The re-emergence of H1N1 influenza virus in 1977: a cautionary tale for estimating divergence times using biologically unrealistic sampling dates. by Joel O Wertheim

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A challenge to the ancient origin of SIVagm based on African green monkey mitochondrial genomes. by Joel O Wertheim, Michael Worobey

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Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment. by Sepideh Mazrouee, Susan J Little, Joel O Wertheim

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Using HIV transmission networks to investigate community effects in HIV prevention trials. by Joel O Wertheim, Sergei L Kosakovsky Pond, Susan J Little, Victor De Gruttola

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Detecting individual sites subject to episodic diversifying selection. by Ben Murrell, Joel O Wertheim, Sasha Moola, Thomas Weighill, Konrad Scheffler, Sergei L Kosakovsky Pond

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Phylogeographic analysis reveals an ancient East African origin of human herpes simplex virus 2 dispersal out-of-Africa by Jennifer L. Havens, Sébastien Calvignac-Spencer, Kevin Merkel, Sonia Burrel, David Boutolleau, Joel O. Wertheim

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Natural selection favoring more transmissible HIV detected in United States molecular transmission network by Joel O. Wertheim, Alexandra M. Oster, William M. Switzer, Chenhua Zhang, Nivedha Panneer, Ellsworth Campbell, Neeraja Saduvala, Jeffrey A. Johnson, Walid Heneine

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Impact of molecular sequence data completeness on HIV cluster detection and a network science approach to enhance detection by Sepideh Mazrouee, Camden J. Hallmark, Ricardo Mora, Natascha Del Vecchio, Rocio Carrasco Hernandez, Michelle Carr, Marlene McNeese, Kayo Fujimoto, Joel O. Wertheim

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Analysis of Hepatitis B Virus Genotype D in Greenland Suggests the Presence of a Novel Quasi-Subgenotype by Adriano de Bernardi Schneider, Carla Osiowy, Reilly Hostager, Henrik Krarup, Henrik Krarup, Henrik Krarup, Malene Børresen, Yasuhito Tanaka, Taylor Morriseau, Joel O. Wertheim

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AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters by Steven Weaver, Vanessa M. Dávila Conn, Daniel Ji, Hannah Verdonk, Santiago Ávila-Ríos, Andrew J. Leigh Brown, Joel O. Wertheim, Sergei L. Kosakovsky Pond

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Using HIV networks to inform real time prevention interventions. by Susan J Little, Sergei L Kosakovsky Pond, Christy M Anderson, Jason A Young, Joel O Wertheim, Sanjay R Mehta, Susanne May, Davey M Smith

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Social and Genetic Networks of HIV-1 Transmission in New York City. by Joel O Wertheim, Sergei L Kosakovsky Pond, Lisa A Forgione, Sanjay R Mehta, Ben Murrell, Sharmila Shah, Davey M Smith, Konrad Scheffler, Lucia V Torian

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Tracking SARS-COV-2 variants using Nanopore sequencing in Ukraine in 2021 by Anna Yakovleva, Ganna Kovalenko, Matthew Redlinger, Mariia G. Liulchuk, Eric Bortz, Viktoria I. Zadorozhna, Alla M. Scherbinska, Joel O. Wertheim, Ian Goodfellow, Luke Meredith, Tetyana I. Vasylyeva

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Author Correction: Tracking SARS-COV-2 variants using Nanopore sequencing in Ukraine in 2021 by Anna Yakovleva, Ganna Kovalenko, Matthew Redlinger, Mariia G. Liulchuk, Eric Bortz, Viktoria I. Zadorozhna, Alla M. Scherbinska, Joel O. Wertheim, Ian Goodfellow, Luke Meredith, Tetyana I. Vasylyeva

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Unveiling ecological/evolutionary insights in HIV viral load dynamics: Allowing random slopes to observe correlational changes to CpG-contents and other molecular and clinical pred... by Rocío Carrasco-Hernández, Humberto Valenzuela-Ponce, Maribel Soto-Nava, Claudia García-Morales, Margarita Matías-Florentino, Joel O. Wertheim, Davey M. Smith, Gustavo Reyes-Terán, Santiago Ávila-Ríos

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The role of socio-economic disparities in the relative success and persistence of SARS-CoV-2 variants in New York City in early 2021. by Tetyana I Vasylyeva, Jennifer L Havens, Jade C Wang, Elizabeth Luoma, Gabriel W Hassler, Helly Amin, Steve Di Lonardo, Faten Taki, Enoma Omoregie, Scott Hughes, Joel O Wertheim

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Establishing a framework towards monitoring HCV microelimination among men who have sex with men living with HIV in Germany: A modeling analysis. by Lara K Marquez, Patrick Ingiliz, Christoph Boesecke, Ivanka Krznaric, Knud Schewe, Thomas Lutz, Stefan Mauss, Stefan Christensen, Jürgen K Rockstroh, Sonia Jain, Feng He, Joel O Wertheim, Natasha K Martin

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Establishing a framework towards monitoring HCV microelimination among men who have sex with men living with HIV in Germany: A modeling analysis by Lara K. Marquez, Patrick Ingiliz, Christoph Boesecke, Ivanka Krznaric, Knud Schewe, Thomas Lutz, Stefan Mauss, Stefan Christensen, Jürgen K. Rockstroh, Sonia Jain, Feng He, Joel O. Wertheim, Natasha K. Martin

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Prevalence of resistance-associated substitutions and phylogenetic analysis of hepatitis C virus infection in Russia by Vasily Isakov, Charlotte Hedskog, Joel O. Wertheim, Reilly E. Hostager, Bandita Parhy, Adriano De Bernardi Schneider, Vithika Suri, Hongmei Mo, Natalia Geivandova, Vyacheslav Morozov, Elena Bessonova, Natalya Gankina, Konstantin Zhdanov, Dzhamal Abdurakhmanov, Evguenia Svarovskaia

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HIV Transmission Networks in the San Diego–Tijuana Border Region by Sanjay R. Mehta, Joel O. Wertheim, Kimberly C. Brouwer, Karla D. Wagner, Antoine Chaillon, Steffanie Strathdee, Thomas L. Patterson, Maria G. Rangel, Mlenka Vargas, Ben Murrell, Richard Garfein, Susan J. Little, Davey M. Smith

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