Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. - Sergei L. Kosakovsky Pond; Simon D. W. Frost (Bioinform., 2005)

HyPhy: hypothesis testing using phylogenies. - Sergei L. Kosakovsky Pond; Simon D. W. Frost; Spencer V. Muse (Bioinform., 2005)

GARD: a genetic algorithm for recombination detection. - Sergei L. Kosakovsky Pond; David Posada; Michael B. Gravenor; Christopher H. Woelk; Simon D. W. Frost (Bioinform., 2006)

Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses. - Sergei L. Kosakovsky Pond; Simon D. W. Frost; Zehava Grossman; Michael B. Gravenor; Douglas D. Richman; Andrew J. Leigh Brown (PLoS Comput. Biol., 2006)

A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes. - Wen-Yu Chung; Samir Wadhawan; Radek Szklarczyk; Sergei L. Kosakovsky Pond; Anton Nekrutenko (PLoS Comput. Biol., 2007)

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics. - Philippe Lemey; Sergei L. Kosakovsky Pond; Alexei J. Drummond; Oliver G. Pybus; Beth Shapiro; Helena Barroso; Nuno Taveira; Andrew Rambaut (PLoS Comput. Biol., 2007)

Coping with Viral Diversity in HIV Vaccine Design. - David C. Nickle; Morgane Rolland; Mark A. Jensen; Sergei L. Kosakovsky Pond; Wenjie Deng; Mark Seligman; David Heckerman; James I. Mullins; Nebojsa Jojic (PLoS Comput. Biol., 2007)

Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope. - Art F. Y. Poon; Fraser I. Lewis; Sergei L. Kosakovsky Pond; Simon D. W. Frost (PLoS Comput. Biol., 2007)

An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope. - Art F. Y. Poon; Fraser I. Lewis; Sergei L. Kosakovsky Pond; Simon D. W. Frost (PLoS Comput. Biol., 2007)

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models. - Art F. Y. Poon; Fraser I. Lewis; Simon D. W. Frost; Sergei L. Kosakovsky Pond (Bioinform., 2008)

Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al. - David C. Nickle; Nebojsa Jojic; David Heckerman; Vladimir Jojic; Darko Kirovski; Morgane Rolland; Sergei L. Kosakovsky Pond; James I. Mullins (PLoS Comput. Biol., 2008)

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1. - Sergei L. Kosakovsky Pond; David Posada; Eric W. Stawiski; Colombe Chappey; Art F. Y. Poon; Gareth Hughes; Esther Fearnhill; Mike B. Gravenor; Andrew J. Leigh Brown; Simon D. W. Frost (PLoS Comput. Biol., 2009)

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. - Wayne Delport; Art F. Y. Poon; Simon D. W. Frost; Sergei L. Kosakovsky Pond (Bioinform., 2010)

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences. - Wayne Delport; Konrad Scheffler; Gordon Botha; Mike B. Gravenor; Spencer V. Muse; Sergei L. Kosakovsky Pond (PLoS Comput. Biol., 2010)

Computational analysis of HIV-1 evolution and epidemiology. - Sergei L. Kosakovsky Pond (BIBM Workshops, 2011)

Workshop: Error correction, noise filtering, and phylogenetic analysis of HIV sequences using the 454 platform. - Konrad Scheffler; N. Lance Hepler; Martin D. Smith; Wayne Delport; Art F. Y. Poon; Douglas D. Richman; Sergei L. Kosakovsky Pond (ICCABS, 2012)

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. - Philippe Lemey; Vladimir N. Minin; Filip Bielejec; Sergei L. Kosakovsky Pond; Marc A. Suchard (Bioinform., 2012)

Modeling HIV-1 Drug Resistance as Episodic Directional Selection. - Ben Murrell; Tulio de Oliveira; Chris Seebregts; Sergei L. Kosakovsky Pond; Konrad Scheffler (PLoS Comput. Biol., 2012)

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform. - N. Lance Hepler; Konrad Scheffler; Steven Weaver; Ben Murrell; Douglas D. Richman; Dennis R. Burton; Pascal Poignard; Davey M. Smith; Sergei L. Kosakovsky Pond (PLoS Comput. Biol., 2014)

: Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial. - Paul Thatcher Edlefsen; Morgane Rolland; Tomer Hertz; Sodsai Tovanabutra; Andrew J. Gartland; Allan C. deCamp; Craig A. Magaret; Hasan Ahmed; Raphael Gottardo; Michal Juraska; Connor McCoy; Brendan B. Larsen; et al. (PLoS Comput. Biol., 2015)

Lorenzo-Redondo et al. reply. - Ramon Lorenzo-Redondo; Helen R. Fryer; Trevor Bedford; Eun-Young Kim; John A. C. Archer; Sergei L. Kosakovsky Pond; Yoon-Seok Chung; Sudhir Penugonda; Jeffrey G. Chipman; Courtney V. Fletcher; Timothy W. Schacker; Michael H. Malim; et al. (Nat., 2017)

phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics. - Stephen D. Shank; Steven Weaver; Sergei L. Kosakovsky Pond (BMC Bioinform., 2018)

Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons. - Kemal Eren; Steven Weaver; Robert Ketteringham; Morné Valentyn; Melissa Laird Smith; Venkatesh Kumar; Sanjay Mohan; Sergei L. Kosakovsky Pond; Ben Murrell (PLoS Comput. Biol., 2018)

A new method for inferring timetrees from temporally sampled molecular sequences. - Sayaka Miura; Koichiro Tamura; Qiqing Tao; Louise A. Huuki; Sergei L. Kosakovsky Pond; Jessica Priest; Jiamin Deng; Sudhir Kumar 001 (PLoS Comput. Biol., 2020)

TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. - Marcos A. Caraballo-Ortiz; Sayaka Miura; Maxwell D. Sanderford; Tenzin Dolker; Qiqing Tao; Steven Weaver; Sergei L. Kosakovsky Pond; Sudhir Kumar 001 (Bioinform., 2022)

WIP: Identifying Tutorial Affordances for Interdisciplinary Learning Environments. - Hannah Kim 003; Sergei L. Kosakovsky Pond; Stephen MacNeil (FIE, 2024)

The evolution of mammalian Rem2: unraveling the impact of purifying selection and coevolution on protein function, and implications for human disorders. - Alexander G. Lucaci; William E. Brew; Jason Lamanna; Avery Selberg; Vincenzo Carnevale; Anna R. Moore; Sergei L. Kosakovsky Pond (Frontiers Bioinform., 2024)

AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters. - Steven Weaver; Vanessa M. Dávila Conn; Daniel Ji; Hannah Verdonk; Santiago Ávila-Rios; Andrew J. Leigh Brown; Joel O. Wertheim; Sergei L. Kosakovsky Pond (Frontiers Bioinform., 2024)

Conversations over Clicks: Impact of Chatbots on Information Search in Interdisciplinary Learning. - Hannah Kim 003; Sergei L. Kosakovsky Pond; Stephen MacNeil (CoRR, 2025)