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Biorxiv : the Preprint Server for Biology|July 19, 2024
Memory-bound k -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 MirarabMolecular Phylogenetics and Evolution|February 9, 2018
DiscoVista: Interpretable visualizations of gene tree discordanceErfan Sayyari, James B Whitfield, Siavash MirarabMolecular Biology and Evolution|October 14, 2017
Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree ReconstructionErfan Sayyari, James B Whitfield, Siavash MirarabJournal of Acquired Immune Deficiency Syndromes (1999)|January 4, 2021
HIV Care Prioritization Using Phylogenetic Branch LengthNiema Moshiri, Davey M Smith, Siavash MirarabSystematic Biology|August 29, 2014
Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage SortingSiavash Mirarab, Md Shamsuzzoha Bayzid, Tandy WarnowNature Biotechnology|July 27, 2023
Greengenes2 unifies microbial data in a single reference treeDaniel McDonald, Yueyu Jiang, Metin Balaban, et al.Annual Review of Nutrition|July 20, 2021
Nutritional Interventions and the Gut Microbiome in ChildrenSaurabh Mehta, Samantha L Huey, Daniel McDonald, et al.Nature Methods|September 7, 2010
Microbial community resemblance methods differ in their ability to detect biologically relevant patternsJustin Kuczynski, Zongzhi Liu, Catherine Lozupone, et al.The Journal of Nutrition|February 24, 2023
Diet Quality and the Fecal Microbiota in Adults in the American Gut ProjectAlexis D Baldeon, Daniel McDonald, Antonio Gonzalez, et al.Pageof 102