Sergei L. Kosakovsky Pond

31 papers C 1Journal 28Unranked 2

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Changing the Optics: Comparing Traditional and Retrieval-Augmented GenAI E-Tutorials in Interdisciplinary Learning. CoRR Hannah Kim, Rahad Arman Nabid, Jeni Sorathiya, Minh Doan, Elijah Jordan, Rayhana Nasimova, Sergei L. Kosakovsky Pond, Stephen MacNeil
2025	J	`jnl`	Conversations over Clicks: Impact of Chatbots on Information Search in Interdisciplinary Learning. CoRR Hannah Kim, Sergei L. Kosakovsky Pond, Stephen MacNeil
2024	J	`jnl`	AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters. Frontiers Bioinform. Steven Weaver, Vanessa M. Dávila Conn, Daniel Ji, Hannah Verdonk, Santiago Ávila-Rios, Andrew J. Leigh Brown, Joel O. Wertheim, Sergei L. Kosakovsky Pond
2024	J	`jnl`	The evolution of mammalian Rem2: unraveling the impact of purifying selection and coevolution on protein function, and implications for human disorders. Frontiers Bioinform. Alexander G. Lucaci, William E. Brew, Jason Lamanna, Avery Selberg, Vincenzo Carnevale, Anna R. Moore, Sergei L. Kosakovsky Pond
2024	C	`conf`	WIP: Identifying Tutorial Affordances for Interdisciplinary Learning Environments. FIE Hannah Kim, Sergei L. Kosakovsky Pond, Stephen MacNeil
2024	J	`jnl`	WIP: Identifying Tutorial Affordances for Interdisciplinary Learning Environments. CoRR Hannah Kim, Sergei L. Kosakovsky Pond, Stephen MacNeil
2022	J	`jnl`	TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity. Bioinform. Marcos A. Caraballo-Ortiz, Sayaka Miura, Maxwell D. Sanderford, Tenzin Dolker, Qiqing Tao, Steven Weaver, Sergei L. Kosakovsky Pond, Sudhir Kumar
2020	J	`jnl`	A new method for inferring timetrees from temporally sampled molecular sequences. PLoS Comput. Biol. Sayaka Miura, Koichiro Tamura, Qiqing Tao, Louise A. Huuki, Sergei L. Kosakovsky Pond, Jessica Priest, Jiamin Deng, Sudhir Kumar
2018	J	`jnl`	Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons. PLoS Comput. Biol. Kemal Eren, Steven Weaver, Robert Ketteringham, Morné Valentyn, Melissa Laird Smith, Venkatesh Kumar, Sanjay Mohan, Sergei L. Kosakovsky Pond, Ben Murrell
2018	J	`jnl`	phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics. BMC Bioinform. Stephen D. Shank, Steven Weaver, Sergei L. Kosakovsky Pond
2017	J	`jnl`	Lorenzo-Redondo Nat. 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, Andrew Rambaut, Ashley T. Haase, Angela R. McLean, Steven M. Wolinsky
2015	J	`jnl`	: Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial. PLoS Comput. Biol. 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, Eric Sanders-Buell, Chris Carrico, Sergey Menis, Meera Bose, Miguel A. Arroyo, Robert J. O'Connell, Sorachai Nitayaphan, Punnee Pitisuttithum, Jaranit Kaewkungwal, Supachai Rerks-Ngarm, Merlin L. Robb, Tatsiana Kirys, Ivelin Georgiev, Peter D. Kwong, Konrad Scheffler, Sergei L. Kosakovsky Pond, Jonathan M. Carlson, Nelson Michael, William R. Schief, James I. Mullins, Jerome H. Kim, Peter B. Gilbert
2014	J	`jnl`	IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform. PLoS Comput. Biol. N. Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D. Richman, Dennis R. Burton, Pascal Poignard, Davey M. Smith, Sergei L. Kosakovsky Pond
2012	J	`jnl`	A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. Bioinform. Philippe Lemey, Vladimir N. Minin, Filip Bielejec, Sergei L. Kosakovsky Pond, Marc A. Suchard
2012	J	`jnl`	Modeling HIV-1 Drug Resistance as Episodic Directional Selection. PLoS Comput. Biol. Ben Murrell, Tulio de Oliveira, Chris Seebregts, Sergei L. Kosakovsky Pond, Konrad Scheffler
2012	—	`conf`	Workshop: Error correction, noise filtering, and phylogenetic analysis of HIV sequences using the 454 platform. ICCABS Konrad Scheffler, N. Lance Hepler, Martin D. Smith, Wayne Delport, Art F. Y. Poon, Douglas D. Richman, Sergei L. Kosakovsky Pond
2011	—	`conf`	Computational analysis of HIV-1 evolution and epidemiology. BIBM Workshops Sergei L. Kosakovsky Pond
2010	J	`jnl`	CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences. PLoS Comput. Biol. Wayne Delport, Konrad Scheffler, Gordon Botha, Mike B. Gravenor, Spencer V. Muse, Sergei L. Kosakovsky Pond
2010	J	`jnl`	Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinform. Wayne Delport, Art F. Y. Poon, Simon D. W. Frost, Sergei L. Kosakovsky Pond
2009	J	`jnl`	An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1. PLoS Comput. Biol. 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
2008	J	`jnl`	Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al. PLoS Comput. Biol. David C. Nickle, Nebojsa Jojic, David Heckerman, Vladimir Jojic, Darko Kirovski, Morgane Rolland, Sergei L. Kosakovsky Pond, James I. Mullins
2008	J	`jnl`	Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models. Bioinform. Art F. Y. Poon, Fraser I. Lewis, Simon D. W. Frost, Sergei L. Kosakovsky Pond
2007	J	`jnl`	A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes. PLoS Comput. Biol. Wen-Yu Chung, Samir Wadhawan, Radek Szklarczyk, Sergei L. Kosakovsky Pond, Anton Nekrutenko
2007	J	`jnl`	An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope. PLoS Comput. Biol. Art F. Y. Poon, Fraser I. Lewis, Sergei L. Kosakovsky Pond, Simon D. W. Frost
2007	J	`jnl`	Coping with Viral Diversity in HIV Vaccine Design. PLoS Comput. Biol. David C. Nickle, Morgane Rolland, Mark A. Jensen, Sergei L. Kosakovsky Pond, Wenjie Deng, Mark Seligman, David Heckerman, James I. Mullins, Nebojsa Jojic
2007	J	`jnl`	Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope. PLoS Comput. Biol. Art F. Y. Poon, Fraser I. Lewis, Sergei L. Kosakovsky Pond, Simon D. W. Frost
2007	J	`jnl`	Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics. PLoS Comput. Biol. Philippe Lemey, Sergei L. Kosakovsky Pond, Alexei J. Drummond, Oliver G. Pybus, Beth Shapiro, Helena Barroso, Nuno Taveira, Andrew Rambaut
2006	J	`jnl`	Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses. PLoS Comput. Biol. Sergei L. Kosakovsky Pond, Simon D. W. Frost, Zehava Grossman, Michael B. Gravenor, Douglas D. Richman, Andrew J. Leigh Brown
2006	J	`jnl`	GARD: a genetic algorithm for recombination detection. Bioinform. Sergei L. Kosakovsky Pond, David Posada, Michael B. Gravenor, Christopher H. Woelk, Simon D. W. Frost
2005	J	`jnl`	Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinform. Sergei L. Kosakovsky Pond, Simon D. W. Frost
2005	J	`jnl`	HyPhy: hypothesis testing using phylogenies. Bioinform. Sergei L. Kosakovsky Pond, Simon D. W. Frost, Spencer V. Muse