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Genome 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.
Trends in Genetics : TIG|May 27, 2026
Phylogenomics beyond the 'bag-of-genes' modelIker Rivas-González, Siavash Mirarab, Edward L Braun
Molecular Ecology Resources|January 17, 2020
The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filtersEleonora Rachtman, Metin Balaban, Vineet Bafna, et al.
Bioinformatics (Oxford, England)|March 16, 2024
CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashingAli Osman Berk Şapcı, Eleonora Rachtman, Siavash Mirarab
BMC Genomics|October 10, 2015
Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transferRuth Davidson, Pranjal Vachaspati, Siavash Mirarab, 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.
BMC Bioinformatics|May 11, 2018
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene treesChao Zhang, Maryam Rabiee, Erfan Sayyari, et al.
Bioinformatics (Oxford, England)|June 30, 2023
Phylogenomic branch length estimation using quartetsYasamin Tabatabaee, Chao Zhang, Tandy Warnow, et al.
Cell Systems|October 20, 2022
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsamplingEleonora Rachtman, Shahab Sarmashghi, Vineet Bafna, et al.
IEEE Transactions on Signal Processing : a Publication of the IEEE Signal Processing Society|August 22, 2025
Principal Component Analysis in Space FormsPuoya Tabaghi, Michael Khanzadeh, Yusu Wang, et al.
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