Sergei L. Kosakovsky Pond

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• Beyond Invariable Sites: Using Evolutionary Stasis to Map Multi-Layered Constraints on the Evolution of Viral and Mammalian Genomes

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-10

• Dynamics of natural selection preceding human viral epidemics and pandemics

  Cell · 2026-03-06 · 4 citations

• Changing the Optics: Comparing Traditional and Retrieval-Augmented GenAI E-Tutorials in Interdisciplinary Learning

  arXiv (Cornell University) · 2026-02-24

• Changing the Optics: Comparing Traditional and Retrieval-Augmented GenAI E-Tutorials in Interdisciplinary LearningPreprint

  Open MIND · 2026-02-24

• MoleRate: comparing molecular relative evolutionary rates to detect convergent evolution

  Evolution · 2025-12-11

• Conversations Over Clicks: Impact of Chatbots on Information Search in Interdisciplinary Learning

  2025-11-02 · 1 citations

• From data to publication in a browser with BRC-Analytics: Evolutionary dynamics of coding overlaps in measles virusPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-14 · 2 citations

• WITHDRAWN: Defective HIV DNA genomes provide ancestralrelevance critical for phylogenetic inference of reservoir dynamicsPreprint

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-03

• Author response: Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models

  2025-09-30

• The persistent pool of HIV-1-infected cells is formed episodically during untreated infection.

  UNC Libraries · 2025-09-25

• Author response: Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models

  2025-08-29

• Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models

  eLife · 2025-08-29

• Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models

  eLife · 2025-08-28

• Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution modelsPreprint

  Research Square · 2025-08-08

• Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment ErrorsPreprint

  eLife · 2025-06-26 · 3 citations

• Author response: Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors

  2025-06-26

• Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment ErrorsPreprint

  eLife · 2025-06-26 · 1 citations

• Ecological interactions and genomic innovation fueled the evolution of ray-finned fish endothermy

  Science Advances · 2025-06-25 · 8 citations

• Nationwide Implementation of HIV Molecular Cluster Detection by Centers for Disease Control and Prevention and State and Local Health Departments, United States

  Emerging infectious diseases · 2025-05-01 · 5 citations

• A New Comparative Framework for Estimating Selection on Synonymous Substitutions

  Molecular Biology and Evolution · 2025-03-23 · 1 citations