Persistence and emergence of X4 virus in HIV infection by Ariel D. Weinberger, Alan S. Perelson

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MHC-Linked Syngeneic Developmental Preference inThymic Lobes Colonized with Bone Marrow Cells: A Mathematical model by Amiela Globerson, Ramit Mehr, Alan S. Perelson, Ayala Sharp, Lee Segel

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Recombination Enhances HIV-1 Envelope Diversity by Facilitating the Survival of Latent Genomic Fragments in the Plasma Virus Population. by Taina T Immonen, Jessica M Conway, Ethan O Romero-Severson, Alan S Perelson, Thomas Leitner

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An Age-Structured Model of HIV Infection that Allows for Variations in the Production Rate of Viral Particles and the Death Rate of Productively Infected Cells by Patrick W. Nelson, Michael A. Gilchrist, Daniel Coombs, James M. Hyman, Alan S. Perelson

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Understanding early HIV-1 rebound dynamics following antiretroviral therapy interruption: The importance of effector cell expansion. by Tin Phan, Jessica M Conway, Nicole Pagane, Jasmine Kreig, Narmada Sambaturu, Sarafa Iyaniwura, Jonathan Z Li, Ruy M Ribeiro, Ruian Ke, Alan S Perelson

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Mechanistic basis of post-treatment control of SIV after anti-α4β7 antibody therapy. by Chad R Wells, Youfang Cao, David P Durham, Siddappa N Byrareddy, Aftab A Ansari, Nancy H Ruddle, Jeffrey P Townsend, Alison P Galvani, Alan S Perelson

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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

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A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV, and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-2. by Kwang Su Kim, Keisuke Ejima, Shoya Iwanami, Yasuhisa Fujita, Hirofumi Ohashi, Yoshiki Koizumi, Yusuke Asai, Shinji Nakaoka, Koichi Watashi, Kazuyuki Aihara, Robin N Thompson, Ruian Ke, Alan S Perelson, Shingo Iwami

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Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers. by Kosaku Kitagawa, Kwang Su Kim, Masashi Iwamoto, Sanae Hayashi, Hyeongki Park, Takara Nishiyama, Naotoshi Nakamura, Yasuhisa Fujita, Shinji Nakaoka, Kazuyuki Aihara, Alan S Perelson, Lena Allweiss, Maura Dandri, Koichi Watashi, Yasuhito Tanaka, Shingo Iwami

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Quantification of heterogeneity in human CD8+ T cell responses to vaccine antigens: an HLA-guided perspective by Duane C. Harris, Apoorv Shanker, Makaela M. Montoya, Trent R. Llewellyn, Anna R. Matuszak, Aditi Lohar, Jessica Z. Kubicek-Sutherland, Ying Wai Li, Kristen Wilding, Ben Mcmahon, Sandrasegaram Gnanakaran, Ruy M. Ribeiro, Alan S. Perelson, Carmen Molina-París

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Modeling the emergence of viral resistance for SARS-CoV-2 during treatment with an anti-spike monoclonal antibody. by Tin Phan, Carolin Zitzmann, Kara W Chew, Davey M Smith, Eric S Daar, David A Wohl, Joseph J Eron, Judith S Currier, Michael D Hughes, Manish C Choudhary, Rinki Deo, Jonathan Z Li, Ruy M Ribeiro, Ruian Ke, Alan S Perelson, ACTIV-2/A5401 Study Team

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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

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