The paper introduces parallel algorithms to improve the computational efficiency of structured coalescent models for phylogeographic analysis, enabling faster and larger-scale studies of pathogen spread.

Proceedings of the National Academy of Sciences · Apr 28, 2026Peer-reviewedBioinformatics

Genomic Epidemiology of Monkeypox Virus During the 2022 Outbreak in New York City

Saymon Akther, Michelle Su, Jade C. Wang, Helly Amin, Faten Taki, Nelson De La Cruz, Moinuddin A. Chowdhury, Tyler Clabby, Erik J. Kopping, Victoria E. Ruiz, Mindy Leelawong, Julia Latash, Kimberly Johnson, Jennifer Baumgartner, Marcia Wong, , Enoma O. Omoregie

This study analyzes MPXV genomic data from NYC during the 2022 outbreak, identifying NYC-specific lineages and estimating multiple infections, while highlighting gaps in epidemiological-genetic concordance.

bioRxiv · Jul 23, 2024 · PreprintGenomics

Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York

Anthony P. West, Joel O. Wertheim, Jade C. Wang, Tetyana I. Vasylyeva, Jennifer L. Havens, Moinuddin A. Chowdhury, Edimarlyn Gonzalez, Courtney E. Fang, Steve S. Di Lonardo, Scott Hughes, Jennifer L. Rakeman, Henry H. Lee, Christopher O. Barnes, Priyanthi N.P. Gnanapragasam, Zhi Yang, , Pamela J. Björkman

The paper detects and characterizes the SARS-CoV-2 lineage B.1.526 in New York, showing its rapid growth and potential impact on neutralization.

Nature Communications · Aug 9, 2021Peer-reviewedBioinformatics