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Algorithms for Molecular Biology : AMB|March 14, 2024
Median quartet tree search algorithms using optimal subtree prune and regraftShayesteh Arasti, Siavash MirarabGenome Biology and Evolution|November 26, 2025
Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and LossYasamin Tabatabaee, Chao Zhang, Shayesteh Arasti, et al.Biorxiv : the Preprint Server for Biology|March 3, 2025
Species tree branch length estimation despite incomplete lineage sorting, duplication, and lossYasamin Tabatabaee, Chao Zhang, Shayesteh Arasti, et al.Biorxiv : the Preprint Server for Biology|May 15, 2024
Branch Length Transforms using Optimal Tree Metric MatchingShayesteh Arasti, Puoya Tabaghi, Yasamin Tabatabaee, et al.Biorxiv : the Preprint Server for Biology|April 27, 2026
Phlag: Scalable detection of genomics regions with unexplained phylogenetic heterogeneityAli Osman Berk Şapcı, Shayesteh Arasti, Edward L Braun, et al.Bioinformatics (Oxford, England)|July 7, 2026
Phlag: scalable detection of genomics regions with unexplained phylogenetic heterogeneityAli Osman Berk Şapcı, Shayesteh Arasti, Edward L Braun, et al.Systematic Biology|March 10, 2026
Branch Length Transforms using Optimal Tree Metric MatchingShayesteh Arasti, Puoya Tabaghi, Yasamin Tabatabaee, et al.Biorxiv : the Preprint Server for Biology|February 6, 2026
Deconvolving Phylogenetic Distance MixturesShayesteh Arasti, Ali Osman Berk Şapcı, Eleonora Rachtman, et al.Bioinformatics (Oxford, England)|January 3, 2022
Completing gene trees without species trees in sub-quadratic timeUyen Mai, Siavash MirarabBMC Genomics|April 18, 2020
Forcing external constraints on tree inference using ASTRALMaryam Rabiee, Siavash MirarabPageof 11