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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phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics by Stephen D. Shank, Steven Weaver, Sergei L. Kosakovsky Pond

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Molecular modeling and phylogenetic analyses highlight the role of amino acid 347 of the N1 subtype neuraminidase in influenza virus host range and interspecies adaptation by Stefano Elli, Giuseppina Raffaini, Marco Guerrini, Sergei Kosakovsky Pond, Mikhail Matrosovich

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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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Benchmarking multi-rate codon models. by Wayne Delport, Konrad Scheffler, Mike B Gravenor, Spencer V Muse, Sergei Kosakovsky Pond

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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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Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia. by Lam, T, Hon, C, Pybus, O, Kosakovsky Pond, S, Wong, RT, Yip, C, Zeng, F, Leung, F

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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