Biowulf users with COVID-related projects should contact the HPC staff to get increased priority for their jobs.
Covid-Related Projects
83.2+ Million CPU hours used
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Biowulf was used for screening of large virtual libraries containing billions of compounds
and allowed for identification of small molecules that bind to SARS-CoV2 spike protein and inhibit viral infection.
The image depicts one of such molecules bound to the receptor-binding domain of the protein. [Nadya Tarasova, NCI]
| ![]() 3D structural model | of the coronavirus spike protein [Mario Borgnia, NIEHS] |
- MD simulation of SARS-CoV-2 spike protein [Peter Kwong group, NIAID_VRC]
- (1) Identification of drugs that can be repurposed for COVID-19 (2) Using genetic interactions like synthetic lethality and genome scale metabolic modeling to identify new drug targets and combination therapy for COVID-19 [Eytan Ruppin group, NCI]
- Simulations of infection spread in populations [Vipul Periwal group, NIDDK]
- Image processing and text mining of clinical data for the NIAID COVID Data Management Working Group [Robert Hohman group, NIAID]
- Modeling unreported SARS-Cov2 infection from observed cases, computational modeling of Covid-19 biological systems. [Carson Chow group, NIDDK]
- Cryo-electron microscopy of virus proteins and complexes [Natalia de Val & Eric Freed group, NCI_CCR]
- MD Simulations and Glycan Network Analysis of SARS-COV-2 spike protein [Bernard Brooks group, NHLBI]
- Determining the incidence of age-related clonal hematopoiesis in mild vs. severe COVID-19 patient [Cynthia Dunbar group, NHLBI]
- Transcriptomics and network analysis of SARS-CoV-2 infection [Mehdi Pirooznia & Robert Balaban group, NHLBI]
- Stochastic modeling of COVID-19 pandemic infection patterns [Michael Stern group, NIA]
- Investigation of pathogenic characteristics of COVID-19 by analysis of RNA-seq data from human patients [Lothar Hennighausen group, NIDDK]
- SARS-CoV-2 RNA structural analyses [Markus Hafner group, NIAMS]
- Structure of complexes of the SARS-CoV-2 ectodomain with a variety of ligands [Mario Borgnia & William Copeland group, NIEHS]
- Modeling, global surveillance, real-time genomic sequencing and phylodynamics of SARS-CoV-2 [Cecile Viboud group, FIC]
- Genome-wide association study of COVID-19 genetic variants vs. phenotypes in the UK BioBank [Andrew Johnson group, NHLBI]
- Surveillance sequencing of SARS-CoV-2 and tracking of emerging variants of concern, Microbiome analysis of respiratory samples from covid19 patients. [Elodie Ghedin group, NIAID]
- Assessing newly generated and previously known compounds for activity against SARS-Cov-2 [Hiroaki Mitsuya group, NCI]
- Metagenomics of Covid-19 family [Xiaofang Jiang group, NLM]
- Studying Interferon-induced variability in ACE2 expression levels [Liudmila Prokunina-Olsson group, NCI]
- In silico screening of drug candidates [Nadya Tarasova group, NCI]
- Investigating the transcriptional regulators of hyper-inflammatory responses to SARs-CoV2 infection [Behdad Afzali group, NIDDK]
- Genome-wide association studies to identify common and rare germline genetic variants associated with susceptibility to severe or fatal COVID-19 disease [Stephen Chanock group, NCI_DCEG]
- Atomic-level structure of the SARS-CoV-2 spike using cryo-electron microscopy [Peter Kwong group, NIAID_VRC]
- Deep Learning models of chest Xray and CT images [Ronald Summers group, CC]
- Text mining of COVID-related scientific literature in LitCovid and CORD-19 [Zhiyong Lu group, NLM/NCBI]
- Covid-19 transmission modeling and crossover trials. Developing models for flow cytometry data that will be used to gain insights into cellular immune responses to COVID-19 [Dean Follman group, NIAID]
- Genetic Determinants of Susceptibility to Severe COVID-19 Infection [NIAID Consortium. Director: Helen Su group, NIAID]
- Studying maturation of the SARS Cov2 main protease [Robert Best group, NIDDK]
Biowulf users with COVID-related projects should contact the HPC staff to get increased priority for their jobs.
BNT162b2 vaccination enhances interferon-JAK-STAT-regulated antiviral programs in COVID-19 patients infected with the SARS-CoV-2 Beta variant
Knabl, L; Lee, HK; Wieser, M et al.
Commun Med (Lond) (2022)
Evolutionary history and introduction of SARS-CoV-2 Alpha VOC/B.1.1.7 in Pakistan through international travelers
Nasir, A; Bukhari, AR; Trovão, NS et al.
Virus Evol (2022)
mRNA vaccination in octogenarians 15 and 20 months after recovery from COVID-19 elicits robust immune and antibody responses that include Omicron
Lee, HK; Knabl, L; Moliva, JI et al.
Cell Rep (2022)
Yearlong COVID-19 Infection Reveals Within-Host Evolution of SARS-CoV-2 in a Patient With B-Cell Depletion
Nussenblatt, V; Roder, AE; Das, S et al.
J Infect Dis (2022)
Parsing Immune Correlates of Protection Against SARS-CoV-2 from Biomedical Literature
Foote, SL; Jones, S; Lockmuller, J et al.
AMIA Annu Symp Proc (2021)
Preintubation Sequential Organ Failure Assessment Score for Predicting COVID-19 Mortality: External Validation Using Electronic Health Record From 86 U.S. Healthcare Systems to Appraise Current Ventilator Triage Algorithms
Keller, MB; Wang, J; Nason, M et al.
Crit Care Med (2022)
A year of COVID-19 GWAS results from the GRASP portal reveals potential genetic risk factors
Thibord, F; Chan, MV; Chen, MH; Johnson, AD; ,
HGG Adv (2022)
Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa
Okoh, OS; Nii-Trebi, NI; Jakkari, A et al.
iScience (2022)
Genome-scale metabolic modeling reveals SARS-CoV-2-induced metabolic changes and antiviral targets
Cheng, K; Martin-Sancho, L; Pal, LR et al.
Mol Syst Biol (2021)
Deconstructing the Treatment Effect of Remdesivir in the Adaptive COVID-19 Treatment Trial-1: Implications for Critical Care Resource Utilization
Fintzi, J; Bonnett, T; Sweeney, DA et al.
Clin Infect Dis (2021)
Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome
Sulaiman, I; Chung, M; Angel, L et al.
Nat Microbiol (2021)
SARS-CoV-2 S2P spike ages through distinct states with altered immunogenicity
Olia, AS; Tsybovsky, Y; Chen, SJ et al.
J Biol Chem (2021)
Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants
Xu, J; Xu, K; Jung, S et al.
Nature (2021)
Genome-wide covariation in SARS-CoV-2
Cresswell-Clay, E; Periwal, V; ,
Math Biosci (2021)
JAK inhibitors dampen activation of interferon-activated transcriptomes and the SARS-CoV-2 receptor ACE2 in human renal proximal tubules
Jankowski, J; Lee, HK; Wilflingseder, J; Hennighausen, L; ,
iScience (2021)
Host-Virus Chimeric Events in SARS-CoV-2-Infected Cells Are Infrequent and Artifactual
Yan, B; Chakravorty, S; Mirabelli, C et al.
J Virol (2021)
Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan
Tamim, S; Trovao, NS; Thielen, P et al.
Infect Genet Evol (2021)
Host-virus chimeric events in SARS-CoV2 infected cells are infrequent and artifactual
Yan, B; Chakravorty, S; Mirabelli, C et al.
bioRxiv (2021)
Assessing vaccine durability in randomized trials following placebo crossover
Fintzi, J; Follmann, D; ,
Stat Med (2021)
Predictable fold switching by the SARS-CoV-2 protein ORF9b
Porter, LL
Protein Sci (2021)
JAK inhibitors dampen activation of interferon-stimulated transcription of ACE2 isoforms in human airway epithelial cells
Lee, HK; Jung, O; Hennighausen, L; ,
Commun Biol (2021)
COVID-19-CT-CXR: A Freely Accessible and Weakly Labeled Chest X-Ray and CT Image Collection on COVID-19 From Biomedical Literature
Peng, Y; Tang, Y; Lee, S et al.
IEEE Trans Big Data (2021)
Social Heterogeneity Drives Complex Patterns of the COVID-19 Pandemic: Insights From a Novel Stochastic Heterogeneous Epidemic Model (SHEM)
Alexander V. Maltsev & Michael D. Stern*
Front. Phys. (2021)
FIB-SEM as a Volume Electron Microscopy Approach to Study Cellular Architectures in SARS-CoV-2 and Other Viral Infections: A Practical Primer for a Virologist
Baena, V; Conrad, R; Friday, P et al.
Viruses (2021)
COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support
Shea, K; Borchering, RK; Probert, WJM et al.
medRxiv (2020)
SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation
Yan, B; Freiwald, T; Chauss, D et al.
Sci Immunol (2021)
Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection
Singh, K; Chen, YC; Hassanzadeh, S et al.
Front Genet (2021)
SARS-CoV-2 infection of the oral cavity and saliva
Huang, N; Pérez, P; Kato, T et al.
Nat Med (2021)
Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2
Ghorbani, M; Brooks, BR; Klauda, JB; ,
Biophys J (2021)
Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area
Thielen, PM; Wohl, S; Mehoke, T et al.
JCI Insight (2021)
Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community
Lee, HK; Knabl, L; Pipperger, L et al.
Sci Rep (2021)
Inborn errors of type I IFN immunity in patients with life-threatening COVID-19
Zhang, Q; Bastard, P; Liu, Z et al.
Science (2020)
Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics
Pillon, MC; Frazier, MN; Dillard, LB et al.
Nat Commun (2021)
A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication
Hattori, SI; Higashi-Kuwata, N; Hayashi, H et al.
Nat Commun (2021)
An immune-based biomarker signature is associated with mortality in COVID-19 patients
Abers, MS; Delmonte, OM; Ricotta, EE et al.
JCI Insight (2020)
Characterizing transcriptional regulatory sequences in coronaviruses and their role in recombination
Yang, Y; Yan, W; Hall, AB; Jiang, X; ,
Mol Biol Evol (2020)
Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations
Ghorbani, M; Brooks, BR; Klauda, JB; ,
J Phys Chem B (2020)
Interferons and viruses induce a novel truncated ACE2 isoform and not the full-length SARS-CoV-2 receptor
Onabajo, OO; Banday, AR; Stanifer, ML et al.
Nat Genet (2020)
Activation of the SARS-CoV-2 Receptor Ace2 through JAK/STAT-Dependent Enhancers during Pregnancy
Hennighausen, L; Lee, HK; ,
Cell Rep (2020)
Serological Responses to Human Virome Define Clinical Outcomes of Italian Patients Infected with SARS-CoV-2
Wang, L; Candia, J; Ma, L et al.
medRxiv (2020)
In silico Drug Repurposing to combat COVID-19 based on Pharmacogenomics of Patient Transcriptomic Data
Das, S; Camphausen, K; Shankavaram, U; ,
Res Sq (2020)
GRL-0920, an Indole Chloropyridinyl Ester, Completely Blocks SARS-CoV-2 Infection
Hattori, SI; Higshi-Kuwata, N; Raghavaiah, J et al.
mBio (2020)
In vitro and in vivo identification of clinically approved drugs that modify ACE2 expression
Sinha, S; Cheng, K; Schäffer, AA; Aldape, K; Schiff, E; Ruppin, E;
Mol. Syst. Biol. (2020)
Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing
Riva, L; Yuan, S; Yin, X et al.
Nature (2020)
Preprints are complete and public drafts of scientific documents, not yet peer reviewed. (More about preprints)
Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein
Zhao, H; Nguyen, A; Wu, D et al.
bioRxiv (2022)
Putative host-derived insertions in the genome of circulating SARS-CoV-2 variants
Yang, Y; Dufault-Thompson, K; Fontenele, RS; Jiang, X; ,
bioRxiv (2022)
Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion
Nussenblatt, V; Roder, AE; Das, S et al.
medRxiv (2021)
Robust immune response to the BNT162b mRNA vaccine in an elderly population vaccinated 15 months after recovery from COVID-19
Lee, HK; Knabl, L; Knabl, L et al.
medRxiv (2021)
Synthetic lethality-based prediction of anti-SARS-CoV-2 targets
Pal, LR; Cheng, K; Nair, NU et al.
bioRxiv (2021)
Regulation of the Dimerization and Activity of SARS-CoV-2 Main Protease through Reversible Glutathionylation of Cysteine 300
Davis, DA; Bulut, H; Shrestha, P et al.
bioRxiv (2021)
Genetic regulation of OAS1 nonsense-mediated decay underlies association with risk of severe COVID-19
Banday, AR; Stanifer, ML; Florez-Vargas, O et al.
medRxiv (2021)
Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation
Lee, HK; Knabl, L; Knabl, L et al.
medRxiv (2021)
Impact of BNT162b first vaccination on the immune transcriptome of elderly patients infected with the B.1.351 SARS-CoV-2 variant
Knabl, L; Lee, HK; Wieser, M et al.
medRxiv (2021)
Furin cleavage of the SARS-CoV-2 spike is modulated by O-glycosylation
Zhang, L; Mann, M; Syed, Z et al.
bioRxiv (2021)
Cryo-EM Structures of the SARS-CoV-2 Endoribonuclease Nsp15
Pillon, MC; Frazier, MN; Dillard, LB et al.
bioRxiv (2020)
Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules
Jankowski, J; Lee, HK; Wilflingseder, J; Hennighausen, L; ,
bioRxiv (2021)
Integrated Single-Cell Atlases Reveal an Oral SARS-CoV-2 Infection and Transmission Axis
Huang, N; Perez, P; Kato, T et al.
medRxiv (2020)
Assessing Durability of Vaccine Effect Following Blinded Crossover in COVID-19 Vaccine Efficacy Trials
Follmann, D; Fintzi, J; Fay, MP et al.
medRxiv (2020)
Activation of Interferon-Stimulated Transcriptomes and ACE2 Isoforms in Human Airway Epithelium Is Curbed by Janus Kinase Inhibitors
Lee, HK; Jung, O; Hennighausen, L; ,
Res Sq (2020)
Activation of ACE2 and interferon-stimulated transcriptomes in human airway epithelium is curbed by Janus Kinase inhibitors
Lee, HK; Jung, O; Hennighausen, L; ,
bioRxiv (2020)
Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences
Karasik A, Jones D, DePass A, Guydosh N
bioRxiv (2020)
Using multiple data streams to estimate and forecast SARS-CoV-2 transmission dynamics, with application to the virus spread in Orange County, California
Fintzi, J; Bayer, D; Goldstein, I et al.
ArXiv (2020)
Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region
Theilen PM; Wohl S; Mehoke T; et al
medRxiv (202)
An autocrine Vitamin D-driven Th1 shutdown program can be exploited for COVID-19
McGregor, R; Chauss, D; Freiwald, T et al.
bioRxiv (2020)
SARS-CoV2 drives JAK1/2-dependent local and systemic complement hyper-activation
Yan, B; Freiwald, T; et al
researchsquare (2020)
Statistical Physics of Epidemic on Network Predictions for SARS-CoV-2 Parameters
Han, J; Cresswell-Clay, EC; Periwal, V
ArXiv (2020)
Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations
Ghorbani, M; Brooks, BR; Klauda JB
bioRxiv (2020)
Global prediction of unreported SARS-CoV2 infection from observed COVID-19 cases
Chow, CC; Chang, JC; Gerkin, RC; Vattikuti, S;
medRxiv (2020)
Activation of the SARS-CoV-2 receptor Ace2 by cytokines through pan JAK-STAT enhancers
Hennighausen, L; Lee, HK;
bioRxiv (2020)