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Author Details

Siavash Mirarab
University of California San Diego
2011
84
36
PMIDPaper TitleJournal TitlePublished Year
37500913Greengenes2 unifies microbial data in a single reference tree.Nat Biotechnol2024
37853258Author Correction: Greengenes2 unifies microbial data in a single reference tree.Nat Biotechnol2024
37853257Author Correction: Generation of accurate, expandable phylogenomic trees with uDance.Nat Biotechnol2024
37500914Generation of accurate, expandable phylogenomic trees with uDance.Nat Biotechnol2024
36637196Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates.Bioinformatics2023
35485976DEPP: Deep Learning Enables Extending Species Trees using Single Genes.Syst Biol2023
37387151Phylogenomic branch length estimation using quartets.Bioinformatics2023
34643995Fast and accurate distance-based phylogenetic placement using divide and conquer.Mol Ecol Resour2022
35758818QuCo: quartet-based co-estimation of species trees and gene trees.Bioinformatics2022
36618367A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods.Front Immunol2022
36138735Learning Hyperbolic Embedding for Phylogenetic Tree Placement and Updates.Biology (Basel)2022
35992043Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model.Bioinform Adv2022
36201617Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees.Mol Biol Evol2022
36265468Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling.Cell Syst2022
36094339ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees.Bioinformatics2022
36009839Distance-Based Phylogenetic Placement with Statistical Support.Biology (Basel)2022
36083447Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies.Methods Mol Biol2022
34978565Completing gene trees without species trees in sub-quadratic time.Bioinformatics2022
32886788Log Transformation Improves Dating of Phylogenies.Mol Biol Evol2021
33555318SODA: multi-locus species delimitation using quartet frequencies.Bioinformatics2021
33833441Author Correction: Dense sampling of bird diversity increases power of comparative genomics.Nature2021
34377979CONSULT: accurate contamination removal using locality-sensitive hashing.NAR Genom Bioinform2021
34780468Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT.PLoS Comput Biol2021
34417619Corrigendum to: ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy.Mol Biol Evol2021
33394616HIV Care Prioritization Using Phylogenetic Branch Length.J Acquir Immune Defic Syndr2021
33289889Multiple Sequence Alignment for Large Heterogeneous Datasets Using SATé, PASTA, and UPP.Methods Mol Biol2021
31545363APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments.Syst Biol2020
31943790The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters.Mol Ecol Resour2020
33177665Dense sampling of bird diversity increases power of comparative genomics.Nature2020
32886770ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy.Mol Biol Evol2020
32657414Phylogenetic double placement of mixed samples.Bioinformatics2020
32562819More is needed-Thousands of loci are required to elucidate the relationships of the 'flowers of the sea' (Sabellida, Annelida).Mol Phylogenet Evol2020
32299337Forcing external constraints on tree inference using ASTRAL.BMC Genomics2020
32542933Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification.Mol Ecol2020
32427907Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.Nat Commun2020
31290974INSTRAL: Discordance-Aware Phylogenetic Placement Using Quartet Scores.Syst Biol2020
30393186Multi-allele species reconstruction using ASTRAL.Mol Phylogenet Evol2019
31794747Interspecific Gene Flow Shaped the Evolution of the Genus Canis.Curr Biol2019
31792218Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.Nat Commun2019
31437182TreeCluster: Clustering biological sequences using phylogenetic trees.PLoS One2019
31221828Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits.Science2019
30760303Skmer: assembly-free and alignment-free sample identification using genome skims.Genome Biol2019
30903685ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization.Bioinformatics2019
30395173FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences.Bioinformatics2019
29165679A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition.Syst Biol2018
30344120Interspecific Gene Flow Shaped the Evolution of the Genus Canis.Curr Biol2018
29421312DiscoVista: Interpretable visualizations of gene tree discordance.Mol Phylogenet Evol2018
29495636Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies.Genes (Basel)2018
29745866ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees.BMC Bioinformatics2018
29745847TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees.BMC Genomics2018
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Collaborators

Metin Balaban
University of California San Diego
Co-authored papers 13
Qiyun Zhu
Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University
Co-authored papers 9
Daniel McDonald
University of California San Diego
Co-authored papers 7
Vineet Bafna
University of California San Diego
Co-authored papers 7
Uyen Mai
University of California San Diego
Co-authored papers 6
Guojie Zhang
University of Copenhagen, Universitetsparken 15
Co-authored papers 6
Niema Moshiri
Bonita Vista High School, University of California San Diego, University of California, San Diego
Co-authored papers 4
Antonio Gonzalez
University of California San Diego School of Medicine
Co-authored papers 4
Oliver A Ryder
Co-authored papers 4
Rob Knight
University of California
Co-authored papers 4
David W Burt
The Roslin Institute & R(D)SVS, University of Edinburgh
Co-authored papers 4
Klaus-Peter Koepfli
Co-authored papers 3
Morgan Wirthlin
Co-authored papers 3
Jian Wang
Institute of Medical Research, Northwestern Polytechnical University
Co-authored papers 3
Huanming Yang
Experimental Research Center, China Academy of Chinese Medical Sciences
Co-authored papers 3
Stefan Janssen
Co-authored papers 3
David Haussler
Genomics Institute, University of California Santa Cruz
Co-authored papers 3
John Gordon Burleigh
University of Florida
Co-authored papers 3
Beth Shapiro
Co-authored papers 3
Andre Franke
Institute of Clinical Molecular Biology, Kiel University
Co-authored papers 2
James H Leebens-Mack
Co-authored papers 2
Curtis Huttenhower
Broad Institute of MIT and Harvard
Co-authored papers 2
Dennis W Stevenson
University of British Columbia
Co-authored papers 2
Cai Li
Sun Yat-sen University
Co-authored papers 2
Kim Rutherford
University of Cambridge
Co-authored papers 2
Benedict Paten
UC Santa Cruz Genomics Institute, University of California
Co-authored papers 2
Veikko Salomaa
Co-authored papers 2
Aki S Havulinna
Co-authored papers 2
Timothy B Sackton
Harvard University
Co-authored papers 2
Qi Fang
The First Affiliated Hospital of Soochow University
Co-authored papers 2
Release 1.2