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

Covid-Related Research on Biowulf 0 Million CPU hours used 0 Million jobs run 105 Peer-Reviewed papers 0 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:

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

105 peer-reviewed papers

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

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)

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)

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)

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

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)

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)

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)

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)

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)

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)

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)

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)

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

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)

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)

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)

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)

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)

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

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)

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)

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)

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)

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)

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

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

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

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)

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)

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

Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa
Okoh, OS; Nii-Trebi, NI; Jakkari, A et al.
iScience (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)

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)

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

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)

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)

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)

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)

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)

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)

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 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)

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)

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)

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)

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)

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)

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 reveal insight into nuclease specificity and dynamics
Pillon, MC; Frazier, MN; Dillard, LB et al.
Nat Commun (2021)

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

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)

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)

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 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 SARS-CoV-2 Receptor Ace2 through JAK/STAT-Dependent Enhancers during Pregnancy
Hennighausen, L; Lee, HK; ,
Cell Rep (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)

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

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

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

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

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

The cv19 enhanced priority on Biowulf ended in June 2023

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