Estimating the Timing of Early Simian-Human Immunodeficiency Virus Infections: a Comparison between Poisson Fitter and BEAST

by Elena E. Giorgi, Hui Li, Tanmoy Bhattacharya, George M. Shaw, Bette Korber
Published 2020-03-01

CAT: computer aided triage improving upon the Bayes risk through ε-refusal triage rules

by Nicolas Hengartner, Leticia Cuellar, Xiao-Cheng Wu, Georgia Tourassi, John Qiu, Blair Christian, Tanmoy Bhattacharya
Published 2018-12-01

Nucleon momentum fraction, helicity and transversity from 2+1-flavor lattice QCD

by Nucleon Matrix Elements (NME) collaboration, Santanu Mondal, Rajan Gupta, Sungwoo Park, Boram Yoon, Tanmoy Bhattacharya, Bálint Joó, Frank Winter
Published 2021-04-01

Reversion and T cell escape mutations compensate the fitness loss of a CD8+ T cell escape mutant in their cognate transmitted/founder virus.

by Hongshuo Song, Bhavna Hora, Tanmoy Bhattacharya, Nilu Goonetilleke, Michael K P Liu, Kevin Wiehe, Hui Li, Shilpa S Iyer, Andrew J McMichael, Alan S Perelson, Feng Gao
Published 2014-01-01

Genital tract sequestration of SIV following acute infection.

by James B Whitney, Peter T Hraber, Corinne Luedemann, Elena E Giorgi, Marcus G Daniels, Tanmoy Bhattacharya, Srinivas S Rao, John R Mascola, Gary J Nabel, Bette T Korber, Norman L Letvin
Published 2011-02-01

A strongly selected mutation in the HIV-1 genome is independent of T cell responses and neutralizing antibodies

by Donglai Liu, Chu Wang, Bhavna Hora, Tao Zuo, Nilu Goonetilleke, Michael K. P. Liu, Mark Berrong, Guido Ferrari, Andrew J. McMichael, Tanmoy Bhattacharya, Alan S. Perelson, Feng Gao
Published 2017-10-01

A signature in HIV-1 envelope leader peptide associated with transition from acute to chronic infection impacts envelope processing and infectivity.

by Mohammed Asmal, Ina Hellmann, Weimin Liu, Brandon F Keele, Alan S Perelson, Tanmoy Bhattacharya, S Gnanakaran, Marcus Daniels, Barton F Haynes, Bette T Korber, Beatrice H Hahn, George M Shaw, Norman L Letvin
Published 2011-01-01

Quantifying the diversification of hepatitis C virus (HCV) during primary infection: estimates of the in vivo mutation rate.

by Ruy M Ribeiro, Hui Li, Shuyi Wang, Mark B Stoddard, Gerald H Learn, Bette T Korber, Tanmoy Bhattacharya, Jeremie Guedj, Erica H Parrish, Beatrice H Hahn, George M Shaw, Alan S Perelson
Published 2012-01-01

HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC.

by Natasha Wood, Tanmoy Bhattacharya, Brandon F Keele, Elena Giorgi, Michael Liu, Brian Gaschen, Marcus Daniels, Guido Ferrari, Barton F Haynes, Andrew McMichael, George M Shaw, Beatrice H Hahn, Bette Korber, Cathal Seoighe
Published 2009-05-01

Human APOBEC3 induced mutation of human immunodeficiency virus type-1 contributes to adaptation and evolution in natural infection.

by Eun-Young Kim, Ramon Lorenzo-Redondo, Susan J Little, Yoon-Seok Chung, Prabhjeet K Phalora, Irina Maljkovic Berry, John Archer, Sudhir Penugonda, Will Fischer, Douglas D Richman, Tanmoy Bhattacharya, Michael H Malim, Steven M Wolinsky
Published 2014-07-01

Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies.

by S Gnanakaran, Marcus G Daniels, Tanmoy Bhattacharya, Alan S Lapedes, Anurag Sethi, Ming Li, Haili Tang, Kelli Greene, Hongmei Gao, Barton F Haynes, Myron S Cohen, George M Shaw, Michael S Seaman, Amit Kumar, Feng Gao, David C Montefiori, Bette Korber
Published 2010-01-01

Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1.

by Zabrina L Brumme, Chanson J Brumme, David Heckerman, Bette T Korber, Marcus Daniels, Jonathan Carlson, Carl Kadie, Tanmoy Bhattacharya, Celia Chui, James Szinger, Theresa Mo, Robert S Hogg, Julio S G Montaner, Nicole Frahm, Christian Brander, Bruce D Walker, P Richard Harrigan
Published 2007-07-01

Correction: Evidence of Differential HLA Class I-Mediated Viral Evolution in Functional and Accessory/Regulatory Genes of HIV-1.

by Zabrina L Brumme, Chanson J Brumme, David Heckerman, Bette T Korber, Marcus Daniels, Jonathan Carlson, Carl Kadie, Tanmoy Bhattacharya, Celia Chui, James Szinger, Theresa Mo, Robert S Hogg, Julio S. G Montaner, Nicole Frahm, Christian Brander, Bruce D Walker, P. Richard Harrigan
Published 2007-08-01

AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing

by Tanmoy Bhattacharya, Thomas Brettin, James H. Doroshow, Yvonne A. Evrard, Emily J. Greenspan, Amy L. Gryshuk, Thuc T. Hoang, Carolyn B. Vea Lauzon, Dwight Nissley, Lynne Penberthy, Eric Stahlberg, Rick Stevens, Rick Stevens, Fred Streitz, Georgia Tourassi, Fangfang Xia, George Zaki
Published 2019-10-01

Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing.

by Hui Li, Mark B Stoddard, Shuyi Wang, Lily M Blair, Elena E Giorgi, Erica H Parrish, Gerald H Learn, Peter Hraber, Paul A Goepfert, Michael S Saag, Thomas N Denny, Barton F Haynes, Beatrice H Hahn, Ruy M Ribeiro, Alan S Perelson, Bette T Korber, Tanmoy Bhattacharya, George M Shaw
Published 2012-01-01

Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants

by Peter Hraber, Bette Korber, Kshitij Wagh, Elena E. Giorgi, Tanmoy Bhattacharya, S. Gnanakaran, Alan S. Lapedes, Gerald H. Learn, Edward F. Kreider, Yingying Li, George M. Shaw, Beatrice H. Hahn, David C. Montefiori, S. Munir Alam, Mattia Bonsignori, M. Anthony Moody, Hua-Xin Liao, Feng Gao, Barton F. Haynes
Published 2015-10-01

Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing.

by Will Fischer, Vitaly V Ganusov, Elena E Giorgi, Peter T Hraber, Brandon F Keele, Thomas Leitner, Cliff S Han, Cheryl D Gleasner, Lance Green, Chien-Chi Lo, Ambarish Nag, Timothy C Wallstrom, Shuyi Wang, Andrew J McMichael, Barton F Haynes, Beatrice H Hahn, Alan S Perelson, Persephone Borrow, George M Shaw, Tanmoy Bhattacharya, Bette T Korber
Published 2010-08-01

Optimal Combinations of Broadly Neutralizing Antibodies for Prevention and Treatment of HIV-1 Clade C Infection.

by Kshitij Wagh, Tanmoy Bhattacharya, Carolyn Williamson, Alex Robles, Madeleine Bayne, Jetta Garrity, Michael Rist, Cecilia Rademeyer, Hyejin Yoon, Alan Lapedes, Hongmei Gao, Kelli Greene, Mark K Louder, Rui Kong, Salim Abdool Karim, Dennis R Burton, Dan H Barouch, Michel C Nussenzweig, John R Mascola, Lynn Morris, David C Montefiori, Bette Korber, Michael S Seaman
Published 2016-03-01

High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men.

by Hui Li, Katharine J Bar, Shuyi Wang, Julie M Decker, Yalu Chen, Chuanxi Sun, Jesus F Salazar-Gonzalez, Maria G Salazar, Gerald H Learn, Charity J Morgan, Joseph E Schumacher, Peter Hraber, Elena E Giorgi, Tanmoy Bhattacharya, Bette T Korber, Alan S Perelson, Joseph J Eron, Myron S Cohen, Charles B Hicks, Barton F Haynes, Martin Markowitz, Brandon F Keele, Beatrice H Hahn, George M Shaw
Published 2010-05-01

Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection

by Hongshuo Song, Elena E. Giorgi, Vitaly V. Ganusov, Fangping Cai, Gayathri Athreya, Hyejin Yoon, Oana Carja, Bhavna Hora, Peter Hraber, Ethan Romero-Severson, Chunlai Jiang, Xiaojun Li, Shuyi Wang, Hui Li, Jesus F. Salazar-Gonzalez, Maria G. Salazar, Nilu Goonetilleke, Brandon F. Keele, David C. Montefiori, Myron S. Cohen, George M. Shaw, Beatrice H. Hahn, Andrew J. McMichael, Barton F. Haynes, Bette Korber, Tanmoy Bhattacharya, Feng Gao
Published 2018-05-01