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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 TurakhiaProceedings 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 TurakhiaBiology|September 23, 2022
Learning Hyperbolic Embedding for Phylogenetic Tree Placement and UpdatesYueyu Jiang, Puoya Tabaghi, 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 MirarabScience (New York, N.Y.)|January 23, 2025
CASTER: Direct species tree inference from whole-genome alignmentsChao Zhang, Rasmus Nielsen, Siavash MirarabMolecular Ecology Resources|October 13, 2025
Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer FrequenciesEleonora Rachtman, Yueyu Jiang, 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 MirarabPageof 12