Relative evolutionary rate inference in HyPhy with LEISR by Stephanie J. Spielman, Sergei L. Kosakovsky Pond

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The evolution of mammalian Rem2: unraveling the impact of purifying selection and coevolution on protein function, and implications for human disorders by Alexander G. Lucaci, Alexander G. Lucaci, William E. Brew, Jason Lamanna, Jason Lamanna, Avery Selberg, Avery Selberg, Vincenzo Carnevale, Vincenzo Carnevale, Anna R. Moore, Sergei L. Kosakovsky Pond, Sergei L. Kosakovsky Pond

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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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Correction: Somatic genome architecture and molecular evolution are decoupled in "young" linage-specific gene families in ciliates. by Xyrus X Maurer-Alcalá, Auden Cote-L'Heureux, Sergei L Kosakovsky Pond, Laura A Katz

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Somatic genome architecture and molecular evolution are decoupled in “young” linage-specific gene families in ciliates by Xyrus X. Maurer-Alcalá, Auden Cote-L’Heureux, Sergei L. Kosakovsky Pond, Laura A. Katz

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Somatic genome architecture and molecular evolution are decoupled in "young" linage-specific gene families in ciliates. by Xyrus X Maurer-Alcalá, Auden Cote-L'Heureux, Sergei L Kosakovsky Pond, Laura A Katz

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Susceptibility of SARS-CoV-2 Omicron Variants to Therapeutic Monoclonal Antibodies: Systematic Review and Meta-analysis by Kaiming Tao, Philip L. Tzou, Sergei L. Kosakovsky Pond, John P. A. Ioannidis, Robert W. Shafer

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A new method for inferring timetrees from temporally sampled molecular sequences. by Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A Huuki, Sergei L Kosakovsky Pond, Jessica Priest, Jiamin Deng, Sudhir Kumar

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HIV-1 Group M Capsid Amino Acid Variability: Implications for Sequence Quality Control of Genotypic Resistance Testing by Kaiming Tao, Soo-Yon Rhee, Philip L. Tzou, Zachary A. Osman, Sergei L. Kosakovsky Pond, Susan P. Holmes, Robert W. Shafer

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DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites by Wenjie Deng, Brandon S. Maust, David C. Nickle, Gerald H. Learn, Yi Liu, Laura Heath, Sergei L Kosakovsky Pond, James I. Mullins

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Coping with viral diversity in HIV vaccine design. by David C Nickle, Morgane Rolland, Mark A Jensen, Sergei L Kosakovsky Pond, Wenjie Deng, Mark Seligman, David Heckerman, James I Mullins, Nebojsa Jojic

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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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Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein by Jordan D. Zehr, Sergei L. Kosakovsky Pond, Darren P. Martin, Kristina Ceres, Gary R. Whittaker, Jean K. Millet, Laura B. Goodman, Michael J. Stanhope

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IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform. by N Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D Richman, Dennis R Burton, Pascal Poignard, Davey M Smith, Sergei L Kosakovsky Pond

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RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis. by Alexander G Lucaci, Jordan D Zehr, Stephen D Shank, Dave Bouvier, Alexander Ostrovsky, Han Mei, Anton Nekrutenko, Darren P Martin, Sergei L Kosakovsky Pond

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Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the Embecovirus subgenus by Jordan D. Zehr, Sergei L. Kosakovsky Pond, Stephen D. Shank, Holly McQueary, Jennifer K. Grenier, Gary R. Whittaker, Michael J. Stanhope, Laura B. Goodman

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Parsing social network survey data from hidden populations using stochastic context-free grammars. by Art F Y Poon, Kimberly C Brouwer, Steffanie A Strathdee, Michelle Firestone-Cruz, Remedios M Lozada, Sergei L Kosakovsky Pond, Douglas D Heckathorn, Simon D W Frost

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Phylogenomic Signatures of a Lineage of Vesicular Stomatitis Indiana Virus Circulating During the 2019–2020 Epidemic in the United States by Selene Zarate, Miranda Bertram, Case Rodgers, Kirsten Reed, Angela Pelzel-McCluskey, Ninnet Gomez-Romero, Luis L. Rodriguez, Christie Mayo, Chad Mire, Sergei L. Kosakovsky Pond, Lauro Velazquez-Salinas

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Ecological diversification of sea catfishes is accompanied by genome-wide signatures of positive selection by Melissa Rincon-Sandoval, Rishi De-Kayne, Stephen D. Shank, Stacy Pirro, Alfred Ko’ou, Linelle Abueg, Alan Tracey, Jackie Mountcastle, Brian O’Toole, Jennifer Balacco, Giulio Formenti, Erich D. Jarvis, Dahiana Arcila, Sergei L. Kosakovsky Pond, Aaron Davis, Devin D. Bloom, Ricardo Betancur-R

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Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas. by Naomi L Forrester, Joel O Wertheim, Vivian G Dugan, Albert J Auguste, David Lin, A Paige Adams, Rubing Chen, Rodion Gorchakov, Grace Leal, Jose G Estrada-Franco, Jyotsna Pandya, Rebecca A Halpin, Kumar Hari, Ravi Jain, Timothy B Stockwell, Suman R Das, David E Wentworth, Martin D Smith, Sergei L Kosakovsky Pond, Scott C Weaver

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