Biowulf High Performance Computing at the NIH

Covid-19 Research Support on Biowulf

Covid-Related Projects

79.4+ Million CPU hours used
1.8+ Million jobs run

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]
Coronavirus-related work being performed on Biowulf by NIH intramural researchers includes:

Biowulf users with COVID-related projects should contact the HPC staff to get increased priority for their jobs.

Peer-Reviewed Scientific Papers Utilizing Biowulf

thumbnail image from paper 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)

thumbnail image from paper SARS-CoV-2 S2P spike ages through distinct states with altered immunogenicity
Olia, AS; Tsybovsky, Y; Chen, SJ et al.
J Biol Chem (2021)

thumbnail image from paper Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants
Xu, J; Xu, K; Jung, S et al.
Nature (2021)

thumbnail image from paper Genome-wide covariation in SARS-CoV-2
Cresswell-Clay, E; Periwal, V; ,
Math Biosci (2021)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper Host-virus chimeric events in SARS-CoV2 infected cells are infrequent and artifactual
Yan, B; Chakravorty, S; Mirabelli, C et al.
bioRxiv (2021)

thumbnail image from paper Assessing vaccine durability in randomized trials following placebo crossover
Fintzi, J; Follmann, D; ,
Stat Med (2021)

thumbnail image from paper Predictable fold switching by the SARS-CoV-2 protein ORF9b
Porter, LL
Protein Sci (2021)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper SARS-CoV-2 drives JAK1/2-dependent local complement hyperactivation
Yan, B; Freiwald, T; Chauss, D et al.
Sci Immunol (2021)

thumbnail image from paper 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)

thumbnail image from paper SARS-CoV-2 infection of the oral cavity and saliva
Huang, N; Pérez, P; Kato, T et al.
Nat Med (2021)

thumbnail image from paper Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2
Ghorbani, M; Brooks, BR; Klauda, JB; ,
Biophys J (2021)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper Inborn errors of type I IFN immunity in patients with life-threatening COVID-19
Zhang, Q; Bastard, P; Liu, Z et al.
Science (2020)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper An immune-based biomarker signature is associated with mortality in COVID-19 patients
Abers, MS; Delmonte, OM; Ricotta, EE et al.
JCI Insight (2020)

thumbnail image from paper Characterizing transcriptional regulatory sequences in coronaviruses and their role in recombination
Yang, Y; Yan, W; Hall, AB; Jiang, X; ,
Mol Biol Evol (2020)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper In silico Drug Repurposing to combat COVID-19 based on Pharmacogenomics of Patient Transcriptomic Data
Das, S; Camphausen, K; Shankavaram, U; ,
Res Sq (2020)

thumbnail image from paper GRL-0920, an Indole Chloropyridinyl Ester, Completely Blocks SARS-CoV-2 Infection
Hattori, SI; Higshi-Kuwata, N; Raghavaiah, J et al.
mBio (2020)

thumbnail image from paper 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)

thumbnail image from paper Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing
Riva, L; Yuan, S; Yin, X et al.
Nature (2020)

Covid-Related Preprint Papers Utilizing Biowulf

Preprints are complete and public drafts of scientific documents, not yet peer reviewed. (More about preprints)

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)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa
Okoh, OS; Nii-Trebi, NI; Jakkari, A et al.
medRxiv (2021)

thumbnail image from paper 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)

thumbnail image from paper Genome-scale metabolic modeling reveals SARS-CoV-2-induced host metabolic reprogramming and identifies metabolic antiviral targets
Cheng, K; Riva, L; Sinha, S et al.
bioRxiv (2021)

thumbnail image from paper Cryo-EM Structures of the SARS-CoV-2 Endoribonuclease Nsp15
Pillon, MC; Frazier, MN; Dillard, LB et al.
bioRxiv (2020)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences
Karasik A, Jones D, DePass A, Guydosh N
bioRxiv (2020)

thumbnail image from paper Societal heterogeneity contributes to complex dynamic patterns of the COVID-19 pandemics: insights from a novel Stochastic Heterogeneous Epidemic Model (SHEM)
Maltsev, AV; Stern, M; ,
medRxiv (2020)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper An autocrine Vitamin D-driven Th1 shutdown program can be exploited for COVID-19
McGregor, R; Chauss, D; Freiwald, T et al.
bioRxiv (2020)

thumbnail image from paper SARS-CoV2 drives JAK1/2-dependent local and systemic complement hyper-activation
Yan, B; Freiwald, T; et al
researchsquare (2020)

thumbnail image from paper Statistical Physics of Epidemic on Network Predictions for SARS-CoV-2 Parameters
Han, J; Cresswell-Clay, EC; Periwal, V
ArXiv (2020)

thumbnail image from paper Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations
Ghorbani, M; Brooks, BR; Klauda JB
bioRxiv (2020)

thumbnail image from paper Systematic Cell Line-Based Identification of Drugs Modifying ACE2 Expression
Sinha, S; Cheng, K; Aldape, K; Schiff, E; Ruppin, E
preprints.org (2020)

thumbnail image from paper Global prediction of unreported SARS-CoV2 infection from observed COVID-19 cases
Chow, CC; Chang, JC; Gerkin, RC; Vattikuti, S;
medRxiv (2020)

thumbnail image from paper Activation of the SARS-CoV-2 receptor Ace2 by cytokines through pan JAK-STAT enhancers
Hennighausen, L; Lee, HK;
bioRxiv (2020)