Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 49

1.

APPLES: Scalable Distance-based Phylogenetic Placement with or without Alignments.

Balaban M, Sarmashghi S, Mirarab S.

Syst Biol. 2019 Sep 23. pii: syz063. doi: 10.1093/sysbio/syz063. [Epub ahead of print]

PMID:
31545363
2.

TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification.

Sayyari E, Kawas B, Mirarab S.

Bioinformatics. 2019 Jul 15;35(14):i31-i40. doi: 10.1093/bioinformatics/btz394.

3.

TreeCluster: Clustering biological sequences using phylogenetic trees.

Balaban M, Moshiri N, Mai U, Jia X, Mirarab S.

PLoS One. 2019 Aug 22;14(8):e0221068. doi: 10.1371/journal.pone.0221068. eCollection 2019.

4.

INSTRAL: Discordance-aware Phylogenetic Placement using Quartet Scores.

Rabiee M, Mirarab S.

Syst Biol. 2019 Jul 10. pii: syz045. doi: 10.1093/sysbio/syz045. [Epub ahead of print]

PMID:
31290974
5.

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits.

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.

Science. 2019 Jun 21;364(6446). pii: eaav6202. doi: 10.1126/science.aav6202.

PMID:
31221828
6.

ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization.

Yin J, Zhang C, Mirarab S.

Bioinformatics. 2019 Oct 15;35(20):3961-3969. doi: 10.1093/bioinformatics/btz211.

PMID:
30903685
7.

Skmer: assembly-free and alignment-free sample identification using genome skims.

Sarmashghi S, Bohmann K, P Gilbert MT, Bafna V, Mirarab S.

Genome Biol. 2019 Feb 13;20(1):34. doi: 10.1186/s13059-019-1632-4.

8.

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences.

Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S.

Bioinformatics. 2019 Jun 1;35(11):1852-1861. doi: 10.1093/bioinformatics/bty921.

PMID:
30395173
9.

Multi-allele species reconstruction using ASTRAL.

Rabiee M, Sayyari E, Mirarab S.

Mol Phylogenet Evol. 2019 Jan;130:286-296. doi: 10.1016/j.ympev.2018.10.033. Epub 2018 Oct 26.

PMID:
30393186
10.

Interspecific Gene Flow Shaped the Evolution of the Genus Canis.

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, Heide-Jørgensen MP, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig Ø, Hansen AJ, Gilbert MTP.

Curr Biol. 2018 Nov 5;28(21):3441-3449.e5. doi: 10.1016/j.cub.2018.08.041. Epub 2018 Oct 18.

11.

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees.

Zhang C, Rabiee M, Sayyari E, Mirarab S.

BMC Bioinformatics. 2018 May 8;19(Suppl 6):153. doi: 10.1186/s12859-018-2129-y.

12.

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees.

Mai U, Mirarab S.

BMC Genomics. 2018 May 8;19(Suppl 5):272. doi: 10.1186/s12864-018-4620-2.

13.

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information.

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.

mSystems. 2018 Apr 17;3(3). pii: e00021-18. doi: 10.1128/mSystems.00021-18. eCollection 2018 May-Jun.

14.

A roadmap for global synthesis of the plant tree of life.

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.

Am J Bot. 2018 Mar;105(3):614-622. doi: 10.1002/ajb2.1041. Epub 2018 Mar 30.

15.

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies.

Sayyari E, Mirarab S.

Genes (Basel). 2018 Feb 28;9(3). pii: E132. doi: 10.3390/genes9030132.

16.

Identifying the favored mutation in a positive selective sweep.

Akbari A, Vitti JJ, Iranmehr A, Bakhtiari M, Sabeti PC, Mirarab S, Bafna V.

Nat Methods. 2018 Apr;15(4):279-282. doi: 10.1038/nmeth.4606. Epub 2018 Feb 19.

17.

DiscoVista: Interpretable visualizations of gene tree discordance.

Sayyari E, Whitfield JB, Mirarab S.

Mol Phylogenet Evol. 2018 May;122:110-115. doi: 10.1016/j.ympev.2018.01.019. Epub 2018 Feb 5.

PMID:
29421312
18.

A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition.

Moshiri N, Mirarab S.

Syst Biol. 2018 May 1;67(3):475-489. doi: 10.1093/sysbio/syx088.

19.

A communal catalogue reveals Earth's multiscale microbial diversity.

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.

Nature. 2017 Nov 23;551(7681):457-463. doi: 10.1038/nature24621. Epub 2017 Nov 1.

20.

Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction.

Sayyari E, Whitfield JB, Mirarab S.

Mol Biol Evol. 2017 Dec 1;34(12):3279-3291. doi: 10.1093/molbev/msx261.

PMID:
29029241
21.

Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?

Shekhar S, Roch S, Mirarab S.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep-Oct;15(5):1738-1747. doi: 10.1109/TCBB.2017.2757930. Epub 2017 Sep 29.

PMID:
28976320
22.

Phylogenomics: Constrained gene tree inference.

Mirarab S.

Nat Ecol Evol. 2017 Jan 13;1(2):56. doi: 10.1038/s41559-016-0056. No abstract available.

PMID:
28812612
23.

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction.

Mai U, Sayyari E, Mirarab S.

PLoS One. 2017 Aug 11;12(8):e0182238. doi: 10.1371/journal.pone.0182238. eCollection 2017.

24.

Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction.

Sayyari E, Mirarab S.

BMC Genomics. 2016 Nov 11;17(Suppl 10):783. doi: 10.1186/s12864-016-3098-z.

25.

HIPPI: highly accurate protein family classification with ensembles of HMMs.

Nguyen NP, Nute M, Mirarab S, Warnow T.

BMC Genomics. 2016 Nov 11;17(Suppl 10):765. doi: 10.1186/s12864-016-3097-0.

26.

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies.

Sayyari E, Mirarab S.

Mol Biol Evol. 2016 Jul;33(7):1654-68. doi: 10.1093/molbev/msw079. Epub 2016 Apr 15.

27.

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference.

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.

Genome Biol Evol. 2016 Jan 5;8(2):330-44. doi: 10.1093/gbe/evv261.

28.

Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer.

Davidson R, Vachaspati P, Mirarab S, Warnow T.

BMC Genomics. 2015;16 Suppl 10:S1. doi: 10.1186/1471-2164-16-S10-S1. Epub 2015 Oct 2.

29.

Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree".

Mirarab S, Bayzid MS, Boussau B, Warnow T.

Science. 2015 Oct 9;350(6257):171. doi: 10.1126/science.aaa7719.

30.

A comparative study of SVDquartets and other coalescent-based species tree estimation methods.

Chou J, Gupta A, Yaduvanshi S, Davidson R, Nute M, Mirarab S, Warnow T.

BMC Genomics. 2015;16 Suppl 10:S2. doi: 10.1186/1471-2164-16-S10-S2. Epub 2015 Oct 2.

31.

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

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.

Science. 2015 Sep 25;349(6255):1460. doi: 10.1126/science.aab1578.

PMID:
26404820
32.

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses.

Bayzid MS, Mirarab S, Boussau B, Warnow T.

PLoS One. 2015 Jun 18;10(6):e0129183. doi: 10.1371/journal.pone.0129183. eCollection 2015.

33.

Ultra-large alignments using phylogeny-aware profiles.

Nguyen NP, Mirarab S, Kumar K, Warnow T.

Genome Biol. 2015 Jun 16;16:124. doi: 10.1186/s13059-015-0688-z.

34.

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes.

Mirarab S, Warnow T.

Bioinformatics. 2015 Jun 15;31(12):i44-52. doi: 10.1093/bioinformatics/btv234.

35.

Phylogenomic analyses data of the avian phylogenomics project.

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.

Gigascience. 2015 Feb 12;4:4. doi: 10.1186/s13742-014-0038-1. eCollection 2015.

36.

Data access for the 1,000 Plants (1KP) project.

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.

Gigascience. 2014 Oct 27;3:17. doi: 10.1186/2047-217X-3-17. eCollection 2014. Review.

37.

BBCA: Improving the scalability of *BEAST using random binning.

Zimmermann T, Mirarab S, Warnow T.

BMC Genomics. 2014;15 Suppl 6:S11. doi: 10.1186/1471-2164-15-S6-S11. Epub 2014 Oct 17.

38.

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

Mirarab S, Nguyen N, Guo S, Wang LS, Kim J, Warnow T.

J Comput Biol. 2015 May;22(5):377-86. doi: 10.1089/cmb.2014.0156. Epub 2014 Dec 30.

39.

Statistical binning enables an accurate coalescent-based estimation of the avian tree.

Mirarab S, Bayzid MS, Boussau B, Warnow T.

Science. 2014 Dec 12;346(6215):1250463. doi: 10.1126/science.1250463. Epub 2014 Dec 11.

40.

Whole-genome analyses resolve early branches in the tree of life of modern birds.

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.

Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.

41.

TIPP: taxonomic identification and phylogenetic profiling.

Nguyen NP, Mirarab S, Liu B, Pop M, Warnow T.

Bioinformatics. 2014 Dec 15;30(24):3548-55. doi: 10.1093/bioinformatics/btu721. Epub 2014 Oct 29.

42.

Phylotranscriptomic analysis of the origin and early diversification of land plants.

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.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):E4859-68. doi: 10.1073/pnas.1323926111. Epub 2014 Oct 29.

43.

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting.

Mirarab S, Bayzid MS, Warnow T.

Syst Biol. 2016 May;65(3):366-80. doi: 10.1093/sysbio/syu063. Epub 2014 Aug 26.

PMID:
25164915
44.

ASTRAL: genome-scale coalescent-based species tree estimation.

Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T.

Bioinformatics. 2014 Sep 1;30(17):i541-8. doi: 10.1093/bioinformatics/btu462.

45.

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

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.

BMC Bioinformatics. 2013 May 13;14:158. doi: 10.1186/1471-2105-14-158.

46.

Inferring optimal species trees under gene duplication and loss.

Bayzid MS, Mirarab S, Warnow T.

Pac Symp Biocomput. 2013:250-61.

47.

MRL and SuperFine+MRL: new supertree methods.

Nguyen N, Mirarab S, Warnow T.

Algorithms Mol Biol. 2012 Jan 26;7(1):3. doi: 10.1186/1748-7188-7-3.

48.

SEPP: SATé-enabled phylogenetic placement.

Mirarab S, Nguyen N, Warnow T.

Pac Symp Biocomput. 2012:247-58.

49.

FastSP: linear time calculation of alignment accuracy.

Mirarab S, Warnow T.

Bioinformatics. 2011 Dec 1;27(23):3250-8. doi: 10.1093/bioinformatics/btr553. Epub 2011 Oct 7.

PMID:
21984754

Supplemental Content

Loading ...
Support Center