Publications
In Press
  • MdS Bayzid, T Hunt, and T Warnow (2014) Disk covering methods improve phylogenomic analyses. To appear in BMC Genomics and Proceedings of RECOMB-CG (Comparative Genomics).
  • T Zimmermann, S Mirarab, and T Warnow (2014) BBCA: Improving the scalability of *BEAST using random binning. To appear in BMC Genomics and Proceedings of RECOMB-CG (Comparative Genomics).
2014
  • K Liu, J Dai, K Truong, Y Song, MH Kohn, and L Nakhleh (2014) An HMM-based comparative genomic framework for detecting introgression in eukaryotes. PLoS Computational Biology 10(6):e1003649. [PDF]
  • S Mirarab, N Nguyen, and T Warnow (2014) PASTA: ultra-large multiple sequence alignment. Proceedings RECOMB 2014. [Full Text]
  • S Mirarab, R Reaz, MdS Bayzid, T Zimmermann, MS Swenson, and T Warnow (2014) ASTRAL: Genome-Scale Coalescent-Based Species Tree Estimation. Bioinformatics 30(17):i541-i548. [PDF]
  • S Mirarab, MdS Bayzid and T Warnow (2014) Evaluating summary methods for multi-locus species tree estimation in the presence of incomplete lineage sorting. Systematic Biology doi: 10.1093/sysbio/syu063. [PDF]
  • CV Than and N Rosenberg (2014) Mean deep coalescence cost under exchangeable probability distributions. Discrete Applied Mathematics 174:11-26 [PDF]
  • M DeGiorgio, J Syring, AJ Eckert, AI Liston, R Cronn, DB Neale, and NA Rosenberg (2014) An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines. BMC Evolutionary Biology 14:67 [PDF]
  • EM Jewett and N Rosenberg (2014) Theory and applications of a deterministic approximation to the coalescent model. Theoretical Population Biology 93:14-29 [PDF]
2013
  • L Nakhleh (2013) Computational approaches to species phylogeny inference and gene tree reconciliation. Trends in Ecology and Evolution 28(12):719-728. [PDF]
  • Y Yu, N Ristic, and L Nakhleh (2013) Fast Algorithms and Heuristics for Phylogenomics under ILS and Hybridization. BMC Bioinformatics 14(15):S6. [PDF]
  • Y Yu, RM Barnett, and L Nakhleh (2013) Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting. Systematic Biology 62(5):738-751. [PDF]
  • MS Bayzid and T Warnow (2013) Naive binning improves phylogenomic analyses. Bioinformatics 29:2277-2284. [PDF]
  • MS Bayzid, S. Mirarab, and T Warnow (2013) Inferring optimal species trees under gene duplication and loss. Pacific Symposium on Biocomputing 18:250-261. [PDF]
  • NA Rosenberg (2013) Coalescent histories for caterpillar-like families. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10:1253-1262 [PDF]
  • NA Rosenberg (2013) Discordance of species trees with their most likely gene trees: a unifying principle. Molecular Biology and Evolution 30:2709-2713 [PDF]
  • CV Than and N Rosenberg (2013) Mathematical properties of the deep coalescence cost. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10:61-72 [PDF]
  • NM Kopelman, L Stone, O Gascuel, and L Nakhleh (2013) The behavior of admixed populations in neighbor-joining inference of population trees. Pacific Symposium on Biocomputing 18:263-274 [PDF]
2012
  • HJ Park and L Nakhleh (2012) Inference of Reticulate Evolutionary Histories by Maximum Likelihood: The Performance of Information Criteria. BMC Bioinformatics 13(S19):S12. [PDF]
  • HJ Park and L Nakhleh (2012) MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees. The 8th International Symposium on Bioinformatics Research and Applications (ISBRA) [PDF]
  • JH Degnan, NA Rosenberg, and T Stadler (2012) A characterization of the set of species trees that produce anomalous ranked gene trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9: 1558-156. [Abstract].
  • EO Buzbas (2012) On the article titled "Estimating species trees using approximate Bayesian computation" (Fan and Kubatko, Molecular Phylogenetics and Evolution 59:354-363). Phylogenetics and Evolution 65: 1014-1016. [Full Text]
  • T Warnow (2012) Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent. PLoS Currents Tree of Life doi: 10.1371/currents.RRN1308. [Full Text]
  • N Nguyen, S Mirarab, and T Warnow (2012) MRL and SuperFine+MRL: new supertree methods. Algorithms for Molecular Biology 7:3. [Full Text]
  • DT Neves, T Warnow, JL Sobral, and K Pingali. (2012) Parallelizing SuperFine. 27th Symposium on Applied Computing (ACM-SAC), Bioinformatics. [Full Text]
  • LJ Helmkmap, EM Jewett and NA Rosenberg (2012) Improvements to a class of distance matrix methods for inferring species trees from gene trees. Journal of Computational Biology 19: 632-649. [Full Text]
  • MdS Bayzid and T Warnow (2012) Estimating optimal species trees from incomplete gene trees under deep coalescence. Journal of Computational Biology 19: 591-605. [Full Text]
  • Y Yu, JH Degnan, and L Nakhleh (2012) The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. PLoS Genetics 8: e1002660. [Full Text].
  • EM Jewett and NA Rosenberg (2012) iGLASS: an improvement to the GLASS method for estimating species trees from gene trees. Journal of Computational Biology 19: 293-315. [Full Text]
  • JH Degnan, NA Rosenberg, and T Stadler (2012) The probability distribution of ranked gene trees on a species tree. Mathematical Biosciences 235:45-55. [Abstract].
2011
  • J Yang and T Warnow (2011) Fast and accurate methods for phylogenomic analyses. BMC Bioinformatics 12(Suppl 9): S4. [PDF]
  • Y Yu, T Warnow, and L Nakhleh (2011) Algorithms for MDC-based Multi-locus Phylogeny Inference: beyond rooted binary gene trees on single alleles. Journal of Computational Biology18: 1543-1559. [PDF]
  • CV Than, NA Rosenberg (2011) Consistency properties of species tree inference by minimizing deep coalescences. Journal of Computational Biology 18: 1-15. [PDF]
Last updated 9/3/2014