Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness by Guinevere Q. Lee

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Prolonged and substantial discordance in prevalence of raltegravir-resistant HIV-1 in plasma versus PBMC samples revealed by 454 "deep" sequencing. by Guinevere Q Lee, Luke C Swenson, Art F Y Poon, Jeffrey N Martin, Hiroyu Hatano, Steven G Deeks, P Richard Harrigan

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Limited evolution of inferred HIV-1 tropism while viremia is undetectable during standard HAART therapy. by Guinevere Q Lee, Winnie Dong, Theresa Mo, David J H F Knapp, Chanson J Brumme, Conan K Woods, Steve Kanters, Benita Yip, P Richard Harrigan

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Differences in HIV-1 reservoir size, landscape characteristics, and decay dynamics in acute and chronic treated HIV-1 Clade C infection by Kavidha Reddy, Guinevere Q Lee, Nicole Reddy, Tatenda JB Chikowore, Kathy Baisley, Krista L Dong, Bruce D Walker, Xu G Yu, Mathias Lichterfeld, Thumbi Ndung'u

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HIV-1 DNA sequence diversity and evolution during acute subtype C infection by Guinevere Q. Lee, Kavidha Reddy, Kevin B. Einkauf, Kamini Gounder, Joshua M. Chevalier, Krista L. Dong, Bruce D. Walker, Xu G. Yu, Thumbi Ndung’u, Mathias Lichterfeld

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Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5. by Steven W Jin, Francis M Mwimanzi, Jaclyn K Mann, Mwebesa Bosco Bwana, Guinevere Q Lee, Chanson J Brumme, Peter W Hunt, Jeff N Martin, David R Bangsberg, Thumbi Ndung'u, Zabrina L Brumme, Mark A Brockman

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Effect of analytical treatment interruption and reinitiation of antiretroviral therapy on HIV reservoirs and immunologic parameters in infected individuals. by Katherine E Clarridge, Jana Blazkova, Kevin Einkauf, Mary Petrone, Eric W Refsland, J Shawn Justement, Victoria Shi, Erin D Huiting, Catherine A Seamon, Guinevere Q Lee, Xu G Yu, Susan Moir, Michael C Sneller, Mathias Lichterfeld, Tae-Wook Chun

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Intra- and inter-individual HIV diversity limits the application of the intact proviral detection assay (IPDA) by Natalie N. Kinloch, Yanqin Ren, Winiffer Conce Alberto, Winnie Dong, Szu Han Huang, Andrew Wilson, Talia M. Mota, Don Kikby, Perla M. Del Rio Estrada, Chanson J. Brumme, Guinevere Q. Lee, Rebecca M. Lynch, Zabrina L. Brumme, R. Brad Jones

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HIV reservoirs are dominated by genetically younger and clonally enriched proviruses by Natalie N. Kinloch, Aniqa Shahid, Winnie Dong, Don Kirkby, Bradley R. Jones, Charlotte J. Beelen, Daniel MacMillan, Guinevere Q. Lee, Talia M. Mota, Hanwei Sudderuddin, Evan Barad, Marianne Harris, Chanson J. Brumme, R. Brad Jones, Mark A. Brockman, Jeffrey B. Joy, Zabrina L. Brumme

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HIV-1 subtype A1, D, and recombinant proviral genome landscapes during long-term suppressive therapy by Guinevere Q. Lee, Pragya Khadka, Sarah N. Gowanlock, Dennis C. Copertino, Maggie C. Duncan, F. Harrison Omondi, Natalie N. Kinloch, Jingo Kasule, Taddeo Kityamuweesi, Paul Buule, Samiri Jamiru, Stephen Tomusange, Aggrey Anok, Zhengming Chen, R. Brad Jones, Ronald M. Galiwango, Steven J. Reynolds, Thomas C. Quinn, Zabrina L. Brumme, Andrew D. Redd, Jessica L. Prodger

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Attenuated HIV-1 Nef But Not Vpu Function in a Cohort of Rwandan Long-Term Survivors by Gisele Umviligihozo, Jaclyn K. Mann, Steven W. Jin, Francis M. Mwimanzi, Hua-Shiuan A. Hsieh, Hanwei Sudderuddin, Guinevere Q. Lee, Helen Byakwaga, Helen Byakwaga, Conrad Muzoora, Peter W. Hunt, Jeff N. Martin, Jessica E. Haberer, Jessica E. Haberer, Etienne Karita, Susan Allen, Eric Hunter, Eric Hunter, Zabrina L. Brumme, Zabrina L. Brumme, Mark A. Brockman, Mark A. Brockman, Mark A. Brockman

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HLA-C downregulation by HIV-1 adapts to host HLA genotype. by Nathaniel D Bachtel, Gisele Umviligihozo, Suzanne Pickering, Talia M Mota, Hua Liang, Gregory Q Del Prete, Pramita Chatterjee, Guinevere Q Lee, Rasmi Thomas, Mark A Brockman, Stuart Neil, Mary Carrington, Bosco Bwana, David R Bangsberg, Jeffrey N Martin, Esper G Kallas, Camila S Donini, Natalia B Cerqueira, Una T O'Doherty, Beatrice H Hahn, R Brad Jones, Zabrina L Brumme, Douglas F Nixon, Richard Apps

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HIV-1 diversity considerations in the application of the Intact Proviral DNA Assay (IPDA) by Natalie N. Kinloch, Yanqin Ren, Winiffer D. Conce Alberto, Winnie Dong, Pragya Khadka, Szu Han Huang, Talia M. Mota, Andrew Wilson, Aniqa Shahid, Don Kirkby, Marianne Harris, Colin Kovacs, Erika Benko, Mario A. Ostrowski, Perla M. Del Rio Estrada, Avery Wimpelberg, Christopher Cannon, W. David Hardy, Lynsay MacLaren, Harris Goldstein, Chanson J. Brumme, Guinevere Q. Lee, Rebecca M. Lynch, Zabrina L. Brumme, R. Brad Jones

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Author Correction: HIV-1 diversity considerations in the application of the Intact Proviral DNA Assay (IPDA) by Natalie N. Kinloch, Yanqin Ren, Winiffer D. Conce Alberto, Winnie Dong, Pragya Khadka, Szu Han Huang, Talia M. Mota, Andrew Wilson, Aniqa Shahid, Don Kirkby, Marianne Harris, Colin Kovacs, Erika Benko, Mario A. Ostrowski, Perla M. Del Rio Estrada, Avery Wimpelberg, Christopher Cannon, W. David Hardy, Lynsay MacLaren, Harris Goldstein, Chanson J. Brumme, Guinevere Q. Lee, Rebecca M. Lynch, Zabrina L. Brumme, R. Brad Jones

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Extensive virologic and immunologic characterization in an HIV-infected individual following allogeneic stem cell transplant and analytic cessation of antiretroviral therapy: A cas... by Nathan W Cummins, Stacey Rizza, Mark R Litzow, Stephane Hua, Guinevere Q Lee, Kevin Einkauf, Tae-Wook Chun, Frank Rhame, Jason V Baker, Michael P Busch, Nicolas Chomont, Patrick G Dean, Rémi Fromentin, Ashley T Haase, Dylan Hampton, Sheila M Keating, Steven M Lada, Tzong-Hae Lee, Sekar Natesampillai, Douglas D Richman, Timothy W Schacker, Stephen Wietgrefe, Xu G Yu, Joseph D Yao, John Zeuli, Mathias Lichterfeld, Andrew D Badley

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HIV-specific T cell responses reflect substantive in vivo interactions with antigen despite long-term therapy by Eva M. Stevenson, Adam R. Ward, Ronald Truong, Allison S. Thomas, Szu-Han Huang, Thomas R. Dilling, Sandra Terry, John K. Bui, Talia M. Mota, Ali Danesh, Guinevere Q. Lee, Andrea Gramatica, Pragya Khadka, Winiffer D. Conce Alberto, Rajesh T. Gandhi, Deborah K. McMahon, Christina M. Lalama, Ronald J. Bosch, Bernard Macatangay, Joshua C. Cyktor, Joseph J. Eron, John W. Mellors, R. Brad Jones, for the AIDS Clinical Trials Group A5321 Team

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SARS CoV-2 mRNA vaccination exposes latent HIV to Nef-specific CD8+ T-cells by Eva M. Stevenson, Sandra Terry, Dennis Copertino, Louise Leyre, Ali Danesh, Jared Weiler, Adam R. Ward, Pragya Khadka, Evan McNeil, Kevin Bernard, Itzayana G. Miller, Grant B. Ellsworth, Carrie D. Johnston, Eli J. Finkelsztein, Paul Zumbo, Doron Betel, Friederike Dündar, Maggie C. Duncan, Hope R. Lapointe, Sarah Speckmaier, Nadia Moran-Garcia, Michelle Premazzi Papa, Samuel Nicholes, Carissa J. Stover, Rebecca M. Lynch, Marina Caskey, Christian Gaebler, Tae-Wook Chun, Alberto Bosque, Timothy J. Wilkin, Guinevere Q. Lee, Zabrina L. Brumme, R. Brad Jones

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