Sergei L. Kosakovsky Pond

National Health Laboratory Service — South Africa

Immunology and Microbiology · Life Sciences

80h-index40.9kcitations324works5.92yr avg
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Research Topics

HIV Research and Treatment(120), Genomics and Phylogenetic Studies(82), HIV/AIDS Research and Interventions(59), SARS-CoV-2 and COVID-19 Research(48), HIV/AIDS drug development and treatment(48)

Publications324 total

MoleRate: comparing molecular relative evolutionary rates to detect convergent evolution
Evolution·2025
From data to publication in a browser with BRC-Analytics: Evolutionary dynamics of coding overlaps in measles virus
2025Open Access
WITHDRAWN: Defective HIV DNA genomes provide ancestralrelevance critical for phylogenetic inference of reservoir dynamics
2025Open Access
Author response: Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models
2025Open Access
The persistent pool of HIV-1-infected cells is formed episodically during untreated infection.
UNC Libraries·2025Open Access
Author response: Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models
2025Open Access
Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models
2025Open Access
Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models
eLife·2025Open Access
Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models
2025Open Access
Author response: Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors
2025Open Access
Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors
2025· 1 citedOpen Access
Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors
2025Open Access
Ecological interactions and genomic innovation fueled the evolution of ray-finned fish endothermy
Science Advances·2025· 5 citedOpen Access
Nationwide Implementation of HIV Molecular Cluster Detection by Centers for Disease Control and Prevention and State and Local Health Departments, United States
Emerging infectious diseases·2025· 3 citedOpen Access
A New Comparative Framework for Estimating Selection on Synonymous Substitutions
Molecular Biology and Evolution·2025Open Access
Dynamics of natural selection preceding human viral epidemics and pandemics
2025· 2 citedOpen Access
HIV-1 Rebound Virus Consists of a Small Number of Lineages That Entered the Reservoir Close to ART Initiation
2025· 2 citedOpen Access
The persistent pool of HIV-1-infected cells is formed episodically during untreated infection
Journal of Virology·2024· 2 citedOpen Access
Correction: Somatic genome architecture and molecular evolution are decoupled in “young” linage-specific gene families in ciliates
PLoS ONE·2024Open Access
Ecological diversification of sea catfishes is accompanied by genome-wide signatures of positive selection
Nature Communications·2024· 5 citedOpen Access
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Frequent Co-authors

Simon D. W. Frost(15), Steven Weaver(13), Joel O. Wertheim(12), Ben Murrell(9), Konrad Scheffler(8), Davey M. Smith(8), Darren P. Martin(7), Andrew Rambaut(7), Túlio de Oliveira(7), Houriiyah Tegally(6), Deelan Doolabh(6), Jennifer Giandhari(6), Richard Lessells(6), Eduan Wilkinson(6), Carolyn Williamson(6), Oliver G. Pybus(6), Spencer V. Muse(5), Susan Engelbrecht(5), Marta Giovanetti(5), Arash Iranzadeh(5)