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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 TurakhiaMolecular Phylogenetics and Evolution|November 6, 2018
Multi-allele species reconstruction using ASTRALMaryam Rabiee, Erfan Sayyari, Siavash MirarabNAR Genomics and Bioinformatics|August 11, 2021
CONSULT: accurate contamination removal using locality-sensitive hashingEleonora Rachtman, Vineet Bafna, Siavash MirarabBiorxiv : the Preprint Server for Biology|July 9, 2025
A k -mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placementAli Osman Berk Şapcı, Siavash MirarabGenome Research|August 29, 2024
Memory-bound k-mer selection for large and evolutionarily diverse reference librariesAli Osman Berk Şapcı, Siavash MirarabMsystems|May 31, 2022
Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed IncreaseIgor Sfiligoi, George Armstrong, Antonio Gonzalez, et al.Science (New York, N.Y.)|January 23, 2025
CASTER: Direct species tree inference from whole-genome alignmentsChao Zhang, Rasmus Nielsen, Siavash MirarabSystematic Biology|September 24, 2019
APPLES: Scalable Distance-Based Phylogenetic Placement with or without AlignmentsMetin Balaban, Shahab Sarmashghi, Siavash MirarabPlos One|August 12, 2017
Minimum variance rooting of phylogenetic trees and implications for species tree reconstructionUyen Mai, Erfan Sayyari, Siavash MirarabMolecular Biology and Evolution|July 16, 2025
ASTER: A Package for Large-Scale Phylogenomic ReconstructionsChao Zhang, Rasmus Nielsen, Siavash MirarabPageof 102