Siavash Mirarab - Publications

2015- Electrical and Computer Engineering University of California, San Diego, La Jolla, CA 

80 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Balaban M, Jiang Y, Zhu Q, McDonald D, Knight R, Mirarab S. Generation of accurate, expandable phylogenomic trees with uDance. Nature Biotechnology. PMID 37500914 DOI: 10.1038/s41587-023-01868-8  0.426
2023 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, ... ... Mirarab S, et al. Greengenes2 unifies microbial data in a single reference tree. Nature Biotechnology. PMID 37500913 DOI: 10.1038/s41587-023-01845-1  0.352
2023 Tabatabaee Y, Zhang C, Warnow T, Mirarab S. Phylogenomic branch length estimation using quartets. Bioinformatics (Oxford, England). 39: i185-i193. PMID 37387151 DOI: 10.1093/bioinformatics/btad221  0.626
2022 Zhang C, Bzikadze AV, Safonova Y, Mirarab S. A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods. Frontiers in Immunology. 13: 1014439. PMID 36618367 DOI: 10.3389/fimmu.2022.1014439  0.303
2022 Rachtman E, Sarmashghi S, Bafna V, Mirarab S. Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling. Cell Systems. 13: 817-829.e3. PMID 36265468 DOI: 10.1016/j.cels.2022.06.007  0.303
2022 Zhang C, Mirarab S. Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees. Molecular Biology and Evolution. PMID 36201617 DOI: 10.1093/molbev/msac215  0.384
2022 Jiang Y, Tabaghi P, Mirarab S. Learning Hyperbolic Embedding for Phylogenetic Tree Placement and Updates. Biology. 11. PMID 36138735 DOI: 10.3390/biology11091256  0.387
2022 Zhang C, Mirarab S. ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees. Bioinformatics (Oxford, England). PMID 36094339 DOI: 10.1093/bioinformatics/btac620  0.359
2022 Zhu Q, Mirarab S. Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies. Methods in Molecular Biology (Clifton, N.J.). 2569: 137-165. PMID 36083447 DOI: 10.1007/978-1-0716-2691-7_7  0.364
2022 Hasan NB, Balaban M, Biswas A, Bayzid MS, Mirarab S. Distance-Based Phylogenetic Placement with Statistical Support. Biology. 11. PMID 36009839 DOI: 10.3390/biology11081212  0.332
2022 Balaban M, Bristy NA, Faisal A, Bayzid MS, Mirarab S. Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model. Bioinformatics Advances. 2: vbac055. PMID 35992043 DOI: 10.1093/bioadv/vbac055  0.351
2022 Rabiee M, Mirarab S. QuCo: quartet-based co-estimation of species trees and gene trees. Bioinformatics (Oxford, England). 38: i413-i421. PMID 35758818 DOI: 10.1093/bioinformatics/btac265  0.382
2022 Jiang Y, Balaban M, Zhu Q, Mirarab S. DEPP: Deep Learning Enables Extending Species Trees using Single Genes. Systematic Biology. PMID 35485976 DOI: 10.1093/sysbio/syac031  0.404
2022 Mai U, Mirarab S. Completing Gene Trees Without Species Trees in Sub-quadratic Time. Bioinformatics (Oxford, England). PMID 34978565 DOI: 10.1093/bioinformatics/btab875  0.388
2021 Balaban M, Jiang Y, Roush D, Zhu Q, Mirarab S. Fast and Accurate Distance-based Phylogenetic Placement using Divide and Conquer. Molecular Ecology Resources. PMID 34643995 DOI: 10.1111/1755-0998.13527  0.428
2021 Zhang C, Scornavacca C, Molloy EK, Mirarab S. Corrigendum to: ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy. Molecular Biology and Evolution. PMID 34417619 DOI: 10.1093/molbev/msab232  0.332
2021 Rachtman E, Bafna V, Mirarab S. CONSULT: accurate contamination removal using locality-sensitive hashing. Nar Genomics and Bioinformatics. 3: lqab071. PMID 34377979 DOI: 10.1093/nargab/lqab071  0.313
2021 Rabiee M, Mirarab S. SODA: Multi-locus species delimitation using quartet frequencies. Bioinformatics (Oxford, England). PMID 33555318 DOI: 10.1093/bioinformatics/btaa1010  0.334
2021 Warnow T, Mirarab S. Multiple Sequence Alignment for Large Heterogeneous Datasets Using SATé, PASTA, and UPP. Methods in Molecular Biology (Clifton, N.J.). 2231: 99-119. PMID 33289889 DOI: 10.1007/978-1-0716-1036-7_7  0.621
2021 Mirarab S, Nakhleh L, Warnow T. Multispecies Coalescent: Theory and Applications in Phylogenetics Annual Review of Ecology, Evolution, and Systematics. 52: 247-268. DOI: 10.1146/annurev-ecolsys-012121-095340  0.373
2020 Moshiri N, Smith DM, Mirarab S. HIV Care Prioritization using Phylogenetic Branch Length. Journal of Acquired Immune Deficiency Syndromes (1999). PMID 33394616 DOI: 10.1097/QAI.0000000000002612  0.648
2020 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, ... ... Mirarab S, et al. Dense sampling of bird diversity increases power of comparative genomics. Nature. 587: 252-257. PMID 33177665 DOI: 10.1038/s41586-020-2873-9  0.314
2020 Mai U, Mirarab S. Log Transformation Improves Dating of Phylogenies. Molecular Biology and Evolution. PMID 32886788 DOI: 10.1093/Molbev/Msaa222  0.469
2020 Zhang C, Scornavacca C, Molloy EK, Mirarab S. ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy. Molecular Biology and Evolution. PMID 32886770 DOI: 10.1093/Molbev/Msaa139  0.52
2020 Balaban M, Mirarab S. Phylogenetic double placement of mixed samples. Bioinformatics (Oxford, England). 36: i335-i343. PMID 32657414 DOI: 10.1093/Bioinformatics/Btaa489  0.416
2020 Tilic E, Sayyari E, Stiller J, Mirarab S, Rouse GW. More is needed - Thousands of loci are required to elucidate the relationships of the 'flowers of the sea' (Sabellida, Annelida). Molecular Phylogenetics and Evolution. 106892. PMID 32562819 DOI: 10.1016/J.Ympev.2020.106892  0.451
2020 Bohmann K, Mirarab S, Bafna V, Gilbert MTP. Beyond DNA barcoding: The unrealised potential of genome skim data in sample identification. Molecular Ecology. PMID 32542933 DOI: 10.1111/Mec.15507  0.396
2020 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, et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nature Communications. 11: 2500. PMID 32427907 DOI: 10.1038/S41467-020-16366-7  0.434
2020 Rabiee M, Mirarab S. Forcing external constraints on tree inference using ASTRAL. Bmc Genomics. 21: 218. PMID 32299337 DOI: 10.1186/S12864-020-6607-Z  0.455
2020 Rachtman E, Balaban M, Bafna V, Mirarab S. On the impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters. Molecular Ecology Resources. PMID 31943790 DOI: 10.1111/1755-0998.13135  0.381
2019 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, ... ... Mirarab S, et al. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea. Nature Communications. 10: 5477. PMID 31792218 DOI: 10.1038/S41467-019-13443-4  0.42
2019 Balaban M, Sarmashghi S, Mirarab S. APPLES: Scalable Distance-based Phylogenetic Placement with or without Alignments. Systematic Biology. PMID 31545363 DOI: 10.1093/Sysbio/Syz063  0.485
2019 Balaban M, Moshiri N, Mai U, Jia X, Mirarab S. TreeCluster: Clustering biological sequences using phylogenetic trees. Plos One. 14: e0221068. PMID 31437182 DOI: 10.1371/Journal.Pone.0221068  0.706
2019 Rabiee M, Mirarab S. INSTRAL: Discordance-aware Phylogenetic Placement using Quartet Scores. Systematic Biology. PMID 31290974 DOI: 10.1093/Sysbio/Syz045  0.504
2019 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, ... ... Mirarab S, et al. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science (New York, N.Y.). 364. PMID 31221828 DOI: 10.1126/Science.Aav6202  0.427
2019 Yin J, Zhang C, Mirarab S. ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization. Bioinformatics (Oxford, England). PMID 30903685 DOI: 10.1093/Bioinformatics/Btz211  0.492
2019 Sarmashghi S, Bohmann K, P Gilbert MT, Bafna V, Mirarab S. Skmer: assembly-free and alignment-free sample identification using genome skims. Genome Biology. 20: 34. PMID 30760303 DOI: 10.1186/S13059-019-1632-4  0.406
2019 Rabiee M, Sayyari E, Mirarab S. Multi-allele species reconstruction using ASTRAL. Molecular Phylogenetics and Evolution. 130: 286-296. PMID 30393186 DOI: 10.1016/J.Ympev.2018.10.033  0.482
2019 Houde P, Braun EL, Narula N, Minjares U, Mirarab S. Phylogenetic Signal of Indels and the Neoavian Radiation Diversity. 11: 108. DOI: 10.3390/D11070108  0.507
2018 Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S. FAVITES: simultaneous simulation of transmission networks, phylogenetic trees, and sequences. Bioinformatics (Oxford, England). PMID 30395173 DOI: 10.1093/Bioinformatics/Bty921  0.703
2018 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, et al. Interspecific Gene Flow Shaped the Evolution of the Genus Canis. Current Biology : Cb. PMID 30344120 DOI: 10.1016/J.Cub.2018.08.041  0.395
2018 Zhang C, Rabiee M, Sayyari E, Mirarab S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. Bmc Bioinformatics. 19: 153. PMID 29745866 DOI: 10.1186/S12859-018-2129-Y  0.491
2018 Mai U, Mirarab S. TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees. Bmc Genomics. 19: 272. PMID 29745847 DOI: 10.1186/S12864-018-4620-2  0.422
2018 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. Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. Msystems. 3. PMID 29719869 DOI: 10.1128/mSystems.00021-18  0.344
2018 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, et al. A roadmap for global synthesis of the plant tree of life. American Journal of Botany. PMID 29603138 DOI: 10.1002/Ajb2.1041  0.605
2018 Sayyari E, Mirarab S. Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies. Genes. 9. PMID 29495636 DOI: 10.3390/Genes9030132  0.497
2018 Sayyari E, Whitfield JB, Mirarab S. DiscoVista: interpretable visualizations of gene tree discordance. Molecular Phylogenetics and Evolution. PMID 29421312 DOI: 10.1016/J.Ympev.2018.01.019  0.448
2018 Moshiri N, Mirarab S. A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition. Systematic Biology. 67: 475-489. PMID 29165679 DOI: 10.1093/Sysbio/Syx088  0.723
2018 Shekhar S, Roch S, Mirarab S. Species Tree Estimation Using ASTRAL: How Many Genes Are Enough? Ieee/Acm Transactions On Computational Biology and Bioinformatics. 15: 1738-1747. PMID 28976320 DOI: 10.1109/Tcbb.2017.2757930  0.498
2017 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, ... ... Mirarab S, et al. A communal catalogue reveals Earth's multiscale microbial diversity. Nature. PMID 29088705 DOI: 10.1038/Nature24621  0.383
2017 Sayyari E, Whitfield JB, Mirarab S. Fragmentary gene sequences negatively impact gene tree and species tree reconstruction. Molecular Biology and Evolution. PMID 29029241 DOI: 10.1093/Molbev/Msx261  0.499
2017 Mirarab S. Phylogenomics: Constrained gene tree inference. Nature Ecology & Evolution. 1: 56. PMID 28812612 DOI: 10.1038/S41559-016-0056  0.45
2017 Mai U, Sayyari E, Mirarab S. Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction. Plos One. 12: e0182238. PMID 28800608 DOI: 10.1371/Journal.Pone.0182238  0.512
2016 Sayyari E, Mirarab S. Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction. Bmc Genomics. 17: 783. PMID 28185574 DOI: 10.1186/S12864-016-3098-Z  0.477
2016 Nguyen NP, Nute M, Mirarab S, Warnow T. HIPPI: highly accurate protein family classification with ensembles of HMMs. Bmc Genomics. 17: 765. PMID 28185571 DOI: 10.1186/S12864-016-3097-0  0.58
2016 Sayyari E, Mirarab S. Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies. Molecular Biology and Evolution. 33: 1654-68. PMID 27189547 DOI: 10.1093/Molbev/Msw079  0.495
2016 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. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biology and Evolution. PMID 26733575 DOI: 10.1093/Gbe/Evv261  0.617
2015 Davidson R, Vachaspati P, Mirarab S, Warnow T. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. Bmc Genomics. 16: S1. PMID 26450506 DOI: 10.1186/1471-2164-16-S10-S1  0.641
2015 Mirarab S, Bayzid MS, Boussau B, Warnow T. Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree". Science (New York, N.Y.). 350: 171. PMID 26450204 DOI: 10.1126/Science.Aaa7719  0.597
2015 Chou J, Gupta A, Yaduvanshi S, Davidson R, Nute M, Mirarab S, Warnow T. A comparative study of SVDquartets and other coalescent-based species tree estimation methods. Bmc Genomics. 16: S2. PMID 26449249 DOI: 10.1186/1471-2164-16-S10-S2  0.669
2015 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. Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds". Science (New York, N.Y.). 349: 1460. PMID 26404820 DOI: 10.1126/Science.Aab1578  0.592
2015 Bayzid MS, Mirarab S, Boussau B, Warnow T. Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses. Plos One. 10: e0129183. PMID 26086579 DOI: 10.1371/Journal.Pone.0129183  0.695
2015 Nguyen NP, Mirarab S, Kumar K, Warnow T. Ultra-large alignments using phylogeny-aware profiles. Genome Biology. 16: 124. PMID 26076734 DOI: 10.1186/S13059-015-0688-Z  0.637
2015 Mirarab S, Warnow T. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics (Oxford, England). 31: i44-52. PMID 26072508 DOI: 10.1093/Bioinformatics/Btv234  0.669
2015 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, et al. Phylogenomic analyses data of the avian phylogenomics project. Gigascience. 4: 4. PMID 25741440 DOI: 10.1186/S13742-014-0038-1  0.62
2015 Mirarab S, Nguyen N, Guo S, Wang LS, Kim J, Warnow T. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 377-86. PMID 25549288 DOI: 10.1089/Cmb.2014.0156  0.708
2015 Nguyen NP, Mirarab S, Kumar K, Warnow T. Ultra-large alignments using ensembles of hidden Markov models Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9029: 259-260. DOI: 10.1007/978-3-319-16706-0_26  0.497
2014 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, et al. Data access for the 1,000 Plants (1KP) project. Gigascience. 3: 17. PMID 25625010 DOI: 10.1186/2047-217X-3-17  0.588
2014 Zimmermann T, Mirarab S, Warnow T. BBCA: Improving the scalability of *BEAST using random binning. Bmc Genomics. 15: S11. PMID 25572469 DOI: 10.1186/1471-2164-15-S6-S11  0.691
2014 Mirarab S, Bayzid MS, Boussau B, Warnow T. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science (New York, N.Y.). 346: 1250463. PMID 25504728 DOI: 10.1126/Science.1250463  0.679
2014 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, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science (New York, N.Y.). 346: 1320-31. PMID 25504713 DOI: 10.1126/Science.1253451  0.658
2014 Nguyen NP, Mirarab S, Liu B, Pop M, Warnow T. TIPP: taxonomic identification and phylogenetic profiling. Bioinformatics (Oxford, England). 30: 3548-55. PMID 25359891 DOI: 10.1093/Bioinformatics/Btu721  0.586
2014 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, et al. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences of the United States of America. 111: E4859-68. PMID 25355905 DOI: 10.1073/Pnas.1323926111  0.604
2014 Mirarab S, Bayzid MS, Warnow T. Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting. Systematic Biology. PMID 25164915 DOI: 10.1093/Sysbio/Syu063  0.674
2014 Mirarab S, Reaz R, Bayzid MS, Zimmermann T, S. Swenson M, Warnow T. ASTRAL: Genome-scale coalescent-based species tree estimation Bioinformatics. 30. PMID 25161245 DOI: 10.1093/Bioinformatics/Btu462  0.689
2013 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, et al. Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. Bmc Bioinformatics. 14: 158. PMID 23668630 DOI: 10.1186/1471-2105-14-158  0.344
2013 Bayzid MS, Mirarab S, Warnow T. Inferring optimal species trees under gene duplication and loss 18th Pacific Symposium On Biocomputing, Psb 2013. 250-261. PMID 23424130  0.602
2012 Nguyen N, Mirarab S, Warnow T. MRL and SuperFine+MRL: new supertree methods. Algorithms For Molecular Biology : Amb. 7: 3. PMID 22280525 DOI: 10.1186/1748-7188-7-3  0.597
2012 Mirarab S, Nguyen N, Warnow T. SEPP: SATé-enabled phylogenetic placement 17th Pacific Symposium On Biocomputing, Psb 2012. 247-258. PMID 22174280  0.645
2011 Mirarab S, Warnow T. FastSP: linear time calculation of alignment accuracy. Bioinformatics (Oxford, England). 27: 3250-8. PMID 21984754 DOI: 10.1093/Bioinformatics/Btr553  0.601
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