High throughput analysis of B cell dynamics and neutralizing antibody development during immunization with a novel clade C HIV-1 envelope. by Rohini Mopuri, Sarah Welbourn, Tysheena Charles, Pooja Ralli-Jain, David Rosales, Samantha Burton, Areeb Aftab, Kirti Karunakaran, Kathryn Pellegrini, William Kilembe, Etienne Karita, Sandrasegaram Gnanakaran, Amit A Upadhyay, Steven E Bosinger, Cynthia A Derdeyn

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Infiltration of inflammatory macrophages and neutrophils and widespread pyroptosis in lung drive influenza lethality in nonhuman primates. by Jacqueline Corry, Gwenddolen Kettenburg, Amit A Upadhyay, Megan Wallace, Michelle M Marti, Elizabeth R Wonderlich, Stephanie J Bissel, Kyndal Goss, Timothy J Sturgeon, Simon C Watkins, Douglas S Reed, Steven E Bosinger, Simon M Barratt-Boyes

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IL-21 and IFNα therapy rescues terminally differentiated NK cells and limits SIV reservoir in ART-treated macaques by Justin Harper, Nicolas Huot, Luca Micci, Gregory Tharp, Colin King, Philippe Rascle, Neeta Shenvi, Hong Wang, Cristin Galardi, Amit A. Upadhyay, Francois Villinger, Jeffrey Lifson, Guido Silvestri, Kirk Easley, Beatrice Jacquelin, Steven Bosinger, Michaela Müller-Trutwin, Mirko Paiardini

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BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data by Amit A. Upadhyay, Robert C. Kauffman, Amber N. Wolabaugh, Alice Cho, Nirav B. Patel, Samantha M. Reiss, Colin Havenar-Daughton, Reem A. Dawoud, Gregory K. Tharp, Iñaki Sanz, Bali Pulendran, Shane Crotty, F. Eun-Hyung Lee, Jens Wrammert, Steven E. Bosinger

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Rapid Germinal Center and Antibody Responses in Non-human Primates after a Single Nanoparticle Vaccine Immunization by Colin Havenar-Daughton, Diane G. Carnathan, Archana V. Boopathy, Amit A. Upadhyay, Ben Murrell, Samantha M. Reiss, Chiamaka A. Enemuo, Etse H. Gebru, Yury Choe, Pallavi Dhadvai, Federico Viviano, Kirti Kaushik, Jinal N. Bhiman, Bryan Briney, Dennis R. Burton, Steven E. Bosinger, William R. Schief, Darrell J. Irvine, Guido Silvestri, Shane Crotty

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Tissue-specific transcriptional profiling of plasmacytoid dendritic cells reveals a hyperactivated state in chronic SIV infection. by Michelle Y-H Lee, Amit A Upadhyay, Hasse Walum, Chi N Chan, Reem A Dawoud, Christine Grech, Justin L Harper, Kirti A Karunakaran, Sydney A Nelson, Ernestine A Mahar, Kyndal L Goss, Diane G Carnathan, Barbara Cervasi, Kiran Gill, Gregory K Tharp, Elizabeth R Wonderlich, Vijayakumar Velu, Simon M Barratt-Boyes, Mirko Paiardini, Guido Silvestri, Jacob D Estes, Steven E Bosinger

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Frequency-potency analysis of IgG+ memory B cells delineates neutralizing antibody responses at single-cell resolution by Michelle K. Tenggara, Seo-Ho Oh, Catherine Yang, Hardik K. Nariya, Amanda M. Metz, Amit A. Upadhyay, Dedeepya R. Gudipati, Lizheng Guo, Emily G. McGhee, Kiran Gill, Elise G. Viox, Rosemarie D. Mason, Nicole A. Doria-Rose, Kathryn E. Foulds, John R. Mascola, Yuhong Du, Haian Fu, John D. Altman, Qi Yan, Zizhang Sheng, Steven E. Bosinger, Rui Kong

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Intradermal but not intramuscular modified vaccinia Ankara immunizations protect against intravaginal tier2 simian-human immunodeficiency virus challenges in female macaques by Venkata S. Bollimpelli, Pradeep B. J Reddy, Sailaja Gangadhara, Tysheena P. Charles, Samantha L. Burton, Gregory K. Tharp, Tiffany M. Styles, Celia C. Labranche, Justin C. Smith, Amit A. Upadhyay, Anusmita Sahoo, Traci Legere, Ayalnesh Shiferaw, Vijayakumar Velu, Tianwei Yu, Mark Tomai, John Vasilakos, Sudhir P. Kasturi, George M. Shaw, David Montefiori, Steven E. Bosinger, Pamela A. Kozlowski, Bali Pulendran, Cynthia A. Derdeyn, Eric Hunter, Rama R. Amara

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A neutralizing antibody target in early HIV-1 infection was recapitulated in rhesus macaques immunized with the transmitted/founder envelope sequence. by Sarah Welbourn, Srirupa Chakraborty, Jie E Yang, Anne S Gleinich, Sailaja Gangadhara, Salar Khan, Courtney Ferrebee, Bhrugu Yagnik, Samantha Burton, Tysheena Charles, S Abigail Smith, Danielle Williams, Rohini Mopuri, Amit A Upadhyay, Justin Thompson, Matt A Price, Shiyu Wang, Zhaohui Qin, Xiaoying Shen, LaTonya D Williams, Nathan Eisel, Tiffany Peters, Lu Zhang, William Kilembe, Etienne Karita, Georgia D Tomaras, Steven E Bosinger, Rama R Amara, Parastoo Azadi, Elizabeth R Wright, Sandrasegaram Gnanakaran, Cynthia A Derdeyn

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TREM2+ and interstitial-like macrophages orchestrate airway inflammation in SARS-CoV-2 infection in rhesus macaques by Amit A. Upadhyay, Elise G. Viox, Timothy N. Hoang, Arun K. Boddapati, Maria Pino, Michelle Y.-H. Lee, Jacqueline Corry, Zachary Strongin, David A. Cowan, Elizabeth N. Beagle, Tristan R. Horton, Sydney Hamilton, Hadj Aoued, Justin L. Harper, Christopher T. Edwards, Kevin Nguyen, Kathryn L. Pellegrini, Gregory K. Tharp, Anne Piantadosi, Rebecca D. Levit, Rama R. Amara, Simon M. Barratt-Boyes, Susan P. Ribeiro, Rafick P. Sekaly, Thomas H. Vanderford, Raymond F. Schinazi, Mirko Paiardini, Steven E. Bosinger

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