S. L. Kosakovsky Pond

PyEuk: a tool suite for catalogue-free multilocus typing

PyEuk is a catalogue-free tool for multilocus typing of eukaryotic parasites, enabling accurate strain identification and transmission analysis without organism-specific tuning.

HyphAeon: Attention on Evolution Across Deep Time Transforms Comparative Genomics

HyphAeon is a transformer model that accelerates detection of episodic diversifying selection in mammalian genomes and enables new analytical capabilities beyond traditional dN/dS methods.

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

This study identifies natural selection differences in key protein domains between non-pathogenic FECV and pathogenic FIPV FCoVs, highlighting sites under positive selection associated with FIP development.

Human HspB1, HspB3, HspB5 and HspB8: Shaping these Disease Factors during Vertebrate Evolution

This study examines the evolutionary forces shaping four sHSPs (HspB1, HspB3, HspB5, HspB8) in vertebrates and links their selective pressures to disease-associated mutations.

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

The paper identifies 13 rare mutations in the Omicron S-gene that cluster in functionally important regions and likely impact Spike function, suggesting cooperative interactions that mitigate fitness costs.

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.

This paper analyzes the evolutionary changes in the spike protein of a Canine Coronavirus isolate, identifying relaxed selection and amino acid substitutions associated with a shift in tropism from enteric to respiratory.

Identification of site-specific evolutionary trajectories shared across human betacoronaviruses

The paper identifies site-specific evolutionary trajectories shared across human betacoronaviruses by analyzing mutations and positive selection in four viruses.

Exploring the natural origins of SARS-CoV-2 in the light of recombination

This paper traces the origins of SARS-CoV-2 to horseshoe bats in China and Southeast Asia, identifies recombination events in Sarbecoviruses, and highlights the need for more wildlife sampling to understand zoonotic spillover risks.

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

The paper reconstructs the progenitor SARS-CoV-2 genome and traces its evolution and spread globally, showing multiple dominant strains and lineage replacements in different regions.

Genomics of a killifish from the Seychelles islands supports transoceanic island colonization and reveals relaxed selection of developmental genes

The study uses genomic data from Seychelles killifish to support trans-oceanic colonization and identifies relaxed selection on developmental genes.

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

This study examines HIV-1 compartmentalization in semen of men with and without STI-associated urethritis, finding stable viral populations and limited replication despite STI treatment.

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

The paper shows SARS-CoV-2's ability to infect humans stems from its evolutionary history in bats, not human adaptation, with evidence of positive selection in bat viruses and weak purifying selection in SARS-CoV-2.

Recombination and purifying selection preserves covariant movements of mosaic SARS-CoV-2 protein S

The paper analyzes SARS-CoV-2 evolution and structure to show recombination and purifying selection shape the S glycoprotein's function and efficiency in human infection.

A new method for inferring timetrees from temporally sampled molecular sequences

This paper introduces RTDT, a new method for inferring timetrees from temporally sampled molecular sequences, which is more accurate and computationally efficient than existing Bayesian methods.

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

This study shows that HIV-1 evolves differently in monocytes compared to T cells, suggesting monocytes may be a significant viral reservoir.

Relative evolutionary rates in proteins are largely insensitive to the substitution model

The paper investigates how substitution models affect site-wise relative rates in proteins and finds that rates are robust to model choice.