List of works by Sergei L. Kosakovsky Pond

28-way vertebrate alignment and conservation track in the UCSC Genome Browser

scientific article (publication date: December 2007)

A Dirichlet process model for detecting positive selection in protein-coding DNA sequences.

scholarly article

A case for the ancient origin of coronaviruses

scientific article (publication date: June 2013)

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection

scientific article published on 12 October 2012

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

scientific article

A genetic algorithm approach to detecting lineage-specific variation in selection pressure.

scientific article published on 27 October 2004

A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses

scientific article (publication date: 2011)

A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus.

scientific article published on 29 May 2008

A new method for inferring timetrees from temporally sampled molecular sequences

scientific article published on 17 January 2020

A public health model for the molecular surveillance of HIV transmission in San Diego, California

scientific article published on January 2009

A random effects branch-site model for detecting episodic diversifying selection.

scientific article published on 13 June 2011

A simple hierarchical approach to modeling distributions of substitution rates.

scientific article published on 13 October 2004

A structural basis for antibody-mediated neutralization of Nipah virus reveals a site of vulnerability at the fusion glycoprotein apex

scientific article published on 25 November 2019

Active Methamphetamine Use is Associated with Transmitted Drug Resistance to Non-Nucleoside Reverse Transcriptase Inhibitors in Individuals with HIV Infection of Unknown Duration

article

Active methamphetamine use is associated with transmitted drug resistance to non-nucleoside reverse transcriptase inhibitors in individuals with HIV infection of unknown duration

scientific article published on 22 October 2007

Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus

scientific article (publication date: March 2007)

Adaptation to different human populations by HIV-1 revealed by codon-based analyses

scientific article

Adaptation to different human populations by HIV-1 revealed by codon-based analysis

article

An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic

scientific article published on 01 July 2021

An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope

scientific article published on 11 October 2007

An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1

scientific article

An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic

scientific article published on 24 September 2020

An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope.

scientific article

Analysis of unusual and signature APOBEC-mutations in HIV-1 pol next-generation sequences

scientific article published on 26 February 2020

Antiretroviral drug resistance and risk behavior among recently HIV-infected men who have sex with men.

scientific article

Are all subtypes created equal? The effectiveness of antiretroviral therapy against non-subtype B HIV-1.

scientific article published on May 2009

Assigning and visualizing germline genes in antibody repertoires

scientific article

Associations between phylogenetic clustering and HLA profile among HIV-infected individuals in San Diego, California.

scientific article

Automated phylogenetic detection of recombination using a genetic algorithm.

scientific article published on 3 July 2006

Benchmarking multi-rate codon models

scientific article

Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort

scientific article published on 14 January 2016

Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B.

scientific article

Characterizing HIV transmission networks across the United States

scientific article

Characterizing the multiplicity of HIV founder variants during sexual transmission among MSM.

scientific article

Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men.

scientific article published on January 2012

Codon volatility does not reflect selective pressure on the HIV-1 genome

article

CodonTest: modeling amino acid substitution preferences in coding sequences

scientific article

Column sorting: rapid calculation of the phylogenetic likelihood function.

scientific article published in October 2004

Combining Phylogenetic and Network Approaches to Identify HIV-1 Transmission Links in San Mateo County, California

article

Comparative Analysis of Cell-Associated HIV DNA Levels in Cerebrospinal Fluid and Peripheral Blood by Droplet Digital PCR

scientific article published on 2 October 2015

Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1.

scientific article published on 11 April 2007

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

scientific article published on January 2008

Comparison of methods to detect HIV dual infection

scientific article

Compartmentalized HIV rebound in the central nervous system after interruption of antiretroviral therapy

scientific article published on July 2016

Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial

scientific article

Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines.

scientific article published on 17 May 2007

Contrast-FEL - a test for differences in selective pressures at individual sites among clades and sets of branches

scientific article published on 16 October 2020

Coping with viral diversity in HIV vaccine design

scientific article

Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons

scientific article published on 09 March 2022

Correcting the bias of empirical frequency parameter estimators in codon models

scientific article

Correction: Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al.

scientific article published on 21 March 2008

DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites

scientific article

Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes

scientific article published on 2 January 2018

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

scientific article (publication date: October 2010)

Datamonkey: rapid detection of selective pressure on individual sites of codon alignments

scientific article (publication date: 15 May 2005)

Deep Sequencing Reveals Compartmentalized HIV-1 in the Semen of Men With and Without STI-Associated Urethritis

scientific article published on 08 April 2020

Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen.

scientific article

Detecting individual sites subject to episodic diversifying selection

scientific article

Detecting phylogenetic signal in mutualistic interaction networks using a Markov process model

scientific article

Detecting signatures of selection from DNA sequences using Datamonkey.

scientific article

Detection in 2009 of the swine origin influenza A (H1N1) virus by a subtyping microarray

scientific article published on 15 July 2009

Detection of a SARS-CoV-2 variant of concern in South Africa

scientific article

Detection of mammalian virulence determinants in highly pathogenic avian influenza H5N1 viruses: multivariate analysis of published data

scientific article

Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants.

scientific article

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus

scientific article

Diversity of Functionally Distinct Clonal Sets of Human Conventional Memory B Cells That Bind Staphylococcal Protein A

scientific article published on 28 April 2021

Dynamics of viral evolution and neutralizing antibody response after HIV-1 superinfection

scientific article published on 18 September 2013

Early Antibody Lineage Diversification and Independent Limb Maturation Lead to Broad HIV-1 Neutralization Targeting the Env High-Mannose Patch

scientific article published on May 2016

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa

scientific article

Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability

scientific article published on 02 March 2020

Estimating selection pressures on HIV-1 using phylogenetic likelihood models.

scientific article published on October 2008

Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts.

scientific article published in January 2018

Evidence for positive selection on a sexual reproduction gene in the diatom genus Thalassiosira (Bacillariophyta).

scientific article published on 7 July 2006

Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans

scientific article published on 29 May 2020

Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas

scientific article published on 3 August 2017

Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces

scientific article published on 01 January 2019

Evolution of duplicated alpha-tubulin genes in ciliates

scientific article

Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors

scientific article published on 14 September 2017

Evolution of the interferon alpha gene family in eutherian mammals

scientific article

Evolution of viral genomes: interplay between selection, recombination, and other forces.

scientific article published on January 2012

Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia.

scientific article

Evolutionary fingerprinting of genes.

scientific article

Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope

scientific article

Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope

scientific article published on 08 December 2006

Evolutionary model selection with a genetic algorithm: a case study using stem RNA.

scientific article published on 12 October 2006

Evolutionary origins of human herpes simplex viruses 1 and 2

scientific article

FUBAR: a fast, unconstrained bayesian approximation for inferring selection

scientific article published on 18 February 2013

Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring

scientific article

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

GARD: a genetic algorithm for recombination detection

scientific article published on 16 November 2006

Gene-wide identification of episodic selection

scientific article published on 19 February 2015

Genetic attributes of cerebrospinal fluid-derived HIV-1 env.

scientific article

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

scientific article

Genotype-Specific Evolution of Hepatitis E Virus

scientific article published on 15 February 2017

Growth of HIV-1 Molecular Transmission Clusters in New York City

article

HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage

scientific article published in November 2017

HIV-1 clade B pol evolution following primary infection

scientific article

HIV-1 neutralizing antibody response and viral genetic diversity characterized with next generation sequencing

scientific article

HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens

scientific article published on 31 January 2018

HIV-associated neurocognitive disorder is associated with HIV-1 dual infection

scientific article

HIV-specific probabilistic models of protein evolution

scientific article

Higher HIV-1 genetic diversity is associated with AIDS and neuropsychological impairment

scientific article

HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

scientific article published on 01 January 2020

HyPhy: Hypothesis Testing Using Phylogenies

scholarly article

HyPhy: hypothesis testing using phylogenies

scientific article (publication date: 27 October 2004)

IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform

scientific article (publication date: September 2014)

Identification of a clade A HIV envelope immunogen from Protocol G that elicits neutralizing antibodies to tier 2 viruses

scientific article published on 13 September 2012

Identification of an HIV-1 clade A envelope that exhibits broad antigenicity and neutralization sensitivity and elicits antibodies targeting three distinct epitopes

scientific article published on 6 March 2013

Impact of seminal cytomegalovirus replication on HIV-1 dynamics between blood and semen

scientific article

In vivo VL-targeted microbial superantigen induced global shifts in the B cell repertoire.

scientific article published on 13 June 2012

Incidence and prevalence of intrasubtype HIV-1 dual infection in at-risk men in the United States.

scientific article

Inconsistencies in estimating the age of HIV-1 subtypes due to heterotachy

scientific article

Intrasubtype B HIV-1 Superinfection Correlates with Delayed Neutralizing Antibody Response

scientific article published on 14 June 2017

Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection

scientific article

Lorenzo-Redondo et al. reply

scientific article published in November 2017

Maintenance of Nef-mediated modulation of major histocompatibility complex class I and CD4 after sexual transmission of human immunodeficiency virus type 1

scientific article published on 28 February 2007

Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients.

scientific article

Mode and rate of evolution of haemosporidian mitochondrial genomes: timing the radiation of avian parasites

scientific article

Modeling HIV-1 drug resistance as episodic directional selection

scientific article

Molecular Features of the V1-V4 Coding Region of Sexually Transmitted Human Immunodeficiency Virus Type 1.

scientific article published on 17 April 2017

Multiple Recombination Events and Strong Purifying Selection at the Origin of SARS-CoV-2 Spike Glycoprotein Increased Correlated Dynamic Movements

scientific article published on 23 December 2020

Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage.

scientific article

National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort

article published in 2019

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen

scholarly article

Neuropathy- and myopathy-associated mutations in human small heat shock proteins: Characteristics and evolutionary history of the mutation sites

scientific article

Neutral theory and rapidly evolving viral pathogens.

scientific article published on 24 April 2018

Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection

scientific article

Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure

scientific article

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

scientific article published on 13 August 2020

No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics

scientific article published on 22 February 2020

Not so different after all: a comparison of methods for detecting amino acid sites under selection

scientific article

On the validity of evolutionary models with site-specific parameters

scientific article

Parsing social network survey data from hidden populations using stochastic context-free grammars

scientific article

Partner services in adults with acute and early HIV infection

scientific article published on 7 November 2016

Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection.

scientific article published on 19 March 2008

Persistent HIV-1 replication maintains the tissue reservoir during therapy

scientific article published on 27 January 2016

Phyloanatomic characterization of the distinct T cell and monocyte contributions to the peripheral blood HIV population within the host

scientific article published on 01 January 2020

Phylodynamic analysis of ebola virus in the 2014 sierra leone epidemic

scientific article published on 24 October 2014

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

scientific article

Phylodynamics of infectious disease epidemics

scientific article

Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.

scientific article

Phylogenetic relatedness of HIV-1 donor and recipient populations.

scientific article published on 11 January 2013

Population structure of the genes encoding the polymorphic Plasmodium falciparum apical membrane antigen 1: implications for vaccine design

scholarly article

Protease polymorphisms in HIV-1 subtype CRF01_AE represent selection by antiretroviral therapy and host immune pressure

scientific article

Purifying selection can obscure the ancient age of viral lineages

scientific article (publication date: December 2011)

RELAX: detecting relaxed selection in a phylogenetic framework

scientific article

Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples

scientific article published on 8 July 2016

Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function

scientific article

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

scientific article

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

scientific article published on 07 January 2022

Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model

scientific article published on 01 September 2018

Relative evolutionary rate inference in HyPhy with LEISR.

scientific article published on 5 February 2018

Response to Comment on "The Origins of Sexually Transmitted HIV Among Men Who Have Sex with Men"

scientific article

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

scientific article published on 07 May 2020

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

scientific article published on 01 April 2022

Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy

scientific article published on 24 July 2018

Semen-specific genetic characteristics of human immunodeficiency virus type 1 env.

scientific article

Sexual transmission of predicted CXCR4-tropic HIV-1 likely originating from the source partner's seminal cells.

scientific article

Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates

scientific article published on 24 December 2019

Site-to-site variation of synonymous substitution rates

scientific article

Social and Genetic Networks of HIV-1 Transmission in New York City

scientific article

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models.

scientific article published on 18 June 2008

Statistics and truth in phylogenomics

scientific article published on 26 August 2011

Structure-function analysis of hepatitis C virus envelope glycoproteins E1 and E2.

scientific article published on 15 October 2014

Suppressors of RNAi from plant viruses are subject to episodic positive selection.

scientific article published on 26 June 2013

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics

scientific article published on 02 January 2007

Synonymous site-to-site substitution rate variation dramatically inflates false positive rates of selection analyses: ignore at your own peril

scientific article published on 18 February 2020

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

scientific article

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

article

The Replication-Competent HIV-1 Latent Reservoir is Primarily Established Near the Time of Therapy Initiation: Supplemental Material for Abrahams et al

article

The biological and clinical significance of emerging SARS-CoV-2 variants

scientific article

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

The global transmission network of HIV-1

scientific article

The origins of sexually transmitted HIV among men who have sex with men.

scientific article

The relatedness of HIV epidemics in the United States-Mexico border region

scientific article

The replication-competent HIV-1 latent reservoir is primarily established near the time of therapy initiation

scientific article published on 01 October 2019

Transmitted HIV type 1 drug resistance among individuals with recent HIV infection in East and Southern Africa

scientific article

Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted Human Immunodeficiency Virus Type 1 Drug Resistance in a Large US Clinic Population

scientific article published on 01 January 2019

Unbiased RACE-Based Massive Parallel Surveys of Human IgA Antibody Repertoires

scientific article published in January 2017

Using HIV Sequence and Epidemiologic Data to Assess the Effect of Self-referral Testing for Acute HIV Infection on Incident Diagnoses in San Diego, California

scientific article

Using HIV networks to inform real time prevention interventions

scientific article

Using HIV transmission networks to investigate community effects in HIV prevention trials

scientific article

Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania

scientific article

Using ultradeep pyrosequencing to study HIV-1 coreceptor usage in primary and dual infection.

scientific article published on 18 April 2013

Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2

scientific article published on 13 July 2020

Viral Evolution and Cytotoxic T Cell Restricted Selection in Acute Infant HIV-1 Infection

scientific article published on 12 July 2016

Waiting for the truth: is reluctance in accepting an early origin hypothesis for SARS-CoV-2 delaying our understanding of viral emergence?

scientific article published in 2022

Windshield splatter analysis with the Galaxy metagenomic pipeline

scientific article published on 09 October 2009

Workshop: Error correction, noise filtering, and phylogenetic analysis of HIV sequences using the 454 platform

scholarly article published February 2012

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

article

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