Estimating the Timing of Early Simian-Human Immunodeficiency Virus Infections: a Comparison between Poisson Fitter and BEAST por Elena E. Giorgi, Hui Li, Tanmoy Bhattacharya, George M. Shaw, Bette Korber

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CAT: computer aided triage improving upon the Bayes risk through ε-refusal triage rules por Nicolas Hengartner, Leticia Cuellar, Xiao-Cheng Wu, Georgia Tourassi, John Qiu, Blair Christian, Tanmoy Bhattacharya

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Nucleon momentum fraction, helicity and transversity from 2+1-flavor lattice QCD por Nucleon Matrix Elements (NME) collaboration, Santanu Mondal, Rajan Gupta, Sungwoo Park, Boram Yoon, Tanmoy Bhattacharya, Bálint Joó, Frank Winter

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

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

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

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

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

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

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

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

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

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

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

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Quantum Simulation for High-Energy Physics por Christian W. Bauer, Zohreh Davoudi, A. Baha Balantekin, Tanmoy Bhattacharya, Marcela Carena, Wibe A. de Jong, Patrick Draper, Aida El-Khadra, Nate Gemelke, Masanori Hanada, Dmitri Kharzeev, Henry Lamm, Ying-Ying Li, Junyu Liu, Mikhail Lukin, Yannick Meurice, Christopher Monroe, Benjamin Nachman, Guido Pagano, John Preskill, Enrico Rinaldi, Alessandro Roggero, David I. Santiago, Martin J. Savage, Irfan Siddiqi, George Siopsis, David Van Zanten, Nathan Wiebe, Yukari Yamauchi, Kübra Yeter-Aydeniz, Silvia Zorzetti

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High dimensional predictions of suicide risk in 4.2 million US Veterans using ensemble transfer learning por Sayera Dhaubhadel, Kumkum Ganguly, Ruy M. Ribeiro, Judith D. Cohn, James M. Hyman, Nicolas W. Hengartner, Beauty Kolade, Anna Singley, Tanmoy Bhattacharya, Patrick Finley, Drew Levin, Haedi Thelen, Kelly Cho, Lauren Costa, Yuk-Lam Ho, Amy C. Justice, John Pestian, Daniel Santel, Rafael Zamora-Resendiz, Silvia Crivelli, Suzanne Tamang, Susana Martins, Jodie Trafton, David W. Oslin, Jean C. Beckham, Nathan A. Kimbrel, Million Veteran Program Suicide Exemplar Work Group, Benjamin H. McMahon

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Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections. por S Gnanakaran, Tanmoy Bhattacharya, Marcus Daniels, Brandon F Keele, Peter T Hraber, Alan S Lapedes, Tongye Shen, Brian Gaschen, Mohan Krishnamoorthy, Hui Li, Julie M Decker, Jesus F Salazar-Gonzalez, Shuyi Wang, Chunlai Jiang, Feng Gao, Ronald Swanstrom, Jeffrey A Anderson, Li-Hua Ping, Myron S Cohen, Martin Markowitz, Paul A Goepfert, Michael S Saag, Joseph J Eron, Charles B Hicks, William A Blattner, Georgia D Tomaras, Mohammed Asmal, Norman L Letvin, Peter B Gilbert, Allan C Decamp, Craig A Magaret, William R Schief, Yih-En Andrew Ban, Ming Zhang, Kelly A Soderberg, Joseph G Sodroski, Barton F Haynes, George M Shaw, Beatrice H Hahn, Bette Korber

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