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

Correcting the bias of empirical frequency parameter estimators in codon models.

by Sergei Kosakovsky Pond, Wayne Delport, Spencer V Muse, Konrad Scheffler
Published 2010-07-01

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

A first look at ARFome: dual-coding genes in mammalian genomes.

by Wen-Yu Chung, Samir Wadhawan, Radek Szklarczyk, Sergei Kosakovsky Pond, Anton Nekrutenko
Published 2007-05-01

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

Benchmarking multi-rate codon models.

by Wayne Delport, Konrad Scheffler, Mike B Gravenor, Spencer V Muse, Sergei Kosakovsky Pond
Published 2010-07-01

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

Comparison of immunogen designs that optimize peptide coverage: reply to Fischer et al.

by David C Nickle, Nebojsa Jojic, David Heckerman, Vladimir Jojic, Darko Kirovski, Morgane Rolland, Sergei Kosakovsky Pond, James I Mullins
Published 2008-01-01