Biowulf High Performance Computing at the NIH

Covid-19 Research Support on Biowulf

Covid-Related Projects

50.9+ Million CPU hours used
1.2+ Million jobs run

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 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 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 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)

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 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)

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 Cryo-EM Structures of the SARS-CoV-2 Endoribonuclease Nsp15
Pillon, MC; Frazier, MN; Dillard, LB et al.
bioRxiv (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 An autocrine Vitamin D-driven Th1 shutdown program can be exploited for COVID-19
McGregor R; Chauss, D; et al.
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 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 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)

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)

thumbnail image from paper Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection
Singh, K; Chen, YC; Judy, JT; Seifuddin, F; Tunc, I; Pirooznia, M;
bioRxiv (2020)