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2017 (82 papers)

• Genome-Wide Association Study to Identify Susceptibility Loci That Modify Radiation-Related Risk for Breast Cancer After Childhood Cancer   Lindsay M. Morton Joshua N. Sampson Gregory T. Armstrong et al. J. Natl. Cancer. Inst., DOI: https://doi.org/10.1093/jnci/djx058 (2017)
• Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome  Zhao, Z; Xie, L; Bourne, PE; PLoS ONE, DOI://10.1371/journal.pone.0179936 (2017)
• The Transcription Factor T-bet Limits Amplification of Type I IFN Transcriptome and Circuitry in T Helper 1 Cells  Iwata, S; Mikami, Y; Sun, HW et al. Immunity, DOI://10.1016/j.immuni.2017.05.005 (2017)

• Graphite-Templated Amyloid Nanostructures Formed by A Potential Pentapeptide Inhibitor for Alzheimer's disease: A Combined Study of Real-Time Atomic Force Microscopy and Molecular Dynamics Simulations  Li, N; Jang, H; Yuan, M et al. Langmuir, DOI://10.1021/acs.langmuir.7b00414 (2017)
• Monte Carlo simulations of randomized clinical trials in epilepsy  DM Goldenholz, J Tharayil, R Moss, E Myers, WH Theodore Annals of Clinical and Translational Neurology, DOI: 10.1002/acn3.426 (2017)
• Heightened amygdala responsiveness in s-carriers of 5-HTTLPR genetic polymorphism reflects enhanced cortical rather than subcortical inputs: An MEG study  Luo, Q; Holroyd, T; Mitchell, D et al. Hum Brain Mapp, DOI://10.1002/hbm.23616 (2017)
• Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly  Chereji, RV; Bharatula, V; Elfving, N et al. Nucleic Acids Res., DOI://10.1093/nar/gkx491 (2017)
• High-fidelity PCR enzyme with DNA-binding domain facilitates de novo gene synthesis  Dolgova, AS; Stukolova, OA; 3 Biotech, DOI://10.1007/s13205-017-0745-2 (2017)
• Release of Cytochrome C from Bax Pores at the Mitochondrial Membrane  Zhang, M; Zheng, J; Nussinov, R; Ma, B; Sci Rep, DOI://10.1038/s41598-017-02825-7 (2017)
• Identification and Analysis of Protein Phosphorylation by Mass Spectrometry  DE McNulty, TW Sikorski, RS Annan in 'Analysis of Protein Post-Translational Modifications by , ed John R. Griffiths, Richard D. Unwin. Wiley (2017)
• PDEδ Binding to Ras Isoforms Provides a Route to Proper Membrane Localization  Muratcioglu, S; Jang, H; Gursoy, A; Keskin, O; Nussinov, R; J Phys Chem B, DOI://10.1021/acs.jpcb.7b03035 (2017)
• BACH2 immunodeficiency illustrates an association between super-enhancers and haploinsufficiency  Afzali, B; Grönholm, J; Vandrovcova, J et al. Nat. Immunol., DOI://10.1038/ni.3753 (2017)
• Pathology of callosal damage in ALS: An ex-vivo, 7 T diffusion tensor MRI study   Agustin M. Cardenas, Joelle E. Sarlls, Justin Y. Kwan, Devin Bageac, Zachary S. Gala, Laura E. Danielian, Abhik Ray-Chaudhury, Hao-Wei Wang, Karla L. Miller, Sean Foxley, Saad Jbabdid, Robert C. Welsh, Mary Kay Floeter NeuroImage: Clinical, doi://10.1016/j.nicl.2017.04.024 (2017)
• Unsupervised Joint Mining of Deep Features and Image Labels for Large-Scale Radiology Image Categorization and Scene Recognition  Xiaosong Wang, Le Lu, Hoo-chang Shin, Lauren Kim, Mohammadhadi Bagheri, Isabella Nogues, Jianhua Yao, Ronald M. Summers IEEE Winter Conference on Applications of Computer Vision, DOI 10.1109/WACV.2017.116 (2017)
• Simulating clinical trials with and without intracranial EEG data  Goldenholz D, Tharayil J, Kuzniecky R, et al. Epilepsia Open, DOI: 10.1002/epi4.12038 (2017)

• Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults  Yang, H; Basquin, D; Pauli, D; Oliver, B; BMC Genomics, DOI://10.1186/s12864-017-3755-x (2017)
• Pias3 is necessary for dorso-ventral patterning and visual response of retinal cones but is not required for rod photoreceptor differentiation  Campla, CK; Breit, H; Dong, L; Gumerson, JD; Roger, JE; Swaroop, A; Biol Open, DOI://10.1242/bio.024679 (2017)
• Conformational Changes in Active and Inactive States of Human PP2Cα Characterized by Hydrogen/Deuterium Exchange-Mass Spectrometry  Mazur, SJ; Gallagher, ES; Debnath, S et al. Biochemistry, DOI://10.1021/acs.biochem.6b01220 (2017)
• A Genome-Wide Association Study Using a Custom Genotyping Array Identifies Variants in GPR158 Associated with Reduced Energy Expenditure in American Indians  Piaggi, P; Masindova, I; Muller, YL et al. Diabetes, DOI://10.2337/db16-1565 (2017)
• Molecular codes for cell type specification in Brn3 retinal ganglion cells  Sajgo, S; Ghinia, MG; Brooks, M et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1618551114 (2017)
• A population MRI brain template and analysis tools for the macaque  Seidlitz, J; Sponheim, C; Glen, D et al. Neuroimage, DOI://10.1016/j.neuroimage.2017.04.063 (2017)

• Median Analysis of Repeated Measures Associated with Recurrent Events in Presence of Terminal Event  Sundaram, R; Ma, L; Ghoshal, S; Int J Biostat, DOI://10.1515/ijb-2016-0057 (2017)
• The isomeric preference of an atypical dopamine transporter inhibitor contributes to its selection of the transporter conformation  Abramyan, AM; Stolzenberg, S; Li, Z; Loland, CJ; Noé, F; Shi, L; ACS Chem Neurosci, DOI://10.1021/acschemneuro.7b00094 (2017)
• Behavioral and Neural Sustained Attention Deficits in Disruptive Mood Dysregulation Disorder and Attention-Deficit/Hyperactivity Disorder  Pagliaccio, D; Wiggins, JL; Adleman, NE et al. J Am Acad Child Adolesc Psychiatry, DOI://10.1016/j.jaac.2017.02.008 (2017)
• Synthesis of Dopamine in E.coli Using Plasmid Based Expression System and Its Marked Effect on Host Growth Profiles  Das, A; Verma, A; Mukherjee, KJ; Prep. Biochem. Biotechnol., DOI://10.1080/10826068.2017.1320291 (2017)
• fMRI clustering and false-positive rates  Cox, RW; Chen, G; Glen, DR; Reynolds, RC; Taylor, PA; Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1614961114 (2017)
• Sequence and Structural Analyses Reveal Distinct and Highly Diverse Human CD8(+) TCR Repertoires to Immunodominant Viral Antigens  Chen, G; Yang, X; Ko, A et al. Cell Rep, DOI://10.1016/j.celrep.2017.03.072 (2017)

• H3K4 demethylase KDM5B regulates global dynamics of transcription elongation and alternative splicing in embryonic stem cells  He, R; Kidder, BL; Nucleic Acids Res., DOI://10.1093/nar/gkx251 (2017)
• Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly  Schneider, VA; Graves-Lindsay, T; Howe, K et al. Genome Res., DOI://10.1101/gr.213611.116 (2017)
• FMRI Clustering in AFNI: False-Positive Rates Redux  Cox, RW; Chen, G; Glen, DR; Reynolds, RC; Taylor, PA; Brain Connect, DOI://10.1089/brain.2016.0475 (2017)
• Intrinsic Functional Connectivity of the Central Nucleus of the Amygdala and Bed Nucleus of the Stria Terminalis  Gorka, AX; Torrisi, S; Shackman, AJ; Grillon, C; Ernst, M; Neuroimage, DOI://10.1016/j.neuroimage.2017.03.007 (2017)
• Hydrophobic-Hydrophilic Forces in Protein Folding  Durell, SR; Ben-Naim, A; Biopolymers, DOI://10.1002/bip.23020 (2017)
• Detection of genetic loci associated with plasma fetuin-A: A meta-analysis of genome-wide association studies from the CHARGE Consortium  Jensen, MK; Jensen, RA; Mukamal, KJ et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddx091 (2017)
• A big data approach to the development of mixed-effects models for seizure count data  Tharayil, JJ; Chiang, S; Moss, R; Stern, JM; Theodore, WH; Goldenholz, DM; Epilepsia, DOI://10.1111/epi.13727 (2017)
• Retrospective correction of frequency drift in spectral editing: The GABA editing example  van der Veen, JW; Marenco, S; Berman, KF; Shen, J; NMR Biomed, DOI://10.1002/nbm.3725 (2017)
• Engineering efficient production of itaconic acid from diverse substrates in Escherichia coli  Chang, P; Chen, GS; Chu, HY; Lu, KW; Shen, CR; J. Biotechnol., DOI://10.1016/j.jbiotec.2017.03.026 (2017)
• REEP6 mediates trafficking of a subset of Clathrin-coated vesicles and is critical for rod photoreceptor function and survival  Veleri, S; Nellissery, J; Mishra, B et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddx111 (2017)
• Stable functional networks exhibit consistent timing in the human brain  Chapeton, JI; Inati, SK; Zaghloul, KA; Brain, DOI://10.1093/brain/aww337 (2017)
• Characterization of four arginine kinases in the ciliate Paramecium tetraurelia: Investigation on the substrate inhibition mechanism  Yano, D; Suzuki, T; Hirokawa, S; Fuke, K; Suzuki, T; Int. J. Biol. Macromol., DOI://10.1016/j.ijbiomac.2017.03.133 (2017)

• Gramicidin A Channel Formation Induces Local�Lipid Redistribution II: A 3D Continuum Elastic Model  Sodt, AJ; Beaven, AH; Andersen, OS; Im, W; Pastor, RW; Biophys. J., DOI://10.1016/j.bpj.2017.01.035 (2017)
• Automatic MR prostate segmentation by deep learning with holistically-nested networks   Ruida Cheng ; Holger R. Roth ; Nathan Lay ; Le Lu ; Baris Turkbey ; William Gandler ; Evan S. McCreedy ; Peter Choyke ; Ronald M. Summers ; Matthew J. McAuliffe Proc. SPIE 10133, Medical Imaging 2017, doi:10.1117/12.2254558 (2017)
• Macrophilone A: Structure Elucidation, Total Synthesis, and Functional Evaluation of a Biologically Active Iminoquinone from the Marine Hydroid Macrorhynchia philippina  Zlotkowski, K; Hewitt, WM; Yan, P et al. Org. Lett., DOI://10.1021/acs.orglett.7b00496 (2017)
• Expressed Structurally-stable Inverted Duplicates in Mammalian Genomes as Functional Noncoding Elements  Chen, ZX; Oliver, B; Zhang, YE; Gao, G; Long, M; Genome Biol Evol, DOI://10.1093/gbe/evx054 (2017)
• Korean Pediatric and Adult Head Computational Phantoms and Application to Photon Specific Absorbed Fractions Calculations  Villoing, D; McMillan, D; Kim, KP et al. Radiat Prot Dosimetry, DOI://10.1093/rpd/ncx009 (2017)
• Determining Cysteines Available for Covalent Inhibition Across the Human Kinome  Zhao, Z; Liu, Q; Bliven, S; Xie, L; Bourne, PE; J. Med. Chem., DOI://10.1021/acs.jmedchem.6b01815 (2017)

• The Role of TM5 in Na2 Release and the Conformational Transition of Neurotransmitter:Sodium Symporters toward the Inward-Open State  Stolzenberg, S; Li, Z; Quick, M et al. J. Biol. Chem., DOI://10.1074/jbc.M116.757153 (2017)
• Whole-Exome Sequencing for Diagnosis of Turner Syndrome: Toward Next-Generation Sequencing and Newborn Screening  Murdock, DR; Donovan, FX; Chandrasekharappa, SC et al. J. Clin. Endocrinol. Metab., DOI://10.1210/jc.2016-3414 (2017)
• Predicting drug-drug interactions through drug structural similarities and interaction networks incorporating pharmacokinetics and pharmacodynamics knowledge  Takeda, T; Hao, M; Cheng, T; Bryant, SH; Wang, Y; J Cheminform, DOI://10.1186/s13321-017-0200-8 (2017)
• Modulation of opioid receptor affinity and efficacy via N-substitution of 9β-hydroxy-5-(3-hydroxyphenyl)morphan: Synthesis and computer simulation study  Truong, PM; Hassan, SA; Lee, YS et al. Bioorg. Med. Chem., DOI://10.1016/j.bmc.2017.02.064 (2017)
• Computational Study of the Forces Driving Aggregation of Ultrasmall Nanoparticles in Biological Fluids  Hassan, SA ACS Nano, DOI://10.1021/acsnano.7b00981 (2017)
• Identification of β-Catenin-Interacting Proteins in Nuclear Fractions of Native Rat Collecting Duct Cells  Hwang, JR; Chou, CL; Medvar, B; Knepper, MA; Jung, HJ; Am. J. Physiol. Renal Physiol., DOI://10.1152/ajprenal.00054.2017 (2017)
• Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation  Koren, S; Walenz, BP; Berlin, K; Miller, JR; Bergman, NH; Phillippy, AM; Genome Res., DOI://10.1101/gr.215087.116 (2017)
• BTBD18 Regulates a Subset of piRNA-Generating Loci through Transcription Elongation in Mice  Zhou, L; Canagarajah, B; Zhao, Y et al. Dev. Cell, DOI://10.1016/j.devcel.2017.02.007 (2017)
• Dynamic Role of trans Regulation of Gene Expression in Relation to Complex Traits  Yao, C; Joehanes, R; Johnson, AD et al. Am. J. Hum. Genet., DOI://10.1016/j.ajhg.2017.02.003 (2017)
• Effect of Detergent Micelle Environment on P-glycoprotein (ABCB1)-Ligand Interactions  Shukla, S; Abel, B; Chufan, EE; Ambudkar, SV; J. Biol. Chem., DOI://10.1074/jbc.M116.771634 (2017)
• Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome  Bickhart, DM; Rosen, BD; Koren, S et al. Nat. Genet., DOI://10.1038/ng.3802 (2017)
• SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation  Kidder, BL; Hu, G; Cui, K; Zhao, K; Epigenetics Chromatin, DOI://10.1186/s13072-017-0115-7 (2017)

• FMRI Clustering in AFNI: False Positive Rates Redux  Robert W. Cox, Gang Chen, Daniel R. Glen, Richard C. Reynolds, Paul A. Taylor Brain Connectivity, DOI: 10.1089/brain.2016.047 (2017)
• Circulating tumor cells capture disease evolution in advanced prostate cancer  Lack, J; Gillard, M; Cam, M; Paner, GP; VanderWeele, DJ; J Transl Med, DOI://10.1186/s12967-017-1138-3 (2017)
• The effects of shared information on semantic calculations in the gene ontology  Bible, PW; Sun, HW; Morasso, MI; Loganantharaj, R; Wei, L; Comput Struct Biotechnol J, DOI://10.1016/j.csbj.2017.01.009 (2017)
• Quaternary contact in the initial interaction of CD4 with the HIV-1 envelope trimer  Liu, Q; Acharya, P; Dolan, MA et al. Nat. Struct. Mol. Biol., DOI://10.1038/nsmb.3382 (2017)
• Epigenetic Patterns in Blood Associated With Lipid Traits Predict Incident Coronary Heart Disease Events and Are Enriched for Results From Genome-Wide Association Studies  Hedman, ÅK; Mendelson, MM; Marioni, RE et al. Circ Cardiovasc Genet, DOI://10.1161/CIRCGENETICS.116.001487 (2017)
• Circulating miRNA Associated with Posttraumatic Stress Disorder in a Cohort of Military Combat Veterans  Christiana G. Martin, Hyungsuk Kim, Sijung Yun, Whitney Livingston, Joseph Fetta, Vincent Mysliwiec, Tristin Baxter, Jessica M. Gill Psychiatry Research, doi://10.1016/j.psychres.2017.01.081 (2017)

• The dynamic mechanism of RASSF5 and MST kinase activation by Ras  Liao, TJ; Jang, H; Tsai, CJ; Fushman, D; Nussinov, R; Phys Chem Chem Phys, DOI://10.1039/c6cp08596b (2017)
• Multivariate meta-analysis with an increasing number of parameters  Boca, SM; Pfeiffer, RM; Sampson, JN; Biom J, DOI://10.1002/bimj.201600013 (2017)
• MNase-Sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers  Chereji, RV; Ocampo, J; Clark, DJ; Mol. Cell, DOI://10.1016/j.molcel.2016.12.009 (2017)
• Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing  Jansen, IE; Ye, H; Heetveld, S et al. Genome Biol., DOI://10.1186/s13059-017-1147-9 (2017)
• Amyloid β Ion Channels in a Membrane Comprising Brain Total Lipid Extracts  Lee, J; Kim, YH; T Arce, F et al. ACS Chem Neurosci, DOI://10.1021/acschemneuro.7b00006 (2017)
• Secretory Expression and Characterization of Chinese Narcissus GNA-Like Lectin in Pichia pastoris  Li, X; Zhang, P; Zhang, N et al. Appl. Biochem. Biotechnol., DOI://10.1007/s12010-017-2408-5 (2017)

• Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm  Zimin, AV; Puiu, D; Luo, MC et al. Genome Res., DOI://10.1101/gr.213405.116 (2017)
• Differential methylation of genes in individuals exposed to maternal diabetes in utero  Chen, P; Piaggi, P; Traurig, M et al. Diabetologia, DOI://10.1007/s00125-016-4203-1 (2017)
• Frequent inactivating germline mutations in DNA repair genes in patients with Ewing sarcoma  Brohl, AS; Patidar, R; Turner, CE et al. Genet. Med., DOI://10.1038/gim.2016.206 (2017)
• Dose coefficients for ICRP reference pediatric phantoms exposed to idealised external gamma fields  Chang, LA; Simon, SL; Jorgensen, TJ; Schauer, DA; Lee, C; J Radiol Prot, DOI://10.1088/1361-6498/aa559e (2017)
• SDHD promoter mutations ablate GABP transcription factor binding in melanoma  Zhang, T; Xu, M; Makowski, MM et al. Cancer Res., DOI://10.1158/0008-5472.CAN-16-0919 (2017)
• Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach  Mendelson, MM; Marioni, RE; Joehanes, R et al. PLoS Med., DOI://10.1371/journal.pmed.1002215 (2017)

• Designer Drugs 2.0  Huestis, MA; Tyndale, RF; Clin. Pharmacol. Ther., DOI://10.1002/cpt.575 (2017)
• Sequence of Reston Virus Isolate AZ-1435, an Ebolavirus Isolate Obtained during the 1989-1990 Reston Virus Epizootic in the United States  Cornish, JP; Diaz, L; Ricklefs, SM et al. Genome Announc, DOI://10.1128/genomeA.01448-16 (2017)
• Genetic stability of genome-scale deoptimized RNA virus vaccine candidates under selective pressure  Le Nouën, C; McCarty, T; Brown, M et al. Proc. Natl. Acad. Sci. U.S.A., DOI://10.1073/pnas.1619242114 (2017)
• Mapping Polyclonal HIV-1 Antibody Responses via Next-Generation Neutralization Fingerprinting  Doria-Rose, NA; Altae-Tran, HR; Roark, RS et al. PLoS Pathog., DOI://10.1371/journal.ppat.1006148 (2017)
• Data integration in physiology using Bayes' rule and minimum Bayes' factors: deubiquitylating enzymes in the renal collecting duct  Xue, Z; Chen, JX; Zhao, Y; Medvar, B; Knepper, MA; Physiol. Genomics, DOI://10.1152/physiolgenomics.00120.2016 (2017)
• Structural studies of influenza virus RNPs by electron microscopy indicate molecular contortions within NP supra-structures  Gallagher, JR; Torian, U; McCraw, DM; Harris, AK; J. Struct. Biol., DOI://10.1016/j.jsb.2016.12.007 (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)

2016 (324 papers)

• 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)
• 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)
• 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)
• 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)
• 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)
• 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)
• 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)

• 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)
• 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)
• 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)
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• MultiDimensional ClinOmics for Precision Therapy of Children and Adolescent Young Adults with Relapsed and Refractory Cancer: A Report from the Center for Cancer Research  Wendy Chang, Andrew Brohl, Rajesh Patidar, Sivasish Sindiri, Jack F. Shern, Jun S. Wei, Young K. Song, Marielle E Yohe, Berkley E. Gryder, Shile Zhang, Kathleen A Calzone, Nityashree Shivaprasad, Xinyu Wen, Thomas Badgett, Markku Miettinen, Kip R Hartman, James C League-Pascual, Toby Trahair, Brigitte C. Widemann, Melinda S. Merchant, Rosandra N Kaplan, Jimmy C Lin, and Javed Khan Clinical Cancer Research, doi: 10.1158/1078-0432.CCR-15-2717 (2016)
• Erratum: The evolutionary turnover of recombination hot spots contributes to speciation in mice  Smagulova, F; Brick, K; Pu, Y; Camerini-Otero, RD; Petukhova, GV; Genes Dev., DOI://10.1101/gad.280677.116 (2016)

• Cajal bodies are linked to genome conformation   Qiuyan Wang, Iain A. Sawyer, Myong-Hee Sung, David Sturgill, Sergey P. Shevtsov, Gianluca Pegoraro, Ofir Hakim, Songjoon Baek, Gordon L. Hager & Miroslav Dundr Nature Communications, doi:10.1038/ncomms10966 (2016)
• Cryo-electron Microscopy Structures of Chimeric Hemagglutinin Displayed on a Universal Influenza Vaccine Candidate  Erin E. H. Tran, Kira A. Podolsky, Alberto Bartesaghi, Oleg Kuybeda, Giovanna Grandinetti, Teddy John Wohlbold, Gene S. Tan, Raffael Nachbagauer, Peter Palese, Florian Krammer, Sriram Subramaniam mBio, doi: 10.1128/mBio.00257-16 (2016)
• Subtle in-scanner motion biases automated measurement of brain anatomy from in vivo MRI  Aaron Alexander-Bloch, Liv Clasen, Michael Stockman, Lisa Ronan, Francois Lalonde, Jay Giedd and Armin Raznahan Human Brain Mapping, DOI: 10.1002/hbm.23180 (2016)
• Detection of benign prostatic hyperplasia nodules in T2W MR images using fuzzy decision forest  Nathan Lay ; Sabrina Freeman ; Baris Turkbey ; Ronald Summers SPIE Proceedings, doi:10.1117/12.2217906 (2016)
• 2.3 Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition  Soojay Banerjee, Alberto Bartesaghi, Alan Merk, Prashant Rao, Stacie L. Bulfer, Yongzhao Yan, Neal Green, Barbara Mroczkowski, R. Jeffrey Neitz, Peter Wipf, Veronica Falconieri, Raymond J. Deshaies, Jacqueline L. S. Milne, Donna Huryn, Michelle Arkin, Sriram Subramaniam Science, DOI: 10.1126/science.aad7974 (2016)
• Design and synthesis of small molecule-sulfotyrosine mimetics that inhibit HIV-1 entry  Dogo-Isonagie, C; Lee, SL; Lohith, K et al. Bioorg. Med. Chem., DOI://10.1016/j.bmc.2016.02.044 (2016)

• Detection and Whole-Genome Sequencing of Carbapenemase-Producing Aeromonas hydrophila Isolates from Routine Perirectal Surveillance Culture  Hughes, HY; Conlan, SP; Lau, AF et al. J. Clin. Microbiol., DOI://10.1128/JCM.03229-15 (2016)
• Whole-Exome Sequencing Analyses of Inflammatory Bowel Disease-Associated Colorectal Cancers  Robles, AI; Traverso, G; Zhang, M et al. Gastroenterology, DOI://10.1053/j.gastro.2015.12.036 (2016)
• caOmicsV: an R package for visualizing multidimensional cancer genomic data  Zhang H, Meltzer PS, Davis SR BMC Bioinformatics, DOI://10.1186/s12859-016-0989-6 (2016)
• A molecular threshold for effector CD8(+) T cell differentiation controlled by transcription factors Blimp-1 and T-bet  Xin, A; Masson, F; Liao, Y et al. Nat. Immunol., DOI://10.1038/ni.3410 (2016)
• Brain-Derived Neurotrophic Factor Val66Met Polymorphism Affects the Relationship Between an Anxiety-Related Personality Trait and Resting Regional Cerebral Blood Flow  Wei, SM; Eisenberg, DP; Nabel, KG et al. Cereb. Cortex, DOI://10.1093/cercor/bhw072 (2016)
• Redox-induced activation of the proton pump in the respiratory complex I  Vivek Sharma, Galina Belevich, Ana P. Gamiz-Hernandez, Tomasz Ròg, Ilpo Vattulainen, Marina L. Verkhovskaya Mårten Wikström, Gerhard Hummer, and Ville R. I. Kaila PNAS, doi://10.1073/pnas.1503761112 (2016)
• High-level expression and characterization of a novel serine protease in Pichia pastoris by multi-copy integration  Min Shu, Wei Shen, Shihui Yang , Xiaojuan Wang , Fei Wang , Yaping Wang , Lixin Ma Enzyme and Microbioal Technology, doi:10.1016/j.enzmictec.2016.06.007 (2016)
• NMDA Receptors Multiplicatively Scale Visual Signals and Enhance Directional Motion Discrimination in Retinal Ganglion Cells   Poleg-Polsky A, Diamond JS Neuron, DOI://10.1016/j.neuron.2016.02.013 (2016)
• MEGSA: A Powerful and Flexible Framework for Analyzing Mutual Exclusivity of Tumor Mutations  Xing Hua, Paula L. Hyland, Jing Huang, Lei Song, Bin Zhu, Neil E. Caporaso, Maria Teresa Landi, Nilanjan Chatterjee, and Jianxin Shi Am J. Hum. Genet. , doi://10.1016/j.ajhg.2015.12.021 (2016)
• Characterizing the Covalent Targets of a Small Molecule Inhibitor of the Lysine Acetyltransferase P300  Shrimp JH, Sorum AW, Garlick JM, Guasch L, Nicklaus MC, Meier JL ACS Med Chem Lett, DOI://10.1021/acsmedchemlett.5b00385 (2016)
• Critical Nucleus Structure and Aggregation Mechanism of the C-terminal Fragment of Copper-Zinc Superoxide Dismutase Protein  Zou Y, Sun Y, Zhu Y, Ma B, Nussinov R, Zhang Q ACS Chem Neurosci, DOI://10.1021/acschemneuro.5b00242 (2016)
• Seeking Optimal Region-Of-Interest (ROI) Single-Value Summary Measures for fMRI Studies in Imaging Genetics  Tong, Y; Chen, Q; Nichols, TE et al. PLoS ONE, DOI://10.1371/journal.pone.0151391 (2016)

• Microscopic interpretation of folding φ-values using the transition path ensemble  Robert B. Best and Gerhard Hummer PNAS, doi: 10.1073/pnas.1520864113 (2016)
• Structural insights of a PI3K/mTOR dual inhibitor with the morpholino-triazine scaffold  Takako Takeda, Yanli Wang , Stephen H. Bryant J. Computer-Aided Molecular Design, doi://10.1007/s10822-016-9905-4 (2016)
• Modulation of Folding Internal Friction by Local and Global Barrier Heights  Wenwei Zheng, David de Sancho, and Robert B. Best J. Phys. Chem. Letters, DOI: 10.1021/acs.jpclett.6b00329 (2016)
• The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo  Josefina Ocampo, Razvan V. Chereji, Peter R. Eriksson and David J. Clark Nucleic Acids Research, doi://10.1093/nar/gkw068 (2016)
• Biointeractions of ultrasmall glutathione-coated gold nanoparticles: effect of small size variations  Alioscka A. Sousa, Sergio A. Hassan, Luiza L. Knittel, Andrea Balbo, Maria A. Aronova, Patrick H. Brown, Peter Schuck and Richard D. Leapman Nanoscale, DOI: 10.1039/C5NR07642K (2016)
• The ubiquitin ligase Ubr4 controls stability of podocin/MEC-2 supercomplexes  Rinschen, MM; Bharill, P; Wu, X et al. Hum. Mol. Genet., DOI://10.1093/hmg/ddw016 (2016)

• Mucolipidosis types II and III and non-syndromic stuttering are associated with different variants in the same genes   Raza, MH; Domingues, CE; Webster, R et al. Eur. J. Hum. Genet., DOI://10.1038/ejhg.2015.154 (2016)
• 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)
• Chemical shift guided homology modeling of larger proteins  Yang Shen and Ad Bax Nat Methods., doi: 10.1038/nmeth.3437 (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)
• 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)
• Hyperphopsphorylation Promotes Tau Aggregation by Modulating 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)
• 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)
• 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 (344 papers)

• Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens PS006  Rocío M. Gamez, Fernando Rodríguez, Johan F. Bernal, Richa Agarwala, David Landsman, Leonardo Mariño-Ramírez Genome Announc., doi: 10.1128/genomeA.00329-16 (2015)
• 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)
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• Distinct profiles for mitochondrial t-RNAs and small nucleolar RNAs in locally invasive and metastatic colorectal cancer  Lai Xu, Joseph Ziegelbauer, Rong Wang, Wells W Wu, Rong-Fong Shen, Hartmut H Juhl, Yaqin Zhang, and Amy S Rosenberg Clinical Cancer Research, doi: 10.1158/1078-0432.CCR-15-0737 (2015)
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• 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 (194 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)
• Prospective Associations of Coronary Heart Disease Loci in African Americans Using the MetaboChip: The PAGE Study  Nora Franceschini, Yijuan Hu, Alex P. Reiner, et al. PLoS One, DOI: 10.1371/journal.pone.0113203 (2014)

• Behçet disease-associated MHC class I residues implicate antigen binding and regulation of cell-mediated cytotoxicity.  Ombrello MJ, Kirino Y, de Bakker PI, Gül A, Kastner DL, Remmers EF PNAS, doi: 10.1073/pnas.1406575111 (2014)
• Integrated transcriptome analysis of mouse spermatogenesis  Margolin G, Khil PP, Kim J, Bellani MA, Camerini-Otero RD BMC Genomics, doi: 10.1186/1471-2164-15-39 (2014)
• Integromic Analysis of Genetic Variation and Gene Expression Identifies Networks for Cardiovascular Disease Phenotypes  Chen Yao, Brian H. Chen, Roby Joehanes, et al. Circulation, doi: 10.1161/CIRCULATIONAHA.114.010696 (2014)
• Sex- and Tissue-Specific Functions of Drosophila Doublesex Transcription Factor Target Genes  Clough E, Jimenez E, Kim YA, Whitworth C, Neville MC, Hempel LU, Pavlou HJ, Chen ZX, Sturgill D, Dale RK, Smith HE, Przytycka TM, Goodwin SF, Van Doren M, Oliver B Dev. Cell, doi: 10.1016/j.devcel.2014.11.021 (2014)
• Leveraging Local identity-by-descent increases the power of Case/Control GWAS with Related Individuals  Joshua N Sampson, Bill Wheeler, Peng Li, Jianxin Shi Ann Appl Stat. 8(2):974-998. (2014)
• Genome sequencing accuracy by RCA-seq versus long PCR template cloning and sequencing in identification of human papillomavirus type 58  Wang X, Li Y, Ni T, Xie X, Zhu J, Zheng ZM Cell Biosci. , doi: 10.1186/2045-3701-4-5 (2014)

• Complex interactions of transcription factors in mediating cytokine biology in T cells  Li P, Spolski R, Liao W, Leonard WJ. Immunol Rev, doi: 10.1111/imr.12199. (2014)
• Opposing actions of IL-2 and IL-21 on Th9 differentiation correlate with their differential regulation of BCL6 expression  Liao W, Spolski R, Li P, Du N, West EE, Ren M, Mitra S, Leonard WJ. PNAS, doi: 10.1073/pnas.1301138111 (2014)
• Enhanced potency of a broadly neutralizing HIV-1 antibody in vitro improves protection against lentiviral infection in vivo.  Rudicell RS1, Kwon YD, Ko SY et al. Journal of Virology, doi: 10.1128/JVI.02213-14 (2014)
• High Accuracy of Karplus Equations for Relating Three-Bond J Couplings to Protein Backbone Torsion Angles  Fang Li, Jung Ho Lee, Alexander Grishaev, Jinfa Ying and Ad Bax Eur. J. Chem. Phys. Chem. , DOI: 10.1002/cphc.201402704 (2014)
• Challenges and solutions for gene identification in the presence of familial locus heterogeneity  Atteeq U Rehman, Regie Lyn P Santos-Cortez et al. Eur. J. Human Genetics, doi: 10.1038/ejhg.2014.266 (2014)
• Linear Energy Relationships in Ground State Proton Transfer and Excited State Proton-Coupled Electron Transfer  Ana-Patricia Gàmiz-Hernàndez , Artiom Magomedov , Gerhard Hummer , and Ville R. I. Kaila J. Phys. Chem. B, DOI: 10.1021/jp508790n (2014)

• B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity  Jason Qian, Qiao Wang, Marei Dose et al. Cell, doi:10.1016/j.cell.2014.11.013 (2014)
• Free energies from dynamic weighted histogram analysis using unbiased Markov state model  Edina Rosta and Gerhard Hummer J. Chem. Theory Comput., DOI: 10.1021/ct500719p (2014)
• High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes  Raghunath Chatterjee, Ximiao He, Di Huang, Peter Fitzgerald, Andrew Smith and Charles Vinson Epigenetics and Chromatin, doi:10.1186/1756-8935-7-35 (2014)
• Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes  Ximiao He, Raghunath Chatterjee, Desiree Tillo, Andrew Smith, Peter FitzGerald and Charles Vinson Epigenetics and Chromatin, doi:10.1186/1756-8935-7-34 (2014)
• Genetic diversity is a predictor of mortality in humans  Bihlmeyer NA, Brody JA, et al. BMC Genetics, doi:10.1186/s12863-014-0159-7 (2014)
• TCF-1 and LEF-1 act upstream of Th-POK to promote the CD4(+) T cell fate and interact with Runx3 to silence Cd4 in CD8(+) T cells  Steinke FC, Yu S, Zhou X, He B, Yang W, Zhou B, Kawamoto H, Zhu J, Tan K8, Xue HH Naturesteinc Immunol. , doi: 10.1038/ni.2897. (2014)

• Brain Structural Substrates of Reward Dependence during Behavioral Performance  Dayan E, Hamann JM, Averbeck BB, Cohen LG J. Neurosci. , doi: 10.1523/JNEUROSCI.3141-14.2014 (2014)
• Early-Onset Stroke and Vasculopathy Associated with Mutations in ADA2  Zhou Q, Yang D, Ombrello AK, et al. N. Engl. J. Med. , doi: 10.1056/NEJMoa1307361 (2014)
• Modern perspectives on numerical modeling of cardiac pacemaker cell  Maltsev VA, Yaniv Y, Maltsev AV, Stern MD, Lakatta EG J. Pharmacological Sci. , doi://10.1254/jphs.13R04CR (2014)
• Risk estimation using probability machines.  Dasgupta A1, Szymczak S, Moore JH, Bailey-Wilson JE, Malley JD BioData Min. , doi: 10.1186/1756-0381-7-2. (2014)
• Rbfox3 controls the biogenesis of a subset of microRNAs  Kim KK, Yang Y, Zhu J, Adelstein RS, Kawamoto S. Nat Struct Mol Biol., doi: 10.1038/nsmb.2892 (2014)
• Bayesian analysis of individual electron microscopy images: Towards structures of dynamic and heterogeneous biomolecular assemblies  Pilar Cossio and Gerhard Hummer J Struct Biol. , doi: 10.1016/j.jsb.2013.10.006 (2014)

• Valence-specific effects of BDNF Val66Met polymorphism on dopaminergic stress and reward processing in humans  Peciña M, Martìnez-Jauand M, Love T, Heffernan J, Montoya P, Hodgkinson C, Stohler CS, Goldman D, Zubieta JK. J. Neurosci., doi: 10.1523/JNEUROSCI.2152-13 (2014)
• Comparative phosphoproteomic analysis of mammalian glomeruli reveals conserved podocin C-terminal phosphorylation as a determinant of slit diaphragm complex architecture  Markus M. Rinschen, Caroline Pahmeyer, Trairak Pisitkun, Nicole Schnell, Xiongwu Wu, Martina Maa, Malte P. Bartram, Tobias Lamkemeyer, Bernhard Schermer, Thomas Benzing andPaul T. Brinkkoetter Proteomics, DOI: 10.1002/pmic.201400235 (2014)
• A Systems Genetics Approach Identifies CXCL14, ITGAX, and LPCAT2 as Novel Aggressive Prostate Cancer Susceptibility Genes  Kendra A. Williams, Minnkyong Lee, Ying Hu et al. PLoS Genetics, doi: 10.1371/journal.pgen.1004809 (2014)
• Charge Neutralization of the Central Lysine Cluster in Prion Protein (PrP) Promotes PrPSc-Like Folding of Recombinant PrP Amyloids  Bradley R. Groveman, Allison Kraus, Lynne D. Raymond, Michael A. Dolan, Kelsie J. Anson, David W. Dorward and Byron Caughey J. Biol. Chem. , doi: 10.1074/jbc.M114.619627 (2014)
• Pathogenic Ischemic Stroke Phenotypes in the NINDS-Stroke Genetics Network  Hakan Ay, Ethem Murat Arsava et al. Stroke, doi: 10.1161/STROKEAHA.114.007362 (2014)
• Variant GADL1 and response to lithium in bipolar I disorder  Consortium on Lithium Genetics, Hou L, Heilbronner U, Rietschel M, Kato T, Kuo PH, McMahon FJ, Schulze TG. N. Engl. J. Med. , doi: 10.1056/NEJMc1401817#SA4 (2014)

• Investigation of the interactions between the EphB2 receptor and SNEW peptide variants  Buyong Ma, Stephanie Kolb, Michael Diprima, Molleshree Karna, Giovanna Tosato, Qiqi Yang, Qiang Huang, and Ruth Nussinov Growth Factors, DOI: 10.3109/08977194.2014.985786 (2014)
• Self-assembled monolayers improve protein distribution on holey carbon cryo-EM supports  Joel R. Meyerson, Prashant Rao, Janesh Kumar, Sagar Chittori, Soojay Banerjee, Jason Pierson, Mark L. Mayer & Sriram Subramaniam Nature, doi:10.1038/srep07084 (2014)
• Diversity and dynamics of the Drosophila transcriptome.  Brown JB, Boley N, Eisman R, May GE et al Nature, doi:10.1038/nature12962 (2014)
• Database of osmoregulated proteins in mammalian cells  Cameron R. Grady , Mark A. Knepper , Maurice B. Burg , Joan D. Ferraris Physiological Reports, DOI: 10.14814/phy2.12180 (2014)
• Simple subgroup approximations to optimal treatment regimes from randomized clinical trial data  Jared C. Foster, Jeremy M.G. Taylor, Niko Kaciroti and Bin Nan Biostatistics, doi: 10.1093/biostatistics/kxu049 (2014)
• Mitochondrial DNA Sequence Variation Associated With Peripheral Nerve Function in the Elderly  Shana M. Katzman, Elsa S. Strotmeyer, Michael A. Nalls et al. J. Gerontology A, doi: 10.1093/gerona/glu175 (2014)

• Role of solvation in pressure-induced helix stabilization  Robert B. Best, Cayla Miller and Jeetain Mittal J. Chem. Physics, doi:///10.1063/1.4901112 (2014)
• Mass spectrometry based protein identification with accurate statistical significance assignment  Gelio Alves and Yi-Kuo Yu Bioinformatics, doi: 10.1093/bioinformatics/btu717 (2014)
• Modeling vocalization with ECoG cortical activity recorded during vocal production in the macaque monkey  Makoto Fukushima, Richard C Saunders, Naotaka Fujii, Bruno B Averbeck, Mortimer Mishkin Engineering in Medicine and Biology, DOI://10.1109/EMBC.2014.6945188 (2014)
• 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. Human Molecular Genetics (2014)
• Development and Implementation of (Q)SAR Modeling Within the CHARMMing Web-User Interface  Iwona E. Weidlich, Yuri Pevzner, Benjamin T. Miller, Igor V. Filippov, H. Lee Woodcock, and Bernard R. Brooks J. Comp. Chem., DOI: 10.1002/jcc.23765 (2014)
• Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes  Serdar Bozdag, Aiguo Li, Mehmet Baysan, and Howard A Fine Cancer Informatics, doi: 10.4137/CIN.S14027 (2014)

• Variants associated with type 2 diabetes identified by the transethnic meta-analysis study: assessment in American Indians and evidence for a new signal in LPP  Nair AK, Muller YL, McLean NA, Abdussamad M, Piaggi P, Kobes S, Weil EJ, Curtis JM, Nelson RG, Knowler WC, Hanson RL, Baier LJ Diabetologia, doi: 10.1007/s00125-014-3351-4 (2014)
• DLX3 regulates bone mass by targeting genes supporting osteoblast differentiation and mineral homeostasis in vivo  Isaac J, Erthal J, Gordon J, Duverger O, Sun HW, Lichtler AC, Stein GS, Lian JB, Morasso MI Cell Death Differ. , doi: 10.1038/cdd.2014.82 (2014)
• Human syndromes of immunodeficiency and dysregulation are characterized by distinct defects in T-cell receptor repertoire development.  Yu X, Almeida JR2, Darko S et al. J Allergy Clin Immunol., doi: 10.1016/j.jaci.2013.11.018. (2014)
• Autosomal recessive phosphoglucomutase 3 (PGM3) mutations link glycosylation defects to atopy, immune deficiency, autoimmunity, and neurocognitive impairment.  Zhang Y, Yu X, Ichikawa M et al. J Allergy Clin Immunol. , doi: 10.1016/j.jaci.2014.02.013 (2014)
• FAAH selectively influences placebo effects  Peciña M, Martìnez-Jauand M, Hodgkinson C, Stohler CS, Goldman D, Zubieta JK Molecular Psychiatry, doi: 10.1038/mp.2013.124 (2014)
• Essential dynamics analysis captures the concerted motion of the integrin-binding site in jerdostatin, an RTS disintegrin  Luisa Calvanese, Lucia Falcigno andGabriella D'Auria Biopolymers, DOI: 10.1002/bip.22578 (2014)

• Role of the Fast Kinetics of Pyroglutamate-Modified Amyloid-β Oligomers in Membrane Binding and Membrane Permeability  Joon Lee, Alan L. Gillman, Hyunbum Jang, Srinivasan Ramachandran, Bruce L. Kagan, Ruth Nussinov, Fernando Teran Arce Biochemistry, doi: 10.1021/bi500587p (2014)
• Pathogenic Properties of Alzheimer's β-Amyloid Identified from Structure-Property Patient-Phenotype Correlations  Manish K. Tiwari and Kasper P. Kepp Dalt. Transac. , DOI: 10.1039/C4DT03122A (2014)
• Using fMRI to decode true thoughts independent of intention to conceal  Yang Z, Huang Z, Gonzalez-Castillo J, Dai R, Northoff G, Bandettini P NeuroImage, doi: 10.1016/j.neuroimage.2014.05.034 (2014)
• Probing the Flexibility of Tropomyosin and Its Binding to Filamentous Actin Using Molecular Dynamics Simulations  Wenjun Zheng, Bipasha Barua, and Sarah E. Hitchcock-DeGregori Biophysical J. , doi: 10.1016/j.bpj.2013.09.003 (2014)
• Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe  Takeshi Mizuguchi, Geoffrey Fudenberg, Sameet Mehta, Jon-Matthew Belton, Nitika Taneja, Hernan Diego Folco, Peter FitzGerald, Job Dekker, Leonid Mirny, Jemima Barrowman & Shiv I. S. Grewal Nature, doi:10.1038/nature13833 (2014)
• Direct Evidence for a Peroxide Intermediate and a Reactive Enzyme-Substrate-Dioxygen Configuration in a Cofactor-free Oxidase  Soi Bui, David von Stetten, Pablo G. Jambrina, Thierry Prangé, Nathalie Colloc'h, Daniele de Sanctis, Antoine Royant, Edina Rosta and Roberto A. Steiner Angewandte Chemie, DOI: 10.1002/anie.201405485 (2014)

• Sequential monte carlo tracking of the marginal artery by multiple cue fusion and random forest regression  Kevin M. Cherry, Brandon Peplinski, Lauren Kim, Shijun Wang, Le Lu, Weidong Zhang, Jianfei Liu, Zhuoshi Wei, Ronald M. Summers Medical Image Analysis, DOI: 10.1016/j.media.2014.09.006 (2014)
• Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association  Robert B. Best, Wenwei Zheng, and Jeetain Mittal J. Chem. Theory and Computation, DOI: 10.1021/ct500569b (2014)
• Phactr3/Scapinin, a Member of Protein Phosphatase 1 and Actin Regulator (Phactr) Family, Interacts with the Plasma Membrane via Basic and Hydrophobic Residues in the N-Terminus  Akihiro Itoh, Atsushi Uchiyama, Shunichiro Taniguchi, and Junji Sagara PLoS One, doi: 10.1371/journal.pone.0113289 (2014)
• Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA  Christopher P Jones andAdrian R Ferr�-D'Amarè EMBO J., DOI: 10.15252/embj.201489209 (2014)
• A system for multilocus chromosomal integration and transformation-free selection marker rescue  Michael S. Siddiqui, Atri Choksi andChristina D. Smolke Yeast Research, DOI: 10.1111/1567-1364.12210 (2014)
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• 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)

• Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity  Minghui Li , Marharyta Petukh , Emil Alexov , and Anna R. Panchenko J. Chem. Theory & Computation, DOI: 10.1021/ct401022c (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 (142 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)
• Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy  Alberto Bartesaghi, Alan Merk, Mario J Borgnia, Jacqueline L S Milne & Sriram Subramaniam Nature Structural & Molecular Biology, doi:10.1038/nsmb.2711 (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)
• Massively Parallel Sequencing Reveals an Accumulation of De Novo Mutations and an Activating Mutation of LPAR1 in a Patient with Metastatic Neuroblastoma  JS Wei, P Johansson, L Chen et al PLoS One, doi:10.1371/journal.pone.0077731 (2013)
• Mitochondrial DNA sequence associations with dementia and amyloid-β in elderly African Americans  GJ Tranah, JS Yokoyoma, SM Katzman et al. Neurobiology of Aging, doi:/10.1016/j.neurobiolaging.2013.05.02 (2013)
• Functional Linear Models for Association Analysis of Quantitative Traits  Ruzong Fan, Yifan Wang, James L. Mills, Alexander F. Wilson, Joan E. Bailey-Wilson, Momiao Xiong Genetic Epidemiology, DOI: 10.1002/gepi.21757 (2013)

• Singular Value Decomposition of the Radial Distribution Function for Hard Sphere and Square Well Potentials  Travis Hoppe PLoS One, doi:10.1371/journal.pone.0075792 (2013)
• Brain Docosahexaenoic Acid [DHA] Incorporation and Blood Flow Are Increased in Chronic Alcoholics: A Positron Emission Tomography Study Corrected for Cerebral Atrophy  J.C. Umhau, W. Zhou, S. Thada et al PLoS One, doi:10.1371/journal.pone.0075333 (2013)
• Cyclic N-Terminal Loop of Amylin Forms Non Amyloid Fibers  Stephanie M. Cope, Sandip Shinde, Robert B. Best, Giovanna Ghirlanda, Sara M. Vaiana Biophys. J. , doi: 10.1016/j.bpj.2013.08.026 (2013)
• Infrared, Raman, and Ultraviolet Absorption Spectra and Theoretical Calculations and Structure of 2, 6-Difluoropyridine in its Ground and Excited Electronic States  Hong-Li Sheu, Sunghwan Kim, and Jaan Laane J. Phys. Chem. A, DOI://10.1021/jp407592r (2013)
• Assessment of Parkinson's disease risk loci in Greece  E. Kara, G. Xiromerisiou, C. Spanaki et al Neurobiology of Aging, doi://10.1016/j.neurobiolaging.2013.07.011 (2013)
• Sequential Monte Carlo Tracking for Marginal Artery Segmentation on CT Angiography by Multiple Cue Fusion  Shijun Wang, Brandon Peplinski, Le Lu, Weidong Zhang, Jianfei Liu, Zhuoshi Wei, Ronald M. Summers Medical Image Computing and Computer-Assisted Intervention  8150:518-525 (2013)
• Strategies for developing prediction models from genome-wide association studies.  Jincao Wu, Ruth M. Pfeiffer andMitchell H. Gail Genet Epidemiol. , doi: 10.1002/gepi.21762 (2013)
• Phosphate release coupled to rotary motion of F1-ATPase  Kei-ichi Okazaki and Gerhard Hummer PNAS, doi: 10.1073/pnas.1305497110 (2013)
• Genome-wide analysis of blood pressure variability and ischemic stroke  Yadav, S; Cotlarciuc, I; Munroe, PB et al. Stroke, DOI://10.1161/STROKEAHA.113.002186 (2013)
• Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation  Gangqing Hu, Qingsong Tang, Suveena Sharma, Fang Yu, Thelma M Escobar, Stefan A Muljo, Jinfang Zhu & Keji Zhao Nature Immunology, doi:10.1038/ni.2712 (2013)
• Specific and Non-Specific Protein Association in Solution: Computation of Solvent Effects and Prediction of First-Encounter Modes for Efficient Configurational Bias Monte Carlo Simulations  Antonio Cardone , Harish C. Pant , and Sergio A Hassan J. Phys. Chem. B, DOI: 10.1021/jp4050594 (2013)
• Molecular Structure of β-Amyloid Fibrils in Alzheimer's Disease Brain Tissue  Jun-Xia Lu, Wei Qiang, Wai-Ming Yau, Charles D. Schwieters, Stephen C. Meredith, Robert Tycko Cell, doi: 10.1016/j.cell.2013.08.035 (2013)

• A fast multilocus test with adaptive SNP selection for large-scale genetic-association studies  Han Zhang, Jianxin Shi, Faming Liang, William Wheeler, Rachael Stolzenberg-Solomon and Kai Yu Eur. J. Human Genetics, doi: 10.1038/ejhg.2013.201 (2013)
• Sequence selectivity of the cleavage sites induced by topoisomerase I inhibitors: a molecular dynamics study  Fung-Ming Siu and Yves Pommier Nucleic Acids Research, doi://10.1093/nar/gkt791 (2013)
• Gene Synthesis Method Based on Overlap Extension PCR and DNAWorks Program  Gang Li, Bing-Xue Dong, Yu-Huan Liu, Chang-Jie Li, Li-Ping Zhang Synthetic Biology - Methods in Molecular Biology 1073:9-17 (2013)
• Proteomic profiling of the rat renal proximal convoluted tubule in response to chronic metabolic acidosis  Dana Marie Freund Ph.D. Thesis, Colorado State University (2013)
• Effect of acute acid-base disturbances on ErbB1/2 tyrosine phosphorylation in rabbit renal proximal tubules  Lara A. Skelton, Walter F. Boron Am. J. Physiol. - Renal Physiol., DOI: 10.1152/ajprenal.00307.2013 (2013)
• Engineering domain fusion chimeras from I-OnuI family LAGLIDADG homing endonucleases for genome engineering applications  Sarah Baxter Ph.D thesis, U. Washington (2013)

• Genetic comorbidities in Parkinson's disease  MA Nalls,M Saad et al. Human Molecular Genetics, doi: 10.1093/hmg/ddt465 (2013)
• Design and Rationale for a Genome-Wide Association Study of Ischemic Stroke Subtypes  Meschia, Arnett, Ay et al. Stroke, doi: 10.1161/​STROKEAHA.113.001857 (2013)
• Familial Alzheimer's Disease Osaka Mutant (ΔE22) β-Barrels Suggest an Explanation for the Different Aβ1-40/42 Preferred Conformational States Observed by Experiment  Hyunbum Jang , Fernando Teran Arce , Srinivasan Ramachandran , Bruce L. Kagan , Ratnesh Lal , and Ruth Nussinov J. Phys. Chem. B, DOI: 10.1021/jp405389n (2013)
• Life and death of a cardiac calcium spark  Michael D. Stern, Eduardo Ríos, and Victor A. Maltsev J. Gen. Physiol. , doi: 10.1085/jgp.201311034 (2013)
• Conformational Analysis of NMDA Receptor GluN1, GluN2, and GluN3 Ligand-Binding Domains Reveals Subtype-Specific Characteristics  Yongneng Yao, John Belcher, Anthony J. Berger, Mark L. Mayer, Albert Y. Lau Structure, doi: 10.1016/j.str.2013.07.011 (2013)
• Correlated vibrations in ion-pair dynamics in mechanoactivation identify functional domains of force-dependent titin kinase  Ming-Chya Wu, Jeffrey G. Forbes and Kuan Wang Soft Matter, DOI: 10.1039/C3SM51539G (2013)

• Genome-Wide Association of Body Fat Distribution in African Ancestry Populations Suggests New Loci  Ching-Ti Liu, Keri L. Monda, Kira C. Taylor et al PLoS Genetics, doi:10.1371/journal.pgen.1003681 (2013)
• Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition  Alika K Maunakea, Iouri Chepelev, Kairong Cui and Keji Zhao Cell Research, doi: 10.1038/cr.2013.110 (2013)
• RCircos: an R package for Circos 2D track plots  Hongen Zhang, Paul Meltzer, Sean Davis BMC Bioinformatics, doi:10.1186/1471-2105-14-244 (2013)
• Top3 β is an RNA topoisomerase that works with fragile X syndrome protein to promote synapse formation  Xu D, Shen W, Guo R, Xue Y, Peng W, Sima J, Yang J, Sharov A, Srikantan S, Yang J, Fox D 3rd, Qian Y, Martindale JL, Piao Y, Machamer J, Joshi SR, Mohanty S, Shaw AC, Lloyd TE, Brown GW, Ko MS, Gorospe M, Zou S, Wang W. Nature Neuroscience, doi: 10.1038/nn.3479 (2013)
• Computational detection of abundant long-range nucleotide covariation in Drosophila genomes  Eckart Bindewald and Bruce A Shapiro RNA, doi: 10.1261/rna.037630.112 (2013)
• Multi-SNP Analysis of GWAS Data Identifies Pathways Associated with Nonalcoholic Fatty Liver Disease  Qing-Rong Chen, Rosemary Braun, Ying Hu, Chunhua Yan, Elizabeth M. Brunt, Daoud Meerzaman, Arun J. Sanyal, Kenneth Buetow PLoS One, doi:10.1371/journal.pone.0065982 (2013)

• Genomic Analysis of Stress Response against Arsenic in Caenorhabditis elegans  Surasri N. Sahu, Jada Lewis, Isha Patel, Serdar Bozdag, Jeong H. Lee, Robert Sprando, and Hediye Nese Cinar PLoS One, doi://10.1371/journal.pone.0066431 (2013)
• Reduced thalamic volumes in major depressive disorder  AC Nugent, RM Davis, CA Zarate Jr, WC Drevets Psych. Res. Neuroimaging, doi://10.1016/j.pscychresns.2013.05.004 (2013)
• Graph theoretical analysis of resting magnetoencephalographic functional connectivity networks  Lindsay Rutter, Sreenivasan R. Nadar, Tom Holroyd, Frederick W. Carver, Jose Apud, Daniel R. Weinberger and Richard Coppola Frontiers in Computational Neuroscience, doi://10.3389/fncom.2013.00093 (2013)
• Evaluation of the Use of Surrogate Tissues for Calculating Radiation Dose to Lymphatic Nodes from External Photon Beams  Stephanie Lamart, Brian E. Moroz and Choonsik Lee Radiation Protection Dosimetry, doi: 10.​1152/​ajprenal.​00210.​2013 (2013)
• Visual Phrase Learning and Its Application in Computed Tomographic Colonography  Shijun Wang, Matthew McKenna, Zhuoshi Wei, Jiamin Liu, Peter Liu, Ronald M. Summers Medical Image Computing and Computer-Assisted Intervention  8149:243 (2013)
• Ordinal latent variable models and their application in the study of newly licensed teenage drivers  John C Jackson, Paul S. Albert, Zhiwei Zhang and Bruce Simons-Morton Appl. Statist. , DOI: 10.1111/j.1467-9876.2012.01065.x (2013)

• Striatal dopamine release and genetic variation of the serotonin 2C receptor in humans  Brian J Mickey, Benjamin J Sanford, Tiffany M Love, Pei-Hong Shen, Colin Hodgkinson, Christian S Stohler, David Goldman, Jon-Kar Zubieta J Neurosci., doi: 10.1523/JNEUROSCI.1260-12.2012 (2013)
• DRD2/ANKK1 Taq1A polymorphism (rs1800497) has opposing effects on D2/3 receptor binding in healthy controls and patients with major depressive disorder  Savitz J, Hodgkinson CA, Martin-Soelch C, Shen PH, Szczepanik J, Nugent AC, Herscovitch P, Grace AA, Goldman D, Drevets WC Int J Neuropsychopharmacol., doi: 10.1017/S146114571300045X (2013)
• DockoMatic 2.0: High Throughput Inverse Virtual Screening and Homology Modeling  Casey Bullock , Nic Cornia , Reed Jacob , Andrew Remm , Thomas Peavey , Ken Weekes , Chris Mallory , Julia Thom Oxford , Owen M. McDougal , and Timothy Lyon Andersen J. Chem. Inf. and Modeling, DOI: 10.1021/ci400047w (2013)
• Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding  X He, R Chatterjee, S John, H Bravo, Bk Sathyanarayana, SC Biddie, PC FitzGerald, JA Stamatoyannopoulos, GL Hager, C Vinson BMC Genomics, doi:10.1186/1471-2164-14-428 (2013)
• Probing the transient dark state of substrate binding to GroEL by relaxation-based solution NMR  David S. Libich, Nicolas L. Fawzia, Jinfa Ying, and G. Marius Clore PNAS, doi: 10.1073/pnas.1305715110 (2013)
• HASP server: a database and structural visualization platform for comparative models of influenza A hemagglutinin proteins  Xavier I Ambroggio, Jennifer Dommer, Vivek Gopalan, Eleca J Dunham, Jeffery K Taubenberger and Darrell E Hurt BMC Bioinformatics, doi:10.1186/1471-2105-14-197 (2013)

• Host immune constraints on malaria transmission: insights from population biology of within-host parasites  Philip G McQueen, Kim C Williamson and F Ellis McKenzie Malaria Journal, doi:10.1186/1475-2875-12-206 (2013)
• VLDP web server: a powerful geometric tool for analysing protein structures in their environment  Jérémy Esque, Sylvain Léonard, Alexandre G. de Brevern and Christophe Oguey Nucleic Acids Research, doi: 10.1093/nar/gkt509 (2013)
• mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex.  Dillman AA, Hauser DN, Gibbs JR, Nalls MA, McCoy MK, Rudenko IN, Galter D, Cookson MR. Nature Neuroscience, doi: 10.1038/nn.3332 (2013)
• Proteome-Wide Measurement of Protein Half-Lives and Translation Rates in Vasopressin-Sensitive Collecting Duct Cells  Pablo C. Sandoval, Dane H. Slentz, Trairak Pisitkun, Fahad Saeed, Jason D. Hoffert and Mark A. Knepper J. Am. Soc. Nephrologu, doi: 10.1681/ASN.2013030279 (2013)
• Anatomical coupling among distributed cortical regions in youth varies as a function of individual differences in vocabulary abilities  Nancy Raitano Lee, Armin Raznahan, Gregory L. Wallace, Aaron Alexander-Bloch, Liv S. Clasen, Jason P. Lerch, Jay N. Giedd Human Brain Mapping, DOI://10.1002/hbm.22299 (2013)
• Serum Iron Levels and the Risk of Parkinson Disease: A Mendelian Randomization Study  I Pichler, F Del Greco et al. PLoS Medicine, doi:10.1371/journal.pmed.1001462 (2013)

• HIV-1 Envelope Glycoprotein Trimers Display Open Quaternary Conformation When Bound to the gp41 Membrane-Proximal External-Region-Directed Broadly Neutralizing Antibody Z13e1  Audray K. Harris, Alberto Bartesaghi, Jacqueline L. S. Milne and Sriram Subramaniam J. Virology, doi:10.1128/JVI.03284-12 (2013)
• DRD2 polymorphisms modulate reward and emotion processing, dopamine neurotransmission and openness to experience  Peciña M, Mickey BJ, Love T, Wang H, Langenecker SA, Hodgkinson C, Shen PH, Villafuerte S, Hsu D, Weisenbach SL, Stohler CS, Goldman D, Zubieta JK Cortex, doi: 10.1016/j.cortex.2012.01.010 (2013)
• Prefrontal white matter impairment in substance users depends upon the catechol-o-methyl transferase (COMT) val158met polymorphism  Zhang X, Lee MR, Salmeron BJ, Stein DJ, Hong LE, Geng X, Ross TJ, Li N, Hodgkinson C, Shen PH, Yang Y, Goldman D, Stein EA. Neuroimage, doi: 10.1016/j.neuroimage.2012.11.056 (2013)
• The functional DRD3 Ser9Gly polymorphism (rs6280) is pleiotropic, affecting reward as well as movement  Savitz J, Hodgkinson CA, Martin-Soelch C, Shen PH, Szczepanik J, Nugent A, Herscovitch P, Grace AA, Goldman D, Drevets WC. PLoS One, doi: 10.1371/journal.pone.0054108 (2013)
• Association of genetic variation in pharmacodynamic factors with methadone dose required for effective treatment of opioid addiction  Levran O, Peles E, Randesi M, Shu X, Ott J, Shen PH, Adelson M, Kreek MJ. Pharmacogenomics, doi: 10.2217/pgs.13.58 (2013)
• Atomic-resolution structural information from scattering experiments on macromolecules in solution  Jürgen Köfinger & Gerhard Hummer Phys. Rev. E , DOI:10.1103/PhysRevE.87.052712 (2013)

• Evolutionary Pressure on the Topology of Protein Interface Interaction Networks  Margaret E Johnson & Gerhard Hummer J. Phys. Chem. B, DOI: 10.1021/jp402944e (2013)
• Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila  Lim SJ, Boyle PJ, Chinen M, Dale RK, Lei EP Nucleic Acids Research, doi: 10.1093/nar/gkt037 (2013)
• A compendium of RNA-binding motifs for decoding gene regulation  Ray D1, Kazan H, Cook KB, et al. Nature, doi: 10.1038/nature12311 (2013)
• Messenger RNA is a functional component of a chromatin insulator complex  Matzat LH1, Dale RK, Lei EP EMBO Rep., DOI: 10.1038/embor.2013.118 (2013)
• Global analysis of the effects of the V2 receptor antagonist satavaptan on protein phosphorylation in collecting duct.  Hoffert JD, Pisitkun T, Saeed F, Wilson JL, Knepper MA Am J Physiol Renal Physiol., DOI: 10.1152/ajprenal.00497.2013 (2013)
• CAMS-RS: Clustering Algorithm for Large-Scale Mass Spectrometry Data Using Restricted Search Space and Intelligent Random Sampling  Saeed F, Hoffert JD, Knepper MA IEEE/ACM Trans Comput Biol Bioinform., doi://10.1109/TCBB.2013.152 (2013)

• A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code  Hirotaka Nakahashi, Kyong-Rim Kieffer Kwon, Wolfgang Resch, Laura Vian, Marei Dose, Diana Stavreva, Ofir Hakim, Nathanael Pruett, Steevenson Nelson, Arito Yamane, Jason Qian, Wendy Dubois, Scott Welsh, Robert D. Phair, B. Franklin Pugh, Victor Lobanenkov, Gordon L. Hager, and Rafael Casellas Cell Reports, doi://10.1016/j.celrep.2013.04.024 (2013)
• Global Regulation of Promoter Melting in Naive Lymphocytes  Fedor Kouzine, Damian Wojtowicz, Arito Yamane, Wolfgang Resch, Kyong-Rim Kieffer-Kwon, Russell Bandle, Steevenson Nelson, Hirotaka Nakahashi, Parirokh Awasthi, Lionel Feigenbaum, Herve Menoni, Jan Hoeijmakers, Wim Vermeulen, Hui Ge, Teresa M. Przytycka, David Levens, and Rafael Casellas Cell , doi://10.1016/j.cell.2013.04.033 (2013)
• Therapeutic Response in Feline Sandhoff Disease Despite Immunity to Intracranial Gene Therapy  Bradbury AM, Cochran JN, McCurdy VJ, Johnson AK et al Mol. Ther. , doi: 10.1038/mt.2013.86 (2013)
• A next generation sequencing approach to constructing a genetic map for Populus tremula  Tahir Mujtaba Master's Thesis, Swedish University of Agricultural Science (2013)
• A 5′-Flanking Region of Gonadotropin-Regulated Testicular RNA Helicase (GRTH/DDX25) Gene Directs Its Cell-Specific Androgen-Regulated Gene Expression in Testicular Germ Cells  Raghuveer Kavarthapu, Chon-Hwa Tsai-Morris, Masato Fukushima, James Pickel and Maria L. Dufau Endocrinology, doi: 10.1210/en.2012-2230 (2013)
• Improving Peptide Identification Sensitivity in Shotgun Proteomics by Stratification of Search Space  Gelio Alves and Yi-Kuo Yu J. Proteome Research, DOI: 10.1021/pr301139y (2013)
• Strategies for recombinant protein production in maize  Xing Xu PhD Thesis, Iowa State University (2013)
• A simplified representation of anisotropic charge distributions within proteins  Travis Hoppe J. Chem. Phys., doi://10.1063/1.4803099 (2013)
• Proteomic Profiling and Pathway Analysis of the Response of Rat Renal Proximal Convoluted Tubules to Metabolic Acidosis  Kevin L. Schauer, Dana M Freund, Jessica E. Prenni, and Norman P. Curthoys Renal Physiology, doi: 10.​1152/​ajprenal.​00210.​2013 (2013)
• Three-Dimensional Structure of CAP-Gly Domain of Mammalian Dynactin Determined by Magic Angle Spinning NMR Spectroscopy: Conformational Plasticity and Interactions with End Binding Protein EB1  S. Yan, G. Hou, CD Schwieters, S Ahmed, JC Williams T Polenova J. Mol. Biol. , doi://10.1016/j.jmb.2013.04.027 (2013)
• CG methylated microarrays identify a novel methylated sequence bound by the CEBPB| ATF4 heterodimer that is active in vivo  Ishminder K. Mann, Raghunath Chatterjee, Jianfei Zhao et al. Genome Research, doi:10.1101/gr.146654.112 (2013)
• Pointwise confidence intervals for a survival distribution with small samples or heavy censoring  Michael P. Fay, Erica H. Brittain and Michael A. Proschan Biostatistics, doi: 10.1093/biostatistics/kxt016 (2013)
• Degenerate polymerase chain reaction strategy with DNA microarray for detection of multiple and various subtypes of virus during blood screening  K. Takizawa, T. Nakashima, T Mizukami et al. Transfusion, DOI: 10.1111/trf.12193 (2013)
• Genome-wide association study of age at menarche in African-American women  EW Demerath, C-T Liu, N Franceschini et al. Human Molecular Genetics, doi: 10.1093/hmg/ddt181 (2013)
• Reconciling Mediating and Slaving Roles of Water in Protein Conformational Dynamics  Li Zhao, Wenzhao Li, and Pu Tian PLoS One, doi://10.1371/journal.pone.0060553 (2013)
• Vasopressin and the regulation of aquaporin-2  Justin L. L. Wilson, Carlos A. Miranda, Mark A. Knepper Clinical and Experimental Nephrology, doi://10.1007/s10157-013-0789-5 (2013)
• Apolipoprotein E genotype, cardiovascular biomarkers and risk of stroke: Systematic review and meta-analysis of 14 015 stroke cases and pooled analysis of primary biomarker data from up to 60 883 individuals  TA Khan, T Shah, D Prieto et al. Int. J. Epidemiol. , doi: 10.1093/ije/dyt034 (2013)
• Controlling the local false discovery rate in the adaptive Lasso  Joshua N Sampson & Nilanjan Chatterjee Biostatistics, doi: 10.1093/biostatistics/kxt008 (2013)

• Molecular mechanisms for the subversion of MyD88 signaling by TcpC from virulent uropathogenic Escherichia coli  GA Snyder, C Cirl, J Jiang et al PNAS, doi: 10.1073/pnas.1215770110 (2013)
• A crossed random effects modeling approach for estimating diagnostic accuracy from ordinal ratings without a gold standard  Yunlong Xie, Zhen Chen, Paul S. Albert Statistics in Medicine, DOI: 10.1002/sim.5784 (2013)
• Pharmacophore and 3D-QSAR Characterization of 6-arylquinazolin-4-amines as Cdc2-like kinase 4 (Clk4) and Dual Specificity Tyrosine-phosphorylation-regulated Kinase 1A (Dyrk1A) Inhibitors  Yongmei Pan , Yanli Wang, and Stephen H. Bryant J. Chem. Inf. Model. , DOI: 10.1021/ci300625c (2013)
• Effects of pre-existing anti-carrier immunity and antigenic element multiplicity on efficacy of a modular virus-like particle vaccine  Yap P. Chuan, Tania Rivera-Hernandez, Nani Wibowo, Natalie K. Connors, Yang Wu, Fiona K. Hughes, Linda H. L. Lua, Anton P. J. Middelberg Biotech. & Bioengg. , DOI: 10.1002/bit.24907 (2013)
• Global Analysis of Neuronal Phosphoproteome Regulation by Chondroitin Sulfate Proteoglycans  Panpan Yu, Trairak Pisitkun, Guanghui Wang, Rong Wang, Yasuhiro Katagiri, Marjan Gucek, Mark A. Knepper, Herbert M. Geller PLoS One, doi:10.1371/journal.pone.0059285 (2013)
• The alkaline pectate lyase PEL168 of Bacillus subtilis heterologously expressed in Pichia pastoris is more stable and efficient for degumming ramie fiber  Chengjie Zhang, Jia Yao,Cheng Zhou,Liangwei Mao, Guimin Zhang, Yanhe Ma BMC Biotechnology, doi:10.1186/1472-6750-13-26 (2013)

• In Silico, In Vitro, and In Vivo Studies Indicate the Potential Use of Bolaamphiphiles for Therapeutic siRNAs Delivery  Taejin Kim, Kirill A. Afonin, Mathias Viard, Alexey Y Koyfman, Selene Sparks, Eliahu Heldman, Sarina Grinberg, Charles Linder, Robert P Blumenthal and Bruce A Shapiro Mol. Therapy - Nuc. Acids, doi:10.1038/mtna.2013.5 (2013)
• RNAi triggered by specialized machinery silences developmental genes and retrotransposons  Soichiro Yamanaka, Sameet Mehta, Francisca E. Reyes-Turcu, Fanglei Zhuang, Ryan T. Fuchs, Yikang Rong, Gregory B. Robb & Shiv I. S. Grewal Nature, doi:10.1038/nature11716 (2013)
• Transcription-dependent dynamic supercoiling is a short-range genomic force  Fedor Kouzine, Ashutosh Gupta, Laura Baranello, Damian Wojtowicz, Khadija Ben-Aissa, Juhong Liu, Teresa M Przytycka & David Levens Nature Structural & Molecular Biology, doi:10.1038/nsmb.2517 (2013)
• X-Ray crystallographic structural characteristics of Arabidopsis hemoglobin I and their functional implications  Nitika Mukhi, Sonali Dhindwal, Sheetal Uppal, Pravindra Kumar, Jagreet Kaur, Suman Kundu Biochim. et Biophys. Acta, doi://10.1016/j.bbapap.2013.02.024 (2013)
• Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing  David Zanuy, Francisco J. Sayago, Guillem Revilla-López, Gema Ballano, Lilach Agemy, Venkata Ramana Kotamraju, Ana I. Jiménez, Carlos Cativiela, Ruth Nussinov, April M. Sawvel, Galen Stucky, Erkki Ruoslahti, Carlos Alemán J. Computer-Aided Mol. Design, doi:10.1007/s10822-012-9623-5 (2013)
• A novel taurocyamine kinase found in the protist Phytophthora infestans  Kouji Uda, Michihiro Hoshijima, Tomohiko Suzuki Comp. Biochem. Phys. Part B: Biochem & Mol. Bio. , doi://10.1016/j.cbpb.2013.03.003 (2013)

• Structure and accessibility of HA trimers on intact 2009 H1N1 pandemic influenza virus to stem region-specific neutralizing antibodies  AK Harris, JR Meyerson, Y Matsuoka, O Kuybeda, A Moran, D Bliss, SR Das, JW Yewdell, G Sapiro, K Subbarao, and S Subramaniam PNAS, doi: 10.1073/pnas.1214913110 (2013)
• Gene Synthesis by Assembly of Deoxyuridine-Containing Oligonucleotides  Romualdas Vaisvila, Jurate Bitinaite Methods in Molecular Biology, doi: 10.1007/978-1-62703-293-3_12 (2013)
• The Molecular Mechanism of Substrate Engagement and Immunosuppressant Inhibition of Calcineurin  Simina Grigoriu, Rachel Bond, Pilar Cossio, Jennifer A. Chen, Nina Ly, Gerhard Hummer, Rebecca Page, Martha S. Cyert, Wolfgang Peti PLoS Biology, doi:10.1371/journal.pbio.1001492 (2013)
• Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network  Z Chen, H Tang, R Qayyum, UM Schick, MA Nalls et al. Human Molecular Genetics, doi: 10.1093/hmg/ddt087 (2013)
• Common Variants Within Oxidative Phosphorylation Genes Influence Risk of Ischemic Stroke and Intracerebral Hemorrhage  CD Anderson, A Biffi, MA Nalls, et al. & the International Stroke Genetics Consortium Stroke, doi: 10.1161/​STROKEAHA.112.672089 (2013)
• Antedependence models for nonstationary categorical longitudinal data with ignorable missingness likelihood-based inference  Yunlong Xie, Dale Zimmerman Statistics in Medicine, DOI: 10.1002/sim.5763 (2013)

• Sequence dependence of C-end rule peptides in binding and activation of neuropilin-1 receptor  David Zanuy, Rohith Kotla, Ruth Nussinov, Tambet Teesalu, Kazuki N. Sugahara, Carlos Alemán, Nurit Haspel J. Struct. Biol. , doi://10.1016/j.jsb.2013.02.006 (2013)
• Electrostatic spectral tuning mechanism of the green fluorescent protein  Ville R. I. Kaila , Robert Send and Dage Sundholm Phys. Chem. Chem. Phys., DOI: 10.1039/C3CP00058C (2013)
• Alzheimer's disease: Which type of amyloid-preventing drug agents to employ?  Hyunbum Jang , Laura Connelly , Fernando Teran Arce , Srinivasan Ramachandran , Ratnesh Lal , Bruce L Kagan and Ruth Nussinov Phys. Chem. Chem. Phys., DOI: 10.1039/C3CP00017F (2013)
• Control of breathing by interacting pontine and pulmonary feedback loops  Yaroslav I. Molkov, Bartholomew J. Bacak, Thomas E. Dick, and Ilya A. Rybak Frontiers in Neural Circuits, doi: 10.3389/fncir.2013.00016 (2013)
• Protein charge and mass contribute to the spatio-temporal dynamics of protein-protein interactions in a minimal proteome  Yu Xu, Hong Wang, Ruth Nussinov, Buyong Ma Proteomics, DOI: 10.1002/pmic.201100540 (2013)
• Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly  C Park, X Chen, J-R Yang, J Zhang PNAS, doi: 10.1073/pnas.1218066110 (2013)

• The Val158Met COMT polymorphism is a modifier of the age at onset in Parkinson's disease with a sexual dimorphism  S Klebe, J-L Golmard, MA Nalls et al, French Parkinson's Disease Genetics Study Group and the International Parkinson's Disease Genomics Consortium J Neurol Neurosurg Psychiatry , doi:10.1136/jnnp-2012-304475 (2013)
• The Convergence of Maturational Change and Structural Covariance in Human Cortical Networks  Aaron Alexander-Bloch, Armin Raznahan, Ed Bullmore, and Jay Giedd J. Neuroscience , doi: 10.1523/​JNEUROSCI.3554-12.2013 (2013)
• Genome-wide profiles of CtBP link metabolism with genome stability and epithelial reprogramming in breast cancer  Li-Jun Di, Jung S. Byun, Madeline M. Wong, Clay Wakano, Tara Taylor, Sven Bilke, Songjoon Baek, Kent Hunter, Howard Yang, Maxwell Lee, Cecilia Zvosec, Galina Khramtsova, Fan Cheng, Charles M. Perou, C. Ryan Miller, Rachel Raab, Olufunmilayo I. Olopade & Kevin Gardner Nature Communications, doi:10.1038/ncomms2438 (2013)
• 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 (148 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)
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• 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)
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• 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)
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• 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)
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• 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)
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• 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)
• Origin of Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in SN2 Reactions  Edina Rosta and Arieh Warshel J. Chem. Theory & Computation, DOI: 10.1021/ct2009329 (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)
• 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, and Buyong Ma J. Biol. Chem. , doi: 10.1074/jbc.M112.340794 (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 (135 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)
• Dehydratase Mediated 1-Propanol Production in Metabolically Engineered Escherichia coli  Rachit Jain and Yajun Yan Microbial Cell Factories, doi:10.1186/1475-2859-10-97 (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)
• 3D structures of sCD4-bound states of trimeric SIV envelope glycoproteins determined 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)
• 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)
• The influence of tumor oxygenation on 18F-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, doi:10.1186/1748-717X-1-3 (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)
• 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)
• 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 (87 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< sub> 17-42</sub>(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< sub> 2</sub> and PIP< sub> 3</sub> 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)
• Copper and cadmium metallothioneins of the ectomycorrhizal fungus Hebeloma cylindrosporum have different patterns of regulation  G. Ramesh, G. K. Podila, G. Gay, R. Marmeisse, and M. S. Reddy App. Env. Microbiology :doi:10.1128/AEM.0214 (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  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< sub> 17-42</sub> 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 (58 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)
• Interleukin (IL)-15 and IL-2 reciprocally regulate expression of the chemokine receptor CX3CR1 through selective NFAT1- and NFAT2-dependent mechanisms  Barlic J, McDermott DH, Merrell MN, Gonzales J, Via LE, Murphy PM. J. Biol. Chem.  279(47):48520-34 (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 (29 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)
• Characterization of a new γTuRC subunit with WD repeats  Gunawardane RN, Martin OC, Zheng Y. Mol. Biol. Cell 14(3):1017-26 (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)
• DBParser:? Web-Based Software for Shotgun Proteomic Data Analyses  Xiaoyu Yang, Vijay Dondeti, Rebecca Dezube, Dawn M. Maynard, Sanford P. Markey, Lewis Y. Geer, Jonathan Epstein, and Jeffrey A. Kowalak Mass Spec. in the Health & Life Sciences S41:B.30 (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)