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Siavash Mirarab

Title(s)Professor, Electrical and Computer Engineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Coalescent-based branch length estimation improves dating of species trees. Syst Biol. 2026 May 22. Tabatabaee Y, Claramunt S, Mirarab S. PMID: 42172051.
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    2. Phlag: Scalable detection of genomics regions with unexplained phylogenetic heterogeneity. bioRxiv. 2026 Apr 13. Sapci AOB, Arasti S, Braun EL, Mirarab S. PMID: 42039534; PMCID: PMC13104820.
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    3. SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation. Mol Ecol Resour. 2026 Apr; 26(3):e70145. Melendez D, Sapci AOB, Bafna V, Mirarab S. PMID: 42026820; PMCID: PMC13106921.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    4. Branch Length Transforms using Optimal Tree Metric Matching. Syst Biol. 2026 Mar 10. Arasti S, Tabaghi P, Tabatabaee Y, Mayer AK, Mirarab S. PMID: 41806191.
      View in: PubMed   Mentions:
    5. krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement. Genome Biol. 2026 Feb 21; 27(1). Sapci AOB, Mirarab S. PMID: 41723514; PMCID: PMC13032499.
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    6. Deconvolving Phylogenetic Distance Mixtures. bioRxiv. 2026 Jan 21. Arasti S, Sapci AOB, Rachtman E, El-Kebir M, Mirarab S. PMID: 41648417; PMCID: PMC12871782.
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    7. Quantifying Hierarchical Conflicts in Homology Statements. J Mol Evol. 2025 Dec; 93(6):830-842. Swenson KM, Elghraoui A, Valafar F, Mirarab S, Weller M. PMID: 41454034.
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    8. Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss. Genome Biol Evol. 2025 10 29; 17(11). Tabatabaee Y, Zhang C, Arasti S, Mirarab S. PMID: 41293994; PMCID: PMC12648238.
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    9. Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies. Mol Ecol Resour. 2025 Nov; 25(8):e70055. Rachtman E, Jiang Y, Mirarab S. PMID: 41077897; PMCID: PMC12550494.
      View in: PubMed   Mentions: 2     Fields:    
    10. ASTER: A Package for Large-Scale Phylogenomic Reconstructions. Mol Biol Evol. 2025 Jul 30; 42(8). Zhang C, Nielsen R, Mirarab S. PMID: 40668947; PMCID: PMC12343031.
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    11. A k -mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placement. bioRxiv. 2025 Jul 01. Berk Sapci AO, Mirarab S. PMID: 40631226; PMCID: PMC12236853.
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    12. Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES. Proc Natl Acad Sci U S A. 2025 May 13; 122(19):e2500553122. Gupta A, Mirarab S, Turakhia Y. PMID: 40314967; PMCID: PMC12088440.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    13. Branch Length Transforms using Optimal Tree Metric Matching. bioRxiv. 2025 Mar 02. Arasti S, Tabaghi P, Tabatabaee Y, Mirarab S. PMID: 38746464; PMCID: PMC11092445.
      View in: PubMed   Mentions:
    14. Coalescent-based branch length estimation improves dating of species trees. bioRxiv. 2025 Feb 28. Tabatabaee Y, Claramunt S, Mirarab S. PMID: 40060389; PMCID: PMC11888464.
      View in: PubMed   Mentions:
    15. CASTER: Direct species tree inference from whole-genome alignments. Science. 2025 Feb 28; 387(6737):eadk9688. Zhang C, Nielsen R, Mirarab S. PMID: 39847611; PMCID: PMC12038793.
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    16. Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss. bioRxiv. 2025 Feb 20. Tabatabaee Y, Zhang C, Arasti S, Mirarab S. PMID: 40027742; PMCID: PMC11870528.
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    17. Net rate of lateral gene transfer in marine prokaryoplankton. ISME J. 2025 Jan 02; 19(1). Stepanauskas R, Brown JM, Arasti S, Mai U, Gavelis G, Pachiadaki M, Bezuidt O, Munson-McGee JH, Chang T, Biller SJ, Berube PM, Mirarab S. PMID: 40910370; PMCID: PMC12416821.
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    18. Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model. Syst Biol. 2024 10 30; 73(5):823-838. Mai U, Charvel E, Mirarab S. PMID: 38970346; PMCID: PMC11524793.
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    19. Memory-bound k-mer selection for large and evolutionarily diverse reference libraries. Genome Res. 2024 10 11; 34(9):1455-1467. Sapci AOB, Mirarab S. PMID: 39209553; PMCID: PMC11529837.
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    20. Principal Component Analysis in Space Forms. IEEE Trans Signal Process. 2024; 72:4428-4443. Tabaghi P, Khanzadeh M, Wang Y, Mirarab S. PMID: 40843461; PMCID: PMC12366648.
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    21. Memory-bound k -mer selection for large and evolutionary diverse reference libraries. bioRxiv. 2024 Jul 10. Sapci AOB, Mirarab S. PMID: 39026785; PMCID: PMC11257464.
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    22. Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach. Bioinformatics. 2024 06 03; 40(6). Jiang Y, McDonald D, Perry D, Knight R, Mirarab S. PMID: 38870525; PMCID: PMC11193062.
      View in: PubMed   Mentions: 4     Fields:    
    23. Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES. bioRxiv. 2024 Jun 01. Gupta A, Mirarab S, Turakhia Y. PMID: 38854139; PMCID: PMC11160643.
      View in: PubMed   Mentions:
    24. Author Correction: Generation of accurate, expandable phylogenomic trees with uDance. Nat Biotechnol. 2024 May; 42(5):814. Balaban M, Jiang Y, Zhu Q, McDonald D, Knight R, Mirarab S. PMID: 37853257.
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    25. Author Correction: Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol. 2024 May; 42(5):813. McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton JT, Nicolaou G, Parks DH, Karst SM, Albertsen M, Hugenholtz P, DeSantis T, Song SJ, Bartko A, Havulinna AS, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S, Knight R. PMID: 37853258; PMCID: PMC11098728.
      View in: PubMed   Mentions: 10     Fields:    
    26. Complexity of avian evolution revealed by family-level genomes. Nature. 2024 May; 629(8013):851-860. Stiller J, Feng S, Chowdhury AA, Rivas-González I, Duchêne DA, Fang Q, Deng Y, Kozlov A, Stamatakis A, Claramunt S, Nguyen JMT, Ho SYW, Faircloth BC, Haag J, Houde P, Cracraft J, Balaban M, Mai U, Chen G, Gao R, Zhou C, Xie Y, Huang Z, Cao Z, Yan Z, Ogilvie HA, Nakhleh L, Lindow B, Morel B, Fjeldså J, Hosner PA, da Fonseca RR, Petersen B, Tobias JA, Székely T, Kennedy JD, Reeve AH, Liker A, Stervander M, Antunes A, Tietze DT, Bertelsen MF, Lei F, Rahbek C, Graves GR, Schierup MH, Warnow T, Braun EL, Gilbert MTP, Jarvis ED, Mirarab S, Zhang G. PMID: 38560995; PMCID: PMC11111414.
      View in: PubMed   Mentions: 90     Fields:    Translation:Animals
    27. A region of suppressed recombination misleads neoavian phylogenomics. Proc Natl Acad Sci U S A. 2024 Apr 09; 121(15):e2319506121. Mirarab S, Rivas-González I, Feng S, Stiller J, Fang Q, Mai U, Hickey G, Chen G, Brajuka N, Fedrigo O, Formenti G, Wolf JBW, Howe K, Antunes A, Schierup MH, Paten B, Jarvis ED, Zhang G, Braun EL. PMID: 38557186; PMCID: PMC11009670.
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    28. CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing. Bioinformatics. 2024 03 29; 40(4). Sapci AOB, Rachtman E, Mirarab S. PMID: 38492564; PMCID: PMC10985673.
      View in: PubMed   Mentions: 3     Fields:    
    29. Median quartet tree search algorithms using optimal subtree prune and regraft. Algorithms Mol Biol. 2024 Mar 13; 19(1):12. Arasti S, Mirarab S. PMID: 38481327; PMCID: PMC10938725.
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    30. Analyses of Nuclear Reads Obtained Using Genome Skimming. Methods Mol Biol. 2024; 2744:247-265. Mirarab S, Bafna V. PMID: 38683324.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    31. Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol. 2024 May; 42(5):715-718. McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton JT, Nicolaou G, Parks DH, Karst SM, Albertsen M, Hugenholtz P, DeSantis T, Song SJ, Bartko A, Havulinna AS, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S, Knight R. PMID: 37500913; PMCID: PMC10818020.
      View in: PubMed   Mentions: 262     Fields:    Translation:Cells
    32. Generation of accurate, expandable phylogenomic trees with uDance. Nat Biotechnol. 2024 May; 42(5):768-777. Balaban M, Jiang Y, Zhu Q, McDonald D, Knight R, Mirarab S. PMID: 37500914; PMCID: PMC10818028.
      View in: PubMed   Mentions: 9     Fields:    
    33. Phylogenomic branch length estimation using quartets. Bioinformatics. 2023 06 30; 39(39 Suppl 1):i185-i193. Tabatabaee Y, Zhang C, Warnow T, Mirarab S. PMID: 37387151; PMCID: PMC10311336.
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    34. DEPP: Deep Learning Enables Extending Species Trees using Single Genes. Syst Biol. 2023 05 19; 72(1):17-34. Jiang Y, Balaban M, Zhu Q, Mirarab S. PMID: 35485976; PMCID: PMC10198656.
      View in: PubMed   Mentions:
    35. Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates. Bioinformatics. 2023 01 01; 39(1). Elghraoui A, Mirarab S, Swenson KM, Valafar F. PMID: 36637196; PMCID: PMC9887090.
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    36. A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods. Front Immunol. 2022; 13:1014439. Zhang C, Bzikadze AV, Safonova Y, Mirarab S. PMID: 36618367; PMCID: PMC9815712.
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    37. Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees. Mol Biol Evol. 2022 12 05; 39(12). Zhang C, Mirarab S. PMID: 36201617; PMCID: PMC9750496.
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    38. ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees. Bioinformatics. 2022 10 31; 38(21):4949-4950. Zhang C, Mirarab S. PMID: 36094339.
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    39. Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling. Cell Syst. 2022 10 19; 13(10):817-829.e3. Rachtman E, Sarmashghi S, Bafna V, Mirarab S. PMID: 36265468; PMCID: PMC9589918.
      View in: PubMed   Mentions: 6     Fields:    
    40. Learning Hyperbolic Embedding for Phylogenetic Tree Placement and Updates. Biology (Basel). 2022 Aug 24; 11(9). Jiang Y, Tabaghi P, Mirarab S. PMID: 36138735; PMCID: PMC9495508.
      View in: PubMed   Mentions: 7  
    41. Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model. Bioinform Adv. 2022; 2(1):vbac055. Balaban M, Bristy NA, Faisal A, Bayzid MS, Mirarab S. PMID: 35992043; PMCID: PMC9383262.
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    42. Distance-Based Phylogenetic Placement with Statistical Support. Biology (Basel). 2022 Aug 12; 11(8). Hasan NB, Balaban M, Biswas A, Bayzid MS, Mirarab S. PMID: 36009839; PMCID: PMC9404983.
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    43. QuCo: quartet-based co-estimation of species trees and gene trees. Bioinformatics. 2022 06 24; 38(Suppl 1):i413-i421. Rabiee M, Mirarab S. PMID: 35758818; PMCID: PMC9235488.
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    44. Completing gene trees without species trees in sub-quadratic time. Bioinformatics. 2022 03 04; 38(6):1532-1541. Mai U, Mirarab S. PMID: 34978565.
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    45. Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies. Methods Mol Biol. 2022; 2569:137-165. Zhu Q, Mirarab S. PMID: 36083447.
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    46. Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT. PLoS Comput Biol. 2021 11; 17(11):e1009449. Sarmashghi S, Balaban M, Rachtman E, Touri B, Mirarab S, Bafna V. PMID: 34780468; PMCID: PMC8629397.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    47. Fast and accurate distance-based phylogenetic placement using divide and conquer. Mol Ecol Resour. 2022 Apr; 22(3):1213-1227. Balaban M, Jiang Y, Roush D, Zhu Q, Mirarab S. PMID: 34643995.
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    48. Corrigendum to: ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy. Mol Biol Evol. 2021 Sep 27; 38(10):4655. Zhang C, Scornavacca C, Molloy EK, Mirarab S. PMID: 34417619; PMCID: PMC8476140.
      View in: PubMed   Mentions:
    49. CONSULT: accurate contamination removal using locality-sensitive hashing. NAR Genom Bioinform. 2021 Sep; 3(3):lqab071. Rachtman E, Bafna V, Mirarab S. PMID: 34377979; PMCID: PMC8340999.
      View in: PubMed   Mentions: 13     Fields:    
    50. HIV Care Prioritization Using Phylogenetic Branch Length. J Acquir Immune Defic Syndr. 2021 04 15; 86(5):626-637. Moshiri N, Smith DM, Mirarab S. PMID: 33394616; PMCID: PMC7933099.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    51. SODA: multi-locus species delimitation using quartet frequencies. Bioinformatics. 2021 Apr 05; 36(24):5623-5631. Rabiee M, Mirarab S. PMID: 33555318.
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    52. Author Correction: Dense sampling of bird diversity increases power of comparative genomics. Nature. 2021 Apr; 592(7856):E24. Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, Andreu-Sánchez S, Margaryan A, Howard JT, Parent C, Pacheco G, Sinding MS, Puetz L, Cavill E, Ribeiro ÂM, Eckhart L, Fjeldså J, Hosner PA, Brumfield RT, Christidis L, Bertelsen MF, Sicheritz-Ponten T, Tietze DT, Robertson BC, Song G, Borgia G, Claramunt S, Lovette IJ, Cowen SJ, Njoroge P, Dumbacher JP, Ryder OA, Fuchs J, Bunce M, Burt DW, Cracraft J, Meng G, Hackett SJ, Ryan PG, Jønsson KA, Jamieson IG, da Fonseca RR, Braun EL, Houde P, Mirarab S, Suh A, Hansson B, Ponnikas S, Sigeman H, Stervander M, Frandsen PB, van der Zwan H, van der Sluis R, Visser C, Balakrishnan CN, Clark AG, Fitzpatrick JW, Bowman R, Chen N, Cloutier A, Sackton TB, Edwards SV, Foote DJ, Shakya SB, Sheldon FH, Vignal A, Soares AER, Shapiro B, González-Solís J, Ferrer-Obiol J, Rozas J, Riutort M, Tigano A, Friesen V, Dalén L, Urrutia AO, Székely T, Liu Y, Campana MG, Corvelo A, Fleischer RC, Rutherford KM, Gemmell NJ, Dussex N, Mouritsen H, Thiele N, Delmore K, Liedvogel M, Franke A, Hoeppner MP, Krone O, Fudickar AM, Milá B, Ketterson ED, Fidler AE, Friis G, Parody-Merino ÁM, Battley PF, Cox MP, Lima NCB, Prosdocimi F, Parchman TL, Schlinger BA, Loiselle BA, Blake JG, Lim HC, Day LB, Fuxjager MJ, Baldwin MW, Braun MJ, Wirthlin M, Dikow RB, Ryder TB, Camenisch G, Keller LF, DaCosta JM, Hauber ME, Louder MIM, Witt CC, McGuire JA, Mudge J, Megna LC, Carling MD, Wang B, Taylor SA, Del-Rio G, Aleixo A, Vasconcelos ATR, Mello CV, Weir JT, Haussler D, Li Q, Yang H, Wang J, Lei F, Rahbek C, Gilbert MTP, Graves GR, Jarvis ED, Paten B, Zhang G. PMID: 33833441; PMCID: PMC8081657.
      View in: PubMed   Mentions: 5     Fields:    
    53. Log Transformation Improves Dating of Phylogenies. Mol Biol Evol. 2021 03 09; 38(3):1151-1167. Mai U, Mirarab S. PMID: 32886788; PMCID: PMC7947844.
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    54. Multiple Sequence Alignment for Large Heterogeneous Datasets Using SATé, PASTA, and UPP. Methods Mol Biol. 2021; 2231:99-119. Warnow T, Mirarab S. PMID: 33289889.
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    55. Dense sampling of bird diversity increases power of comparative genomics. Nature. 2020 11; 587(7833):252-257. Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, Andreu-Sánchez S, Margaryan A, Howard JT, Parent C, Pacheco G, Sinding MS, Puetz L, Cavill E, Ribeiro ÂM, Eckhart L, Fjeldså J, Hosner PA, Brumfield RT, Christidis L, Bertelsen MF, Sicheritz-Ponten T, Tietze DT, Robertson BC, Song G, Borgia G, Claramunt S, Lovette IJ, Cowen SJ, Njoroge P, Dumbacher JP, Ryder OA, Fuchs J, Bunce M, Burt DW, Cracraft J, Meng G, Hackett SJ, Ryan PG, Jønsson KA, Jamieson IG, da Fonseca RR, Braun EL, Houde P, Mirarab S, Suh A, Hansson B, Ponnikas S, Sigeman H, Stervander M, Frandsen PB, van der Zwan H, van der Sluis R, Visser C, Balakrishnan CN, Clark AG, Fitzpatrick JW, Bowman R, Chen N, Cloutier A, Sackton TB, Edwards SV, Foote DJ, Shakya SB, Sheldon FH, Vignal A, Soares AER, Shapiro B, González-Solís J, Ferrer-Obiol J, Rozas J, Riutort M, Tigano A, Friesen V, Dalén L, Urrutia AO, Székely T, Liu Y, Campana MG, Corvelo A, Fleischer RC, Rutherford KM, Gemmell NJ, Dussex N, Mouritsen H, Thiele N, Delmore K, Liedvogel M, Franke A, Hoeppner MP, Krone O, Fudickar AM, Milá B, Ketterson ED, Fidler AE, Friis G, Parody-Merino ÁM, Battley PF, Cox MP, Lima NCB, Prosdocimi F, Parchman TL, Schlinger BA, Loiselle BA, Blake JG, Lim HC, Day LB, Fuxjager MJ, Baldwin MW, Braun MJ, Wirthlin M, Dikow RB, Ryder TB, Camenisch G, Keller LF, DaCosta JM, Hauber ME, Louder MIM, Witt CC, McGuire JA, Mudge J, Megna LC, Carling MD, Wang B, Taylor SA, Del-Rio G, Aleixo A, Vasconcelos ATR, Mello CV, Weir JT, Haussler D, Li Q, Yang H, Wang J, Lei F, Rahbek C, Gilbert MTP, Graves GR, Jarvis ED, Paten B, Zhang G. PMID: 33177665; PMCID: PMC7759463.
      View in: PubMed   Mentions: 208     Fields:    Translation:HumansAnimals
    56. ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy. Mol Biol Evol. 2020 11 01; 37(11):3292-3307. Zhang C, Scornavacca C, Molloy EK, Mirarab S. PMID: 32886770; PMCID: PMC7751180.
      View in: PubMed   Mentions:
    57. Phylogenetic double placement of mixed samples. Bioinformatics. 2020 07 01; 36(Suppl_1):i335-i343. Balaban M, Mirarab S. PMID: 32657414; PMCID: PMC7355250.
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    58. Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification. Mol Ecol. 2020 07; 29(14):2521-2534. Bohmann K, Mirarab S, Bafna V, Gilbert MTP. PMID: 32542933; PMCID: PMC7496323.
      View in: PubMed   Mentions: 37     Fields:    Translation:Animals
    59. More is needed-Thousands of loci are required to elucidate the relationships of the 'flowers of the sea' (Sabellida, Annelida). Mol Phylogenet Evol. 2020 10; 151:106892. Tilic E, Sayyari E, Stiller J, Mirarab S, Rouse GW. PMID: 32562819.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    60. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun. 2020 05 19; 11(1):2500. Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, Mirarab S, Huttenhower C, Segata N. PMID: 32427907; PMCID: PMC7237447.
      View in: PubMed   Mentions: 391     Fields:    Translation:Cells
    61. APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments. Syst Biol. 2020 05 01; 69(3):566-578. Balaban M, Sarmashghi S, Mirarab S. PMID: 31545363; PMCID: PMC7164367.
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    62. Forcing external constraints on tree inference using ASTRAL. BMC Genomics. 2020 Apr 16; 21(Suppl 2):218. Rabiee M, Mirarab S. PMID: 32299337; PMCID: PMC7160890.
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    63. INSTRAL: Discordance-Aware Phylogenetic Placement Using Quartet Scores. Syst Biol. 2020 03 01; 69(2):384-391. Rabiee M, Mirarab S. PMID: 31290974.
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    64. The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters. Mol Ecol Resour. 2020 May; 20(3). Rachtman E, Balaban M, Bafna V, Mirarab S. PMID: 31943790.
      View in: PubMed   Mentions: 17     Fields:    Translation:Humans
    65. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nat Commun. 2019 12 02; 10(1):5477. Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R. PMID: 31792218; PMCID: PMC6889312.
      View in: PubMed   Mentions: 189     Fields:    Translation:Cells
    66. Interspecific Gene Flow Shaped the Evolution of the Genus Canis. Curr Biol. 2019 Dec 02; 29(23):4152. Gopalakrishnan S, Sinding MS, Ramos-Madrigal J, Niemann J, Samaniego Castruita JA, Vieira FG, Carøe C, de Manuel Montero M, Kuderna L, Serres A, González-Basallote VM, Liu YH, Wang GD, Marques-Bonet T, Mirarab S, Fernandes C, Gaubert P, Koepfli KP, Budd J, Rueness EK, Sillero C, Heide-Jørgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig Ø, Hansen AJ, Gilbert MTP. PMID: 31794747; PMCID: PMC6892301.
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    67. ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization. Bioinformatics. 2019 10 15; 35(20):3961-3969. Yin J, Zhang C, Mirarab S. PMID: 30903685.
      View in: PubMed   Mentions:
    68. TreeCluster: Clustering biological sequences using phylogenetic trees. PLoS One. 2019; 14(8):e0221068. Balaban M, Moshiri N, Mai U, Jia X, Mirarab S. PMID: 31437182; PMCID: PMC6705769.
      View in: PubMed   Mentions: 96     Fields:    Translation:HumansCells
    69. TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification. Bioinformatics. 2019 07 15; 35(14):i31-i40. Sayyari E, Kawas B, Mirarab S. PMID: 31510701; PMCID: PMC6612822.
      View in: PubMed   Mentions:
    70. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science. 2019 06 21; 364(6446). Chen L, Qiu Q, Jiang Y, Wang K, Lin Z, Li Z, Bibi F, Yang Y, Wang J, Nie W, Su W, Liu G, Li Q, Fu W, Pan X, Liu C, Yang J, Zhang C, Yin Y, Wang Y, Zhao Y, Zhang C, Wang Z, Qin Y, Liu W, Wang B, Ren Y, Zhang R, Zeng Y, da Fonseca RR, Wei B, Li R, Wan W, Zhao R, Zhu W, Wang Y, Duan S, Gao Y, Zhang YE, Chen C, Hvilsom C, Epps CW, Chemnick LG, Dong Y, Mirarab S, Siegismund HR, Ryder OA, Gilbert MTP, Lewin HA, Zhang G, Heller R, Wang W. PMID: 31221828.
      View in: PubMed   Mentions: 223     Fields:    Translation:Animals
    71. FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences. Bioinformatics. 2019 06 01; 35(11):1852-1861. Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S. PMID: 30395173; PMCID: PMC6931354.
      View in: PubMed   Mentions: 33     Fields:    Translation:Humans
    72. Skmer: assembly-free and alignment-free sample identification using genome skims. Genome Biol. 2019 02 13; 20(1):34. Sarmashghi S, Bohmann K, P Gilbert MT, Bafna V, Mirarab S. PMID: 30760303; PMCID: PMC6374904.
      View in: PubMed   Mentions: 72     Fields:    Translation:Animals
    73. Multi-allele species reconstruction using ASTRAL. Mol Phylogenet Evol. 2019 01; 130:286-296. Rabiee M, Sayyari E, Mirarab S. PMID: 30393186.
      View in: PubMed   Mentions:
    74. Interspecific Gene Flow Shaped the Evolution of the Genus Canis. Curr Biol. 2018 11 05; 28(21):3441-3449.e5. Gopalakrishnan S, Sinding MS, Ramos-Madrigal J, Niemann J, Samaniego Castruita JA, Vieira FG, Carøe C, Montero MM, Kuderna L, Serres A, González-Basallote VM, Liu YH, Wang GD, Marques-Bonet T, Mirarab S, Fernandes C, Gaubert P, Koepfli KP, Budd J, Rueness EK, Sillero C, Heide-Jørgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig Ø, Hansen AJ, Gilbert MTP. PMID: 30344120; PMCID: PMC6224481.
      View in: PubMed   Mentions:
    75. TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees. BMC Genomics. 2018 May 08; 19(Suppl 5):272. Mai U, Mirarab S. PMID: 29745847; PMCID: PMC5998883.
      View in: PubMed   Mentions:
    76. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics. 2018 05 08; 19(Suppl 6):153. Zhang C, Rabiee M, Sayyari E, Mirarab S. PMID: 29745866; PMCID: PMC5998893.
      View in: PubMed   Mentions:
    77. A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition. Syst Biol. 2018 May 01; 67(3):475-489. Moshiri N, Mirarab S. PMID: 29165679; PMCID: PMC5920319.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    78. Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. mSystems. 2018 May-Jun; 3(3). Janssen S, McDonald D, Gonzalez A, Navas-Molina JA, Jiang L, Xu ZZ, Winker K, Kado DM, Orwoll E, Manary M, Mirarab S, Knight R. PMID: 29719869; PMCID: PMC5904434.
      View in: PubMed   Mentions: 294     Fields:    
    79. A roadmap for global synthesis of the plant tree of life. Am J Bot. 2018 03; 105(3):614-622. Eiserhardt WL, Antonelli A, Bennett DJ, Botigué LR, Burleigh JG, Dodsworth S, Enquist BJ, Forest F, Kim JT, Kozlov AM, Leitch IJ, Maitner BS, Mirarab S, Piel WH, Pérez-Escobar OA, Pokorny L, Rahbek C, Sandel B, Smith SA, Stamatakis A, Vos RA, Warnow T, Baker WJ. PMID: 29603138.
      View in: PubMed   Mentions:
    80. Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies. Genes (Basel). 2018 Feb 28; 9(3). Sayyari E, Mirarab S. PMID: 29495636; PMCID: PMC5867853.
      View in: PubMed   Mentions:
    81. Identifying the favored mutation in a positive selective sweep. Nat Methods. 2018 04; 15(4):279-282. Akbari A, Vitti JJ, Iranmehr A, Bakhtiari M, Sabeti PC, Mirarab S, Bafna V. PMID: 29457793; PMCID: PMC6231406.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansCells
    82. DiscoVista: Interpretable visualizations of gene tree discordance. Mol Phylogenet Evol. 2018 05; 122:110-115. Sayyari E, Whitfield JB, Mirarab S. PMID: 29421312.
      View in: PubMed   Mentions:
    83. Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction. Mol Biol Evol. 2017 Dec 01; 34(12):3279-3291. Sayyari E, Whitfield JB, Mirarab S. PMID: 29029241.
      View in: PubMed   Mentions:
    84. A communal catalogue reveals Earth's multiscale microbial diversity. Nature. 2017 11 23; 551(7681):457-463. Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R, Earth Microbiome Project Consortium. PMID: 29088705; PMCID: PMC6192678.
      View in: PubMed   Mentions: 1150     Fields:    Translation:HumansAnimalsCells
    85. Species Tree Estimation Using ASTRAL: How Many Genes Are Enough? IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep-Oct; 15(5):1738-1747. Shekhar S, Roch S, Mirarab S. PMID: 28976320.
      View in: PubMed   Mentions:
    86. Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction. PLoS One. 2017; 12(8):e0182238. Mai U, Sayyari E, Mirarab S. PMID: 28800608; PMCID: PMC5553649.
      View in: PubMed   Mentions:
    87. Phylogenomics: Constrained gene tree inference. Nat Ecol Evol. 2017 Jan 13; 1(2):56. Mirarab S. PMID: 28812612.
      View in: PubMed   Mentions:
    88. HIPPI: highly accurate protein family classification with ensembles of HMMs. BMC Genomics. 2016 11 11; 17(Suppl 10):765. Nguyen NP, Nute M, Mirarab S, Warnow T. PMID: 28185571; PMCID: PMC5123343.
      View in: PubMed   Mentions:
    89. Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction. BMC Genomics. 2016 11 11; 17(Suppl 10):783. Sayyari E, Mirarab S. PMID: 28185574; PMCID: PMC5123309.
      View in: PubMed   Mentions:
    90. Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies. Mol Biol Evol. 2016 07; 33(7):1654-68. Sayyari E, Mirarab S. PMID: 27189547; PMCID: PMC4915361.
      View in: PubMed   Mentions:
    91. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biol Evol. 2016 Jan 05; 8(2):330-44. Tarver JE, Dos Reis M, Mirarab S, Moran RJ, Parker S, O'Reilly JE, King BL, O'Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PC, Pisani D. PMID: 26733575; PMCID: PMC4779606.
      View in: PubMed   Mentions:
    92. Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree". Science. 2015 Oct 09; 350(6257):171. Mirarab S, Bayzid MS, Boussau B, Warnow T. PMID: 26450204.
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    93. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. BMC Genomics. 2015; 16 Suppl 10:S1. Davidson R, Vachaspati P, Mirarab S, Warnow T. PMID: 26450506; PMCID: PMC4603753.
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    94. A comparative study of SVDquartets and other coalescent-based species tree estimation methods. BMC Genomics. 2015; 16 Suppl 10:S2. Chou J, Gupta A, Yaduvanshi S, Davidson R, Nute M, Mirarab S, Warnow T. PMID: 26449249; PMCID: PMC4602346.
      View in: PubMed   Mentions:
    95. Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds". Science. 2015 Sep 25; 349(6255):1460. Cracraft J, Houde P, Ho SY, Mindell DP, Fjeldså J, Lindow B, Edwards SV, Rahbek C, Mirarab S, Warnow T, Gilbert MT, Zhang G, Braun EL, Jarvis ED. PMID: 26404820.
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    96. Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses. PLoS One. 2015; 10(6):e0129183. Bayzid MS, Mirarab S, Boussau B, Warnow T. PMID: 26086579; PMCID: PMC4472720.
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    97. Ultra-large alignments using phylogeny-aware profiles. Genome Biol. 2015 Jun 16; 16:124. Nguyen NP, Mirarab S, Kumar K, Warnow T. PMID: 26076734; PMCID: PMC4492008.
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    98. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics. 2015 Jun 15; 31(12):i44-52. Mirarab S, Warnow T. PMID: 26072508; PMCID: PMC4765870.
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    99. Phylogenomic analyses data of the avian phylogenomics project. Gigascience. 2015; 4:4. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Alfaro-Núñez A, Narula N, Liu L, Burt D, Ellegren H, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G, Avian Phylogenomics Consortium. PMID: 25741440; PMCID: PMC4349222.
      View in: PubMed   Mentions:
    100. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. J Comput Biol. 2015 May; 22(5):377-86. Mirarab S, Nguyen N, Guo S, Wang LS, Kim J, Warnow T. PMID: 25549288; PMCID: PMC4424971.
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    101. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014 Dec 12; 346(6215):1320-31. Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G. PMID: 25504713; PMCID: PMC4405904.
      View in: PubMed   Mentions: 744     Fields:    Translation:AnimalsCells
    102. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science. 2014 Dec 12; 346(6215):1250463. Mirarab S, Bayzid MS, Boussau B, Warnow T. PMID: 25504728.
      View in: PubMed   Mentions:
    103. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A. 2014 Nov 11; 111(45):E4859-68. Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GK, Leebens-Mack J. PMID: 25355905; PMCID: PMC4234587.
      View in: PubMed   Mentions:
    104. TIPP: taxonomic identification and phylogenetic profiling. Bioinformatics. 2014 Dec 15; 30(24):3548-55. Nguyen NP, Mirarab S, Liu B, Pop M, Warnow T. PMID: 25359891; PMCID: PMC4253836.
      View in: PubMed   Mentions:
    105. Data access for the 1,000 Plants (1KP) project. Gigascience. 2014; 3:17. Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J, Wong GK. PMID: 25625010; PMCID: PMC4306014.
      View in: PubMed   Mentions:
    106. BBCA: Improving the scalability of *BEAST using random binning. BMC Genomics. 2014; 15 Suppl 6:S11. Zimmermann T, Mirarab S, Warnow T. PMID: 25572469; PMCID: PMC4239591.
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    107. ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics. 2014 Sep 01; 30(17):i541-8. Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T. PMID: 25161245; PMCID: PMC4147915.
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    108. Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting. Syst Biol. 2016 May; 65(3):366-80. Mirarab S, Bayzid MS, Warnow T. PMID: 25164915.
      View in: PubMed   Mentions:
    109. Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinformatics. 2013 May 13; 14:158. Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, Vaidya G, Pontelli E, Cranston K, Vos R, Webb CO, Harmon LJ, Pirrung M, O'Meara B, Pennell MW, Mirarab S, Rosenberg MS, Balhoff JP, Bik HM, Heath TA, Midford PE, Brown JW, McTavish EJ, Sukumaran J, Westneat M, Alfaro ME, Steele A, Jordan G. PMID: 23668630; PMCID: PMC3669619.
      View in: PubMed   Mentions: 13     Fields:    
    110. Inferring optimal species trees under gene duplication and loss. Pac Symp Biocomput. 2013; 250-61. Bayzid MS, Mirarab S, Warnow T. PMID: 23424130.
      View in: PubMed   Mentions:
    111. MRL and SuperFine+MRL: new supertree methods. Algorithms Mol Biol. 2012 Jan 26; 7(1):3. Nguyen N, Mirarab S, Warnow T. PMID: 22280525; PMCID: PMC3308190.
      View in: PubMed   Mentions:
    112. SEPP: SATé-enabled phylogenetic placement. Pac Symp Biocomput. 2012; 247-58. Mirarab S, Nguyen N, Warnow T. PMID: 22174280.
      View in: PubMed   Mentions:
    113. FastSP: linear time calculation of alignment accuracy. Bioinformatics. 2011 Dec 01; 27(23):3250-8. Mirarab S, Warnow T. PMID: 21984754.
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