Author details

Full Name

Sergei L Kosakovsky Pond

Affiliation

ORCID

Career Start Year

2001

Papers

207

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
34075377	Identification of evolutionary trajectories shared across human betacoronaviruses.		2023
37738247	Recommendations on data sharing in HIV drug resistance research.	PLoS Med	2023
38077089	The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.	bioRxiv	2023
37875683	Anti-COVID drug accelerates viral evolution.		2023
36712007	Natural selection differences detected in key protein domains between non-pathogenic and pathogenic Feline Coronavirus phenotypes.		2023
37395787	Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses.	Mol Biol Evol	2023
37384622	Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies.	PLoS Pathog	2023
37112972	HIV-1 Group M Capsid Amino Acid Variability: Implications for Sequence Quality Control of Genotypic Resistance Testing.	Viruses	2023
37038392	Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes.		2023
37220645	Identification of Evolutionary Trajectories Shared across Human Betacoronaviruses.		2023
35325204	Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function.	Mol Biol Evol	2022
36029839	Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy.	Environmental Research	2022
35760080	Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa.	Nat Med	2022
35700134	Susceptibility of SARS-CoV-2 Omicron Variants to Therapeutic Monoclonal Antibodies: Systematic Review and Meta-analysis.	Microbiol Spectr	2022
35814334	Conserved recombination patterns across coronavirus subgenera.	Virus Evolution	2022
35752633	Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.	Nat Commun	2022
35632597	Recent Zoonotic Spillover and Tropism Shift of a Canine Coronavirus Is Associated with Relaxed Selection and Putative Loss of Function in NTD Subdomain of Spike Protein.	Viruses	2022
35561179	TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity.		2022
36334368	Sierra SARS-CoV-2 sequence and antiviral resistance analysis program.	Journal of Clinical Virology	2022
35678958	Human HspB1, HspB3, HspB5 and HspB8: Shaping these disease factors during vertebrate evolution.	Cell Stress and Chaperones	2022
35732627	The evolution of BDNF is defined by strict purifying selection and prodomain spatial coevolution, but what does it mean for human brain disease?	Translational Psychiatry	2022
36322581	RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis.	PLoS One	2022
36597548	Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models.		2022
35296465	Waiting for the truth: is reluctance in accepting an early origin hypothesis for SARS-CoV-2 delaying our understanding of viral emergence?	BMJ Global Health	2022
35042229	Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.	Nature	2022
35014856	Predicting the mutational drivers of future SARS-CoV-2 variants of concern.	Sci Transl Med	2022
35075458	RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis.	bioRxiv	2022
35075456	Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.	bioRxiv	2022
35263335	Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons.	PLoS ONE	2022
34931186	TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity.		2021
33972434	Weak selection on synonymous codons substantially inflates estimates in bacteria.	Proceedings of the National Academy of Sciences of the United States of America	2021
33853970	Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil.	Science	2021
33690265	Detection of a SARS-CoV-2 variant of concern in South Africa.	Nature	2021
33791701	Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring.	bioRxiv	2021
33998095	Ancestral transoceanic colonization and recent population reduction in a nonannual killifish from the Seychelles archipelago.	Molecular Ecology	2021
33995388	Diversity of Functionally Distinct Clonal Sets of Human Conventional Memory B Cells That Bind Staphylococcal Protein A.	Front Immunol	2021
33942847	An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic.	Molecular Biology and Evolution	2021
33828543	Molecular Evolution of Human Norovirus GII.2 Clusters.	Frontiers in Microbiology	2021
33711070	Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes.	PLoS ONE	2021
33711012	Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.	PLoS Biol	2021
33064823	Contrast-FEL-A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches.	Molecular Biology and Evolution	2021
32995781	An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic.		2021
34505896	Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses.	Mol Biol Evol	2021
34555124	Characterization of changes in the hemagglutinin that accompanied the emergence of H3N2/1968 pandemic influenza viruses.	PLoS Pathog	2021
34492694	Effective Human Immunodeficiency Virus Molecular Surveillance Requires Identification of Incident Cases of Infection.	Clin Infect Dis	2021
34537136	The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.	Cell	2021
34535792	The biological and clinical significance of emerging SARS-CoV-2 variants.	Nature Reviews Genetics	2021
34588690	Ready-to-use public infrastructure for global SARS-CoV-2 monitoring.	Nat Biotechnol	2021
31504749	HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies.	Mol Biol Evol	2020
32269129	Deep Sequencing Reveals Compartmentalized HIV-1 in the Semen of Men with and without Sexually Transmitted Infection-Associated Urethritis.	J Virol	2020