Research · Publications · Software · People · Journal Club

2009

• A Simulation Study Comparing Supertree and Combined Analysis Methods using SMIDGen
  WABI '09: Swenson, Barbançon, Linder, & Warnow


• The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation
  TCBB '09: Wang, Leebens-Mack, Wall, Beckmann, dePamphilis, & Warnow


• Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees
  Science '09: Liu, Raghavan, Nelesen, Linder, & Warnow


• Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy
  TCBB '09: Liu, Nelesen, Raghavan, Linder, & Warnow

2008

• Tutorial on Computational Linguistic Phylogeny
  LLC '08: Nichols & Warnow


• Linguistic History and Computational Cladistics
  Origin and Evolution of Languages: Approaches, Models, Paradigms (B. Laks, editor): Ringe & Warnow


• Short Quartet Puzzling: A New Quartet-based Phylogeny Reconstruction Algorithm
  J. Comp. Biol. '08: Snir, Warnow, & Rao


• The effect of the guide tree on multiple sequence alignment and subsequent phylogenetic analyses
  PSB '08: Nelesen, Liu, Zhao, Linder, & Warnow

2007

• An experimental study comparing linguistic phylogenetic reconstruction methods
  LGC '07: Barbançon, Warnow, Ringe, Evans, & Nakhleh

2006

• Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)
  OMICS '06: Leebens-Mack, Vision, Brenner, Bowers, Cannon, Clement, Cunningham, dePamphilis, deSalle, Doyle, Eisen, Gu,
  Harshman, Jansen, Kellogg, Koonin, Mishler, Philippe, Pires, Qiu, Rhee, Sjölander, Soltis, Soltis, Stevenson, Wall, Warnow, & Zmasek


• Pattern Identification in Biogeography
  TCBB '06: Ganapathy, Goodson, Jansen, Le, Ramachandran, & Warnow


• Distance-based Genome Rearrangement Phylogeny
  J. Mol. Evol. '06: Wang, Jansen, Moret, Raubeson, & Warnow


• Reconstructing Chromosomal Evolution
  SIAM J. Computing '06: Wang & Warnow

2005

• Pattern identification in biogeography: metrics and algorithms for comparing area cladograms
  WABI '05: Ganapathy, Goodson, Jansen, Ramachandran, & Warnow


• An overview of phylogeny reconstruction
  Handbook of Computational Molecular Biology (S. Aluru, editor): Linder & Warnow


• Large-scale Phylogenetic Analysis
  Handbook of Computational Molecular Biology (S. Aluru, editor): Warnow


• Inference of divergence times as a statistical inverse problem
  Phylogenetic Methods and the Prehistory of Languages (Forster & Renfrew, editors): Evans, Ringe, & Warnow


• A stochastic model of language evolution that incorporates homoplasy and borrowing
  Phylogenetic Methods and the Prehistory of Languages (Forster & Renfrew, editors): Warnow, Evans, Ringe, & Nakhleh


• Reconstructing reticulate evolution in species - theory and practice
  J. Comp. Biol. '05: Nakhleh, Warnow, Linder, & St. John


• Advances in phylogeny reconstruction from gene order and content data
  Molecular Evolution: Producing the Biochemical Data, Part B (Zimmer & Roalson, editors): Moret & Warnow


• A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset
  TPS '05: Nakhleh, Warnow, Ringe, & Evans


• Unidentifiable divergence times in rates-across-sites models
  TCBB '05: Evans & Warnow


• Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages
  JLSA '05: Nakhleh, Ringe, & Warnow


• Reconstructing phylogenies from gene-content and gene-order data
  Mathematics of Evolution and Phylogeny (O. Gascuel, editor): Moret, Tang, & Warnow


• Distance-based genome rearrangement phylogeny
  Mathematics of Evolution and Phylogeny (O. Gascuel, editor): Wang & Warnow

2004

• Phylogenetic networks: modeling, reconstructibility, and accuracy
  TCBB '04: Moret, Nakhleh, Warnow, Linder, Tholse, Padolina, Sun, & Timme


• Rec-I-DCM3: A fast algorithmic technique for reconstructing large phylogenetic trees
  CSB '04: Roshan, Moret, Warnow, & Williams


• Reconstructing reticulate evolution in species - theory and practice
  RECOMB '04: Nakhleh, Warnow, & Linder


• On Contract-and-Refine-Transformations Between Phylogenetic Trees
  SODA '04: Ganapathy, Ramachandran, & Warnow


• Performance of supertree methods on various dataset decompositions
  Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life (O.R.P. Bininda-Emonds, editor): Roshan, Moret, Williams, & Warnow

pre-2004