Search Results - "Mirarab, Siavash"

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies by Sayyari, Erfan, Mirarab, Siavash

“…Species tree reconstruction is complicated by effects of incomplete lineage sorting, commonly modeled by the multi-species coalescent model (MSC). While there…”
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TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees by Mai, Uyen, Mirarab, Siavash

“…Sequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level, but when…”
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ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees by Zhang, Chao, Rabiee, Maryam, Sayyari, Erfan, Mirarab, Siavash

“…Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one…”
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Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 by Asnicar, Francesco, Thomas, Andrew Maltez, Beghini, Francesco, Mengoni, Claudia, Manara, Serena, Manghi, Paolo, Zhu, Qiyun, Bolzan, Mattia, Cumbo, Fabio, May, Uyen, Sanders, Jon G., Zolfo, Moreno, Kopylova, Evguenia, Pasolli, Edoardo, Knight, Rob, Mirarab, Siavash, Huttenhower, Curtis, Segata, Nicola

“…Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs)…”
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ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy by Zhang, Chao, Scornavacca, Celine, Molloy, Erin K, Mirarab, Siavash

“…Abstract Phylogenetic inference from genome-wide data (phylogenomics) has revolutionized the study of evolution because it enables accounting for discordance…”
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ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization by Yin, John, Zhang, Chao, Mirarab, Siavash

“…Abstract Motivation Evolutionary histories can change from one part of the genome to another. The potential for discordance between the gene trees has…”
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TreeCluster: Clustering biological sequences using phylogenetic trees by Balaban, Metin, Moshiri, Niema, Mai, Uyen, Jia, Xingfan, Mirarab, Siavash

“…Clustering homologous sequences based on their similarity is a problem that appears in many bioinformatics applications. The fact that sequences cluster is…”
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Forcing external constraints on tree inference using ASTRAL by Rabiee, Maryam, Mirarab, Siavash

“…To account for genome-wide discordance among gene trees, several widely-used methods seek to find a species tree with the minimum distance to input gene trees…”
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DiscoVista: Interpretable visualizations of gene tree discordance by Sayyari, Erfan, Whitfield, James B., Mirarab, Siavash

“…[Display omitted] •We introduce a new tool, DiscoVista, for phylogenomic visualization of discordance.•DiscoVista helps systematists to generate interpretable…”
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Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction by Mai, Uyen, Sayyari, Erfan, Mirarab, Siavash

“…Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream…”
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Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information by Janssen, Stefan, McDonald, Daniel, Gonzalez, Antonio, Navas-Molina, Jose A, Jiang, Lingjing, Xu, Zhenjiang Zech, Winker, Kevin, Kado, Deborah M, Orwoll, Eric, Manary, Mark, Mirarab, Siavash, Knight, Rob

“…Recent algorithmic advances in amplicon-based microbiome studies enable the inference of exact amplicon sequence fragments. These new methods enable the…”
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Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses by Bayzid, Md Shamsuzzoha, Mirarab, Siavash, Boussau, Bastien, Warnow, Tandy

“…Because biological processes can result in different loci having different evolutionary histories, species tree estimation requires multiple loci from across…”
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Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer by Davidson, Ruth, Vachaspati, Pranjal, Mirarab, Siavash, Warnow, Tandy

“…Species tree estimation is challenged by gene tree heterogeneity resulting from biological processes such as duplication and loss, hybridization, incomplete…”
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A comparative study of SVDquartets and other coalescent-based species tree estimation methods by Chou, Jed, Gupta, Ashu, Yaduvanshi, Shashank, Davidson, Ruth, Nute, Mike, Mirarab, Siavash, Warnow, Tandy

“…Species tree estimation is challenging in the presence of incomplete lineage sorting (ILS), which can make gene trees different from the species tree. Because…”
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Statistical binning enables an accurate coalescent-based estimation of the avian tree by Mirarab, Siavash, Bayzid, Md. Shamsuzzoha, Boussau, Bastien, Warnow, Tandy

“…Gene tree incongruence arising from incomplete lineage sorting (ILS) can reduce the accuracy of concatenation-based estimations of species trees. Although…”
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Median quartet tree search algorithms using optimal subtree prune and regraft by Arasti, Shayesteh, Mirarab, Siavash

“…Gene trees can be different from the species tree due to biological processes and inference errors. One way to obtain a species tree is to find one that…”
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Skmer: assembly-free and alignment-free sample identification using genome skims by Sarmashghi, Shahab, Bohmann, Kristine, P Gilbert, M Thomas, Bafna, Vineet, Mirarab, Siavash

“…The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming…”
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Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction by Sayyari, Erfan, Mirarab, Siavash

“…Inferring species trees from gene trees using the coalescent-based summary methods has been the subject of much attention, yet new scalable and accurate…”
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Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea by Zhu, Qiyun, Mai, Uyen, Pfeiffer, Wayne, Janssen, Stefan, Asnicar, Francesco, Sanders, Jon G., Belda-Ferre, Pedro, Al-Ghalith, Gabriel A., Kopylova, Evguenia, McDonald, Daniel, Kosciolek, Tomasz, Yin, John B., Huang, Shi, Salam, Nimaichand, Jiao, Jian-Yu, Wu, Zijun, Xu, Zhenjiang Z., Cantrell, Kalen, Yang, Yimeng, Sayyari, Erfan, Rabiee, Maryam, Morton, James T., Podell, Sheila, Knights, Dan, Li, Wen-Jun, Huttenhower, Curtis, Segata, Nicola, Smarr, Larry, Mirarab, Siavash, Knight, Rob

“…Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of…”
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Greengenes2 unifies microbial data in a single reference tree by McDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T., Nicolaou, Giorgia, Parks, Donovan H., Karst, Søren M., Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S., Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash, Knight, Rob

“…Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a…”
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