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Items: 1 to 50 of 91

1.

Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets.

Nute M, Saleh E, Warnow T.

Syst Biol. 2018 Oct 17. doi: 10.1093/sysbio/syy068. [Epub ahead of print]

PMID:
30329135
2.

Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods.

Roch S, Nute M, Warnow T.

Syst Biol. 2019 Mar 1;68(2):281-297. doi: 10.1093/sysbio/syy061.

PMID:
30247732
3.

Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows.

Shah N, Nute MG, Warnow T, Pop M.

Bioinformatics. 2018 Sep 24. doi: 10.1093/bioinformatics/bty833. [Epub ahead of print] No abstract available.

PMID:
30247621
4.

PASTA for proteins.

Collins K, Warnow T.

Bioinformatics. 2018 Nov 15;34(22):3939-3941. doi: 10.1093/bioinformatics/bty495.

5.

Simultaneous radiation of bird and mammal lice following the K-Pg boundary.

Johnson KP, Nguyen NP, Sweet AD, Boyd BM, Warnow T, Allen JM.

Biol Lett. 2018 May;14(5). pii: 20180141. doi: 10.1098/rsbl.2018.0141.

PMID:
29794007
6.

The performance of coalescent-based species tree estimation methods under models of missing data.

Nute M, Chou J, Molloy EK, Warnow T.

BMC Genomics. 2018 May 8;19(Suppl 5):286. doi: 10.1186/s12864-018-4619-8.

7.

SIESTA: enhancing searches for optimal supertrees and species trees.

Vachaspati P, Warnow T.

BMC Genomics. 2018 May 8;19(Suppl 5):252. doi: 10.1186/s12864-018-4621-1.

8.

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.

PMID:
29603138
9.

OCTAL: Optimal Completion of gene trees in polynomial time.

Christensen S, Molloy EK, Vachaspati P, Warnow T.

Algorithms Mol Biol. 2018 Mar 15;13:6. doi: 10.1186/s13015-018-0124-5. eCollection 2018.

10.

SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space.

Vachaspati P, Warnow T.

Mol Phylogenet Evol. 2018 Jul;124:122-136. doi: 10.1016/j.ympev.2018.03.006. Epub 2018 Mar 9.

PMID:
29530498
11.

The development and application of bioinformatics core competencies to improve bioinformatics training and education.

Mulder N, Schwartz R, Brazas MD, Brooksbank C, Gaeta B, Morgan SL, Pauley MA, Rosenwald A, Rustici G, Sierk M, Warnow T, Welch L.

PLoS Comput Biol. 2018 Feb 1;14(2):e1005772. doi: 10.1371/journal.pcbi.1005772. eCollection 2018 Feb.

12.

Gene tree parsimony for incomplete gene trees: addressing true biological loss.

Bayzid MS, Warnow T.

Algorithms Mol Biol. 2018 Jan 19;13:1. doi: 10.1186/s13015-017-0120-1. eCollection 2018.

13.

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods.

Molloy EK, Warnow T.

Syst Biol. 2018 Mar 1;67(2):285-303. doi: 10.1093/sysbio/syx077.

PMID:
29029338
14.

Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice.

Boyd BM, Allen JM, Nguyen NP, Vachaspati P, Quicksall ZS, Warnow T, Mugisha L, Johnson KP, Reed DL.

Mol Biol Evol. 2017 Jul 1;34(7):1743-1757. doi: 10.1093/molbev/msx117.

15.

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.

16.

An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees.

Uricchio LH, Warnow T, Rosenberg NA.

BMC Bioinformatics. 2016 Nov 11;17(Suppl 14):417. doi: 10.1186/s12859-016-1266-4.

17.

Scaling statistical multiple sequence alignment to large datasets.

Nute M, Warnow T.

BMC Genomics. 2016 Nov 11;17(Suppl 10):764. doi: 10.1186/s12864-016-3101-8.

18.

Phylogenomics from Whole Genome Sequences Using aTRAM.

Allen JM, Boyd B, Nguyen NP, Vachaspati P, Warnow T, Huang DI, Grady PGS, Bell KC, Cronk QCB, Mugisha L, Pittendrigh BR, Leonardi MS, Reed DL, Johnson KP.

Syst Biol. 2017 Sep 1;66(5):786-798. doi: 10.1093/sysbio/syw105.

PMID:
28123117
19.

Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola).

Boyd BM, Allen JM, Nguyen NP, Sweet AD, Warnow T, Shapiro MD, Villa SM, Bush SE, Clayton DH, Johnson KP.

Syst Biol. 2017 Nov 1;66(6):896-911. doi: 10.1093/sysbio/syx027.

20.

FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization.

Vachaspati P, Warnow T.

Bioinformatics. 2017 Mar 1;33(5):631-639. doi: 10.1093/bioinformatics/btw600.

21.

High diversity of picornaviruses in rats from different continents revealed by deep sequencing.

Hansen TA, Mollerup S, Nguyen NP, White NE, Coghlan M, Alquezar-Planas DE, Joshi T, Jensen RH, Fridholm H, Kjartansdóttir KR, Mourier T, Warnow T, Belsham GJ, Bunce M, Willerslev E, Nielsen LP, Vinner L, Hansen AJ.

Emerg Microbes Infect. 2016 Aug 17;5(8):e90. doi: 10.1038/emi.2016.90.

22.

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).

Welch L, Brooksbank C, Schwartz R, Morgan SL, Gaeta B, Kilpatrick AM, Mietchen D, Moore BL, Mulder N, Pauley M, Pearson W, Radivojac P, Rosenberg N, Rosenwald A, Rustici G, Warnow T.

PLoS Comput Biol. 2016 May 13;12(5):e1004943. doi: 10.1371/journal.pcbi.1004943. eCollection 2016 May. No abstract available.

23.

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity.

Nguyen NP, Warnow T, Pop M, White B.

NPJ Biofilms Microbiomes. 2016 Apr 20;2:16004. doi: 10.1038/npjbiofilms.2016.4. eCollection 2016.

24.

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.

25.

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.

26.

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.

27.

ASTRID: Accurate Species TRees from Internode Distances.

Vachaspati P, Warnow T.

BMC Genomics. 2015;16 Suppl 10:S3. doi: 10.1186/1471-2164-16-S10-S3. Epub 2015 Oct 2.

28.

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.

29.

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
30.

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.

31.

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.

32.

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.

33.

Concatenation Analyses in the Presence of Incomplete Lineage Sorting.

Warnow T.

PLoS Curr. 2015 May 22;7. pii: ecurrents.currents.tol.8d41ac0f13d1abedf4c4a59f5d17b1f7. doi: 10.1371/currents.tol.8d41ac0f13d1abedf4c4a59f5d17b1f7.

34.

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods.

Roch S, Warnow T.

Syst Biol. 2015 Jul;64(4):663-76. doi: 10.1093/sysbio/syv016. Epub 2015 Mar 25.

PMID:
25813358
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.

Disk covering methods improve phylogenomic analyses.

Bayzid MS, Hunt T, Warnow T.

BMC Genomics. 2014;15 Suppl 6:S7. doi: 10.1186/1471-2164-15-S6-S7. Epub 2014 Oct 17.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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
45.

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.

46.

Large-scale multiple sequence alignment and tree estimation using SATé.

Liu K, Warnow T.

Methods Mol Biol. 2014;1079:219-44. doi: 10.1007/978-1-62703-646-7_15.

47.

Naive binning improves phylogenomic analyses.

Bayzid MS, Warnow T.

Bioinformatics. 2013 Sep 15;29(18):2277-84. doi: 10.1093/bioinformatics/btt394. Epub 2013 Jul 9.

PMID:
23842808
48.

Inferring optimal species trees under gene duplication and loss.

Bayzid MS, Mirarab S, Warnow T.

Pac Symp Biocomput. 2013:250-61.

49.

Estimating optimal species trees from incomplete gene trees under deep coalescence.

Bayzid MS, Warnow T.

J Comput Biol. 2012 Jun;19(6):591-605. doi: 10.1089/cmb.2012.0037.

PMID:
22697236
50.

DACTAL: divide-and-conquer trees (almost) without alignments.

Nelesen S, Liu K, Wang LS, Linder CR, Warnow T.

Bioinformatics. 2012 Jun 15;28(12):i274-82. doi: 10.1093/bioinformatics/bts218.

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