| Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans PS Arunachalam, F Wimmers, CKP Mok, RAPM Perera, M Scott, T Hagan, ... Science 369 (6508), 1210-1220, 2020 | 1095 | 2020 |
| Antibiotics-driven gut microbiome perturbation alters immunity to vaccines in humans T Hagan, M Cortese, N Rouphael, C Boudreau, C Linde, MS Maddur, ... Cell 178 (6), 1313-1328. e13, 2019 | 472 | 2019 |
| Slow delivery immunization enhances HIV neutralizing antibody and germinal center responses via modulation of immunodominance KM Cirelli, DG Carnathan, B Nogal, JT Martin, OL Rodriguez, ... Cell 177 (5), 1153-1171. e28, 2019 | 350 | 2019 |
| Type I and type III interferons restrict SARS-CoV-2 infection of human airway epithelial cultures A Vanderheiden, P Ralfs, T Chirkova, AA Upadhyay, MG Zimmerman, ... Journal of virology 94 (19), 10.1128/jvi. 00985-20, 2020 | 298 | 2020 |
| Systemic HIV and SIV latency reversal via non-canonical NF-κB signalling in vivo CC Nixon, M Mavigner, GC Sampey, AD Brooks, RA Spagnuolo, ... Nature 578 (7793), 160-165, 2020 | 246 | 2020 |
| Baricitinib treatment resolves lower-airway macrophage inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques TN Hoang, M Pino, AK Boddapati, EG Viox, CE Starke, AA Upadhyay, ... Cell 184 (2), 460-475. e21, 2021 | 188 | 2021 |
| Cache domains that are homologous to, but different from PAS domains comprise the largest superfamily of extracellular sensors in prokaryotes AA Upadhyay, AD Fleetwood, O Adebali, RD Finn, IB Zhulin PLoS computational biology 12 (4), e1004862, 2016 | 170 | 2016 |
| The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen C Havenar-Daughton, A Sarkar, DW Kulp, L Toy, X Hu, I Deresa, ... Science translational medicine 10 (448), eaat0381, 2018 | 125 | 2018 |
| A modified vaccinia Ankara vector-based vaccine protects macaques from SARS-CoV-2 infection, immune pathology, and dysfunction in the lungs NK Routhu, N Cheedarla, S Gangadhara, VS Bollimpelli, AK Boddapati, ... Immunity 54 (3), 542-556. e9, 2021 | 82 | 2021 |
| BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data AA Upadhyay, RC Kauffman, AN Wolabaugh, A Cho, NB Patel, SM Reiss, ... Genome medicine 10, 1-18, 2018 | 59 | 2018 |
| West Nile virus-inclusive single-cell RNA sequencing reveals heterogeneity in the type I interferon response within single cells JT O’Neal, AA Upadhyay, A Wolabaugh, NB Patel, SE Bosinger, ... Journal of virology 93 (6), 10.1128/jvi. 01778-18, 2019 | 57 | 2019 |
| Rapid germinal center and antibody responses in non-human primates after a single nanoparticle vaccine immunization C Havenar-Daughton, DG Carnathan, AV Boopathy, AA Upadhyay, ... Cell reports 29 (7), 1756-1766. e8, 2019 | 53 | 2019 |
| How bacterial chemoreceptors evolve novel ligand specificities JA Gavira, VM Gumerov, M Rico-Jiménez, M Petukh, AA Upadhyay, ... MBio 11 (1), 10.1128/mbio. 03066-19, 2020 | 52 | 2020 |
| Sequence, structure, and evolution of cellulases in glycoside hydrolase family 48 LO Sukharnikov, M Alahuhta, R Brunecky, A Upadhyay, ME Himmel, ... Journal of Biological Chemistry 287 (49), 41068-41077, 2012 | 47 | 2012 |
| Infiltration of inflammatory macrophages and neutrophils and widespread pyroptosis in lung drive influenza lethality in nonhuman primates J Corry, G Kettenburg, AA Upadhyay, M Wallace, MM Marti, ... PLoS Pathogens 18 (3), e1010395, 2022 | 33 | 2022 |
| IL-21 and IFNα therapy rescues terminally differentiated NK cells and limits SIV reservoir in ART-treated macaques J Harper, N Huot, L Micci, G Tharp, C King, P Rascle, N Shenvi, H Wang, ... Nature Communications 12 (1), 2866, 2021 | 29 | 2021 |
| From structure to sequence: antibody discovery using cryoEM A Antanasijevic, CA Bowman, RN Kirchdoerfer, CA Cottrell, G Ozorowski, ... Science Advances 8 (3), eabk2039, 2022 | 23 | 2022 |
| Early T follicular helper cell activity accelerates hepatitis C virus-specific B cell expansion E Salinas, M Boisvert, AA Upadhyay, N Bédard, SA Nelson, J Bruneau, ... The Journal of Clinical Investigation 131 (2), 2021 | 18 | 2021 |
| Clinical and whole genome characterization of SARS-CoV-2 in India R Muttineni, N Kammili, TC Bingi, R Rao M, K Putty, PS Dholaniya, ... PLoS One 16 (2), e0246173, 2021 | 13 | 2021 |
| TREM2+ and interstitial-like macrophages orchestrate airway inflammation in SARS-CoV-2 infection in rhesus macaques AA Upadhyay, EG Viox, TN Hoang, AK Boddapati, M Pino, MYH Lee, ... Nature Communications 14 (1), 1914, 2023 | 12 | 2023 |
