Sergei L. Kosakovsky Pond

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Relative evolutionary rate inference in HyPhy with LEISR

Stephanie J. Spielman, Sergei L. Kosakovsky Pond, 2017, bioRxiv.

Parsing Social Network Survey Data from Hidden Populations Using Stochastic Context-Free Grammars

Douglas D. Heckathorn, Simon D. W. Frost, Art F. Y. Poon, 2009, PloS one.

Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes

Stephen D. Shank, Sergei L. Kosakovsky Pond, Steven Weaver, 2020, bioRxiv.

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

Hilmar Lapp, James P. Balhoff, Todd J. Vision, 2007, Evolutionary Bioinformatics Online.

A new method for inferring timetrees from temporally sampled molecular sequences

Sudhir Kumar, Sayaka Miura, Louise A. Huuki, 2019, bioRxiv.

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

Daniel J. Blankenberg, Sergei L. Kosakovsky Pond, Tom H. Pringle, 2007, Genome research.

Column sorting: rapid calculation of the phylogenetic likelihood function.

Sergei L. Kosakovsky Pond, S. Muse, 2004, Systematic biology.

Phylodynamics of Infectious Disease Epidemics

Sergei L. Kosakovsky Pond, E. Volz, S. Frost, 2009, Genetics.

Phylodynamic Reconstruction Reveals Norovirus GII.4 Epidemic Expansions and their Molecular Determinants

Sergei L. Kosakovsky Pond, P. Lemey, A. Rambaut, 2010, PLoS pathogens.

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

Sergei L. Kosakovsky Pond, S. Frost, 2005, Molecular biology and evolution.

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

Sergei L. Kosakovsky Pond, S. Frost, B. Murrell, 2011, Molecular biology and evolution.

Detecting Individual Sites Subject to Episodic Diversifying Selection

Sergei L. Kosakovsky Pond, Thomas Weighill, B. Murrell, 2012, PLoS genetics.

FUBAR: a fast, unconstrained bayesian approximation for inferring selection.

Sergei L. Kosakovsky Pond, Thomas Weighill, D. Sheward, 2013, Molecular biology and evolution.

Benchmarking Multi-Rate Codon Models

Sergei L. Kosakovsky Pond, S. Muse, M. Gravenor, 2010, PloS one.

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

Sergei L. Kosakovsky Pond, S. Frost, A. Leigh Brown, 2008, Molecular biology and evolution.

UC Office of the President Recent Work Title Less Is More : An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection Permalink

Sergei L. Kosakovsky Pond, B. Murrell, K. Scheffler, 2015 .

Statistics and truth in phylogenomics.

Sergei L. Kosakovsky Pond, Sudhir Kumar, A. Filipski, 2012, Molecular biology and evolution.

Evolution of the interferon alpha gene family in eutherian mammals.

Sergei L. Kosakovsky Pond, D. Richman, S. Frost, 2007, Gene.

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

Sergei L. Kosakovsky Pond, J. Mullins, D. Richman, 2010, Molecular biology and evolution.

Mapping Protease Inhibitor Resistance to Human Immunodeficiency Virus Type 1 Sequence Polymorphisms within Patients

Sergei L. Kosakovsky Pond, D. Richman, S. Frost, 2007, Journal of Virology.

The global transmission network of HIV-1.

Sergei L. Kosakovsky Pond, D. Richman, A. Leigh Brown, 2014, The Journal of infectious diseases.

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

Sergei L. Kosakovsky Pond, Sergei L Kosakovsky Pond, Michael B Gravenor, 2007, Molecular biology and evolution.

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

Sergei L. Kosakovsky Pond, A. Godzik, A. Sigal, 2020, medRxiv.

Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril

Sergei L. Kosakovsky Pond, S. Muse, S. Wisotsky, 2020, Molecular biology and evolution.

Evolutionary Origins of Human Herpes Simplex Viruses 1 and 2

Sergei L. Kosakovsky Pond, Davey M. Smith, K. Scheffler, 2014, Molecular biology and evolution.

Purifying Selection Can Obscure the Ancient Age of Viral Lineages

Sergei L. Kosakovsky Pond, Sergei L Kosakovsky Pond, Joel O Wertheim, 2011, Molecular biology and evolution.

Gene-wide identification of episodic selection.

Ben Murrell, Konrad Scheffler, Steven Weaver, 2015, Molecular biology and evolution.

Windshield splatter analysis with the Galaxy metagenomic pipeline.

Sergei L. Kosakovsky Pond, A. Nekrutenko, F. Chiaromonte, 2009, Genome research.

Using HIV Transmission Networks to Investigate Community Effects in HIV Prevention Trials

Joel O. Wertheim, Sergei L. Kosakovsky Pond, Victor De Gruttola, 2011, PloS one.

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

Ben Murrell, Konrad Scheffler, Joel O. Wertheim, 2017, PLoS pathogens.

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

Sergei L. Kosakovsky Pond, O. Pybus, B. Gutiérrez, 2019, Proceedings of the National Academy of Sciences.

HyPhy 2.5 - a customizable platform for evolutionary hypothesis testing using phylogenies.

Stephanie J. Spielman, Sergei L. Kosakovsky Pond, A. Nekrutenko, 2019, Molecular biology and evolution.

HIV-Specific Probabilistic Models of Protein Evolution

David C. Nickle, Peter B. Gilbert, Sergei L. Kosakovsky Pond, 2007, PloS one.

Detection of Mammalian Virulence Determinants in Highly Pathogenic Avian Influenza H5N1 Viruses: Multivariate Analysis of Published Data

Sergei L. Kosakovsky Pond, F I Lewis, M. Ward, 2009, Journal of Virology.

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

Ben Murrell, Terri Wrin, Sergei L. Kosakovsky Pond, 2017, Immunity.

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

Konrad Scheffler, Ronald J. Ellis, Sergei L. Kosakovsky Pond, 2016, Virus evolution.

Using HIV Networks to Inform Real Time Prevention Interventions

Joel O. Wertheim, Sergei L. Kosakovsky Pond, Christy M. Anderson, 2014, PloS one.

Contrast-FEL—A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches

Sergei L. Kosakovsky Pond, A. Escalante, S. Weaver, 2020, Molecular biology and evolution.

Contrast-FEL—A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches

Sergei L. Kosakovsky Pond, A. Escalante, S. Weaver, 2020, bioRxiv.

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

Sergei L. Kosakovsky Pond, S. Muse, F. Mannino, 2020, PloS one.

On the Validity of Evolutionary Models with Site-Specific Parameters

Sergei L. Kosakovsky Pond, B. Murrell, K. Scheffler, 2014, PloS one.

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

Sergei L. Kosakovsky Pond, Gemma G. R. Murray, Darren J Obbard, 2013, Proceedings of the Royal Society B: Biological Sciences.

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

Cathy H. Wu, Sergei L. Kosakovsky Pond, C. R. Vinayaka, 2007, Virus Genes.

Evidence for Positive Selection on a Sexual Reproduction Gene in the Diatom Genus Thalassiosira (Bacillariophyta)

Sergei L. Kosakovsky Pond, U. Sorhannus, 2006, Journal of Molecular Evolution.

Neutral Theory and Rapidly Evolving Viral Pathogens

Sergei L. Kosakovsky Pond, S. Frost, B. R. Magalis, 2018, Molecular biology and evolution.

Evolutionary and Transmission Dynamics of Reassortant H5N1 Influenza Virus in Indonesia

Sergei L. Kosakovsky Pond, T. Lam, C. Hon, 2008, PLoS pathogens.

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

Sergei L. Kosakovsky Pond, M. Salemi, M. Summers, 2018, Virus evolution.

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

Sergei L. Kosakovsky Pond, D. Richman, S. Little, 2013, The Journal of infectious diseases.

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

Sergei L. Kosakovsky Pond, D. Richman, S. Little, 2012, Virology.

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

Sergei L. Kosakovsky Pond, Jody L. Martin, J. O. Wertheim, 2014, Mutation research. Reviews in mutation research.

Identification of an HIV-1 Clade A Envelope That Exhibits Broad Antigenicity and Neutralization Sensitivity and Elicits Antibodies Targeting Three Distinct Epitopes

Sergei L. Kosakovsky Pond, D. Burton, D. Montefiori, 2013, Journal of Virology.

Deep Sequencing Reveals Minor Protease Resistance Mutations in Patients Failing a Protease Inhibitor Regimen

Simon A. A. Travers, Sergei L. Kosakovsky Pond, S. Travers, 2012, Journal of Virology.

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

Sergei L. Kosakovsky Pond, R. Haubrich, Davey M. Smith, 2015, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

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

Sergei L. Kosakovsky Pond, N. Pattabiraman, R. Mazumder, 2015, Journal of biomolecular structure & dynamics.

The Origins of Sexually Transmitted HIV Among Men Who Have Sex with Men

Sergei L. Kosakovsky Pond, D. Richman, S. Little, 2010, Science Translational Medicine.

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

Sergei L. Kosakovsky Pond, D. Richman, S. Little, 2013, The Journal of infectious diseases.

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

Sergei L. Kosakovsky Pond, A. Godzik, A. Sigal, 2021, Nature.

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

Sergei L. Kosakovsky Pond, R. Ellis, S. Gianella, 2015, PloS one.

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

Sergei L. Kosakovsky Pond, D. Richman, S. Little, 2017, Journal of Virology.

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

Sergei L. Kosakovsky Pond, Joshua B. Singer, P. Lemey, 2021, PLoS biology.

Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen

Sergei L. Kosakovsky Pond, P. Lemey, D. Robertson, 2020, bioRxiv.

HyPhy: hypothesis testing using phylogenies

Sergei L. Kosakovsky Pond, Simon D. W. Frost, Sergei L. Kosakovsky Pond, 2005, Bioinform..

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

Sergei L. Kosakovsky Pond, Yi Liu, Gerald H Learn, 2010, BioTechniques.

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

Stephanie J. Spielman, Sergei L. Kosakovsky Pond, A. Poon, 2019, Methods in molecular biology.

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

Steven Weaver, Stephanie J. Spielman, Sergei L. Kosakovsky Pond, 2018, Molecular biology and evolution.

Mode and Rate of Evolution of Haemosporidian Mitochondrial Genomes: Timing the Radiation of Avian Parasites

Craig E. Stanley, Sergei L. Kosakovsky Pond, P. Parker, 2017, Molecular biology and evolution.

EVOLUTION OF DUPLICATED ALPHA-TUBULIN GENES IN CILIATES

Sergei L. Kosakovsky Pond, L. Katz, S. Muse, 2002 .

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

Sergei L. Kosakovsky Pond, X. Su, O. Doumbo, 2008, Proceedings of the National Academy of Sciences.

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

Timothy B. Stockwell, Sergei L. Kosakovsky Pond, A. P. Adams, 2017, PLoS neglected tropical diseases.

Automated phylogenetic detection of recombination using a genetic algorithm.

David Posada, Sergei L. Kosakovsky Pond, Sergei L Kosakovsky Pond, 2006, Molecular biology and evolution.

RELAX: detecting relaxed selection in a phylogenetic framework.

Ben Murrell, Konrad Scheffler, Sergei L. Kosakovsky Pond, 2014, Molecular biology and evolution.

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

Stephanie J. Spielman, Sergei L. Kosakovsky Pond, Sergei L Kosakovsky Pond, 2018, bioRxiv.

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

Sergei L. Kosakovsky Pond, D. Richman, S. Pillai, 2005, Virology.

Molecular Evolution of Human Norovirus GII.2 Clusters

Sergei L. Kosakovsky Pond, E. Volz, Xingguang Li, 2021, Frontiers in Microbiology.

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

Sergei L. Kosakovsky Pond, J. Ananworanich, M. Salemi, 2020, Virus evolution.

Monocyte Infection Dynamics Shape HIV-1 Phyloanatomy in the Peripheral Blood

Sergei L. Kosakovsky Pond, Jerome H. Kim, R. Paul, 2018, bioRxiv.

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

Sergei L. Kosakovsky Pond, T. de Oliveira, D. Israelski, 2018, Front. Microbiol..

A Massively Parallel Sequencing Approach Uncovers Ancient Origins and High Genetic Variability of Endangered Przewalski's Horses

Sergei L. Kosakovsky Pond, A. Nekrutenko, K. Makova, 2011, Genome biology and evolution.

Weak selection on synonymous codons substantially inflates dN/dS estimates in bacteria

Sergei L. Kosakovsky Pond, J. Hey, A. Webb, 2021, Proceedings of the National Academy of Sciences.

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

Sergei L. Kosakovsky Pond, R. Knight, L. Katz, 2019, mBio.

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

Sergei L. Kosakovsky Pond, P. Lemey, D. Robertson, 2021, Cell.

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

Sergei L. Kosakovsky Pond, R. Shafer, S. Rhee, 2019, Open forum infectious diseases.

Correction: Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models

Sergei L. Kosakovsky Pond, S. Muse, W. Delport, 2014, PLoS ONE.

Correcting the Bias of Empirical Frequency Parameter Estimators in Codon Models

Sergei L. Kosakovsky Pond, S. Muse, W. Delport, 2010, PloS one.

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

Sergei L. Kosakovsky Pond, D. Richman, S. Frost, 2007, PLoS pathogens.

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

Sergei L. Kosakovsky Pond, Mathieu Fourment, Sergei L Kosakovsky Pond, 2012, Molecular biology and evolution.

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

Ben Murrell, Sergei L. Kosakovsky Pond, Sergei L Kosakovsky Pond, 2018, The Journal of infectious diseases.

HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens.

Steven Weaver, Sergei L. Kosakovsky Pond, Sergei L Kosakovsky Pond, 2018, Molecular biology and evolution.

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

Yang Liu, Terri Wrin, Sergei L. Kosakovsky Pond, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses

Sergei L. Kosakovsky Pond, A. Nekrutenko, Han Mei, 2021, Molecular biology and evolution.

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

Sergei L. Kosakovsky Pond, Simon A. Bray, A. Nekrutenko, 2021, bioRxiv.

The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape

Sergei L. Kosakovsky Pond, P. Lemey, D. Robertson, 2021, medRxiv.

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

Sergei L. Kosakovsky Pond, M. Salemi, G. Chillemi, 2020, International journal of molecular sciences.

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

Michael J Silverberg, Sergei L. Kosakovsky Pond, Soo-Yon Rhee, 2018, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

A Case for the Ancient Origin of Coronaviruses

Sergei L. Kosakovsky Pond, J. Peiris, L. Poon, 2013, Journal of Virology.

Detection of Minority Resistance during Early HIV-1 Infection: Natural Variation and Spurious Detection rather than Transmission and Evolution of Multiple Viral Variants

Jun Yong Choi, Sergei L. Kosakovsky Pond, Wayne Delport, 2011, Journal of Virology.

Estimating selection pressures on HIV‐1 using phylogenetic likelihood models

Sergei L. Kosakovsky Pond, D. Richman, S. Little, 2008, Statistics in medicine.

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

Sergei L. Kosakovsky Pond, Philip J Norris, Todd M. Allen, 2016, PLoS pathogens.

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.

Sergei L. Kosakovsky Pond, D. Richman, S. Little, 2016, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

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

Sergei L. Kosakovsky Pond, D. Richman, I. Grant, 2012, Virology.

Deep Sequencing Reveals Compartmentalized HIV-1 in the Semen of Men with and without Sexually Transmitted Infection-Associated Urethritis

Sergei L. Kosakovsky Pond, Shuntai Zhou, R. Swanstrom, 2020, Journal of Virology.

Deep Sequencing Reveals Compartmentalized HIV-1 in the Semen of Men with and without STI-associated Urethritis

Sergei L. Kosakovsky Pond, Shuntai Zhou, R. Swanstrom, 2020, bioRxiv.

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

Sergei L. Kosakovsky Pond, D. Richman, S. Little, 2016, Virus evolution.

Dynamics of Viral Evolution and Neutralizing Antibody Response after HIV-1 Superinfection

Sergei L. Kosakovsky Pond, D. Richman, S. Little, 2013, Journal of Virology.

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

Yan Guo, Ben Murrell, Pham Phung, 2016, Virus evolution.

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

Sergei L. Kosakovsky Pond, Philip L. Tzou, R. Shafer, 2019, bioRxiv.

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

Sergei L. Kosakovsky Pond, Davey M. Smith, 2009, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

EVOLUTION OF DUPLICATED ALPHα‐TUBULIN GENES IN CILIATES

Sergei L. Kosakovsky Pond, L. Katz, S. Muse, 2002, Evolution; international journal of organic evolution.

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

Sergei L. Kosakovsky Pond, Susan Little, Sergei L Kosakovsky Pond, 2012, The Journal of infectious diseases.

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

Sergei L. Kosakovsky Pond, D. Richman, F. Vaida, 2016, AIDS.

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

Ben Murrell, Terri Wrin, Sergei L. Kosakovsky Pond, 2016, Immunity.

In Vivo VL-Targeted Microbial Superantigen Induced Global Shifts in the B Cell Repertoire

Sergei L. Kosakovsky Pond, G. Silverman, C. Grönwall, 2012, The Journal of Immunology.

Ancestral transoceanic colonization and recent population reduction in a nonannual killifish from the Seychelles archipelago

Sergei L. Kosakovsky Pond, D. Valenzano, S. Wisotsky, 2021, Molecular ecology.

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

Sergei L. Kosakovsky Pond, S. Letendre, Davey M. Smith, 2007, The open AIDS journal.

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

Sergei L. Kosakovsky Pond, D. Richman, S. Little, 2012, Journal of medical virology.

Partner services in adults with acute and early HIV infection

Sergei L. Kosakovsky Pond, S. Little, Davey M. Smith, 2017, AIDS.

Viral CpG Deficiency Provides No Evidence That Dogs Were Intermediate Hosts for SARS-CoV-2

Sergei L. Kosakovsky Pond, E. Holmes, R. Goldstein, 2020, Molecular biology and evolution.

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

Darko Kirovski, David Heckerman, Vladimir Jojic, 2008, PLoS Computational Biology.

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

Anton Nekrutenko, Sergei L. Kosakovsky Pond, Sergei L Kosakovsky Pond, 2020, bioRxiv.

UC Office of the President Recent Work Title The Global Transmission Network of HIV-1 Permalink

Sergei L. Kosakovsky Pond, D. Richman, A. Leigh Brown, 2013 .

Sergei L. Kosakovsky Pond, Davey M. Smith, K. Scheffler, 2013, The Journal of infectious diseases.

BIOINFORMATICS APPLICATIONS

Sergei L. Kosakovsky Pond, S. Frost, S. Muse, 2022 .

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform

Ben Murrell, Sergei L. Kosakovsky Pond, Konrad Scheffler, 2014, PLoS Comput. Biol..

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

Sergei L. Kosakovsky Pond, X. Su, O. Doumbo, 2008, Proceedings of the National Academy of Sciences.

Effective HIV Molecular Surveillance Requires Identification of Incident Cases of Infection.

Sergei L. Kosakovsky Pond, S. Little, Davey M. Smith, 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Identification of an HIV-1 Clade A Envelope That Exhibits Broad Antigenicity and Neutralization Sensitivity and Elicits Antibodies Targeting Three Distinct Epitopes

Sergei L. Kosakovsky Pond, D. Burton, D. Montefiori, 2013, Journal of Virology.