S. L. Kosakovsky Pond

发表

Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City

A. Nekrutenko, J. Rakeman, L. Torian, 2022, Nature Communications.

Capturing intrahost recombination of SARS-CoV-2 during superinfection with Alpha and Epsilon variants in New York City

A. Nekrutenko, J. Rakeman, L. Torian, 2022, medRxiv.

Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy

M. Canuti, E. Tanzi, A. Amendola, 2021, Environmental Research.

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

R. Shafer, P. Lemey, A. Nekrutenko, 2022, Molecular biology and evolution.

Evolutionary shortcuts via multi-nucleotide substitutions and their impact on natural selection analyses

Jordan D. Zehr, S. L. Kosakovsky Pond, Alexander G. Lucaci, 2022, bioRxiv.

Sierra SARS-CoV-2 sequence and antiviral resistance analysis program

Philip L. Tzou, R. Shafer, B. Pinsky, 2022, Journal of Clinical Virology.

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

Philip L. Tzou, R. Shafer, S. K. Kosakovsky Pond, 2021, bioRxiv.

Predicting the mutational drivers of future SARS-CoV-2 variants of concern

Bryan D. Bryson, A. Telenti, B. Hie, 2021, Science Translational Medicine.

Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination

D. Robertson, J. Hughes, D. Martin, 2021, bioRxiv.

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

A. Godzik, A. Sigal, B. Sewell, 2021, Nature.

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

M. Kraemer, O. Pybus, L. du Plessis, 2021, Nature.

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

Philip L. Tzou, R. Shafer, T. de Oliveira, 2021, Nature Reviews Genetics.

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

M. Stanhope, G. Whittaker, D. Martin, 2021, bioRxiv.

Natural selection differences detected in key protein domains between non-pathogenic and pathogenic Feline Coronavirus phenotypes

M. Stanhope, G. Whittaker, J. Millet, 2023, bioRxiv.

RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis

A. Nekrutenko, D. Martin, S. K. Kosakovsky Pond, 2022, PloS one.

RASCL: RAPID ASSESSMENT OF SARS-COV-2 CLADES THROUGH MOLECULAR SEQUENCE ANALYSIS

A. Nekrutenko, D. Martin, S. K. Kosakovsky Pond, 2022, bioRxiv.

Conserved recombination patterns across coronavirus subgenera

D. Robertson, M. Stanhope, B. Murrell, 2021, bioRxiv.

Identification of Evolutionary Trajectories Shared across Human Betacoronaviruses

O. Pybus, B. Gutiérrez, T. Bowden, 2021, bioRxiv.

The evolution of BDNF is defined by strict purifying selection and prodomain spatial coevolution, but what does it mean for human brain disease?

D. Çolak, M. Notaras, S. L. Kosakovsky Pond, 2022, bioRxiv.

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

R. Shafer, P. Lemey, A. Nekrutenko, 2022, bioRxiv.

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

Stephen D. Shank, Sergei L. Kosakovsky Pond, Steven Weaver, 2018, BMC Bioinformatics.

Genotype-Specific Evolution of Hepatitis E Virus

Bethany L. Dearlove, S. Frost, Adam B. Brayne, 2017, Journal of Virology.

Ready-to-use public infrastructure for global SARS-CoV-2 monitoring

Simon A. Bray, A. Nekrutenko, Simon Gladman, 2021, Nature Biotechnology.

Susceptibility of SARS-CoV-2 Omicron Variants to Therapeutic Monoclonal Antibodies: Systematic Review and Meta-analysis

Philip L. Tzou, R. Shafer, S. K. Kosakovsky Pond, 2022, Microbiology spectrum.

Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes

M. Stanhope, G. Whittaker, J. Millet, 2023, Virus evolution.

Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies

D. Burton, B. Briney, Collin Joyce, 2023, PLoS pathogens.

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

D. Fenyö, G. Silverman, B. Shopsin, 2021, Frontiers in Immunology.

Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses

J. W. Thornton, D. Enard, S. K. Kosakovsky Pond, 2023, bioRxiv.

Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes

M. Stanhope, G. Whittaker, J. Millet, 2023, Virus evolution.

Genotype-Specific Evolution of Hepatitis E Virus

Bethany L. Dearlove, S. Frost, Adam B. Brayne, 2017, Journal of Virology.

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

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

Assigning and visualizing germline genes in antibody repertoires

S. Frost, B. Murrell, G. Silverman, 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

Comparative Study of Methods for Detecting Sequence Compartmentalization in Human Immunodeficiency Virus Type 1 Samples of Viral Populations Are Collected Either by Examining Brain Tissue from Infected Individuals Post Mortem or by Drawing Samples From

S. Frost, P. Shapshak, Sergei L Kosakovsky Pond, 2006 .