Author

A. A. Upadhyay

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Immunology· 5 Microbiology· 3

Signature Assays, Organisms & Methods

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Approach:experimental assay· 7 Research Focus:host-pathogen & immune response· 4 Organism:rat· 4 Research Focus:cell type annotation· 3 Assay:bulk RNA-seq· 2 Research Focus:cell-cell communication· 2 Research Focus:differential expression· 2 Assay:scRNA-seq· 2

Frequent Co-Authors

S. E. Bosinger· 7 shared G. K. Tharp· 5 shared T. H. Vanderford· 4 shared A. K. Boddapati· 3 shared E. G. Viox· 3 shared G. Silvestri· 3 shared J. L. Harper· 3 shared K. L. Pellegrini· 3 shared

Activity by Year

2018-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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7 shared papersImmunology

S. E. Bosinger

Mutual co-authors in cluster

Author profile →

8 papers

Recent·Most cited

Modulation of type I interferon responses potently inhibits SARS-CoV-2 replication and inflammation in rhesus macaques

T. N. Hoang, E. G. Viox, A. A. Upadhyay, Z. Strongin, G. K. Tharp, M. Pino, R. Nchioua, M. Hirschenberger, M. Gagne, K. Nguyen, J. L. Harper, S. Marciano, A. K. Boddapati, K. L. Pellegrini, J. Tisoncik-Go, , M. Paiardini

This study shows that modulating type I interferon responses in rhesus macaques reduces SARS-CoV-2 viral load and inflammation, suggesting a potential therapeutic strategy for severe COVID-19.

bioRxiv · Oct 21, 2022Immunology

TREM2+ and interstitial macrophages orchestrate airway inflammation in SARS-CoV-2 infection in rhesus macaques

A. A. Upadhyay, T. N. Hoang, M. Pino, A. K. Boddapati, E. G. Viox, M. Y. H. Lee, J. Corry, Z. Strongin, D. A. Cowan, E. N. Beagle, T. R. Horton, S. Hamilton, H. Aoued, J. L. Harper, K. Nguyen, , S. E. Bosinger

This study identifies two macrophage populations driving inflammation in the lower airway during SARS-CoV-2 infection in rhesus macaques and shows baricitinib effectively reduces their influx and cytokine production.

bioRxiv · Oct 5, 2021 · PreprintMicrobiology

From Structure to Sequence: Identification of polyclonal antibody families using cryoEM

A. Antanasijevic, C. A. Bowman, R. N. Kirchdoerfer, C. A. Cottrell, G. Ozorowski, A. A. Upadhyay, K. M. Cirelli, D. G. Carnathan, C. A. Enemuo, L. M. Sewall, B. Nogal, F. Zhao, B. Groschel, W. R. Schief, D. Sok, , A. B. Ward

This paper uses cryoEM and next-generation sequencing to identify monoclonal antibodies from polyclonal sera and validate their antigen-binding properties.

bioRxiv · Apr 13, 2021 · PreprintImmunology

Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques

T. N. Hoang, M. Pino, A. K. Boddapati, E. G. Viox, C. E. Starke, A. A. Upadhyay, S. Gumber, K. Busman-Sahay, Z. Strongin, J. L. Harper, G. K. Tharp, K. L. Pellegrini, S. Kirejczyk, K. Zandi, S. Tao, , Bosinger

This study shows baricitinib reduces lung inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques without affecting viral shedding or immune responses.

bioRxiv · Sep 16, 2020Immunology

Type I and Type III IFN Restrict SARS-CoV-2 Infection of Human Airway Epithelial Cultures

A. Vanderheiden, P. Ralfs, T. Chirkova, A. A. Upadhyay, M. G. Zimmerman, S. Bedoya, H. Aoued, G. K. Tharp, K. Pellegrini, A. C. Lowen, V. D. Menachery, L. J. Anderson, A. Grakoui, S. E. Bosinger, M. S. Suthar

This study shows SARS-CoV-2 infects human airway epithelial cultures, induces pro-inflammatory cytokines, and is inhibited by type I and III IFNs.

bioRxiv · May 19, 2020Microbiology

Microbiome Stability with Chronic SIV Infection in AIDS-resistant Sooty Mangabeys

R. M. Bochart, G. K. Tharp, S. Jean, A. A. Upadhyay, M. M. Crane, T. H. Vanderford, A. M. Ortiz, A. Ericsen, J. Cohen, S. E. Bosinger

This study compares the gut microbiota stability in SIV-infected sooty mangabeys and rhesus macaques, finding that SMs maintain microbiota stability while RMs show community divergence.

bioRxiv · Sep 24, 2019 · PreprintImmunology

West Nile virus-inclusive single-cell RNA sequencing reveals heterogeneity in the type I interferon response within single cells

J. T. O'Neal, A. A. Upadhyay, A. Wolabaugh, N. B. Patel, S. E. Bosinger, M. S. Suthar

The paper uses WNV-inclusive scRNA-seq to show single-cell heterogeneity in IFN-I response and viral RNA abundance during WNV infection.

bioRxiv · Oct 4, 2018Microbiology

Slow delivery immunization enhances HIV neutralizing antibody and germinal center responses via modulation of immunodominance

K. M. Cirelli, D. G. Carnathan, B. Nogal, O. L. Rodriguez, J. T. Martin, A. A. Upadhyay, C. A. Enemuo, E. H. Gebru, Y. Choe, F. Viviano, C. Nakao, M. Pauthner, S. Reiss, C. A. Cottrell, R. Bastidas, , S. Crotty

This study shows that slow delivery immunization in rhesus macaques increases HIV-neutralizing antibody titers and germinal center responses by modulating immunodominance.

bioRxiv · Oct 1, 2018Immunology