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

Covid-Related Research on Biowulf 87.6+ Million CPU hours used 2.1+ Million jobs run 61 Peer-Reviewed papers 27 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:

• Stochastic modeling of COVID-19 pandemic infection patterns [Michael Stern group, NIA]
• 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]
• SARS-CoV-2 RNA structural analyses [Markus Hafner group, NIAMS]
• Cryo-electron microscopy of virus proteins and complexes [Natalia de Val & Eric Freed group, NCI_CCR]
• (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]
• Transcriptomics and network analysis of SARS-CoV-2 infection [Mehdi Pirooznia & Robert Balaban group, NHLBI]
• Deep Learning models of chest Xray and CT images [Ronald Summers group, CC]
• Structure of complexes of the SARS-CoV-2 ectodomain with a variety of ligands [Mario Borgnia & William Copeland group, NIEHS]
• Determining the incidence of age-related clonal hematopoiesis in mild vs. severe COVID-19 patient [Cynthia Dunbar group, NHLBI]
• MD Simulations and Glycan Network Analysis of SARS-COV-2 spike protein [Bernard Brooks group, NHLBI]
• Assessing newly generated and previously known compounds for activity against SARS-Cov-2 [Hiroaki Mitsuya group, NCI]
• Genetic Determinants of Susceptibility to Severe COVID-19 Infection [NIAID Consortium. Director: Helen Su group, NIAID]
• Modeling unreported SARS-Cov2 infection from observed cases, computational modeling of Covid-19 biological systems. [Carson Chow group, NIDDK]
• 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]
• Investigating the transcriptional regulators of hyper-inflammatory responses to SARs-CoV2 infection [Behdad Afzali group, NIDDK]
• Studying maturation of the SARS Cov2 main protease [Robert Best group, NIDDK]
• Modeling, global surveillance, real-time genomic sequencing and phylodynamics of SARS-CoV-2 [Cecile Viboud group, FIC]
• In silico screening of drug candidates [Nadya Tarasova group, NCI]
• 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]
• Simulations of infection spread in populations [Vipul Periwal group, NIDDK]
• Text mining of COVID-related scientific literature in LitCovid and CORD-19 [Zhiyong Lu group, NLM/NCBI]
• Image processing and text mining of clinical data for the NIAID COVID Data Management Working Group [Robert Hohman group, NIAID]
• Atomic-level structure of the SARS-CoV-2 spike using cryo-electron microscopy [Peter Kwong group, NIAID_VRC]
• Genome-wide association study of COVID-19 genetic variants vs. phenotypes in the UK BioBank [Andrew Johnson group, NHLBI]
• Metagenomics of Covid-19 family [Xiaofang Jiang group, NLM]
• Text mining of COVID-related scientific literature in LitCovid and CORD-19 [Zhiyong Lu group, NLM/NCBI]
• Investigation of pathogenic characteristics of COVID-19 by analysis of RNA-seq data from human patients [Lothar Hennighausen group, NIDDK]
• MD simulation of SARS-CoV-2 spike protein [Peter Kwong group, NIAID_VRC]
• Studying Interferon-induced variability in ACE2 expression levels [Liudmila Prokunina-Olsson group, NCI]

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

61 peer-reviewed papers

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)

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)

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)

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)

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)

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 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)

Covid-Related Preprint Papers Utilizing Biowulf

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

27 preprint papers

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)

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)

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

Structures of synthetic nanobody-SARS-CoV-2-RBD complexes reveal distinct sites of interaction and recognition of variants
Ahmad, J; Jiang, J; Boyd, LF et al.
Res Sq (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)

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)

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)