Relative evolutionary rate inference in HyPhy with LEISR

by Stephanie J. Spielman, Sergei L. Kosakovsky Pond
Published 2018-02-01

On the validity of evolutionary models with site-specific parameters.

by Konrad Scheffler, Ben Murrell, Sergei L Kosakovsky Pond
Published 2014-01-01

phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics

by Stephen D. Shank, Steven Weaver, Sergei L. Kosakovsky Pond
Published 2018-07-01

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
Published 2020-01-01

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
Published 2011-01-01

Molecular Evolution of Human Norovirus GII.2 Clusters

by Xingguang Li, Haizhou Liu, Brittany Rife Magalis, Sergei L. Kosakovsky Pond, Erik M. Volz
Published 2021-03-01

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
Published 2019-12-01

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
Published 2021-01-01

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
Published 2007-11-01

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
Published 2007-01-01

Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants.

by J Joukje Siebenga, Philippe Lemey, Sergei L Kosakovsky Pond, Andrew Rambaut, Harry Vennema, Marion Koopmans
Published 2010-05-01

Detecting individual sites subject to episodic diversifying selection.

by Ben Murrell, Joel O Wertheim, Sasha Moola, Thomas Weighill, Konrad Scheffler, Sergei L Kosakovsky Pond
Published 2012-01-01

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
Published 2010-08-01

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
Published 2020-01-01

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
Published 2007-06-01

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
Published 2020-01-01

Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

by Philippe Lemey, Sergei L Kosakovsky Pond, Alexei J Drummond, Oliver G Pybus, Beth Shapiro, Helena Barroso, Nuno Taveira, Andrew Rambaut
Published 2007-02-01

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
Published 2006-06-01

Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons.

by Kemal Eren, Steven Weaver, Robert Ketteringham, Morné Valentyn, Melissa Laird Smith, Venkatesh Kumar, Sanjay Mohan, Sergei L Kosakovsky Pond, Ben Murrell
Published 2018-12-01

Modeling HIV-1 drug resistance as episodic directional selection.

by Ben Murrell, Tulio de Oliveira, Chris Seebregts, Sergei L Kosakovsky Pond, Konrad Scheffler, Southern African Treatment and Resistance Network-SATuRN Consortium
Published 2012-01-01