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Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications.

Tiley GP, Barker MS, Burleigh JG.

Genome Biol Evol. 2018 Nov 1;10(11):2882-2898. doi: 10.1093/gbe/evy200.


Tempo and timing of ecological trait divergence in bird speciation.

McEntee JP, Tobias JA, Sheard C, Burleigh JG.

Nat Ecol Evol. 2018 Jul;2(7):1120-1127. doi: 10.1038/s41559-018-0570-y. Epub 2018 Jun 18.


Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution.

Tiley GP, Kimball RT, Braun EL, Burleigh JG.

BMC Genomics. 2018 May 8;19(1):336. doi: 10.1186/s12864-018-4711-0.


chromploid: An R package for chromosome number evolution across the plant tree of life.

Zenil-Ferguson R, Burleigh JG, Ponciano JM.

Appl Plant Sci. 2018 Apr 11;6(3):e1037. doi: 10.1002/aps3.1037. eCollection 2018 Mar.


Extraction of phenotypic traits from taxonomic descriptions for the tree of life using natural language processing.

Endara L, Cui H, Burleigh JG.

Appl Plant Sci. 2018 Mar 31;6(3):e1035. doi: 10.1002/aps3.1035. eCollection 2018 Mar.


Community assembly of the ferns of Florida.

Sessa EB, Chambers SM, Li D, Trotta L, Endara L, Burleigh JG, Baiser B.

Am J Bot. 2018 Mar;105(3):549-564. doi: 10.1002/ajb2.1073. Epub 2018 May 5.


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.


Evolution of the 3R-MYB Gene Family in Plants.

Feng G, Burleigh JG, Braun EL, Mei W, Barbazuk WB.

Genome Biol Evol. 2017 Apr 20. doi: 10.1093/gbe/evx056. [Epub ahead of print]


Testing the association of phenotypes with polyploidy: An example using herbaceous and woody eudicots.

Zenil-Ferguson R, Ponciano JM, Burleigh JG.

Evolution. 2017 May;71(5):1138-1148. doi: 10.1111/evo.13226. Epub 2017 Mar 29.


Effects of 16S rDNA sampling on estimates of the number of endosymbiont lineages in sucking lice.

Allen JM, Burleigh JG, Light JE, Reed DL.

PeerJ. 2016 Jul 19;4:e2187. doi: 10.7717/peerj.2187. eCollection 2016.


Evaluating the role of genome downsizing and size thresholds from genome size distributions in angiosperms.

Zenil-Ferguson R, Ponciano JM, Burleigh JG.

Am J Bot. 2016 Jul;103(7):1175-86. doi: 10.3732/ajb.1500408. Epub 2016 May 10.


Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data.

Tiley GP, Ané C, Burleigh JG.

Genome Biol Evol. 2016 Apr 11;8(4):1023-37. doi: 10.1093/gbe/evw058.


Erratum to: The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms.

Tiley GP, Burleigh JG.

BMC Evol Biol. 2015 Nov 9;15:244. doi: 10.1186/s12862-015-0525-8. No abstract available.


Synthesis of phylogeny and taxonomy into a comprehensive tree of life.

Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, Crandall KA, Deng J, Drew BT, Gazis R, Gude K, Hibbett DS, Katz LA, Laughinghouse HD 4th, McTavish EJ, Midford PE, Owen CL, Ree RH, Rees JA, Soltis DE, Williams T, Cranston KA.

Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):12764-9. doi: 10.1073/pnas.1423041112. Epub 2015 Sep 18.


MatrixConverter: Facilitating construction of phenomic character matrices.

Liu J, Endara L, Burleigh JG.

Appl Plant Sci. 2015 Feb 9;3(2). pii: apps.1400088. doi: 10.3732/apps.1400088. eCollection 2015 Feb.


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.


Finding our way through phenotypes.

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.

PLoS Biol. 2015 Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection 2015 Jan.


Building the avian tree of life using a large-scale, sparse supermatrix.

Burleigh JG, Kimball RT, Braun EL.

Mol Phylogenet Evol. 2015 Mar;84:53-63. doi: 10.1016/j.ympev.2014.12.003. Epub 2014 Dec 27.


Assessing approaches for inferring species trees from multi-copy genes.

Chaudhary R, Boussau B, Burleigh JG, Fernández-Baca D.

Syst Biol. 2015 Mar;64(2):325-39. doi: 10.1093/sysbio/syu128. Epub 2014 Dec 23.


Deep phylogenetic incongruence in the angiosperm clade Rosidae.

Sun M, Soltis DE, Soltis PS, Zhu X, Burleigh JG, Chen Z.

Mol Phylogenet Evol. 2015 Feb;83:156-66. doi: 10.1016/j.ympev.2014.11.003. Epub 2014 Nov 18.


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.


MulRF: a software package for phylogenetic analysis using multi-copy gene trees.

Chaudhary R, Fernández-Baca D, Burleigh JG.

Bioinformatics. 2015 Feb 1;31(3):432-3. doi: 10.1093/bioinformatics/btu648. Epub 2014 Oct 1.


Duplications and losses in gene families of rust pathogens highlight putative effectors.

Pendleton AL, Smith KE, Feau N, Martin FM, Grigoriev IV, Hamelin R, Nelson CD, Burleigh JG, Davis JM.

Front Plant Sci. 2014 Jun 26;5:299. doi: 10.3389/fpls.2014.00299. eCollection 2014.


Scombroid fishes provide novel insights into the trait/rate associations of molecular evolution.

Qiu F, Kitchen A, Burleigh JG, Miyamoto MM.

J Mol Evol. 2014 Jun;78(6):338-48. doi: 10.1007/s00239-014-9621-4. Epub 2014 May 9.


From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes.

Ruhfel BR, Gitzendanner MA, Soltis PS, Soltis DE, Burleigh JG.

BMC Evol Biol. 2014 Feb 17;14:23. doi: 10.1186/1471-2148-14-23.


Efficient algorithms for knowledge-enhanced supertree and supermatrix phylogenetic problems.

Wehe A, Burleigh JG, Eulenstein O.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov-Dec;10(6):1432-41. doi: 10.1109/TCBB.2012.162.


Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance.

Chaudhary R, Burleigh JG, Fernández-Baca D.

Algorithms Mol Biol. 2013 Nov 1;8(1):28. doi: 10.1186/1748-7188-8-28.


Next-generation phenomics for the Tree of Life.

Burleigh JG, Alphonse K, Alverson AJ, Bik HM, Blank C, Cirranello AL, Cui H, Daly M, Dietterich TG, Gasparich G, Irvine J, Julius M, Kaufman S, Law E, Liu J, Moore L, O'Leary MA, Passarotti M, Ranade S, Simmons NB, Stevenson DW, Thacker RW, Theriot EC, Todorovic S, Velazco PM, Walls RL, Wolfe JM, Yu M.

PLoS Curr. 2013 Jun 26;5. pii: ecurrents.tol.085c713acafc8711b2ff7010a4b03733. doi: 10.1371/currents.tol.085c713acafc8711b2ff7010a4b03733.


Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach.

Soltis DE, Mort ME, Latvis M, Mavrodiev EV, O'Meara BC, Soltis PS, Burleigh JG, Rubio de Casas R.

Am J Bot. 2013 May;100(5):916-29. doi: 10.3732/ajb.1300044. Epub 2013 Apr 29.


Recurrent evolution of dioecy in bryophytes.

McDaniel SF, Atwood J, Burleigh JG.

Evolution. 2013 Feb;67(2):567-72. doi: 10.1111/j.1558-5646.2012.01808.x. Epub 2012 Oct 18.


A scalable method for identifying frequent subtrees in sets of large phylogenetic trees.

Ramu A, Kahveci T, Burleigh JG.

BMC Bioinformatics. 2012 Oct 3;13:256. doi: 10.1186/1471-2105-13-256.


Explaining differences in the lifespan and replicative capacity of cells: a general model and comparative analysis of vertebrates.

Gillooly JF, Hayward A, Hou C, Burleigh JG.

Proc Biol Sci. 2012 Oct 7;279(1744):3976-80. doi: 10.1098/rspb.2012.1129. Epub 2012 Jul 18.


Consensus properties for the deep coalescence problem and their application for scalable tree search.

Lin HT, Burleigh JG, Eulenstein O.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S12. doi: 10.1186/1471-2105-13-S10-S12.


Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence.

Chaudhary R, Burleigh JG, Eulenstein O.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S11. doi: 10.1186/1471-2105-13-S10-S11.


Assessing parameter identifiability in phylogenetic models using data cloning.

Ponciano JM, Burleigh JG, Braun EL, Taper ML.

Syst Biol. 2012 Dec 1;61(6):955-72. doi: 10.1093/sysbio/sys055. Epub 2012 May 30.


Fast local search for unrooted Robinson-Foulds supertrees.

Chaudhary R, Burleigh JG, Fernández-Baca D.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):1004-13. doi: 10.1109/TCBB.2012.47.


Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life.

Katz LA, Grant JR, Parfrey LW, Burleigh JG.

Syst Biol. 2012 Jul;61(4):653-60. doi: 10.1093/sysbio/sys026. Epub 2012 Feb 14.


What makes a leaf tough? Patterns of correlated evolution between leaf toughness traits and demographic rates among 197 shade-tolerant woody species in a neotropical forest.

Westbrook JW, Kitajima K, Burleigh JG, Kress WJ, Erickson DL, Wright SJ.

Am Nat. 2011 Jun;177(6):800-11. doi: 10.1086/659963.


Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees.

Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, Vision TJ.

Syst Biol. 2011 Mar;60(2):117-25. doi: 10.1093/sysbio/syq072. Epub 2010 Dec 24.


Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models.

Bansal MS, Burleigh JG, Eulenstein O.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S42. doi: 10.1186/1471-2105-11-S1-S42.


Robinson-Foulds supertrees.

Bansal MS, Burleigh JG, Eulenstein O, Fernández-Baca D.

Algorithms Mol Biol. 2010 Feb 24;5:18. doi: 10.1186/1748-7188-5-18.


Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots.

Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE.

Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4623-8. doi: 10.1073/pnas.0907801107. Epub 2010 Feb 22.


Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants.

Burleigh JG, Bansal MS, Wehe A, Eulenstein O.

J Comput Biol. 2009 Aug;16(8):1071-83. doi: 10.1089/cmb.2009.0139.


Surviving the K-T mass extinction: new perspectives of polyploidization in angiosperms.

Soltis DE, Burleigh JG.

Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5455-6. doi: 10.1073/pnas.0901994106. Epub 2009 Mar 31. No abstract available.


Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms.

Burleigh JG, Hilu KW, Soltis DE.

BMC Evol Biol. 2009 Mar 17;9:61. doi: 10.1186/1471-2148-9-61.


Triplet supertree heuristics for the tree of life.

Lin HT, Burleigh JG, Eulenstein O.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S8. doi: 10.1186/1471-2105-10-S1-S8.


Phylogenetic signal in matK vs. trnK: a case study in early diverging eudicots (angiosperms).

Hilu KW, Black C, Diouf D, Burleigh JG.

Mol Phylogenet Evol. 2008 Sep;48(3):1120-30. doi: 10.1016/j.ympev.2008.05.021. Epub 2008 May 27.


DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

Wehe A, Bansal MS, Burleigh JG, Eulenstein O.

Bioinformatics. 2008 Jul 1;24(13):1540-1. doi: 10.1093/bioinformatics/btn230. Epub 2008 May 12.


PhyloFinder: an intelligent search engine for phylogenetic tree databases.

Chen D, Burleigh JG, Bansal MS, Fernández-Baca D.

BMC Evol Biol. 2008 Mar 21;8:90. doi: 10.1186/1471-2148-8-90.

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