burkitt transformation of PTLD: loss of CD20 expression accompanied by a switch in light-chain expression Yu-Yan Hwang, Kai Y. Wong, Rock Y. Y. Leung, Simon H. M. Wong, See-Ching Chan, Gopesh Srivastava and Wing Y. Au Annals of Hematology 89(1):1432-0584 (2009)
De novo protein structure generation from incomplete chemical shift assignments Yang Shen, Robert Vernon, David Baker, and Ad Bax J. Biomol. 43(2):63-78 (2009)
In Silico Molecular Engineering for a Targeted Replacement in a Tumor-Homing Peptide. Zanuy D, Flores-Ortega A, Jiménez AI, Calaza MI, Cativiela C, Nussinov R, Ruoslahti E, Alemán C. J. Phys. Chem. B 113(22):7879-89 (2009)

Widespread Reductions of Cortical Thickness in Schizophrenia and Spectrum Disorders and Evidence of Heritability Aaron L. Goldman, Lukas Pezawas, Venkata S. Mattay, Bruce Fischl, Beth A. Verchinski, Qiang Chen, Daniel R. Weinberger, Andreas Meyer-Lindenberg. Archives of General Psychiatry 66(5):467-477 (2009)
Gene Composer: database software for protein construct design, codon engineering, and gene synthesis Don Lorimer, Amy Raymond, John Walchli. Mark Mixon, Adrienne Barrow, Ellen Wallace, Rena Grice, Alex Burgin, Lance Stewart BMC Biotechnology 9:36 (2009)
Available states and available space: static properties that predict self-diffusivity of confined fluids Gaurav Goel, William P Krekelberg, Mark J Pond, Jeetain Mittal, Vincent K Shen, Jeffrey R Errington and Thomas M Truskett J. Stat. Mech., doi:10.1088/1742-5468/2009/04/P04006 (2009)
Identification of cis-regulatory elements in gene co-expression networks using A-GLAM. Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spouge J, Landsman D. Methods Mol. Biol. 541:1-22 (2009)
Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations Edina Rosta, Nicolae-Viorel Buchete and Gerhard Hummer J. Chem. Theory and Computation 5(5):1393-1399 (2009)
Pathway analysis by adaptive combination of P-values Kai Yu, Qizhai Li, Andrew W. Bergen, Ruth M. Pfeiffer, Philip S. Rosenberg, Neil Caporaso, Peter Kraft, Nilanjan Chatterjee Genetic Epidemiology 33(8):700-9 (2009)

Comparison of the Extended Isotropic Periodic Sum and Particle Mesh Ewald Methods for Simulations of Lipid Bilayers and Monolayers Richard M. Venable, Linda E. Chen and Richard W. Pastor J. Phys. Chem B 113(17):5855-5862 (2009)
Genetic background comparison using distance-based regression, with applications in population stratification evaluation and adjustment Qizhai Li, Sholom Wacholder, David J. Hunter, Robert N. Hoover, Stephen Chanock, Gilles Thomas, Kai Yu Genetic Epidemiology 33(5):432-441 (2009)
Self-guided langevin dynamics study of regulatory interactions in NtrC Ana Damjanovic, Betrand Garcia-Moreno E., Bernard R. Brooks Proteins: Structure, Function and Bioinformatics 76(4):1007-19 (2009)
Engineered Integrin Binding Peptides Cochran, Jennifer R., Kimura, Richard, Levin, Aron M., Silverman, Adam, Gambhir, Sanjiv S., Cheng, Zhen, Lahti, Jennifer Patent # 12/418376 (2009)
Different Patterns of Regulation for the Copper and Cadmium Metallothioneins of the Ectomycorrhizal Fungus Hebeloma cylindrosporum G. Ramesh, G. K. Podila, G. Gay, R. Marmeisse, and M. S. Reddy App. Env. Microbiology 75(8):2266-2274 (2009)
Hybrid Structural Model of the Complete Human ESCRT-0 Complex Xuefeng Ren, Daniel P. Kloer, Young C. Kim, Rodolfo Ghirlando, Layla F. Saidi, Gerhard Hummer and James H. Hurley Structure 17(3):406-416 (2009)
Combining heterogeneous features for colonic polyp detection in CTC based on semi-definite programming Shijun Wang ; Jianhua Yao ; Nicholas A. Petrick ; Ronald M. Summers SPIE Proceedings, doi:10.1117/12.811219 (2009)
Identification of active sites of biomolecules II: Saccharide and transition metal ion in aqueous solution Coskuner O, Bergeron DE, Rincon L, Hudgens JW, Gonzalez CA. J. Phys. Chem. A 113(11):2491-9 (2009)
Intramolecular Disulfide Bonds of the Prolactin Receptor Short Form are Required for its Inhibitory Action on the Function of the Long form of the Receptor Y-L. Xie, S. A. Hassan, A. M. Qazi, C. H. Tsai-Morris, and M. L. Dufau Mol. Cell. Biol. 29(10):2546-55 (2009)
Adjacency Method for Finding Connected Subsets of a Graph: An Application of Graph Theory to Spatial Statistics Jun Luo, Lan Huang, Mark Hachey, Ram Tiwari Comm. in Stat.: Simulation and Computation 38(5):1136-1151 (2009)
Genetic Studies on Stuttering Families Muhammed Hashim Raza PhD Thesis, University of the Punjab, Lahore, Pakistan (2009)
Large-scale production and characterization of an engineered human olfactory receptor Brian Lee Cook PhD thesis in Biological Engineering at MIT (2009)

Ionic Hydrogen-Bond Networks and Ion Solvation. 1. An Efficient Monte Carlo/Quantum Mechanical Method for Structural Search and Energy Computations: Ammonium/Water Yi-Lei Zhao, Michael Meot-Ner (Mautner) and Carlos Gonzalez J. Phys. Chem. A 113(12):2967-74 (2009)
Theory and simulation of macromolecular crowding effects on protein folding stability and kinetics Jeetain Mittal and Robert B. Best arXiv.org (2009)
High-Level Production, Solubilization and Purification of Synthetic Human GPCR Chemokine Receptors CCR5, CCR3, CXCR4 and CX3CR1 Hui Ren, Daoyong Yu, Baosheng Ge, Brian Cook, Zhinan Xu, and Shuguang Zhang PLoS ONE 4(2):e4509 (2009)
A Model for Fine Mapping in Family Based Association Studies Stefan Boehringer and Ruth M. Pfeiffer Hum. Heredit. 67(4):226-236 (2009)
The Factor VIIIa C2 Domain (Residues 2228-2240) Interacts with the Factor IXa Gla Domain in the Factor Xase Complex Tetsuhiro Soeda, Keiji Nogami, Katsumi Nishiya, Masahiro Takeyama, Kenichi Ogiwara, Yoichi Sakata, Akira Yoshioka, and Midori Shima J. Biol. Chem. 284(6):3379-3388 (2009)
Proteomic Analysis of Human Urinary Exosomes Patricia Amalia Gonzales Mancilla PhD thesis, U. Maryland (2009)

Optimizing computer-aided colonic polyp detection for CT colonography by evolving the Pareto front Jiang Li, Adam Huang, Jack Yao, Jiamin Liu, Robert L. Van Uitert, Nicholas Petrick, Ronald M. Summers Medical Physics 36:201-212 (2009)
Rigorous treatment of electrostatics for spatially varying dielectrics based on energy minimization O. I. Obolensky, T. P. Doerr, R. Ray, and Yi-Kuo Yu Bulletin of the American Physical Society 54:P40.00008 (2009)
Available states and available space: Static properties that predict dynamics of confined fluids Gaurav Goel, William P. Krekelberg, Mark J. Pond, Jeetain Mittal, Vincent K. Shen, Jeffrey R. Errington, Thomas M. Truskett J. Stat. Mech. :P04006 (2009)
A coarse-grained model for polyethylene oxide and polyethylene glycol: conformation and hydrodynamics. Lee H, de Vries AH, Marrink SJ, Pastor RW. J. Phys. Chem. B 113(40):13186-94 (2009)
Visual Awareness, Emotion, and Gamma Band Synchronization Qian Luo, Derek Mitchell, Xi Cheng, Krystal Mondillo, Daniel McCaffrey, Tom Holroyd, Frederick Carver, Richard Coppola and James Blair Cerebral Cortex 19(8):1896-1904 (2009)
Bayesian Inference for Smoking Cessation with a Latent Cure State Luo S, Crainiceanu, CM, Louis TA, Chatterjee, N Biometrics 65(3):970-8 (2009)
Bio-Sensing Nanodevice Zhang, Shuguang, Mershin, Andreas, Kaiser, Liselotte, Cook, Brian, Graveland-bikker, Johanna F., Prakash, Manu, Kong, David, Maguire, Yael Patent # 12/183916 (2009)

2008 (102 papers)

Dislocation nucleation during nanoindentation of aluminum R. J. Wagner, L. Ma, F. Tavazza, and L. E. Levine J. Applied Physics 104:114311 (2008)
Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl) tetrahydropyran. Woodcock HL, Brooks BR, Pastor RW. JACS 130(20):6345-7 (2008)
Biological Entity Recognition with Conditional Random Fields Ying He and Mehmet Kayaalp AMIA Annu Symp Proc. 2008:293-297 (2008)
Lipid bilayer curvature and pore formation induced by charged linear polymers and dendrimers: the effect of molecular shape Hwankyu Lee and Ronald G. Larson J. Phys. Chem. B 112(39):12279-12285 (2008)
The point mutation A34F causes dimerization of GB1. JunGoo Jee, In-Ja L. Byeon, John M. Louis, Angela M. Gronenborn Proteins 71(3):1420-31 (2008)

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration Alves G, Ogurtsov AY, Yu YK. BMC Genomics 9:505 (2008)
Enhancing peptide identification confidence by combining search methods. Alves G, Wu WW, Wang G, Shen RF, Yu YK J. Proteome Res. 7(8):3102-13 (2008)
Coarse-grained molecular dynamics studies of the concentration and size dependence of fifth-and seventh-generation PAMAM dendrimers on pore formation in DMPC bilayer Hwankyu Lee and Ronald G. Larson J. Phys. Chem. B 112(26):7778-7784 (2008)
RNA binding activity of the recessive parkinsonism protein DJ-1 supports involvement in multiple cellular pathways Marcel P. van der Brug, Jeff Blackinton, Jayanth Chandran, Ling-Yang Hao, Ashish Lal, Krystyna Mazan-Mamczarz, Jennifer Martindale, Chengsong Xie, Rili Ahmad, Kelly J. Thomas, Alexandra Beilina, J. Raphael Gibbs, Jinhui Ding, Amanda J. Myers, Ming Zhan, Huaibin Cai, Nancy M. Bonini, Myriam Gorospe and Mark R. Cookson PNAS 105(29):10244-10249 (2008)
Influence of the dye presence on the conformational preferences of CREKA, a tumor homing linear pentapeptide. Zanuy D, Curcó D, Nussinov R, Alemán C Biopolymers 92(2):83-93 (2008)
Analysis of Smoking Cessation Patterns Using a Stochastic Mixed-Effects Model With a Latent Cured State Sheng Luo, Ciprian M Crainiceanu, Thomas A Louis, Nilanjan Chatterjee J. Am. Stat. Assoc. 103(483):1002-1013 (2008)

Inference of non-centrality parameter of a truncated non-central chi-squared distribution Qizhai Li and Kai Yu J. Stat. Planning and Inference 139(7):2431-2444 (2008)
Static and dynamic correlations in water at hydrophobic interfaces Jeetain Mittal and Gerhard Hummer PNAS 105:20130-20135 (2008)
Thermodynamics and kinetics of protein folding under confinement Jeetain Mittal and Robert Best PNAS 105(51):20233-8 (2008)
Characterization of a protective Escherichia coli-expressed Plasmodium falciparum merozoite surface protein 3 indicates a non-linear, multi-domain structure Tsai CW, Duggan PF, Jin AJ, Macdonald NJ, Kotova S, Lebowitz J, Hurt DE, Shimp RL Jr, Lambert L, Miller LH, Long CA, Saul A, Narum DL. Mol. Biochem. Parasitol. 164(1):45-56 (2008)
Self-assembly of fused homo-oligomers to create nanotubes Buch I, Tsai CJ, Wolfson HJ, Nussinov R. Methods Mol. Biol. 474:117-31 (2008)
Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein Yongsu Jeong, Federico Coluccio Leskow, Kenia El-Jaick, Erich Roessler, Maximilian Muenke, Anastasia Yocum, Christele Dubourg, Xue Li, Xin Geng, Guillermo Oliver & Douglas J Epstein Nature Genetics 40:1348-1353 (2008)

Identification of a signature motif in target mRNAs of RNA-binding protein AUF1 Krystyna Mazan-Mamczarz, Yuki Kuwano, Ming Zhan, Elizabeth J. White, Jennifer L. Martindale, Ashish Lal and Myriam Gorospe Nucleic Acids Research 37(1):204-14 (2008)
GRL-02031, a Novel Nonpeptidic Protease Inhibitor (PI) Containing a Stereochemically Defined Fused Cyclopentanyltetrahydrofuran Potent against Multi-PI-Resistant HIV-1 In Vitro Yasuhiro Koh, Debananda Das, Sofiya Leschenko, Hirotomo Nakata, Hiromi Ogata-Aoki, Masayuki Amano, Maki Nakayama, Arun K. Ghosh, and Hiroaki Mitsuya Antimicrob Agents Chemother. 53(3):997-1006 (2008)
A class comparison method with filtering-enhanced variable selection for high-dimensional data sets Lara Lusa, Edward L. Korn, Lisa M. McShane Stat. Med 28:5834-5849 (2008)
Models of voltage-dependent conformational changes in NaChBac channels Shafrir Y, Durell SR, Guy HR. Biophys. J. 95(8):3663-76 (2008)
Prediction of evolutionarily conserved interologs in Mus musculus. Yellaboina S, Dudekula DB, Ko MS. BMC Genomics 9:465 (2008)
Comparing the Use of Gibbs Ensemble and Grand-Canonical Transition-Matrix Monte Carlo Methods to Determine Phase Equilibria Andrew S. Paluch, Vincent K. Shen and Jeffrey R. Errington Ind. Eng. Chem. Res. 47(13):4533-4541 (2008)
Molecular Dynamics Simulations of Perylene and Tetracene Librations: Comparison With Femtosecond Upconversion Data Tilman Rosales, Jianhua Xu, Xiongwu Wu, Milan Hodoscek, Patrik Callis, Bernard R. Brooks and Jay R. Knutson J. Phys. Chem. A 112(25):5593-5597 (2008)
Efficient cell-free production of olfactory receptors: Detergent optimization, structure, and ligand binding analyses Liselotte Kaiser, Johanna Graveland-Bikker, Dirk Steuerwald, Mélanie Vanberghem, Kara Herlihy, and Shuguang Zhang PNAS 105(41):15726-15731 (2008)
Models of Toxic β-Sheet Channels of Protegrin-1 Suggest a Common Subunit Organization Motif Shared with Toxic Alzheimer β-Amyloid Ion Channels. Jang H, Ma B, Lal R, Nussinov R. Biophys. J. 95(10):4631-42 (2008)
Computer Simulation of Ion Cluster Speciation in Concentrated Aqueous Solutions at Ambient Conditions Sergio A. Hassan J. Phys. Chem. B 112:10573-10584 (2008)
Study on allotopic expression of recoded human mitochondrial ND4L genes in mammalian cells Mou-Chieh Kao Master's thesis, National Tsing Hua University, Taiwan (2008)
Considerations for Lipid Force Field Development Jeffery B. Klauda, Richard M. Venable, Alexander D. MacKerell Jr., Richard W. Pastor in Computational Modeling of Membrane Bilayers, in Current Topics in Membranes Vol 60. (2008)

Developmental and epigenetic regulation of the human TLR3 gene Analia Porrás, Sarah Kozar, Valya Russanova, Paraskevi Salpea, Tazuko Hirai, Nicholas Sammons, Pooja Mittal, Ji Young Kim, Keiko Ozato, Roberto Romero and Bruce H. Howard Mol. Immunol. 46(1):27-36 (2008)
Glycosidic linkage conformation of methyl-α-mannopyranoside Orkid Coskuner, Denis E. Bergeron, Luis Rincon, Jeffrey W. Hudgens, and Carlos A. Gonzalez J. Chem. Phys. 129:045102 (2008)
Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways. Lenz G, Wright GW, Emre NC, Kohlhammer H, Dave SS, Davis RE, Carty S, Lam LT, Shaffer AL, Xiao W, Powell J, Rosenwald A, Ott G, Muller-Hermelink HK, Gascoyne RD, Connors JM, Campo E, Jaffe ES, Delabie J, Smeland EB, Rimsza LM, Fisher RI, Weisenburger DD, Chan WC, Staudt LM. PNAS 105(36):13520-5 (2008)
Ligand Exchange Reactions in the Formation of Diphosphine-Protected Gold Clusters Denis E. Bergeron, Orkid Coskuner, Jeffrey W. Hudgens, and Carlos A. Gonzalez J. Phys. Chem. C 112(33):12808-12814 (2008)
Evidence That Proline Focuses Movement of the Floppy Loop of Arylalkylamine N-Acetyltransferase (EC 2.3. 1.87) Jiri Pavlicek, Steven L. Coon, Surajit Ganguly, Joan L. Weller, Sergio A. Hassan, Dan L. Sackett, and David C. Klein J. Biol. Chem. 283(21):14552-14558 (2008)
NEIBank: Genomics and bioinformatics resources for vision research Graeme Wistow, Katherine Peterson, James Gao, Patee Buchoff, Cynthia Jaworski, Catherine Bowes-Rickman, Jessica N. Ebright, Michael A. Hauser, and David Hoover Molecular Vision 14:1327-1337 (2008)
mRNA Distribution and Heterologous Expression of Orphan Cytochrome P450 20A1 Katarina Stark, Zhong-Liu Wu, Cheryl J. Bartleson and F. Peter Guengerich Drug Metabolism and Disposition 36(9):1930-1937 (2008)
Molecular dynamics studies of polyethylene oxide and polyethylene glycol: Hydrodynamic radius and shape anisotropy Hwankyu Lee, Richard M. Venable, Alexander D. MacKerell, Jr. and Richard W. Pastor Biophysical Journal 95(4):1590-9 (2008)
Positron Emission Tomography Imaging Using an Inverse Agonist Radioligand to Assess Cannabinoid CB1 Receptors in Rodents Terry G, Liow J-S, Chernet E; Zoghbi SS, Phebus L, Felder CC, Tauscher J, Schaus JM, Pike VW, Halldin C, Innis RB. Neuroimage 41(3):690-8 (2008)
p53-Induced DNA Bending: The Interplay between p53-DNA and p53-p53 Interactions Yongpin Pan, Ruth Nussinov J. Phys. Chem. B 112(21):6716-24 (2008)
11C-Loperamide and its N-desmethyl radiometabolite are avid substrates for brain P-glycoprotein efflux Zoghbi SS, Liow J-S,Yasuno F, Hong J, Tuan E; Lazarova N, Gladding RL; Pike VW, Innis RB J. Nucl. Med. 49(4):649-56 (2008)
CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes Klauda JB, Brooks BR J. Chem. Theory and Computation 4(1):107-115 (2008)

Binding-induced folding of a natively unstructured transcription factor Turjanski, A. G., Gutkind, J.S., Best, R. and Hummer. G. PLoS Computational Biology, e1000060 doi:10.1371 (2008)
Privileged scaffolds targeting reverse-turn and helix recognition Che, Ye & Marshall, Garland. Expert Opinion on Therapeutic Targets 12(1):101-114 (2008)
Study of a Synthetic Human Olfactory Receptor 17-4: Expression and Purification from an Inducible Mammalian Cell Line Brian L. Cook, Karin E. Ernberg, Hyeyoun Chung, and Shuguang Zhang PLoS One 3(8):e2920 (2008)
Genotype, haplotype and copy-number variation in worldwide human populations. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA, Degnan JH, Wang K, Guerreiro R, Bras JM, Schymick JC, Hernandez DG, Traynor BJ, Simon-Sanchez J, Matarin M, Britton A, van de Leemput J, Rafferty I, Bucan M, Cann HM, Hardy JA, Rosenberg NA, Singleton AB. Nature 451(7181):998-1003 (2008)
Cluster Without Fluster: The Effect of Correlated Outcomes on Inference in Randomized Clinical Trials Proschan MA, Follmann, DA. Statistics in Medicine 27(6):795-809 (2008)
Sigma Stellation: A Design Strategy for Electron Boxes Irikura, Karl K J. Phys. Chem A 112:983-988 (2008)
Coordination Studies of Al-EDTA in Aqueous Solution Orkid Coskuner, Emily A. A. Jarvis J. Phys. Chem. 112(12):2628-2633 (2008)
Layering and Position-Dependent Diffusive Dynamics of Confined Fluids Jeetain Mittal, Thomas M. Truskett, Jeffrey R. Errington, and Gerhard Hummer Phys. Rev. Let. 100:145901 (2008)
Genetic variation in human NPY expression affects stress response and emotion Zhou Z, Zhu G, Hariri AR, Enoch MA et al. Nature, doi: 10.1038/nature06858 (2008)
Addictions biology: haplotype-based analysis for 130 candidate genes on a single array Hodgkinson CA, Yuan Q, Xu K, Shen PH, Heinz E, Lobos EA, Binder EB, Cubells J, Ehlers CL, Gelernter J, Mann J, Riley B, Roy A, Tabakoff B, Todd RD, Zhou Z, Goldman D. Alcohol and Alcoholism, doi: 10.1093/alcalc/agn032 (2008)
Common Genetic Origins for EEG, Alcoholism and Anxiety: The Role of CRH-BP Enoch MA, Shen PH, Ducci F, Yuan Q, Liu J, White KV, Albaugh B, Hodgkinson CA, Goldman D. PLoS One, doi: 10.1371/journal.pone.0003620 (2008)
Comprehensive Structural Studies of 2', 3'-Difluorinated Nucleosides: Comparison of Theory, Solution, and Solid State Joseph J. Barchi, Jr., Rajeshri G. Karki, Marc C. Nicklaus, Maqbool A. Siddiqui, Clifford George, Igor A. Mikhailopulo and Victor E. Marquez J. Am. Chem. Soc. 130(28):9048-9057 (2008)
A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins Vallat BK, Pillardy J, Elber R. Proteins 72(3):910-28 (2008)
MAX-rank: a simple and robust genome-wide scan for case-control association studies. Li Q, Yu K, Li Z, Zheng G. Hum. Genet. 123(6):617-23 (2008)
Backbone relaxation coupled to the ionization of internal groups in proteins: A self-guided Langevin dynamics study Ana Damjanovic, Xiongwu Wu, Bertrand Garcia-Moreno and Bernard R Brooks Biophys. J. 95(9):4091-101 (2008)
The Cytoplasmic Terminus of Kaposi's Sarcoma-Associated Herpesvirus Glycoprotein B Is Not Essential for Virion Egress and Infectivity{triangledown} R. Subramanian, O. D'Auvergne, Haixia Kong, and K. G. Kousoulas J. Virol. 82(14):7144-7154 (2008)
Expression and purification of orphan cytochrome P450 4X1 and oxidation of anandamide Stark K, Dostalek M, Guengerich FP. FEBS J. 275(14):3706-17 (2008)
Towards an automatic classification of protein structural domains based on structural similarity Sam V, Tai CH, Garnier J, Gibrat JF, Lee B, Munson PJ. BMC Bioinformatics 9(1):74 (2008)
Endogenous retrotransposon sequences of the Schistosoma mansoni intermediate snail host, Biomphalaria glabrata Knight M, Bridger J, Ittiprasert W, Odoemelam E, Masabanda J, Miller A, Raghavan, N. Mobile Genetic Elements in Metazoan Para, Brindley PJ (ed). Landes Bioscience, in press. (2008)
The Imaging Probe Development Center and the Production of Molecular Imaging Probes Gary L Griffiths Curr. Chem. Genomics 1:65-69 (2008)
On estimating diagnostic accuracy from studies with multiple raters and partial gold standard evaluation Paul S. Albert and Lori E Dodd J. Am. Stat. Assoc 103(481):61-73 (2008)
In Situ Gas Phase Diagnostics for Hafnium Oxide Atomic Layer Deposition J.E. Maslar, W.S. Hurst, D.R. Burgess, W.A. Kimes, N.V. Nguyen, E.F. Moore, J.T. Hodges ECS Transactions 13(2):139-149 (2008)
Differences in Cysteine Protease Activity in Schistosoma mansoni-Resistant and-Susceptible Biomphalaria glabrata and Characterization of the Hepatopancreas Cathepsin B Full-length cDNA Jocelyn Myers, Wannaporn Ittiprasert, Nithya Raghavan, André Miller, and Matty Knight J. Parasitol. 94:3:659-668 (2008)
Molecular architecture of native HIV-1 gp 120 trimers Jun Liu, Alberto Bartesaghi, Mario J. Borgnia, Guillermo Sapiro & Sriram Subramaniam Nature 455:109-113 (2008)

Dissecting contact potentials for proteins: relative contributions of individual amino acids Buchete NV, Straub JE, Thirumalai D. Proteins 70(1):119-30 (2008)
Synthesis and evaluation of N-Methyl and S-Methyl 11C-Labeled 6-Methylthio-2-(4'-N,N-dimethylamino)phenylimidazo[1,2-a]pyridines as radioligands for imaging beta-amyloid plaques in Alzheimer's disease Cai L, Liow JS, Zoghbi SS, Cuevas J, Baetas C, Hong J, Shetty HU, Seneca NM, Brown AK, Gladding R, Temme SS, Herman MM, Innis RB, Pike VW. J. Med. Chem. 51(1):148-58 (2008)
Residual multiparticle entropy does not generally change sign near freezing Krekelberg WP, Shen VK, Errington JR, Truskett TM. J. Chem. Phys. 128(16):161101 (2008)
Synthesis and pharmacological effects of the enantiomers of the N-phenethyl analogues of the ortho and para e-and f-oxide-bridged phenylmorphans Josef Zezula, Lisa Singer, Anna K. Przyby, Akihiro Hashimoto, Christina M. Dersch, Richard B. Rothman, Jeffrey Deschamps, Yong Sok Lee, Arthur E. Jacobson and Kenner C. Rice Org. and Biomol. Chem. 6:2868-2883 (2008)
A pseudopotential for improving the packing of ellipsoidal protein structures determined by NMR C.D. Schwieters and G.M. Clore. J. Phys. Chem 112(19):6070-6073 (2008)
PCR-based gene synthesis to produce recombinant proteins for crystallization Damien Marsic, Ronny C Hughes, Miranda L Byrne-Steele and Joseph D Ng BMC Biotechnology 8:44 (2008)

Dynamics of Cholesterol Exchange in the OSBP-Related Protein Family Canagarajah, B., Hummer, G., Prinz, W. and Hurley, J. H. J. Mol. Biol. 378(3):737-48 (2008)
Population Substructure and Control Selection in Genome-Wide Association Studies Kai Yu, Zhaoming Wang, Qizhai Li, Sholom Wacholder, David J. Hunter, Robert N. Hoover, Stephen Chanock, and Gilles Thomas PLoS One 3(7):2551 (2008)
Testing logistic regression coefficients with clustered data and few positive outcomes Sally Hunsberger, Ed Korn, and Barry Graubard. Statistics in Medicine 27(8):1305-24 (2008)
Host Control of Malaria Infections: Constraints on Immune and Erythropoeitic Response Kinetics McQueen PG, McKenzie FE PLoS Computational Biology 4(8):e1000149 (2008)
Identification of the transition states in the inversion of 1, 4-benzodiazepines with the Ab Initio Replica Path Method Yong-Sok Lee, Victor W. Pike, and Milan Hodoscek. J. Phys. Chem A 112:1604-1611 (2008)
A frailty mixture cure model with application to hospital readmission cata Yu, B. Biometrical J. 50(3):386-94 (2008)

Efficient Approximation of P-value of the Maximum of Correlated Tests, with Applications to Genome-Wide Association Studies. Li Q.Z., Zheng G., Li Z.H. and Yu K. Annals of Human Genetics 72(3):397-406 (2008)
Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements Ma B, Levine AJ. Nucleic Acids Research 35(22):7733-7747 (2008)
Improved Classifier for Computer-aided Polyp Detection in CT Colonography by Nonlinear Dimensionality Reduction Shijun Wang, Jianhua Yao and Ronald M. Summers Med. Phys. 35(4):1377-86 (2008)
β2-microglobulin amyloid fragment organization and morphology and its comparison to Aβ suggests that amyloid aggregation pathways are sequence specific Zheng J, Jang H, Nussinov R. Biochemistry. Feb 26;47(8):2497-2509 (2008)
Morphology of Ion Clusters in Aqueous Electrolytes SA Hassan. Phys. Rev. E 77:03151 (2008)
Involvement of the second extracellular loop and transmembrane residues of CCR5 in inhibitor binding and HIV-1 fusion: insights into the mechanism of allosteric inhibition Maeda K, Das D, Yin PD, Tsuchiya K, Ogata-Aoki H, Nakata H, Norman RB, Hackney LA, Takaoka Y, Mitsuya H. J. Mol. Biol. 381:956-974 (2008)

Are Current Molecular Dynamics Force Fields too Helical? Robert B Best, Nicolae-Viorel Buchete and Gerhard Hummer Biophysical Letters 95(1):L07-9 (2008)
Concentration and crowding effects on protein stability from a coarse-grained model J. K. Cheung, V. K. Shen, J. R. Errington, and T. M. Truskett. in Statistical Mechanics of Cellular System, MH Zaman ed, Cambridge University Press. (2008)
Heritability of brain morphology related to schizophrenia: a large-scale automated magnetic resonance imaging segmentation study Goldman AL, Pezawas L, Mattay VS, Fischl B, Verchinski BA, Zoltick B, Weinberger DR, Meyer-Lindenberg A. Biol. Psychiatry 63(5):475-83 (2008)
Models of the Structure and Gating Mechanisms of the Pore Domain of the NaChBac Ion Channel Yinon Shafrir, Stewart R Durell and H. Robert Guy Biophys. J. 95(8):3650-62 (2008)
NIST Computational Chemistry Comparison and Benchmark Database Some of the calculations in the CCBD were performed by Russell Johnson on the Biowulf cluster. (2008)
Modeling Longitudinal Biomarker Data from Multiple Assays that Have Different Known Detection Limits Paul S. Albert Biometrics 64:527-537 (2008)

Application of 1-Aminocyclohexane Carboxylic Acid to Protein Nanostructure Computer Design. Rodriguez-Ropero F, Zanuy D, Casanovas J, Nussinov R, Aleman C. J Chem Inf Model. 48(2):333-43 (2008)
Calcium-dependent inactivation terminates calcium release in skeletal muscle of amphibians Eduardo Rios, Jingsong Zhou, Gustavo Brum, Bradley S. Launikonis, and Michael D. Stern. J. Gen. Physiol. 131(4):335-48 (2008)
Classification and 3D averaging with missing wedge correction in biological electron tomography A. Bartesaghi, P. Sprechmann, J. Liu, G. Randall, G. Sapiro and S. Subramaniam J. Struct. Biol. 162(3):436-450 (2008)
Detection of co-eluted peptides using database search methods Gelio Alves, Aleksey Y Ogurtsov, Siwei Kwok, Wells W Wu, Guanghui Wang, Rong-Fong Shen, and Yi-Kuo Yu Biol. Direct. 3:27 (2008)
Coarse Master Equations for Peptide Folding Dynamics N.V. Buchete and G. Hummer. J. Phys. Chem. B 112(19):6057-69 (2008)
Interfacial polar interactions affect gramicidin channel kinetics Rostovtseva, TK; Petrache, HI; Kazemi, N; Hassanzadeh, E; Bezrukov, SM; Biophys. J., DOI://10.1529/biophysj.107.120261 (2008)
Effective approaches for the production of heterologous proteins using the Thermococcus kodakaraensis-based translation system Takashi Endoha, Tamotsu Kanaia and Tadayuki Imanaka J. Biotech. 133(2):177-182 (2008)
Identification of the Active Sites of Biomolecules I: Methyl-alpha-mannopyranoside and Fe(III) Orkid Coskuner, Denis E. Bergeron, Luis Rincon, Jeffrey W. Hudgens, Carlos A. Gonzalez J. Phys. Chem. A 112(3):2940-2947 (2008)
Metabolic engineering of Escherichia coli for biosynthesis of hyaluronic acid Huimin Yua and Gregory Stephanopoulos Metabolic Engg. 10(1):24-32 (2008)
New structures help the modeling of toxic amyloidβ ion channels Jang H, Zheng J, Lal R, Nussinov R. Trends Biochem Sci. Feb;33(2):91-100 (2008)
Peptide folding kinetics from replica exchange molecular dynamics Nicolae-Viorel Buchete and Gerhard Hummer Phys. Rev. E 77:030902 (2008)
Structure and dynamics of Helix-0 of the N-BAR domain in Lipid Micelles and Bilayers Christian Löw, Ulrich Weininger, Hwankyu Lee, Kristian Schweimer, Ines Neundorf, Annette G. Beck-Sickinger, Richard W. Pastor and Jochen Balbach Biophys. J. 95(9):4315-23 (2008)
Reactions of Glyceraldehyde 3-Phosphate Dehydrogenase Sulfhydryl Groups with Bis-Electrophiles Produce DNA-Protein Cross-Links but Not Mutations Elisabeth M. Loecken and F. Peter Guengerich Chem. Res. Toxicol. 21(2):453-358 (2008)

2007 (82 papers)

Validating Pareto optimal operation parameters of polyp detection algorithms for CT colonography Jiang Li ; Adam Huang ; Nicholas Petrick ; Jianhua Yao ; Ronald M. Summers Proc. SPIE 6514, Medical Imaging 2007, doi:10.1117/12.707965 (2007)
Multiple comparisons distortions of parameter estimates Jeffries, NO. Biostatistics 8(2):500-4 (2007)
Engineering Metal Complexes of Chiral Pentaazacrowns as Privileged Reverse-turn Scaffolds. Y Che, Bernard Brooks, Dennis P Riley, Andrea JH Reaka, Garland R Marshall. Chemical Biology & Drug Design 69 (2) : 99-110 (2007)
RAId_DbS: Peptide identification using database searches with realistic statistics Alves G, Ogurtsov AY, Yu YK. Biol. Direct. 2:25 (2007)
Cysteine-cysteine contact preference leads to target-focusing in protein folding Sardiu ME, Cheung MS, Yu YK. Biophys. J. 93(3):938-51 (2007)

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project The ENCODE Project Consortium Nature 447:799-816 (2007)
The structure of receptor-associated protein (RAP) Donghan Lee, Joseph D. Walsh, Molly Migliorini, Ping Yu Tao Cai, Charles D. Schwieters, Susan Krueger, Dudley K. Strickland, and Yun-Xing Wang. Protein Science 16:1628-1640 (2007)
Accounting for Variability in Sample Size Estimation with Applications to Nonadherence and Estimation of Variance and Effect Size Fay, MP, Halloran, ME, Follmann, DA. Biometrics 63(2): 465-474 (2007)
Modeling the Alzheimer A β 17-42 Fibril Architecture: Tight Intermolecular Sheet-Sheet Association and Intramolecular Hydrated Cavities Zheng J, Jang H, Ma B, Tsai CJ, Nussinov R. Biophys. J. 93(9):3046-57 (2007)
Molecular and functional analyses of a novel class I secretory nuclease from the human pathogen, Leishmania donovani Joshi MB, Dwyer DM. J. Biol. Chem. 282(13):10079-95 (2007)
Induction of Epitope-Specific Neutralizing Antibodies against West Nile Virus Theodore Oliphant, Grant E. Nybakken, S. Kyle Austin, Qing Xu, Jonathan Bramson, Mark Loeb, Mark Throsby, Daved H. Fremont, Theodore C. Pierson, and Michael S. Diamond J. Virol. 81(21):11828-11839 (2007)

Ab Initio Modeling of Glycosyl Torsions and Anomeric Effects in a Model Carbohydrate: 2-Ethoxy Tetrahydropyran H. Lee Woodcock, Damian Moran, Richard W. Pastor, Alexander D. MacKerell, Jr. and Bernard R. Brooks Biophys. J. 93:1-10 (2007)
Analysis of failure time data with multilevel clustering, with application to the child vitamin a intervention trial in Nepal Shih JH, Lu SE. Biometrics 63(3):673-80 (2007)
Liquid-structure forces and electrostatic modulation of biomolecular interactions in solution SA Hassan. J. Phys. Chem B 111(1):227-41 (2007)
Natural resonance structures and aromaticity of the nucleobases Guangyu Sun & Marc Nicklaus. Theoretical Chemistry Accounts: Theory, 117(2): 323-332 (2007)
Understanding the structural and functional differences between mouse thyrotropin-releasing hormone receptors 1 and 2 Francesca Deflorian, Stanislav Engel, Anny-Odile Colson, Bruce M. Raaka, Marvin C. Gershengorn, Stefano Costanzi Proteins: Structure, Function and Bioinf 71(2):783 - 794 (2007)
Stability of Tubular Structures Based on β-Helical Proteins: Self-Assembled versus Polymerized Nanoconstructs and Wild-Type versus Mutated Sequences David Zanuy, Francisco Rodríguez-Ropero, Nurit Haspel, Jie Zheng, Ruth Nussinov, and Carlos Alem´n BIomacromolecules 8(10):3135-3146 (2007)
N-Nitrosation of amines by NO2 and NO: A theoretical study Yi-Lei Zhao, Stephen L. Garrison, Carlos Gonzalez, William David Thweatt, and Manuel Marquez J. Phys. Chem. A 111(11):2200-2205 (2007)
Exploring SCC-DFTB Paths for Mapping QM/MM Reaction Mechanisms H. Lee Woodcock, Milan Hodošček, and Bernard R. Brooks J. Phys. Chem A 111(26):5720-5728 (2007)
Comparative Study of the Effect of Tail Corrections on Surface Tension Determined by Molecular Simulation V. K. Shen, R. D. Mountain, and J. R. Errington. J. Phys. Chem B 111:6198 (2007)
A genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release. Matarin M, Brown WM, Scholz S, Simon-Sanchez J, Fung HC, Hernandez D, Gibbs JR, De Vrieze FW, Crews C, Britton A, Langefeld CD, Brott TG, Brown RD Jr, Worrall BB, Frankel M, Silliman S, Case LD, Singleton A, Hardy JA, Rich SS, Meschia JF. Lancet Neurol. 6(5):414-20 (2007)
A physical picture of atomic motions within the Dickerson DNA dodecamer in solution derived from joint ensemble refinement against NMR and large-angle X-ray scattering data. Schwieters CD, Clore GM. Biochemistry 46(5):1152-66 (2007)
Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure. Klauda JB, Brooks BR. J Mol Biol. 367(5):1523-34 (2007)
Using Pareto fronts to evaluate polyp detection algorithms for CT colonography Adam Huang ; Jiang Li ; Ronald M. Summers ; Nicholas Petrick ; Amy K. Hara Medical Imaging: Computer-Aided Diagnosis, doi:10.1117/12.709426 (2007)
Spiral structure of Escherichia coli HUαβ provides foundation for DNA supercoiling Fusheng Guo and Sankar Adhya PNAS 104:4309-4314 (2007)
Two-sample Comparison Based on Prediction Error, with Applications to Candidate Gene Association Studies K. Yu, R. Martin, N. Rothman, T. Zheng, Q. Lan. Annals of Human Genetics 71 (1) :107- 118 (2007)
Preferred conformation of the glycosidic linkage of methyl-beta-mannose Coskuner O. J. Chem. Phys 127(1):015101 (2007)
Structure and Dynamics of Parallel β-Sheets, Hydrophobic Core, and Loops in Alzheimer's A β Fibrils Buchete NV, Hummer G. Biophys. J. 92(9):3032-9 (2007)
Molecular dynamics simulation of the P2Y 14 receptor. Ligand docking and identification of a putative binding site of the distal hexose moiety Ivanov, A. A.; Fricks, I; Harden, T. K.; Jacobson, K. A. Bioorg. Med. Chem. Lett. 17:761-766 (2007)

Calculation of the Free Energy and Cooperativity of Protein Folding Kentsis A, Gindin T, Mezei M, Osman R. PLoS One 2:e446 (2007)
Coarse-grained strategy for modeling protein stability in concentrated solutions. III: directional protein interactions J. K. Cheung, V. K. Shen, J. R. Errington, and T. M. Truskett. Biophys. J. 92:4316 (2007)
Context-specific amino acid substitution matrices and their use in the detection of protein homologs Goonesekere NC, Lee B. Proteins 71(2):910-919 (2007)
The Origin of Quantal Size Variation: Vesicular Glutamate Concentration Plays a Significant Role Xin-Sheng Wu, Lei Xue, Raja Mohan, Kenneth Paradiso, Kevin D. Gillis, and Ling-Gang Wu. J. Neurosc. 27(11):3046-3056 (2007)
Challenges in Projecting Clustering Results Across Gene Expression-Profiling Datasets Lara Lusa, Lisa M. McShane, James F. Reid, Loris De Cecco, Federico Ambrogi, Elia Biganzoli, Manuela Gariboldi, Marco A. Pierotti. J. National Cancer Institute 99(22): 1715-1723 (2007)
In Situ Monitoring of Hafnium Oxide Atomic Layer Deposition J.E. Maslar, W.S. Hurst, D.R. Burgess, Jr., W.A. Kimes, N.V. Nguyen, and E.F. Moore Frontiers of Char. and Metr. for Nanoelectrics (2007)
The bootstrap variance of the square of a sample mean Dodd, LE and Korn, EL. The American Statistician. 1(2):127-131 (2007)
qPrimerDepot: a primer database for quantitative real time PCR Wenwu Cui, Dennis D. Taub and Kevin Gardner Nucleic Acids Research 35:D805-D809 (2007)
Probes for Narcotic Receptor Mediated Phenomena. 34. Synthesis and Structure-Activity Relationships of a Potent μ-Agonist δ-Antagonist and an Exceedingly Potent Antinociceptive in the Enantiomeric C9-Substituted 5-(3-Hydroxyphenyl)-N-phenylethylmorphan Series Anne-C�cile Hiebel, Yong Sok Lee, Edward Bilsky, Denise Giuvelis, Jeffrey R. Deschamps, Damon A. Parrish, Mario D. Aceto, Everette L. May, Louis S. Harris, Andrew Coop, Christina M. Dersch, John S. Partilla, Richard B. Rothman, Kejun Cheng, Arthur E. Jacobson, and Kenner C. Rice J. Med. Chem. 50(16):3765-3776 (2007)
Effects of Chain Length on the Rates of CC Bond Dissociation in Linear Alkanes and Polyethylene Knyazev V J. Phys. Chem. A 111(19):3875-83 (2007)
Molecular modeling of the human P2Y2 receptor and design of a selective agonist, 2'-amino-2'-deoxy-2-thiouridine 5'-triphosphate. Ivanov AA, Ko H, Cosyn L, Maddileti S, Besada P, Fricks I, Costanzi S, Harden TK, Calenbergh SV, Jacobson KA. J. Med. Chem 50(6):1166-76 (2007)
Testing β-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: A molecular dynamics study D. Zanuy, F. Rodriguez-Ropero, R. Nussinov, C. Aleman. J. Struct. Biol. 160(2): 177-189 (2007)

Nanostructure Design Using Protein Building Blocks Enhanced by Conformationally Constrained Synthetic Residues Zheng J, Zanuy D, Haspel N, Tsai CJ, Alem C and Nussinov R. Biochemistry 46(5):1205 -1218 (2007)
Substrate-induced Conformational Changes and Dynamics of UDP-N-Acetylgalactosamine: Polypeptide N-Acetylgalactosaminyltransferase-2 Adina L Milac, Nicolae-Viorel Buchete, Timothy A Fritz, Gerhard Hummer, Lawrence A Tabak J. Mol. Biol. Oct 19;373(2):439-51 (2007)
A 2-Year Prospective Study of Human Papillomavirus Persistence among Women with a Cytological Diagnosis of Atypical Squamous Cells of Undetermined Significance or Low-Grade Squamous Intraepithelial Lesion Plummer M, Schiffman M, Castle PE, Maucort-Boulch D, Wheeler CM; ALTS Group. J Infect Dis. 195(11):1582-9 (2007)
Nimbus( BgI): An active non-LTR retrotransposon of the Schistosoma mansoni snail host Biomphalaria glabrata Raghavan N, Tettelin H, Miller A, Hostetler J, Tallon L, Knight M. Int. J. Parasitol. 37(12):1307-18 (2007)
Competition between Hydrogen Abstraction and Halogen Displacement in the Reaction of Br with CH3I, CH3Br, and CH3Cl Irikura, Karl K.; Francisco, J. S. J. Phys. Chem 111:6852-6859 (2007)
Elucidation of a C-Rich Signature Motif in Target mRNAs of RNA-Binding Protein TIAR Kim HS, Kuwano Y, Zhan M, Pullmann R Jr, Mazan-Mamczarz K, Li H, Kedersha N, Anderson P, Wilce MC, Gorospe M, Wilce JA. Mol. Cell. Biol. 27(19):6806-17 (2007)
Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4 Fishelovitch D, Hazan C, Shaik S, Wolfson HJ, Nussinov R. J Am Chem Soc. 14;129(6):1602-11 (2007)
Limits on variations in protein backbone dynamics from precise measurements of scalar couplings Vogeli B, Ying J, Grishaev A, Bax A. J. Am. Chem. Soc 129(30):9377-85 (2007)
Effects of chain length on the rates of C-C bond dissociation in linear alkanes and polyethylene Knyazev, VD J Phys Chem A, DOI://10.1021/jp066419e (2007)
Identification and regional distribution in rat brain of radiometabolites of the dopamine transporter PET radioligand [11C]PE2I Shetty HU, Zoghbi SS, Liow JS, Ichise M, Hong J, Musachio JL, Halldin C, Seidel J, Innis RB, Pike VW. Eur. J. Nucl. Med. Mol. Imaging 34(5):667-78 (2007)
Effect of a P-glycoprotein inhibitor, Cyclosporin A, on the disposition in rodent brain and blood of the 5-HT1A receptor radioligand, [11C](R)-(-)-RWAY Liow JS, Lu S, McCarron JA, Hong J, Musachio JL, Pike VW, Innis RB, Zoghbi SS. Synapse 61(2):96-105 (2007)
Electron Transport Pathway for a Streptomyces Cytochrome P450: Cytochrome P450 105D5-catalyzed fatty acid hydroxylation in Streptomyces Coelicolor A3 (2) Young-Jin Chun, Tsutomu Shimada, Raymundo Sanchez-Ponce, Martha V. Martin, Li Lei, Bin Zhao, Steven L. Kelly, Michael R. Waterman, David C. Lamb and F. Peter Guengerich J. Biol. Chem. 282:17486-17500 (2007)

A detailed transcript-level probe annotation reveals alternative splicing based microarray platform differences Joseph C Lee, David Stiles, Jun Lu, and Margaret C Cam. BMC Genomics 8: 284 (2007)
Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. Schymick JC, Scholz SW, Fung HC, Britton A, Arepalli S, Gibbs JR, Lombardo F, Matarin M, Kasperaviciute D, Hernandez DG, Crews C, Bruijn L, Rothstein J, Mora G, Restagno G, Chio A, Singleton A, Hardy J, Traynor BJ. Lancet Neurol. 6(4):322-8 (2007)
The LeFE algorithm, embracing the complexity of gene expression in the interpretation of microarray data Eichler, GS, Reimers, M, Kane, D, Weinstein, JN. Genome Biology 8(9):R185 (2007)
Imputation Approaches for Estimating Diagnostic Accuracy for Multiple Tests from Partially Verified Designs Paul S. Albert. Biometrics 63:947-957 (2007)
An investigation of two multivariate permutation methods for controlling the false discovery proportion Edward L. Korn , Ming-Chung Li , Lisa M. McShane and Richard Simon. Statistics in Medicine 26:4428-4440 (2007)
A survey of genetic human cortical gene expression Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, Marlowe L, Kaleem M, Leung D, Bryden L, Nath P, Zismann VL, Joshipura K, Huentelman MJ, Hu-Lince D, Coon KD, Craig DW, Pearson JV, Holmans P, Heward CB, Reiman EM, Stephan D, Hardy J. Nature Genetics 39(12):1494-9 (2007)

Changing the Charge Distribution of β-Helical-Based Nanostructures Can Provide the Conditions for charge transfer. Haspel N, Zanuy D, Zheng J, Aleman C, Wolfson H, Nussinov R. Biophys. J. 93(1):245-53 (2007)
Similar Binding Sites and Different Partners: Implications to Shared Proteins in Cellular Pathways Keskin O and Nussinov R. Structure 15:341-354 (2007)
Random Effects Modeling Approaches for Estimating ROC Curves from Repeated Ordinal Tests without a Gold Standard Paul Albert. Biometrics 63:593-602 (2007)
Conformational study of the protegrin-1 (PG-1) dimer interaction with lipid bilayers and its effect. Jang H, Ma B, Nussinov R. BMC Struct Biol. 2;7:21 (2007)
Molecular factors and biochemical pathways induced by febrile temperature in intraerythrocytic Plasmodium falciparum parasites Miranda S. M. Oakley, Sanjai Kumar, Vivek Anantharaman, Hong Zheng, Babita Mahajan, J. David Haynes, J. Kathleen Moch Rick Fairhurst Thomas F. McCutchan and L. Aravind. Infection and Immunity 75: 2012-2025 (2007)
Expression and Purification of Recombinant Wheat Translation Initiation Factors eIF1, eIF1A, eIF4A, eIF4B, eIF4F, eIF(iso)4F, and eIF5 Laura K. Mayberry, Michael D. Dennis, M. Leah Allen, Kelley Ruud Nitka, Patricia A. Murphy, Lara Campbell and Karen S. Browning Methods in Enzymology 430:397-408 (2007)
N-MYC Regulates Focal Adhesion Kinase Expression in Human Neuroblastoma Elizabeth A. Beierle, Angelica Trujillo, Abhilasha Nagaram, Elena V. Kurenova, Richard Finch, Xiaojie Ma, Jennifer Vella, William G. Cance and Vita M. Golubovskaya J. Biol. Chem. 282:12503-12516 (2007)
Calibrating E-values for MS2 database search methods Alves G, Ogurtsov AY, Wu WW, Wang G, Shen RF, Yu YK. Biol. Direct. 2:26 (2007)
Structural basis for p53 binding-induced DNA bending. Pan Y, Nussinov R. J Biol Chem. 5;282(1):691-9 (2007)
Confinement, entropy, and single-particle dynamics of equilibrium hard-sphere mixtures. Mittal J, Shen VK, Errington JR, Truskett TM. J Chem Phys. Oct 21;127(15):154513 (2007)
An Evaluation of Power and Type I Error of Single-Nucleotide Polymorphism Transmission/Disequilibrium-Based Statistical Methods under Different Family Structures, Missing Parental Data, and Population Stratification Kristin K. Nicodemus Augustin Luna and Yin Yao Shugart. Am. J. Hum. Genet. 80:178-185 (2007)
Density functional theory study of the clean and hydrated hematite (1[overline 1]02) surfaces Cynthia S. Lo, Kunaljeet S. Tanwar, Anne M. Chaka, and Thomas P. Trainor Phys. Rev. B 75(7):209901 (2007)
Density-functional study of magnetism in bare Au nanoclusters: Evidence of permanent size-dependent spin polarization without geometry relaxation Magyar, R. J.; Mujica, V.; Marquez, M.; Gonzalez, C. Phys. Rev. B 75(14):14421 (2007)
Optimized clonotypic analysis of T-cell receptor repertoire in immune reconstitution Packer AN, Muraro PA. Exp. Hematol. 35(3):516-21 (2007)
Neural dynamics for facial threat processing as revealed by gamma band synchronization using MEG Qian Luo, Tom Holroyd, Matthew Jones, Talma Hendler and James Blair Neuroimage 34:839-847 (2007)
Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. Woodcock HL 3rd, Hodoscek M, Gilbert AT, Gill PM, Schaefer HF 3rd, Brooks BR. J. Comput. Chem 28(9):1485-502 (2007)
Intrinsic Conformational Characteristics of α, α-Diphenylglycine Casanovas J, Zanuy D, Nussinov R, Aleman C. J. Org. Chem. 16;72(6):2174-81 (2007)
Identification and Biochemical Characterization of Unique Secretory Nucleases of the Human Enteric Pathogen, Entamoeba histolytica Glen C. McGugan, Jr., Manju B. Joshi, and Dennis M. Dwyer J. Biol. Chem. 282(43):31789-31802 (2007)
Use of constrained synthetic amino acids in β-helix proteins for conformational control. Zanuy D, Jimenez AI, Cativiela C, Nussinov R, Aleman C. J Phys Chem B. 111(12):3236-42 (2007)
Models of β-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a Dynamic Process. Jang H, Zheng J, Nussinov R. Biophys. J. 93(6):1938-49 (2007)
Structures of the CCR5 N Terminus and of a Tyrosine-Sulfated Antibody with HIV-1 gp120 and CD4 Chih-chin Huang, Son N. Lam, Priyamvada Acharya, Min Tang, Shi-Hua Xiang, Syed Shahzad-ul Hussan, Robyn L. Stanfield, James Robinson, Joseph Sodroski, Ian A. Wilson, Richard Wyatt, Carole A. Bewley, Peter D. Kwong Science 317:1930-1934 (2007)
Protein recognition motifs: Design of peptidomimetics of helix surfaces Ye Che, Bernard Brooks, Garland R Marshall. Biopolymers 86(4):288 - 297 (2007)
Water dissociation in the presence of metal ions Coskuner O, Jarvis EA, Allison TC. Angew. Chem. Int. Ed 46(41): 7853 (2007)

2006 (57 papers)

Functionalized Self-Assembled Monolayers on Ultraflat Gold as Platforms for Single Molecule Force Spectroscopy and Imaging Yadavalli VK, Forbes JG, Wang K. Langmuir 22(16):6969-76 (2006)

Kinetic Study of the Gas-Phase Reaction of OH with Br2 Mikhail G. Bryukov, Barry Dellinger, and Vadim D. Knyazev J. Phys. Chem. A 110(29):9169-9174 (2006)
Surface-modulated motion switch: Capture and release of iron-sulfur protein in the cytochrome bc₁ complex Lothar Esser, Xing Gong, Shaoqing Yang, Linda Yu, Chang-An Yu and Di Xia PNAS 103(35):13045-13050 (2006)
System size and control parameter effects in reverse perturbation nonequilibrium molecular dynamics Mountain RD. J Chem Phys. 124(10):104109 (2006)
Membrane biophysics Joshua Zimmerberg. Current Biology 16:R272-R276 (2006)
De Novo Tubular Nanostructure Design Based on Self-Assembly of β-Helical Protein Motifs Nurit Haspel, David Zanuy, Carlos Alemán, Haim Wolfson and Ruth Nussinov Structure 14(7):1137-1148 (2006)
Structure by design: from single proteins and their building blocks to nanostructures Tsai C-J, Zheng J, Aleman C, Nussinov R. Trends in Biotechnoloy 24:449-454 (2006)
Constant surface tension molecular dynamics simulations of lipid bilayers with trehalose R. M. Venable, A. Skibinsky and R. W. Pastor. Molecular Simulation 32:849-855 (2006)
Effects of electric fields on proton transport through water chains S A Hassan, G Hummer and Y S Lee J. Chem. Phys 124:204510 (2006)
The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements MAQC Consortium. Nature Biotechnology 24: 1151 - 1161 (2006)
Global similarity and local divergence in human and mouse gene co-expression networks. Tsaparas, P., Marino-Ramirez, L., Bodenreider, O., Koonin, E. V. and Jordan, I. K. BMC Evol Biol. 6:70 (2006)
Concordance of residual dipolar couplings, backbone order parameters and crystallographic B-factors for a small alpha/beta protein: a unified picture of high probability, fast atomic motions in proteins Clore GM, Schwieters CD. J. Mol. Biol. 355(5):879-86 (2006)
Determination of surface tension in binary mixtures using transition-matrix Monte Carlo V. K. Shen and J. R. Errington. J. Chem. Phys 124:24721 (2006)

Genes involved in DNA repair and nitrosamine metabolism and those located on chromosome 14q32 are dysregulated in nasopharyngeal carcinoma. Dodd LE, Sengupta S, Chen IH, den Boon JA, Cheng YJ, Westra W, Newton MA, Mittl BF, McShane L, Chen CJ, Ahlquist P, Hildesheim A. Cancer Epidemiol Biomarkers Prev. 15(11):2216-25 (2006)
Predicting domain-domain interactions using a parsimony approach Katia S Guimaraes, Raja Jothi, Elena Zotenko and Teresa M Przytycka. Genome Biol. 7(11): R104 (2006)
De novo peptide sequencing using exhaustive enumeration of peptide composition. Olson MT, Epstein JA, Yergey AL. J. Am. Soc. Mass. Spectrum 17(8):1041-9 (2006)
PET imaging of brain 5-HT1A receptors in rat in vivo with 18F-FCWAY and improvement by successful inhibition of radioligand defluorination with miconazole Tipre DN, Zoghbi SS, Liow JS, Green MV, Seidel J, Ichise M, Innis RB, Pike VW. J. Nucl. Med 47(2):345-53 (2006)
Chemical shift tensors of protonated base carbons in helical RNA and DNA from NMR relaxation and liquid crystal measurements. Ying J, Grishaev A, Bryce DL, Bax A. J. Am. Chem. Soc 128(35):11443-54 (2006)
Using RNA sample titrations to assess microarray platform performance and normalization techniques Shippy R et al. Nature Biotechnology 24: 1123-1131 (2006)

Interaction of Protegrin-1 with Lipid Bilayers: Membrane Thinning Effect Jang H, Ma B, Woolf TB., Nussinov R Biophysical J. 91:2848-2859 (2006)
The snail (Biomphalaria glabrata) genome project Raghavan N. and Knight M. Trends Parasitol. 22(4):148-51 (2006)
CisView: A Browser and Database of cis-regulatory Modules Predicted in the Mouse Genome Sharov A, Dudekula D, Ko MSH. DNA Research 13(3):123-34 (2006)
Using ancestry-informative markers to define populations and detect population stratification Enoch MA, Shen PH, Xu K, Hodgkinson C, Goldman D. J Psychopharmacol 20:19-26 (2006)
Augmented designs to assess immune response in vaccine trials Follmann, DA. Biometrics 62(4):1161-9 (2006)
“Similarity Trap” in Protein-Protein Interactions Could Be Carcinogenic: Simulations of p53 Core Domain Complexed with 53BP1 and BRCA1 BRCT Domains Liu J, Pan Y, Ma B, and Nussinov R. Structure 14(12):1811-21 (2006)

Engineering Cyclic Tetrapeptides Containing Chimeric Amino Acids as Preferred Reverse-Turn Scaffolds Ye Che and Garland Marshall. J. Med. Chem. 49 (1):111 -124, (2006)
Titin as a giant scaffold for integrating stress and Src homology domain 3-mediated signaling pathways Ma K, Forbes JG, Gutierrez-Cruz G, and Wang K. J. Biol Chem. 281(37):27539-56 (2006)
Development of small molecules designed to modulate protein-protein interactions Ye Che, Bernard Brooks, Garland Marshall. J. Computer-Aided Molecular Design 20(2): 109-130 (2006)
Structural Stability and Dynamics of an Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35 Zheng J, Ma B, Tsai C-J, Nussinov R. Biophysical Journal 91: 824-833 (2006)
Development of a substrate-based cyclic phosphopeptide inhibitor of protein phosphatase 2Cδ, Wip1 Yamaguchi H, Durell SR, Feng H, Bai Y, Anderson CW, Appella E. Biochemistry 45(44):13193-202 (2006)
Computational Study of the Fibril Organization of Polyglutamine Repeats Reveals a Common Motif Identified in β-Helices David Zanuy, Kannan Gunasekaran, Arthur M. Lesk and Ruth Nussinov J. Mol. Biol. 358(1):330-345 (2006)

Dynamical motions of lipids and a finite size effect in simulations of bilayers Klauda JB, Brooks BR, Pastor RW. J Chem Phys. 125(14):144710 (2006)
The Stability of Monomeric Intermediates Controls Amyloid Formation: A{beta}25-35 and its N27Q Mutant Ma B, Nussinov R. Biophys. J. 90(10):3365-74 (2006)
Interpretation of Data and Identification of Information are Sine Qua Non for Modern Digital Information Services Ying He, and Mehmet Kayaalp. AMIA Annu Symp Proc. : 946 (2006)
Rat toxicogenomic study reveals analytical consistency across microarray platforms Guo, L, Edward K Lobenhofer, Charles Wang, Richard Shippy, Stephen C Harris, Lu Zhang, Nan Mei, Tao Chen, Damir Herman, Federico M Goodsaid, Patrick Hurban, Kenneth L Phillips, Jun Xu, Xutao Deng, Yongming Andrew Sun, Weida Tong, Yvonne P Dragan & Leming Shi Nature Biotechnology. 24: 1162 - 1169 (2006)
Parallel Computation and Visualization Tools for Codetermination Analysis of Multivariate Gene Expression Relations Edward B. Suh, Edward R. Dougherty, Seungchan Kim, Michael L. Bittner, Yidong Chen, Daniel E. Russ and Robert L. Martino Computational and Statistical Approaches to Genomics (2006)
SCIMS: A new algorithm for associating anticancer drug mechanisms with gene ontology categories Gabriel S. Eichler, Mark Reimers and John N. Weinstein Proc. Amer. Assoc. Cancer Res. 47:1565 (2006)
Getting practical with molecular chaperones VM Longshaw, WS Nicoll, M Botha, MH Ludewig, A Shonhai, LL Stephens and GL Blatch Protein Folding (2006)
Nucleation and cavitation of spherical, cylindrical, and slablike droplets and bubbles in small systems L. G. MacDowell, V. K. Shen, and J. R. Errington. J. Chem. Phys 125(3): 34705 (2006)
Altered HIV-1 Gag protein interactions with cyclophilin A (CypA) on the acquisition of H219Q and H219P substitutions in the CypA binding loop Gatanaga H, Das D, Suzuki Y, Yeh DD, Hussain KA, Ghosh AK, Mitsuya H. J Biol Chem. 281(2):1241-50 (2006)
Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure Jie Zheng, Buyong Ma and Ruth Nussinov. Phys. Biol. 3: 1478-3975 (2006)
Impact of Cis-proline analogs on peptide conformation Ye Che, Garland R. Marshall. Biopolymers 81(5): 392 - 406 (2006)
Coarse-grained strategy for modeling protein stability in concentrated solutions. II: phase behavior. V. K. Shen, J. K. Cheung, J. R. Errington, and T. M. Truskett. Biophys. J. 90:1949 (2006)

The influence of tumor oxygenation on 18 F-FDG (Fluorine-18 Deoxyglucose) uptake: A mouse study using positron emission tomography (PET) Linda W Chan, Sebastien Hapdey, Sean English, Jurgen Seidel, Joann Carson, Anastasia L Sowers, Murali C Krishna, Michael V Green, James B Mitchell and Stephen L Bacharach. Radiation Oncology 1:3 (2006)
A Missense Mutation in the Seven-transmembrane Domain of the Human Ca2+ Receptor Converts a Negative Allosteric Modulator into a Positive Allosteric Modulator Jianxin Hu, Jiankang Jiang, Stefano Costanzi, Craig Thomas, Wu Yang, Jean H. M. Feyen, Kenneth A. Jacobson, and Allen M. Spiegel. J. Biol. Chem Vol. 281(3): 21558-21565 (2006)
The histone database: A comprehensive resource for histones and histone fold-containing proteins Marino-Ramirez, L., Hsu, B., Baxevanis, A. D. and Landsman, D Proteins 62:838-842 (2006)
Structural and Molecular Interactions of CCR5 Inhibitors with CCR5 Maeda K, Das D, Ogata-Aoki H, Nakata H, Miyakawa T, Tojo Y, Norman R, Takaoka Y, Ding J, Arnold GF, Arnold E, Mitsuya H. J Biol Chem. 281(18):12688-98 (2006)
ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification. Sam V, Tai CH, Garnier J, Gibrat JF, Lee B, Munson PJ. BMC Bioinformatics 7:206 (2006)
Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data. Fung HC, Scholz S, Matarin M, Simon-Sanchez J, Hernandez D, Britton A, Gibbs JR, Langefeld C, Stiegert ML, Schymick J, Okun MS, Mandel RJ, Fernandez HH, Foote KD, Rodriguez RL, Peckham E, De Vrieze FW, Gwinn-Hardy K, Hardy JA, Singleton A. Lancet Neurol. 5:911-916 (2006)

Multiple independent evolutionary solutions to core histone gene regulation Marino-Ramirez L, Jordan IK, Landsman D. Genome Biol. 7(12):R122 (2006)
Comparison of the Human and Worm p53 Structures Suggests a Way for Enhancing Stability Pan Y, Ma B, Levine AJ, Nussinov R. Biochemistry 45 (12):3925 -3933 (2006)
PET imaging of the dopamine transporter with 18F-FECNT: a polar radiometabolite confounds brain radioligand measurements Zoghbi SS, Shetty HU, Ichise M, Fujita M, Imaizumi M, Liow JS, Shah J, Musachio JL, Pike VW, Innis RB. J. Nucl. Med 47(3):520-7 (2006)
Appropriateness of some resampling-based inference procedures for assessing performance of prognostic classifiers derived from microarray data Lusa L, McShane LM, Radmacher MD, Shih JH, Wright GW, Simon R. Stat Med. 26(5):1102-13 (2006)
Co-evolutionary Rates of Functionally Related Yeast Genes Leonardo Marino-Ramirez, Olivier Bodenreider, Natalie Kantz and I. King Jordan Evolutionary Bioinformatics, Donald Forsdyke (ed), Springer (2006)
Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. Balaji S, Babu MM, Iyer LM, Luscombe NM, Aravind L. J. Mol. Biol. 360(1):213-27 (2006)
Automatic colonic polyp detection using multiobjective evolutionary techniques Jiang Li, Adam Huang, Jianhua Yao, and Ingmar Bitter, Nicholas Petrick, Ronald M. Summers, Perry J. Pickhardt, J. Richard Choi. In Medical Imaging 2006: Image Processing, Joseph M. Reinhardt, Josien P. W. Pluim (eds) (2006)
Backbone Conformational Preferences and Pseudorotational Ring Puckering of 1-Aminocyclopentane-1-carboxylic Acid Aleman C, Zanuy D, Casanovas J, Cativiela C, Nussinov R. J Phys Chem B 110 (42): 21264 -21271 (2006)

2005 (42 papers)

Score statistics of global sequence alignment from the energy distribution of a modified directed polymer and directed percolation problem Sardiu ME, Alves G, Yu Y-K. Phys. Rev. E 72: 061917 (2005)
Agonist-Induced Conformational Changes in Thyrotropin-Releasing Hormone Receptor Type I: Disulfide Cross-Linking and Molecular Modeling Approaches. Huang W, Osman R, Gershengorn MC. Biochemistry. 44(7):2419-2431 (2005)
CD4 binding partially locks the bridging sheet in gp120 but leaves the β2/3 strands flexible Pan Y, Ma B, Nussinov R. J Mol Biol. 350(3):514-27 (2005)
Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics Alves G, Yu Y-K. Bioinformatics 21(19):3726-3732 (2005)

Molecular Dynamics Simulations of Alzheimer's beta-Amyloid Protofilaments Buchete NV, Tycko R, and Hummer G. Mol. Biol. 353 (4): 804-821 (2005)
PET imaging of brain with the beta-amyloid probe, [11C]6-OH-BTA-1, in a transgenic mouse model of Alzheimer's disease Toyama H, Ye D, Ichise M, Liow JS, Cai L, Jacobowitz D, Musachio JL, Hong J, Crescenzo M, Tipre D, Lu JQ, Zoghbi S, Vines DC, Seidel J, Katada K, Green MV, Pike VW, Cohen RM, Innis RB. Eur. J. Nucl. Med. Mol. Imaging 32(5):593-600 (2005)
Mutations in PIP5K3 are associated with François-Neetens mouchetée fleck corneal dystrophy Li S, Tiab L, Jiao X, Munier FL, Zografos L, Frueh BE, Sergeev Y, Smith J, Rubin B, Meallet MA, Forster RK, Hejtmancik JF, Schorderet DF. Am. J. Hum. Genet. 77(1):54-63 (2005)
Human P2Y(6) receptor: molecular modeling leads to the rational design of a novel agonist based on a unique conformational preference Costanzi S, Joshi BV, Maddileti S, Mamedova L, Gonzalez-Moa MJ, Marquez VE, Harden TK, Jacobson KA. J Med Chem. 48(26):8108-11 (2005)
In the quest for stable rescuing mutants of p53: computational mutagenesis of flexible loop L1. Pan Y, Ma B, Venkataraghavan RB, Levine AJ, Nussinov R. Biochemistry 44(5):1423-32 (2005)
Adjacent Gauche Stabilization in Linear Alkanes: Implications for Polymer Models and Conformational Analysis Jeffery B. Klauda, Richard W. Pastor, and Bernard R. Brooks J. Phys. Chem. 109(33):15684-15686 (2005)

An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer Klauda J, Brooks BR, MacKerell AD, Venable RM, Pastor RW. J. Phys. Chem. B 109 (11): 5300 -5311 (2005)
Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. Tsai HH, Reches M, Tsai CJ, Gunasekaran K, Gazit E, Nussinov R. PNAS 102(23):8174-9 (2005)
Molecular architecture of a eukaryotic DNA transposase. Hickman AB, Perez ZN, Zhou L, Musingarimi P, Ghirlando R, Hinshaw JE, Craig NL, Dyda F. Nat Struct Mol Biol. 12: 715 - 721 (2005)
A Molecular Dynamics Study of the Response of Lipid Bilayers and Monolayers to Trehalose Skibinsky A, Venable RM, Pastor RW. Biophys. J. 89: 4111-4121 (2005)
Sequential testing for efficacy in clinical trials with non-transient effects James F. Troendle, Aiyi Liu, Chengqing Wu, Kai F. Yu. Statistics in Medicine 24(21):3239 - 3250 (2005)
Amino Acid Side Chain Interactions in the Presence of Salts Sergio A. Hassan J. Phys. Chem. 109(46):21989-21996 (2005)
Variable tick protein in two genomic groups of the relapsing fever spirochete Borrelia hermsii in western North America Porcella SF, Raffel SJ, Anderson DE Jr, Gilk SD, Bono JL, Schrumpf ME, Schwan TG. Infect. Immun. 73(10):6647-58 (2005)
Distinguishing Modes of Eukaryotic Gradient Sensing R. Skupsky, W. Losert, and R. J. Nossal Biophys. J. 89(4):2806-2823 (2005)
Bacterial 16S ribosomal DNA in house dust mite cultures Valerio CR, Murray P, Arlian LG, Slater JE. J. Allergy Clin. Immunol. 116(6):1296-300 (2005)
Accurate Determination of Leucine and Valine Side-chain Conformations using U-[15 N/13 C/2H]/[1H-(methine/methyl)-Leu/Val] Isotope Labeling, NOE Pattern Recognition, and Methine Cγ-Hγ/Cβ-Hβ Residual Dipolar Couplings: Application to the 34-kDa Enzyme IIAChitobiose Chun Tang, Junji Iwahara and G. Marius Clore J. Biomol. NMR 33(2):1573-5001 (2005)
Multiple comparisons between two groups on multiple Bernoulli outcomes while accounting for covariates. JF Troendle Stat. Med. 24(23):3581-91 (2005)
Polyproline and the “spectroscopic ruler” revisited with single-molecule fluorescence ? Schuler B, Lipman EA, Steinbach PJ, Kumke M, Eaton WA. PNAS 102(8):2754-9 (2005)

Measurement of Ribose Carbon Chemical Shift Tensors for A-form RNA by Liquid Crystal NMR Spectroscopy David L. Bryce, Alexander Grishaev, and Ad Bax. J. Am. Chem. Soc 127 (20):7387 -7396 (2005)
Molecular Dynamics Simulations of the Influenza Hemagglutinin Fusion Peptide in Micelles and Bilayers: Conformational Analysis of Peptide and Lipids Lague P, Roux B, Pastor RW. J. Mol. Biol 354: 1129-1141 (2005)
From quantum chemistry and the classical theory of polar liquids to continuum approximations in molecular mechanics calculations SA Hassan, EL Mehler. Int.Quantum Chem. 102(5): 986 - 1001 (2005)
A comparative study of amyloid fibril formation by residues 15-19 of the human calcitonin hormone: a single β-sheet model with a small hydrophobic core. Haspel N, Zanuy D, Ma B, Wolfson H, Nussinov R. J Mol Biol. 345(5):1213-27 (2005)
SspA is required for acid resistance in stationary phase by downregulation of H-NS in Escherichia coli Hansen AM, Qiu Y, Yeh N, Blattner FR, Durfee T, Jin DJ. Mol. Microbiol. 56(3):719-34 (2005)
Comparison of the protein-protein interfaces in the p53-DNA crystal structures: towards elucidation of the biological interface Ma B, Pan Y, Gunasekaran K, Venkataraghavan RB, Levine AJ, Nussinov R. PNAS 102(11):3988-93 (2005)

Comprehensive analysis of heterochromatin-and RNAi-mediated epigenetic control of the fission yeast genome Cam H, Sugiyama T, Chen ES, Chen X, Fitzgerald P, Grewal SI. Nat Genet. 37: 809 - 819 (2005)
Modelling longitudinal semicontinuous emesis volume data with serial correlation in an acupuncture clinical trial Paul S. Albert and Joannie Shen Appl. Statist. 54(4):707-720 (2005)
Ion Transport through Membrane-Spanning Nanopores Studied by Molecular Dynamics Simulations and Continuum Electrostatics Calculations Christine Peter and Gerhard Hummer. Biophys. J. 89:2222-2234 (2005)
Identification and functional outcome of mRNAs associated with RNA-binding protein TIA-1 Lopez de Silanes I, Galban S, Martindale JL, Yang X, Mazan-Mamczarz K, Indig FE, Falco G, Zhan M, Gorospe M. Mol. Cell. Biol. 25(21):9520-31 (2005)
The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli Scholl D, Merril C. J. Bacteriol. 187(24):8499-503 (2005)
Utilization of a Common Pathway for the Synthesis of High Affinity Macrocyclic Grb 2 SH 2 Domain-Binding Peptide Mimetics That Differ in the Configuration at One Ring Junction Zhen-Dan Shi, Rajeshri G. Karki, Karen M. Worthy, Lakshman K. Bindu, Marc C. Nicklaus, Robert J. Fisher, and Terrence R. Burke Jr. Chem. & Biodiversity 2:447-456 (2005)

Solution Structure of Enzyme IIAChitobiose from the N, N'-Diacetylchitobiose Branch of the Escherichia coli Phosphotransferase System ? Chun Tang, David C. Williams, Jr., Rodolfo Ghirlando, and G. Marius Clore. J. Biol. Chem 280, Issue 12:11770-11780 (2005)
Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: Calculation of structural and dynamic properties Li X, Hassan SA, Mehler EL. Proteins. 60(3):464 - 484 (2005)
Utilization of a common pathway for the synthesis of high affinity macrocyclic Grb2 SH2 domain-binding peptide mimetics that differ in the configuration at one ring junction Shi ZD, Karki RG, Worthy KM, Bindu LK, Nicklaus MC, Fisher RJ, Burke TR. Chem. & Biodivers 2:447-456 (2005)
Genome-wide assembly and analysis of alternative transcripts in mouse. Sharov AA, Dudekula DB, Ko MSH. Genome Res. 15:748-754 (2005)
Computed tomographic virtual colonoscopy computer-aided polyp detection in a screening population. Summers RM, Yao J, Pickhardt PJ, Franaszek M, Bitter I, Brickman D, Krishna V, Choi JR. Gastroenterology 129(6):1832-44 (2005)
Titin PEVK segment: charge-driven elasticity of the open and flexible polyampholyte Forbes JG, Jin AJ, Ma K, Gutierrez-Cruz G, Tsai WL, Wang K. J Muscle Res Cell Motil. 26(6-8):291-301 (2005)
Expression of estrogen receptor alpha exon-deleted mRNA variants in the human and non-human primate frontal cortex W.R. Perlman, M. Matsumoto, S. Beltaifa, T.M. Hyde, R.C. Saunders, M.J. Webster, D.R. Rubinow, J.E. Kleinman and C.S. Weickert Neuroscience 134(1):81-95 (2005)
Quantification of brain phosphodiesterase 4 in rat with (R)-[11C]Rolipram-PET Fujita M, Zoghbi SS, Crescenzo MS, Hong J, Musachio JL, Lu JQ, Liow JS, Seneca N, Tipre DN, Cropley VL, Imaizumi M, Gee AD, Seidel J, Green MV, Pike VW, Innis RB. Neuroimage 26(4):1201-10 (2005)

2004 (57 papers)

Nucleic acid transport through carbon nanotube membranes In-Chul Yeh and Gerhard Hummer. PNAS 101(33): 12177-12182 (2004)
Performance of a genetic algorithm for mass spectrometry proteomics Jeffries, NO. BMC Bioinformatics 5:180 (2004)
A Spontaneous Translational Fusion of Bacillus cereus PlcR and PapR Activates Transcription of PlcR-Dependent Genes in Bacillus anthracis via Binding with a Specific Palindromic Sequence Andrei P. Pomerantsev, Olga M. Pomerantseva, and Stephen H. Leppla Infection & Immunity 72(10):5814-5823 (2004)
Combinatorial modeling of protein folding kinetics: free energy profiles and rates Eric R. Henry and William A. Eaton Chemical Physics 307:163-185 (2004)
Dynamics of proton transfer in bacteriorhodopsin Lee YS, Krauss M. J Am Chem Soc. 126(7):2225-30 (2004)
Exploring peptide energy landscapes: A test of force fields and implicit solvent models. Steinbach PJ. Proteins 57(4):665-677 (2004)
Correcting log ratios for signal saturation in cDNA microarrays Dodd LE, Korn EL, McShane LM, Chandramouli GV, Chuang EY. Bioinformatics 20(16):2685-93 (2004)
An efficient algorithm for generating two-way contingency tables with fixed marginal totals and arbitrary mean proportions, with applications to permutation tests Craig Borkowf. Comp. Stat. and Data Analysis 44(3): 431-449 (2004)
Modulating Functional Loop Movements: The Role of Highly Conserved Residues in the Correlated Loop Motions Kannan Gunasekaran, Ruth Nussinov Chem.Bio.Chem. 5(2):224-230 (2004)
IL-15 and IL-2 reciprocally regulate expression of the chemokine receptor CX3CR1 through selective NFAT1- and NFAT2-dependent mechanisms Jana Barlic, David H. McDermott, Maya N. Merrell, Jacqueline Gonzales, Laura E. Via, and Philip M. Murphy J. Biol. Chem. 279(47):48520-48534 (2004)
Side chain interactions determine the amyloid organization: a single layer β-sheet molecular structure of the calcitonin peptide segment 15-19 David Zanuy, Nurit Haspel, Hui-Hsu (Gavin) Tsai, Buyong Ma, Kannan Gunasekaran, Haim J Wolfson and Ruth Nussinov Physical Biology 1(2):89-99 (2004)
How Much Backbone Motion in Ubiquitin Is Required To Account for Dipolar Coupling Data Measured in Multiple Alignment Media as Assessed by Independent Cross-Validation? G. Marius Clore and Charles D. Schwieters J. Am. Chem. Soc. 126(9):2923-2938 (2004)
Structure and Reaction in the Active Site of Mammalian Adenylyl Cyclase Yong-Sok Lee and Morris Krauss J. Phys. Chem. B 108(14):4508-4515 (2004)
Large-scale validation of a computer-aided polyp detection algorithm for CT colonography using cluster computing I Bitter, JE Brown, D Brickman, RM Summers Medical Imaging 2004 (2004)
Quantum Chemical Calculations and Mutational Analysis Suggest Heat Shock Protein 90 Catalyzes Trans- Cis Isomerization of Geldanamycin Lee YS, Marcu MG, Neckers L. Chem Biol. 11(7):991-8 (2004)
DBParser: web-based software for shotgun proteomic data analyses. Yang X, Dondeti V, Dezube R, Maynard DM, Geer LY, Epstein J, Chen X, Markey SP, Kowalak JA. J. Proteome Res. 3(5):1002-8 (2004)

Clustering of DNA sequences in human promoters. FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C. Genome Research 14(8):1562-74 (2004)
Amplitudes of Protein Backbone Dynamics and Correlated Motions in a Small α/β Protein: Correspondence of Dipolar Coupling and Heteronuclear Relaxation Measurements G. Marius Clore and Charles D. Schwieters Biochemistry 43(33):10678-10691 (2004)
Semirandom Sampling to Detect Differentiation-Related and Age-Related Epigenome Remodeling Valya R. Russanova, Tazuko H. Hirai and Bruce H. Howard J. Gerontology 59:1221-1233 (2004)
Three Roads to Islet Bursting: Emergent Oscillations in Coupled Phantom Bursters Charles L. Zimliki, David Mears and Arthur Sherman. Biophys. J 87:193-206 (2004)
A chlamydial type III translocated protein is tyrosine-phosphorylated at the site of entry and associated with recruitment of actin D. R. Clifton, K. A. Fields, S. S. Grieshaber, C. A. Dooley, E. R. Fischer, D. J. Mead, R. A. Carabeo, and T. Hackstadt PNAS 101(27):10166-10171 (2004)
β-Hairpin Folding Mechanism of a Nine-Residue Peptide Revealed from Molecular Dynamics Simulations in Explicit Water. Wu X and Bernard R. Brooks. Biophys. J. 86(4):1946-58 (2004)

Visualization of α-helical features in a density map constructed using 9 molecular images of the 1.8 MDa icosahedral core of pyruvate dehydrogenase Borgnia MJ, Shi D, Zhang P, Milne JL J. Struct. Biol. 147(2):136-45 (2004)
A Model of Inverse Agonist Action at Thyrotropin-Releasing Hormone Receptor Type 1: Role of a Conserved Tryptophan in Helix 6. Lu X, Huang W, Worthington S, Drabik P, Osman R, Gershengorn MC. Mol Pharmacol. 66(5):1192-200 (2004)
Simian cytomegalovirus encodes five rapidly evolving chemokine receptor homologues Sahagun-Ruiz A, Sierra-Honigmann AM, Krause P, Murphy PM. Virus Genes 28(1):71-83 (2004)
Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function Goonesekere NC, Lee B. Nucleic Acids Research 32(9):2838-43 (2004)
Absolute quantification of regional cerebral glucose utilization in mice by 18F-FDG small animal PET scanning and 2-14C-DG autoradiography Toyama H, Ichise M, Liow JS, Modell KJ, Vines DC, Esaki T, Cook M, Seidel J, Sokoloff L, Green MV, Innis RB. J. Nucl. Med 45(8):1398-405 (2004)
Identification and functional characterization of novel scorpion venom peptides with no disulfide bridge from Buthus martensii Karsch Zeng XC, Wang SX, Zhu Y, Zhu SY, Li WX. Peptides 25(2):143-50 (2004)
Rydberg-London potential for diatomic molecules and unbonded atom pairs Kevin Cahill, V. Adrian Parsegian J. Chem. Phys. 121:10839 (2004)
Statistical analysis of over-represented words in human promoter sequences. Marino-Ramirez L, Spouge JL, Kanga GC, Landsman D. Nucleic Acids Research 32(3):949-58 (2004)
Comparative analysis of apicomplexa and genomic diversity in eukaryotes. Templeton TJ, Iyer LM, Anantharaman V, Enomoto S, Abrahante JE, Subramanian GM, Hoffman SL, Abrahamsen MS, Aravind L. Genome Res. 14(9):1686-95 (2004)
Evolutionary and functional relationships within the DJ1 superfamily. Bandyopadhyay S, Cookson MR. BMC Evol Biol. 4(1):6 (2004)
Functionalization of tumor necrosis factor-alpha using phage display technique and PEGylation improves its antitumor therapeutic window Shibata H, Yoshioka Y, Ikemizu S, Kobayashi K, Yamamoto Y, Mukai Y, Okamoto T, Taniai M, Kawamura M, Abe Y, Nakagawa S, Hayakawa T, Nagata S, Yamagata Y, Mayumi T, Kamada H, Tsutsumi Y. Clin. Cancer Res. 10(24):8293-300 (2004)
Peptide sequence and amyloid formation: molecular simulations and experimental study of a human islet amyloid polypeptide fragment and its analogs Zanuy D, Porat Y, Gazit E, Nussinov R. Structure 12(3):439-55 (2004)
Synthesis and evaluation of two 18F-labeled 6-iodo-2-(4'-N,N-dimethylamino)phenylimidazo[1,2-a]pyridine derivatives as prospective radioligands for beta-amyloid in Alzheimer's disease Cai L, Chin FT, Pike VW, Toyama H, Liow JS, Zoghbi SS, Modell K, Briard E, Shetty HU, Sinclair K, Donohue S, Tipre D, Kung MP, Dagostin C, Widdowson DA, Green M, Gao W, Herman MM, Ichise M, Innis RB. J. Med. Chem 47(9):2208-18 (2004)
Mechanistic insights from a refined three-dimensional model of integrin alphaIIbbeta3 Filizola M, Hassan SA, Artoni A, Coller BS, Weinstein H. J Biol Chem 279(23):24624-30 (2004)
In silico protein design by combinatorial assembly of protein building blocks Hui-Hsu (Gavin) Tsai, Chung-Jung Tsai, Buyong Ma and Ruth Nussinov. Protein Science 13:2753-2765 (2004)
The stability and dynamics of the human calcitonin amyloid peptide DFNKF Tsai HH, Zanuy D, Haspel N, Gunasekaran K, Ma B, Tsai CJ, Nussinov R. Biophys. J. 87(1):146-58 (2004)
Mapping Development-Related and Age-Related Chromatin Remodeling by a High Throughput ChIP-HPLC Approach Valya R. Russanova, Tazuko H. Hirai, Andrei V. Tchernov and Bruce H. Howard J. Gerontology 59:1234-1243 (2004)
An Example of Slow Convergence of the Bootstrap in High Dimensions. Troendle J.F.; Korn E.L.; McShane L.M. The American Statistician 58(1): 25-29 (2004)

Discriminating the Helical Forms of Peptides by NMR and Molecular Dynamics Simulation Daron I. Freedberg, Richard M. Venable, Angelo Rossi, Thomas E. Bull, and Richard W. Pastor. J. Am. Chem. Soc 126:10478-10484 (2004)
Impact of Azaproline on Peptide Conformation Ye Che and Garland Marshall. J. Org. Chem 69 (26): 9030 -9042 (2004)
Reversible proton transfer dynamics in bacteriorhodopsin Lee YS and Krauss M. J. Mol. Stru. 700(3):243-246 (2004)
Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design Karki RG, Tang Y, Burke TR Jr, Nicklaus MC. J Comput Aided Mol Des. 18(12):739-60 (2004)
Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms Robert J Clifford, Michael N Edmonson, Cu Nguyen, Kenneth J Buetow. Bioinformatics 20(7):1006-1014 (2004)
Controlling the number of false discoveries: application to high-dimensional genomic data Korn EL, Troendle JF, McShane LM, and Simon R. Journal of Statistical Planning and Infe 124(2):379-398 (2004)
Pressure-Based Long-Range Correction for Lennard-Jones Interactions in Molecular Dynamics Simulations: Application to Alkanes and Interfaces Patrick Lague, Richard W. Pastor, Bernard R Brooks. J. Phys. Chem. B 108:363-368 (2004)
Characterization of the conformational state and flexibility of HIV-1 glycoprotein gp120 core domain Pan Y, Ma B, Keskin O, Nussinov R. J Biol Chem 16;279(29):30523-30 (2004)
Diffusion and Electrophoretic Mobility of Single-Stranded RNA from Molecular Dynamics Simulations In-Chul Yeh and Gerhard Hummer. Biophys. J. 86:681-689 (2004)
LdARF1 in Trafficking and Structural Maintenance of the trans-Golgi Cisternal Network in the Protozoan Pathogen Leishmania donovani Johanna M. Porter-Kelley, Noel J. Gerald, Juan C. Engel, Elodie Ghedin and Dennis M. Dwyer Traffic 5(11):868-883 (2004)
Insights into amyloid structural formation and assembly through computational approaches. Zanuy D, Gunasekaran K, Ma B, Tsai HH, Tsai CJ, Nussinov R. Amyloid. 11(3):143-61 (2004)
Identifying multiple changepoints in heterogeneous binary data with an application to molecular genetics Albert PS, Hunsberger SA, Hu N, Taylor PR. Biostatistics 5(4):515-529 (2004)
A cautionary note on the robustness of latent class models for estimating diagnostic error without a gold standard Albert PS, Dodd LE. Biometrics 60(2):427-35 (2004)
Evaluation of anesthesia effects on [18F]FDG uptake in mouse brain and heart using small animal PET Toyama H, Ichise M, Liow JS, Vines DC, Seneca NM, Modell KJ, Seidel J, Green MV, Innis RB. Nucl. Med. Biol. 31(2):251-6 (2004)
Release factors eRF1 and RF2: a universal mechanism controls the large conformational changes. Ma B, Nussinov R. J Biol Chem. 279(51):53875-85 (2004)
MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli Chen S, Zhang A, Blyn LB, Storz G. J. Bacteriol. 186(20):6689-97 (2004)
Intermolecular Potentials of Mean Force of Amino Acid Side Chain Interactions in Aqueous Medium Hassan SA J. Phys. Chem. B. 108 (50):19501-19509 (2004)

2003 (27 papers)

Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup D. Scholl, J. Kieleczawa, P. Kemp, J. Rush, C. C. Richardson, C. Merril. Adhya5 and I. J. Molineux J. Mol. Biol. 335(5):1151-1171 (2003)

Synthesis and Conformational Analysis of a Locked Analogue of Carbovir Built on a Bicyclo [3.1. 0]-hex-2-enyl template. Choi Y, Sun G, George C, Nicklaus MC, Kelley JA, Marquez VE. Nucleotides Nucleic Acids. 22(12):2077-91 (2003)
Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL Zanuy D, Ma B, Nussinov R. Biophys. J. 84(3):1884-94 (2003)
A peptide with three hyaluronan binding motifs inhibits tumor growth and induces apoptosis Xu XM, Chen Y, Chen J, Yang S, Gao F, Underhill CB, Creswell K, Zhang L. Cancer Res. 63(18):5685-90 (2003)
Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase H. Lee Woodcock, Milan Hodoŝĉek, Paul Sherwood, Yong S. Lee, Henry F. Schaefer III and Bernard R. Brooks Theoretical Chemistry Accounts 109(3):140-148 (2003)
Interdependence of Backbone Flexibility, Residue Conservation, and Enzyme Function: A Case Study on β1, 4-Galactosyltransferase-I Gunasekaran K, Ma B, Ramakrishnan B, Qasba PK, Nussinov R. Biochemistry. 42(13):3674-87 (2003)
A Random Effects Transition Model For Longitudinal Binary Data With Informative Missingness Paul S Albert & Dean Follmann. Statistica Neerlandica 57 Issue 1:100-111, (2003)
Binding and Hydrolysis of Ampicillin in the Active Site of a Zinc Lactamase M. Krauss, N. Gresh, and J. Antony J. Phys. Chem B 107(5):1215-1229 (2003)
A super-linear minimization scheme for the nudged elastic band method Jhih-Wei Chu, Bernhardt L. Trout, Bernard R Brooks J. Chem. Phys. 119:12708-12717 (2003)
Changes in mumps virus gene sequence associated with variability in neurovirulent phenotype Rubin SA, Amexis G, Pletnikov M, Li Z, Vanderzanden J, Mauldin J, Sauder C, Malik T, Chumakov K, Carbone KM. J. Virol. 77(21):11616-24 (2003)
On the kinematics of protein folding Sean Cahill, Michael Cahill, Kevin Cahill. J. Comp. Chem Volume 24, Issue 11: Pages 1364-1370 (2003)
Triggering loops and enzyme function: identification of loops that trigger and modulate movements Gunasekaran K, Ma B, Nussinov R. J Mol Biol. 332(1):143-59 (2003)
Characterization of a New γ TuRC Subunit with WD Repeats Ruwanthi N. Gunawardane, Ona C. Martin, and Yixian Zheng Mol. Biol. Cell 14(3):1017-1026 (2003)
The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29. Zanuy D, Nussinov R. J Mol Biol. 329(3):565-84 (2003)
Docking of Protein-Protein Complexes on the Basis of Highly Ambiguous Intermolecular Distance Restraints Derived from 1HN/15N Chemical Shift Mapping and Backbone 15N/1H Residual Dipolar Couplings Using Conjoined Rigid Body/Torsion Angle Dynamics G. Marius Clore and Charles D. Schwieters J. Am. Chem. Soc. 125(10):2902-2912 (2003)
Modeling tumor growth with random onset Albert PS, Shih JH. Biometrics 59(4):897-906 (2003)
Molecular dynamics simulations of the unfolding of β2-microglobulin and its variants Ma B, Nussinov R. Protein Eng. 16(8):561-75 (2003)
Application of NMR, molecular simulation, and hydrodynamics to conformational analysis of trisaccharides Dixon AM, Venable R, Widmalm G, Bull TE, Pastor RW. Biopolymers 69(4):448-60 (2003)
A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy Wu X, Milne JL, Borgnia MJ, Rostapshov AV, Subramaniam S, Brooks BR. J Struct Biol. 141(1):63-76 (2003)

Lathosterolosis: an inborn error of human and murine cholesterol synthesis due to lathosterol 5-desaturase deficiency Krakowiak PA, Wassif CA, Kratz L, Cozma D, Kovárová M, Harris G, Grinberg A, Yang Y, Hunter AG, Tsokos M, Kelley RI, Porter FD. Hum. Mol. Genet. 12(13):1631-41 (2003)
Transcriptome analysis of mouse stem cells and early embryos. Sharov AA, Piao Y, Matoba R, Dudekula DB, Qian Y, VanBuren V, Falco G, Martin PR, Stagg CA, Bassey UC, Wang Y, Carter MG, Hamatani T, Aiba K, Akutsu H, Sharova L, Tanaka TS, Kimber WL, Yoshikawa T, Jaradat SA, Pantano S, Nagaraja R, Boheler KR, Taub D, Hodes RJ, Longo DL, Schlessinger D, Keller J, Klotz E, Kelsoe G, Umezawa A, Vescovi AL, Rossant J, Kunath T, Hogan BL, Curci A, D'Urso M, Kelso J, Hide W, Ko MS. PLoS Biol. 1(3):E74 (2003)
Parallel computation for coefficients of determination in the context of multivariate gene-expression analysis Edward B Suh, Daniel E Russ, Edward R Dougherty, Seungchan Kim, Michael L Bittner, Yidong Chen, Robert L. Martino in Biocomputing, editor Phillip A Laplante (2003)
The influenza A virus PB1-F2 protein targets the inner mitochondrial membrane via a predicted basic amphipathic helix that disrupts mitochondrial function Gibbs JS, Malide D, Hornung F, Bennink JR, Yewdell JW. J. Virol. 77(13):7214-24 (2003)
Direct Observation of the Folding and Unfolding of a Hairpin in Explicit Water through Computer Simulation Xiongwu Wu, Shaomeng Wang, and Bernard R. Brooks. J. Am. Chem. Soc. 124(19):5282-3 (2003)
Microarray reveals differences in both tumors and vascular specific gene expression in de novo CD5+ and CD5− diffuse large B-cell lymphomas Tohru Kobayashi, Motoko Yamaguchi, Seungchan Kim, Jun Morikawa, Shoko Ogawa, Satoshi Ueno, Edward Suh, Edward Dougherty, Ilya Shmulevich, Hiroshi Shiku, and Wei Zhang Cancer Res. 63:60 (2003)

Hydrogen bonding interactions between aldose reductase complexed with NADP(H) and inhibitor tolrestat studied by molecular dynamics simulations and binding assay Lee YS, Hodoscek M, Kador PF, Sugiyama K. Chem. Biol. Interact 143-144:307-16 (2003)
Cyclin E expression during development in Caenorhabditis elegans Brodigan TM, Liu J, Park M, Kipreos ET, Krause M. Dev. Biol. 254(1):102-115 (2003)

2002 (17 papers)

A preliminary transcriptome map of non-small cell lung cancer Fujii T, Dracheva T, Player A, Chacko S, Clifford R, Strausberg RL, Buetow K, Azumi N, Travis WD, Jen J. Cancer Res. 62(12):3340-6 (2002)
The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs Zhang A, Wassarman KM, Ortega J, Steven AC, Storz G. Mol. Cell 9(1):11-22 (2002)
Features of the NIH ATLAS Small Animal PET Scanner and Its Use with a Coaxial Small Animal Volume CT Scanner Seidel J, Vacquero JJ, Pascua J, Desco M, Johnson CA, Green M IEEE International Symposium on Biomedic, Washington, DC, 2002:TP-P1.9 (2002)
Hydrophobicity Maps of the N-Peptide Coiled Coil of HIV-1 gp41 Xavier Siebert and Gerhard Hummer Biochemistry 41(9):2956-2961 (2002)
A Latent Autoregressive Model for Longitudinal Binary Data Subject to Informative Missingness Albert, PS, Follmann, DA, Wang, SA, Suh, EB. Biometrics 58 Issue 3:631-642 (2002)
Micelle-bound conformation of a hairpin-forming peptide: combined NMR and molecular dynamics study Dixon AM, Venable RM, Pastor RW, Bull TE. Biopolymers 65(4):284-98 (2002)
Structure Activity of 3-Aryl-1, 3-diketo-Containing Compounds as HIV-1 Integrase Inhibitors1 Godwin C. G. Pais, Xuechun Zhang, Christophe Marchand, Nouri Neamati, Kiriana Cowansage, Evguenia S. Svarovskaia, Vinay K. Pathak, Yun Tang, Marc Nicklaus, Yves Pommier, and Terrence R. Burke, Jr. J. Med. Chem. 45(15):3184-3194 (2002)
Isolation and sequencing of a putative promoter region of the murine G protein beta 1 subunit (GNB1) gene Kitanaka J, Kitanaka N, Takemura M, Wang XB, Hembree CM, Goodman NL, Uhl GR. DNA Seq. 13(1):39-45 (2002)
Parametric and semiparametric approaches to testing for seasonal trend in serial count data Hunsberger S, Albert PS, Follmann DA, Suh E. Biostatistics. 3(2):289-98 (2002)
Fast-growth Thermodynamic Integration: Results for Sodium Ion Hydration G. Hummer Molecular Simulation 28:81-90 (2002)

Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent Yeh IC, Hummer G. J Am Chem Soc. 124(23):6563-8 (2002)
Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate development Chen L, Segal D, Hukriede NA, Podtelejnikov AV, Bayarsaihan D, Kennison JA, Ogryzko VV, Dawid IB, Westphal H. PNAS 99(22):14320-5 (2002)
Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Aβ_16-22, Aβ_16-35, and Aβ_10-35): Sequence effects Buyong Ma and Ruth Nussinov PNAS 99(22):14126-14131 (2002)
Ixolaris, a novel recombinant tissue factor pathway inhibitor (TFPI) from the salivary gland of the tick, Ixodes scapularis: identification of factor X and factor Xa as scaffolds for the inhibition of factor VIIa/tissue factor complex Francischetti IM, Valenzuela JG, Andersen JF, Mather TN, Ribeiro JM. Blood 99(10):3602-12 (2002)
Assembly, verification, and initial annotation of the NIA mouse 7.4 K cDNA clone set VanBuren V, Piao Y, Dudekula DB, Qian Y, Carter MG, Martin PR, Stagg CA, Bassey UC, Aiba K, Hamatani T, Kargul GJ, Luo AG, Kelso J, Hide W, Ko MS. Genome Res. 12(12):1999-2003 (2002)
Mutant deoxynucleotide carrier is associated with congenital microcephaly Rosenberg MJ, Agarwala R, Bouffard G, Davis J, Fiermonte G, Hilliard MS, Koch T, Kalikin LM, Makalowska I, Morton DH, Petty EM, Weber JL, Palmieri F, Kelley RI, Schaffer AA, Biesecker LG. Nat Genet. 32(1):175-9 (2002)
The neurogenetics of mucolipidosis type IV G. Altarescu, MD, M. Sun, MD, PhD, D. F. Moore, MD, PhD, DIC, J. A. Smith, MD, E. A. Wiggs, PhD, B. I. Solomon, MS, N. J. Patronas, MD, K. P. Frei, MD, S. Gupta, MD, C. R. Kaneski, MS, O. W. Quarrell, MD, S. A. Slaugenhaupt, PhD, E. Goldin, PhD and R. Schiffmann, MD Neurology 59:306-313 (2002)

2001 (14 papers)

Identification of fifteen novel mutations and genotype-phenotype relationship in Fabry disease Altarescu GM, Goldfarb LG, Park KY, Kaneski C, Jeffries N, Litvak S, Nagle JW, Schiffmann R. Clin. Genet. 60(1):46-51 (2001)
Circularly permuted proteins in the protein structure database Jongsun Jung and Byungkook Lee. Protein Science 10:1881-1886 (2001)
Limited heterogeneity of T cell receptor BV usage in aplastic anemia Zeng W, Maciejewski JP, Chen G, Young NS. J. Clin. Invest. 108(5):765-73 (2001)
Molecular Dynamics Simulations of Octyl Glucoside Micelles: Dynamic Properties Stephen Bogusz, Richard M. Venable, and Richard W. Pastor J. Phys. Chem. 105(35):8312-8321 (2001)
ERGL, a novel gene related to ERGIC-53 that is highly expressed in normal and neoplastic prostate and several other tissues Yerushalmi N, Keppler-Hafkemeyer A, Vasmatzis G, Liu XF, Olsson P, Bera TK, Duray P, Lee B, Pastan I. Gene 265(1-2):55-60 (2001)

Simultaneous Determination of Orientational and Order Parameter Distributions from NMR Spectra of Partially Oriented Model Membranes Edward Sternin, Hartmut Schafer, Ivan V. Polozov and Klaus Gawrisch. J. Mag. Res 149(1): 110-113 (2001)
Parallel Computing Methods for Analyzing Gene Expression Relationships Edward B. Suh, Edward R. Dougherty, Seungchan Kim, Daniel E. Russ, and Robert L. Martino Proc. SPIE 4266:213-221 (2001)
Lowering the isoelectric point of the Fv portion of recombinant immunotoxins leads to decreased nonspecific animal toxicity without affecting antitumor activity Onda M, Nagata S, Tsutsumi Y, Vincent JJ, Wang Q, Kreitman RJ, Lee B, Pastan I. Cancer Res. 61(13):5070-7 (2001)
Cloning, mRNA distribution, and functional expression of an avian counterpart of the chemokine receptor/HIV coreceptor CXCR4 Liang TS, Hartt JK, Lu S, Martins-Green M, Gao JL, Murphy PM. J. Leukoc. Biol. 69(2):297-305 (2001)
Fast-growth thermodynamic integration: Error and efficiency analysis G. Hummer J. Chem. Phys. 114(17):7330 (2001)
Genomic Organization of the Murine G Protein (3 Subunit Genes and Related Processed Pseudogenes J. Kitanaka, XB Wang, N Kitanaka, CM Hembree, GR Uhl DNA Sequence 12:345-354 (2001)

PET, CT, and MR Image Registration of the Rat Brain and Skull Juan José Vaquero, Manuel Desco, Javier Pascau, Andrés Santos, E, Injae Lee, Jürgen Seidel, and Michael V. Green IEEE Transactions on Nuclear Science 48(4):1440-1445 (2001)
Crystal structure of the 14-3-3ζ: serotonin N-acetyltransferase complex: a role for scaffolding in enzyme regulation Obsil T, Ghirlando R, Klein DC, Ganguly S, Dyda F. Cell 105(2):257-67 (2001)
A novel myeloid-restricted zebrafish CCAAT/enhancer-binding protein with a potent transcriptional activation domain Lyons SE, Shue BC, Oates AC, Zon LI, Liu PP. Blood 97(9):2611-7 (2001)

2000 (16 papers)

Immunomorphometric Study of Rat Renal Inner Medulla Raymond Mejia and James B Wade Am. J. Physiol. - Renal Physiol. 10.1152:ajprenal.00340.2000 (2000)
Structure and Promoter Analysis of the Human unc-33-like Phosphoprotein Gene Tatsuya Matsuo, Jimmy K. Stauffer, Robert L. Walker , Paul Meltzer , and Carol J. Thiele J. Biol. Chem. 275(22):16560-16568 (2000)
Multiple quantum solid-state NMR indicates a parallel, not antiparallel, organization of beta-sheets in Alzheimer's beta-amyloid fibrils. Antzutkin ON, Balbach JJ, Leapman RD, Rizzo NW, Reed J, Tycko R. PNAS 97(24):13045-50 (2000)

Characterization and Sequencing of Prototypic Human T-Lymphotropic Virus Type 1 (HTLV-1) from an HTLV-1/2 Seroindeterminate Patient Allen Waziri, Samantha S. Soldan, Michael D. Graf, Jim Nagle, and Steven Jacobson J. Virol. 74(5):2178-2185 (2000)
Amyloid fibril formation by Aβ16-22, a seven-residue fragment of the Alzheimer's beta-amyloid peptide, and structural characterization by solid state NMR. Balbach JJ, Ishii Y, Antzutkin ON, Leapman RD, Rizzo NW, Dyda F, Reed J, Tycko R. Biochemistry 39(45):13748-59 (2000)
Oligodendrocytes in aging mice lacking myelin-associated glycoprotein are dystrophic but not apoptotic Weiss MD, Hammer J, Quarles RH. J. Neurosci. Res. 62(6):772-80 (2000)
Genomic imbalance in rat mammary gland carcinomas induced by 2-Amino-1-methyl-6-phenylimidazo(4,5-b)pyridine Minshu Yu, Doug-Young Ryu, Elizabeth G. Snyderwine Molecular Carcinogenesis 27(2):76-83 (2000)
Molecular Dynamics Simulations of Octyl Glucoside Micelles: Structural Properties Stephen Bogusz, Richard M. Venable, and Richard W. Pastor J. Phys. Chem. 104(23):5462-5470 (2000)
General nonlinear framework for the analysis of gene interaction via multivariate expression arrays Kim S, Dougherty ER, Bittner ML, Chen Y, Sivakumar K, Meltzer P, Trent JM. J. Biomed. Opt. 5(4):411-24 (2000)
Multivariate measurement of gene expression relationships. Kim S, Dougherty ER, Chen Y, Sivakumar K, Meltzer P, Trent JM, Bittner M. Genomics 67(2):201-9 (2000)
XAGE-1, a new gene that is frequently expressed in Ewing's sarcoma Liu XF, Helman LJ, Yeung C, Bera TK, Lee B, Pastan I. Cancer Res. 60(17):4752-5 (2000)
Bioactive motifs of agouti signal protein Virador VM, Santis C, Furumura M, Kalbacher H, Hearing VJ. Exp. Cell Res. 259(1):54-63 (2000)
Mutation analysis and description of sixteen RSH/Smith-Lemli-Opitz syndrome patients: Polymerase chain reaction-based assays to simplify genotyping Patrycja A. Krakowiak, Ngozi A. Nwokoro, Christopher A. Wassif, Kevin P. Battaile, Magorzata J.M. Nowaczyk, William E. Connor, Cheryl Maslen, Robert D. Steiner, Forbes D. Porter Am. J. Med. Genetics 94(3):214-227 (2000)
Rhesus and pig-tailed macaque parvoviruses: identification of two new members of the erythrovirus genus in monkeys Green SW, Malkovska I, O'Sullivan MG, Brown KE. Virology 269(1):105-12 (2000)
A stage-specific preparation to study the Ca2+-triggered fusion steps of exocytosis: Rationale and perspectives Joshua Zimmerberg, Paul S. Blank, Irina Kolosova, Myoung-Soon Cho, Masahiro Tahara, and Jens R. Coorssen Biochimie 82(4):303-314 (2000)

Theoretical formalism for kinesin motility I. Bead movement powered by single one-headed kinesins. Chen Y. Biophys. J. 78(1):313-21 (2000)

1999 (9 papers)

The zebrafish genome contains two distinct selenocysteine tRNA[Ser]sec genes Xu XM, Zhou X, Carlson BA, Kim LK, Huh TL, Lee BJ, Hatfield DL FEBS Lett. 454(1-2):16-20 (1999)
Characterization of a multicopy family of genes encoding a surface-expressed serine endoprotease in rat Pneumocystis carinii Russian DA, Andrawis-Sorial V, Goheen MP, Edman JC, Vogel P, Turner RE, Klivington DL, Angus CW, Kovacs JA. Proc. Assoc. Am. Physicians 111(4):347-56 (1999)
Asymmetry and direction reversal in fluctuation-induced biased Brownian motion Chen YD, Yan B, Miura R. Phys Rev E Stat Phys Plasmas Fluids Rela 60(4 Pt A):3771-5 (1999)
Novel Genes in the PAGE and GAGE Family of Tumor Antigens Found by Homology Walking in the dbEST Database Ulrich Brinkmann, George Vasmatzis, Byungkook Lee and Ira Pastan Cancer Res. 59:1445-1448 (1999)
Reduction of the nonspecific animal toxicity of anti-Tac(Fv)-PE38 by mutations in the framework regions of the Fv which lower the isoelectric point Onda M, Kreitman RJ, Vasmatzis G, Lee B, Pastan I. J. Immunol. 163(11):6072-7 (1999)

Expression profiling using cDNA microarrays Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. Nat Genet. 21(1 Suppl):10-4 Review. (1999)
Genomic organization and mapping of the human and mouse neuronal β2-nicotinic acetylcholine receptor genes Lueders KK, Elliott RW, Marenholz I, Mischke D, DuPree M, Hamer D. Mamm. Genome 10(9):900-5 (1999)
GalR mutants defective in repressosome formation Geanacopoulos M, Vasmatzis G, Lewis DE, Roy S, Lee B, Adhya S. Genes Dev. 13(10):1251-62 (1999)
Analysis of selenocysteine (Sec) tRNA([Ser]Sec) genes in Chinese hamsters Xu XM, Carlson BA, Kim LK, Lee BJ, Hatfield DL, Diamond AM. Gene 239(1):49-53 (1999)

1998 (2 papers)

Information technology applications in biomedical research Martino, R.L. Kempner, K.M. Johnson, C.A. Information Technology Applications in B ITAB98:28-34 (1998)
Parallel computing strategies for determining viral capsidstructure by cryoelectron microscopy Lanczycki, C.J. Johnson, C.A. Trus, B.L. Conway, J.F. Steven, A.C. Martino, R.L. Computational Science & Engineering, IEE 5(2):76-91 (1998)