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

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On the validity of evolutionary models with site-specific parameters. by Konrad Scheffler, Ben Murrell, Sergei L Kosakovsky Pond

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Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability. by Frank Mannino, Sadie Wisotsky, Sergei L Kosakovsky Pond, Spencer V Muse

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The evolution of BDNF is defined by strict purifying selection and prodomain spatial coevolution, but what does it mean for human brain disease? by Alexander G. Lucaci, Michael J. Notaras, Sergei L. Kosakovsky Pond, Dilek Colak

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Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons. by Philip L Tzou, Kaiming Tao, Sergei L Kosakovsky Pond, Robert W Shafer

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Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons by Philip L. Tzou, Kaiming Tao, Sergei L. Kosakovsky Pond, Robert W. Shafer

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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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An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. by Art F Y Poon, Fraser I Lewis, Sergei L Kosakovsky Pond, Simon D W Frost

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Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates by Ying Yan, Xyrus X. Maurer-Alcalá, Rob Knight, Sergei L. Kosakovsky Pond, Laura A. Katz

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Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope. by Art F Y Poon, Fraser I Lewis, Sergei L Kosakovsky Pond, Simon D W Frost

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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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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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Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes. by Alexander G Lucaci, Sadie R Wisotsky, Stephen D Shank, Steven Weaver, Sergei L Kosakovsky Pond

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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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CodonTest: modeling amino acid substitution preferences in coding sequences. by Wayne Delport, Konrad Scheffler, Gordon Botha, Mike B Gravenor, Spencer V Muse, Sergei L Kosakovsky Pond

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Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences. by Philip L Tzou, Sergei L Kosakovsky Pond, Santiago Avila-Rios, Susan P Holmes, Rami Kantor, Robert W Shafer

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HIV-specific probabilistic models of protein evolution. by David C Nickle, Laura Heath, Mark A Jensen, Peter B Gilbert, James I Mullins, Sergei L Kosakovsky Pond

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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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Adaptation to different human populations by HIV-1 revealed by codon-based analyses. by Sergei L Kosakovsky Pond, Simon D W Frost, Zehava Grossman, Michael B Gravenor, Douglas D Richman, Andrew J Leigh Brown

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