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Bioinformatics (Oxford, England)|August 31, 2023
Tracking and curating putative SARS-CoV-2 recombinants with RIVETKyle Smith, Cheng Ye, Yatish Turakhia
Molecular Biology and Evolution|October 24, 2025
Highly Recurrent Multinucleotide Mutations in SARS-CoV-2Nicola De Maio, Olivier Anoufa, Kyle Smith, et al.
Nature Genetics|January 12, 2026
Compressive pangenomics using mutation-annotated networksSumit Walia, Harsh Motwani, Yu-Hsiang Tseng, et al.
Nature|August 11, 2022
Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscapeYatish Turakhia, Bryan Thornlow, Angie Hinrichs, et al.
Biorxiv : the Preprint Server for Biology|December 20, 2021
Pandemic-scale phylogeneticsCheng Ye, Bryan Thornlow, Alexander Kramer, et al.
Proceedings of the National Academy of Sciences of the United States of America|May 2, 2025
Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIESAnshu Gupta, Siavash Mirarab, Yatish Turakhia
Biorxiv : the Preprint Server for Biology|June 10, 2024
Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIESAnshu Gupta, Siavash Mirarab, Yatish Turakhia
Bioinformatics (Oxford, England)|July 15, 2025
Ultrafast and ultralarge multiple sequence alignments using TWILIGHTYu-Hsiang Tseng, Sumit Walia, Yatish Turakhia
Plos Computational Biology|March 30, 2026
WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiologyPranav Gangwar, Pratik Katte, Manu Bhat, et al.
Nature Computational Science|July 8, 2026
Ultrafast and ultralarge distance-based phylogenetics using DIPPERSumit Walia, Zexing Chen, Yu-Hsiang Tseng, et al.
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