Covid-Related Projects 61.5+ Million CPU hours used 1.4+ 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:

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

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

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)

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)

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)

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)

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)

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)

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

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, YX; Lee, S; Zhu, Y; Summers, RM; Lu, Z;
ArXiv (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)