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Biology|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 <i>k</i> -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 <i>k</i>-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 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 MirarabBiorxiv : the Preprint Server for Biology|July 19, 2024
Memory-bound <i>k</i> -mer selection for large and evolutionary diverse reference librariesAli Osman Berk Şapcı, Siavash MirarabSystematic Biology|July 6, 2024
Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate ModelUyen Mai, Eduardo Charvel, Siavash MirarabPageof 12