Biowulf High Performance Computing at the NIH

Covid-19 Research Support on Biowulf

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

Covid-Related Research on Biowulf

89.1+ Million CPU hours used
2.2+ Million jobs run
79 Peer-Reviewed papers
26 Preprint papers

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

79 peer-reviewed papers

thumbnail image from paper Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer
McBride, DS; Garushyants, SK; Franks, J et al.
Nat Commun (2023)

thumbnail image from paper Exposure to lung-migrating helminth protects against murine SARS-CoV-2 infection through macrophage-dependent T cell activation
Oyesola, OO; Hilligan, KL; Namasivayam, S et al.
Sci Immunol (2023)

Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data
Roder, AE; Johnson, KEE; Knoll, M et al.
mBio (2023)

thumbnail image from paper Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children
Xu, Q; Milanez-Almeida, P; Martins, AJ et al.
Nat Immunol (2023)

thumbnail image from paper Topoisomerase 3b is dispensable for replication of a positive-sense RNA virus--murine coronavirus
Zhang, T; Su, S; Altouma, V et al.
Antiviral Res (2022)

thumbnail image from paper A conserved oligomerization domain in the disordered linker of coronavirus nucleocapsid proteins
Zhao, H; Wu, D; Hassan, SA et al.
Sci Adv (2023)

thumbnail image from paper Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA
Fontenele, RS; Yang, Y; Driver, EM et al.
Sci Total Environ (2023)

thumbnail image from paper Identification of SARS-CoV-2 Mpro inhibitors containing P1’ 4-fluorobenzothiazole moiety highly active against SARS-CoV-2
Higashi-Kuwata, N; Tsuji, K; Hayashi, H et al.
Nat Commun (2023)

thumbnail image from paper Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD
Chen, Y; Prévost, J; Ullah, I et al.
iScience (2023)

Analysis of immune responses in CLL patients after heterologous COVID-19 vaccination
Lee, HK; Hoechstetter, MA; Buchner, M et al.
Blood Adv (2023)

thumbnail image from paper Direct Cryo-ET observation of platelet deformation induced by SARS-CoV-2 spike protein
Kuhn, CC; Basnet, N; Bodakuntla, S et al.
Nat Commun (2023)

thumbnail image from paper Spleen tyrosine kinase inhibition restores myeloid homeostasis in COVID-19
Wigerblad, G; Warner, SA; Ramos-Benitez, MJ et al.
Sci Adv (2023)

Serological responses to human virome define clinical outcomes of Italian patients infected with SARS-CoV-2
Wang, L; Candia, J; Ma, L et al.
Int J Biol Sci (2022)

Acute worsening of CADASIL in a patient with COVID-19 infection: illustrative case
Rosenblum, JS; Tunacao, JM; Nazari, MA et al.
J Neurosurg Case Lessons (2022)

thumbnail image from paper Temporal Improvements in COVID-19 Outcomes for Hospitalized Adults: A Post Hoc Observational Study of Remdesivir Group Participants in the Adaptive COVID-19 Treatment Trial
Potter, GE; Bonnett, T; Rubenstein, K et al.
Ann Intern Med (2022)

thumbnail image from paper Intranasal delivery of a rationally attenuated SARS-CoV-2 is immunogenic and protective in Syrian hamsters
Liu, S; Stauft, CB; Selvaraj, P et al.
Nat Commun (2022)

thumbnail image from paper Limited cross-variant immune response from SARS-CoV-2 Omicron BA.2 in naïve but not previously infected outpatients
Lee, HK; Knabl, L; Walter, M et al.
iScience (2022)

thumbnail image from paper Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease
Frazier, MN; Wilson, IM; Krahn, JM et al.
Nucleic Acids Res (2022)

thumbnail image from paper Genetic regulation of OAS1 nonsense-mediated decay underlies association with COVID-19 hospitalization in patients of European and African ancestries
Banday, AR; Stanifer, ML; Florez-Vargas, O et al.
Nat Genet (2022)

Clonal Hematopoiesis Is Not Significantly Associated with Covid-19 Disease Severity
Zhou, Y; Shalhoub, RN; Rogers, SN et al.
Blood (2022)

thumbnail image from paper A Path-Based Analysis of Infected Cell Line and COVID-19 Patient Transcriptome Reveals Novel Potential Targets and Drugs Against SARS-CoV-2
Agrawal, P; Sambaturu, N; Olgun, G; Hannenhalli, S; ,
Front Immunol (2022)

thumbnail image from paper Dromedary camel nanobodies broadly neutralize SARS-CoV-2 variants
Hong, J; Kwon, HJ; Cachau, R et al.
Proc Natl Acad Sci U S A (2022)

thumbnail image from paper Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein
Zhao, H; Nguyen, A; Wu, D et al.
PNAS Nexus (2022)

thumbnail image from paper Unraveling the Treatment Effect of Baricitinib on Clinical Progression and Resource Utilization in Hospitalized COVID-19 Patients: Secondary Analysis of the Adaptive COVID-19 Treatment Randomized Trial-2
Fintzi, J; Bonnett, T; Tebas, P et al.
Open Forum Infect Dis (2022)

thumbnail image from paper Prior Vaccination Exceeds Prior Infection in Eliciting Innate and Humoral Immune Responses in Omicron Infected Outpatients
Lee, HK; Knabl, L; Walter, M et al.
Front Immunol (2022)

thumbnail image from paper Putative Host-Derived Insertions in the Genomes of Circulating SARS-CoV-2 Variants
Yang, Y; Dufault-Thompson, K; Salgado Fontenele, R; Jiang, X; ,
mSystems (2022)

thumbnail image from paper Heterologous ChAdOx1-BNT162b2 vaccination in Korean cohort induces robust immune and antibody responses that includes Omicron
Lee, HK; Go, J; Sung, H et al.
iScience (2022)

thumbnail image from paper SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal
Borges, V; Isidro, J; Trovão, NS et al.
Commun Med (Lond) (2022)

thumbnail image from paper Synthetic lethality-based prediction of anti-SARS-CoV-2 targets
Pal, LR; Cheng, K; Nair, NU et al.
iScience (2022)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper 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)

thumbnail image from paper Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module
Lee, HK; Knabl, L; Knabl, L et al.
Sci Rep (2022)

thumbnail image from paper SARS-CoV-2 infection in free-ranging white-tailed deer
Hale, VL; Dennis, PM; McBride, DS et al.
Nature (2022)

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.
iScience (2022)

thumbnail image from paper Structural basis and mode of action for two broadly neutralizing antibodies against SARS-CoV-2 emerging variants of concern
Li, W; Chen, Y; Prévost, J et al.
Cell Rep (2022)

thumbnail image from paper Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U
Frazier, MN; Dillard, LB; Krahn, JM et al.
Nucleic Acids Res (2021)

thumbnail image from paper Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction
Ahmad, J; Jiang, J; Boyd, LF et al.
J Biol Chem (2021)

thumbnail image from paper 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)

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)

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)

The NIH Lipo-COVID Study: A Pilot NMR Investigation of Lipoprotein Subfractions and Other Metabolites in Patients with Severe COVID-19
Ballout, RA; Kong, H; Sampson, M et al.
Biomedicines (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.
mBio (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 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)

Cell-free DNA maps COVID-19 tissue injury and risk of death and can cause tissue injury
Andargie, TE; Tsuji, N; Seifuddin, F et al.
JCI Insight (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)

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)

The cv19 enhanced priority on Biowulf ended in June 2023

Covid-Related Preprint Papers Utilizing Biowulf

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

26 preprint papers

thumbnail image from paper Comprehensive analysis of immune responses in CLL patients after heterologous COVID-19 vaccination
Lee, HK; Hoechstetter, MA; Buchner, M et al.
medRxiv (2022)

thumbnail image from paper Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance
Mushegian, A; Long, SW; Olsen, RJ et al.
medRxiv (2022)

thumbnail image from paper Limited cross-variant immune response from SARS-CoV-2 Omicron BA.2 in naïve but not previously infected outpatients
Lee, HK; Knabl, L; Walter, M et al.
medRxiv (2022)

thumbnail image from paper Camel nanobodies broadly neutralize SARS-CoV-2 variants
Hong, J; Kwon, HJ; Cachau, R et al.
bioRxiv (2021)

thumbnail image from paper Putative host-derived insertions in the genome of circulating SARS-CoV-2 variants
Yang, Y; Dufault-Thompson, K; Fontenele, RS; Jiang, X; ,
bioRxiv (2022)

thumbnail image from paper 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)

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 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 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 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 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)