1. S. Kannan and T. Warnow, 1992. Triangulating Three-Colored Graphs, SIAM J. on Discrete Mathematics, Vol. 5 No. 2, pp. 249-258. (A preliminary version appeared in the Proceedings of the ACM/SIAM Symposium on Discrete Algorithms, 1991.)

2. H. Bodlaender, M. Fellows, and T. Warnow, 1992. Two strikes against perfect phylogeny, Proceedings, International Colloquium on Automata, Languages and Programming. Springer Verlag Lecture Notes in Computer Science, volume 623. pp. 273-283.

3. M. Steel and T. Warnow, 1993. Kaikoura Tree Theorems: The Maximum Agreement Subtree Problem. Information Processing Letters, 48, pp. 77-82.

4. T. Warnow, 1993. Constructing phylogenetic trees efficiently using compatibility criteria. New Zealand Journal of Botany, 31:3, pp. 239-248, DOI:10.1080/0028825X.1993.10419501. (PDF)

5. S. Kannan and T. Warnow, 1994. Inferring Evolutionary History from DNA Sequences. SIAM J. on Computing, Vol. 23, No. 4, pp. 713-737. (A preliminary version of this paper appeared at FOCS 1990.)

6. T. Warnow, 1994. Tree Compatibility and Inferring Evolutionary History. Journal of Algorithms, 16, pp. 388-407. (A preliminary version of this paper appeared at SODA 1993.)

7. F.R. McMorris, T. Warnow, and T. Wimer, 1994. Triangulating Vertex Colored Graphs. SIAM J. on Discrete Mathematics, Vol. 7, No. 2, pp. 296-306. (A preliminary version of this paper appeared at SODA 1993.)

8. M. Farach, S. Kannan, and T. Warnow, 1995. A robust model for finding optimal evolutionary trees. Algorithmica, special issue on Computational Biology, Vol. 13, No. 1, pp. 155-179. (A preliminary version of this paper appeared at the Symposium on the Theory of Computing (STOC) 1993.)

9. S. Kannan and T. Warnow, 1995. Tree Reconstruction from Partial Orders. SIAM J. on Computing, Vol. 24 No. 3, pp. 511-520. (A preliminary version of this paper appeared in the Workshop on Algorithms and Data Structures, 1993.)

10. A. Taylor, D. Ringe, and T. Warnow. Character-based reconstruction of a linguistic cladogram. Proceedings of the 12th International Conference on Historical Linguistics (Manchester, August 1995).

11. T. Warnow, D. Ringe, and A. Taylor. Reconstructing the evolutionary history of natural languages. Association for Computing Machinery and the Society of Industrial and Applied Mathematics, Proceedings of ACM-SIAM Symposium on Discrete Algorithms (SODA), 1996, pp. 314-322.

12. C.A. Phillips and T. Warnow, 1996. The Asymmetric Median Tree: a new model for building consensus trees. Discrete Applied Mathematics, Special Issue on Computational Molecular Biology, 71, pp. 311-335, 1996. (PDF)

13. L.A. Goldberg, P.W. Goldberg, C.A. Phillips, E. Sweedyk, and T. Warnow, 1996. Minimizing phylogenetic number to find good evolutionary trees. Discrete Applied Mathematics, Volume 71, Numbers 1-3, pp. 111-136. (A preliminary version of this paper appeared in Combinatorial Pattern Matching 1995.)

14. C. Benham, S. Kannan, M. Paterson, and T. Warnow, 1996. Hen's Teeth and Whale's Feet: Generalized Character Compatibility. Journal of Computational Biology. Vol 2. No 4. pp 527-536. (A preliminary version of this appeared in Combinatorial Pattern Matching, 1995.)

15. S. Kannan, E. Lawler, and T. Warnow, 1996. Determining the Evolutionary Tree, Journal of Algorithms, 21(1): 26-50. (A preliminary version of this paper appeared at SODA 1990.)

16.
D. Ringe, T. Warnow, A. Taylor, A. Michailov, and L. Levison, 1997. Computational
cladistics and the position of Tocharian. __I__n V. Mair (Ed.), *The
Bronze Age and Early Iron Age Peoples of Eastern Central Asia*, a special
volume of the Journal of Indoeuropean Studies.

17. P.L. Erdos, M. Steel, L. Szekely, and T. Warnow, 1997. Local quartet splits of a binary tree infer all quartet splits via one dyadic inference rule. Computers and Artificial Intelligence, Number 2, Vol 16, pp. 217-227. (PDF)

18. T. Warnow, 1997. Mathematical approaches to comparative linguistics. Proceedings of the National Academy of Sciences, Vol. 94, pp. 6585-6590, 1997. (PDF)

19. S. Kannan and T. Warnow, 1997. A fast algorithm for the computation and enumeration of perfect phylogenies when the number of character states is fixed. SIAM J. Computing, Vol. 26, No. 6, pp. 1749-1763. (A preliminary version appeared in the proceedings of the ACM/SIAM Symposium on Discrete Algorithms, 1995.)

20. K. Rice and T. Warnow, Parsimony is Hard to Beat!, Proceedings, Third Annual International Conference of Computing and Combinatorics (COCOON), Shanghai, China, 1997, pp. 124-133. T. Jiang and D.T. Lee, Eds.

21. P. L. Erdos, M. Steel, L. Szekeley, and T. Warnow. Inferring big trees from short sequences. Proceedings of International Congress on Automata, Languages, and Programming 1997. Bologna, Italy. (This paper also appears as DIMACS Technical Report 97-71.)

22. D. Huson, S. Nettles, L. Parida, T. Warnow, and S. Yooseph. The Disk-Covering Method for Tree Reconstruction. In R. Battiti and A.A. Bertossi, editors, Proceedings of "Algorithms and Experiments" (ALEX'98), pages 62-75. 1998. Trento, Italy, Feb. 9-11, 1998. (PDF)

23. M. Bonet, M. Steel, T. Warnow, and S. Yooseph. Faster algorithms for solving parsimony and compatibility. The Journal of Computational Biology, Vol. 5, No. 3, pp. 409-422, 1998. By invitation, for the special issue on selected papers from RECOMB 1998.

24. S. Kannan, T. Warnow, and S. Yooseph, 1998. Computing the local consensus of trees. SIAM J. Computing, vol. 27, no. 6, pp. 1695-1724, 1998. (A preliminary version appeared in the Association for Computing Machinery and the Society of Industrial Applied Mathematics, Proceedings, ACM/SIAM Symposium on Discrete Algorithms, 1995, pp. 68-77.)

25. Huson, D. K. A. Smith and T. Warnow. 1999. "Correcting Large Distances for Phylogenetic Reconstruction." Proceedings, 3rd Workshop on Algorithms Engineering (WAE), London, England, 1999, pp. 273-286.

26. T. Warnow. Some combinatorial problems in phylogenetics. Invited paper, Proceedings of the International Colloquium on Combinatorics and Graph Theory, Balatonlelle, Hungary, July 15-20, 1996, Volume 7 of Bolyai Society Mathematical Studies, Budapest, pp. 363-413. Eds. A. Gyárfás, L. Lovász, L.A. Székely. (PDF)

27. P.L. Erdos, M. Steel, L. Székély, and T. Warnow, 1999. A few logs suffice to build almost all trees - I. Random Structures and Algorithms, 14 (2): 153-184.

28. P.L. Erdos, M. Steel, L. Székély, and T. Warnow. A few logs suffice to build almost all trees - II. Theoretical Computer Science, 221, pp. 77-118, 1999 (by invitation, special issue of selected papers from ICALP 1997.) (Also appears as DIMACS Technical Report 97-72.) (pdf)

29. M. Bonet, C.A. Phillips, T. Warnow, and S. Yooseph, 1999. Constructing evolutionary trees in the presence of polymorphic characters. SIAM J. Computing, Vol. 29. No. 1, pp. 103-131. (A preliminary version appeared in the ACM Symposium on the Theory of Computing, 1996.)

30. M. Henzinger, V. King, and T. Warnow, 1999. Constructing a tree from homeomorphic subtrees, with applications to computational molecular biology. Algorithmica, 24(1): 1-13 (1999). (A preliminary version appeared in the Association for Computing Machinery and the Society of Industrial and Applied Mathematics, Proceedings, ACM/SIAM Symposium on Discrete Algorithms, 1996, pp. 333-340.)

31. D. Huson, S. Nettles, and T. Warnow. Disk-Covering, a fast converging method for phylogenetic tree reconstruction. Special issue of the Journal of Computational Biology for selected papers from RECOMB 1999, Vol. 6, No. 3, 1999, pp. 369-386. (This appeared in a preliminary form in the Proceedings of RECOMB 1999, as Obtaining highly accurate topology estimates of evolutionary trees from very short sequences. Lyon, France.) (PDF)

32. D. Huson, S. Nettles, K. Rice, T. Warnow, and S. Yooseph. The Hybrid tree reconstruction method. The Journal of Experimental Algorithmics, Volume 4, Article 5, 1999. Special issue for selected papers from The Workshop on Algorithms Engineering, Saarbrucken, Germany, 1998. (pdf).

33. D. Huson, L. Vawter, and T. Warnow. 1999. Solving large scale phylogenetic problems using DCM-2. Proceedings of ISMB (Intelligent Systems for Molecular Biology), (ISMB), Saarbrucken, 1999.

34. J. Kim and T. Warnow. 1999. Tutorial on Phylogenetic Tree Estimation. Intelligent Systems for Molecular Biology, Heidelberg 1999. (PS) (PDF)

35. M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L.-S. Wang, T. Warnow, and S. Wyman. 2000. "A new fast heuristic for computing the breakpoint phylogeny and a phylogenetic analysis of a group of highly rearranged chloroplast genomes." Proceedings of Intelligent Systems for Molecular Biology (ISMB), August 2000. (PS)

36. M. E. Cosner, R. K. Jansen, B.M.E. Moret, L.A. Raubeson, L.-S. Wang, T. Warnow, and S. Wyman, 2000. "An empirical comparison between BPAnalysis and MPBE on the Campanulaceae chloroplast dataset." In Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, D. Sankoff and J. Nadeau, eds., Kluwer Academic, Dordrecht (2000), 99--121. (PS)

37. H.L. Bodlaender, M.R. Fellows, Michael T. Hallett, H. Todd Wareham, and T. Warnow. 2000. The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs, Theoretical Computer Science 244 (2000) 167-188.

38. K. St. John, T. Warnow, B.M.E. Moret, and L. Vawter. 2001. "Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining". Proceedings SODA 2001. An extended version of this paper appears in paper #61 (below), J. Algorithms 48 (2003), 173-193.

39. G. Ganapathy, and T. Warnow, 2001. "Finding the Maximum Compatible Tree for a Bounded Number of Trees with Bounded Degree is Solvable in Polynomial Time." In Proceedings of the First International Workshop on Algorithms and Bioinformatics (WABI), 2001, pp. 156-163, Springer Verlag, Olivier Gascuel and Bernard M.E. Moret, eds. (PS.)

40. T. Warnow, B.M.E. Moret, and K. St. John. 2001. Absolute Convergence: True Trees From Short Sequences. ACM-SIAM Symposium on Discrete Algorithms (SODA) 2001. (PS)

41. L.-S. Wang and T. Warnow. 2001. "Estimating true evolutionary distances between genomes." Proceedings, Symposium on the Theory of Computing (STOC), 2001, pp. 637-646. (PDF).

42. B.M.E. Moret, S. Wyman, D.A. Bader, T. Warnow, and M. Yan, 2001. "A new implementation and detailed study of breakpoint analysis," Proc. 6th Pacific Symp. on Biocomputing (PSB 2001), Hawaii, World Scientific Pub. (2001), 583-594. (pdf)

43. B.M.E. Moret, L.-S. Wang, T. Warnow, and S.K. Wyman, 2001. "New approaches for reconstructing phylogenies based on gene order,'' 9th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB 2001), Copenhagen, in Bioinformatics 17, Suppl. 1, (2001), pp. S165-S173; chosen as one of the 5 best papers at the conference. (pdf)

44. L. Nakhleh, K. St. John, U. Roshan, J. Sun, and T. Warnow, 2001. "Designing fast converging phylogenetic methods." 9th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB 2001), Copenhagen, in Bioinformatics 17, Suppl. 1, (2001), pp. S190-S198. (pdf)

45. L. Nakhleh, U. Roshan, K. St. John, J. Sun, and T. Warnow, 2001. "The performance of phylogenetic methods on trees of bounded diameter." Proceedings, The First International Workshop on Algorithms in Bioinformatics (WABI), 2001, Lecture Notes in Computer Science (LNCS #2149) pp. 214-226, Springer Verlag, Olivier Gascuel and Bernard M.E. Moret, eds. (pdf)

46. B.M.E. Moret, D.A. Bader, and T. Warnow, 2001. "High-performance algorithmic engineering for computational phylogenetics,'' Proc. 2001 Int'l Conf. Computational Science (ICCS 2001), San Francisco (2001), Lecture Notes in Computer Science 2073-2074, Springer Verlag. (pdf)

47. D. Ringe, T. Warnow, and A. Taylor, 2002. "Indo-European and Computational Cladistics", Transactions of the Philological Society, Volume 100: Issue 1, March 2002, pp. 59-129. (PDF)

48. L. Nakhleh, B. M. E. Moret, U. Roshan, K. St. John, J. Sun, and T. Warnow, 2002. "The accuracy of fast phylogenetic methods for large datasets", Proc. 7th Pacific Symposium on BioComputing (PSB02), Kauai, USA (2002), World Scientific Pub, 211-222. (PS) (PDF)

49. G. Ganapathy, and T. Warnow 2002. Approximating the Complement of the Maximum Compatible Subset of Leaves of k Trees. In Proceedings of the Fifth International Workshop on Approximation Algorithms for Combinatorial Optimization, pages 122--134, 2002. (PS.)

50. L.-S. Wang, R. Jansen, B. Moret, L. Raubeson, and T. Warnow, 2002. "Fast Phylogenetic Methods For Genome Rearrangement Evolution: An Empirical Study," Proc. 7th Pacific Symp. on Biocomputing (PSB 2002), Hawaii, World Scientific Pub. (2002), 524-535. (PS)

51. B.M.E. Moret, D.A. Bader, and T. Warnow, 2002. "High-performance algorithm engineering for computational phylogenetics,'' J. Supercomputing (22), 99--111, special issue on best papers from ICCS'01. (PS)

52. B.M.E. Moret, U. Roshan, and T. Warnow, 2002. "Sequence length requirements for phylogenetic methods," Proc. 2nd International Workshop on Algorithms in Bioinformatics (WABI'02), Rome (2002), Lecture Notes in Computer Science (LNCS #2452), pp. 343-356, Springer Verlag, Roderic Guigo and Dan Gusfield, eds (pdf)

53. L. Nakhleh, U. Roshan, L. Vawter, and T. Warnow, 2002. "Estimating the deviation from a molecular clock", Proc. 2nd International Workshop on Algorithms in BioInformatics (WABI02), Rome, Italy (2002), Lecture Notes in Computer Science 2452, 287-299, Springer Verlag, R. Guido and D. Gusfield, eds. (pdf)

54. B.M.E. Moret, J. Tang, L.-S. Wang, and T. Warnow, 2002. "Steps toward accurate reconstruction of phylogenies from gene-order data,'' J. Comput. Syst. Sci. (invited, special issue on computational biology), 65, 3 (2002), 508-525. (PS)

55. C. Stockham, L.-S. Wang, and T. Warnow, 2002. "Statistically-Based Postprocessing of Phylogenetic Analysis Using Clustering," Bioinformatics, Vol. 18, Suppl. 1, special issue for the Proceedings of 10th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB'02). Edmonton, Canada, pp. S285--S293. (PDF)

56. B.M.E. Moret, L.-S. Wang, and T. Warnow, 2002. "Towards New Software for Computational Phylogenetics," IEEE Computer 35, 7 (July 2002), Special issue on Bioinformatics, pp. 55-64. (PDF)

57. B.M.E. Moret, and T. Warnow, 2002. "Reconstructing optimal phylogenetic trees: A challenge in experimental algorithmics," Lecture Notes in Computer Science 2547, Springer Verlag, 2002, 163-180 (2002). (PDF)

58. L. Nakhleh, J. Sun, T. Warnow, C.R. Linder, B.M.E. Moret and A. Tholse, 2003. "Towards the development of computational tools for evaluating phylogenetic network reconstruction methods," Proc. 8th Pacific Symp. on Biocomputing (PSB 2003), January 2003. (PDF)

59. M. Spencer, B. Bordalejo, L.-S. Wang, A. C. Barbrook, L. R. Mooney, P. Robinson, T. Warnow and C. J. Howe. 2003. "Gene Order Analysis Reveals the History of The Canterbury Tales Manuscripts." Computers and the Humanities, 37 (1): 97-109. Feb. 2003. Kluwer Academic Pub.

60. G. Ganapathy, V. Ramachandran, and T. Warnow. 2003. "Better Hill-Climbing Seaches for Parsimony." In Proceedings of the Third International Workshop on Algorithms in Bioinformatics (WABI 2003), pages 245--258, 2003.

61. K. St. John, T. Warnow, B.M.E. Moret, and L. Vawter. 2003. "Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining". J. of Algorithms, 48, 1 (2003), 173-193. Special issue on the best papers from SODA 2001. (PDF)

62. U. Roshan, B. M. E. Moret, T. L. Williams, and T. Warnow. 2004. "Performance of supertree methods on various dataset decompositions". In O. R. P. Bininda-Emonds, editor, Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, Volume 3 of Computational Biology, pages 301-328, Kluwer Academics, 2004 (Andreas Dress, series editor). (PS)

63. G. Ganapathy, V. Ramachandran, and T. Warnow. 2004. "On Contract-and-Refine-Transformations Between Phylogenetic Trees." In Proceedings of the Fifteenth ACM-SIAM Symposium on Discrete Algorithms (SODA), 2004. (SODA 2004.)

64. L. Nakhleh, T. Warnow, and C. R. Linder 2004. "Reconstructing reticulate evolution in species - theory and practice." Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004), pp 337-346. (Also submitted, by special invitation, to the Journal of Computational Biology, for selected papers from RECOMB 2004.) (J. Computational Biology and RECOMB 2004)

65. U. Roshan, B.M.E. Moret, T.L. Williams, and T. Warnow, "Rec-I-DCM3: A fast algorithmic technique for reconstructing large phylogenetic trees," Proc. IEEE Computer Society Bioinformatics Conference CSB 2004, Stanford U., 2004. (PDF)

66. B.M.E. Moret, L. Nakhleh, T. Warnow, C.R. Linder, A. Tholse, A. Padolina, J. Sun, and R. Timme, "Phylogenetic networks: modeling, reconstructibility, and accuracy," IEEE/ACM Transactions on Computational Biology and Biocomputing, 1(1):13-23, 2004. (PDF)

67. S.N. Evans, and Tandy Warnow, "Unidentifiable divergence times in rates-across-sites models." IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1, pp. 130-134. 2005. (PDF)

68. L.-S. Wang and T. Warnow. "Distance-based genome rearrangement phylogeny." In Mathematics of Evolution and Phylogeny, O. Gascuel, ed., Oxford Univ. Press, 2005. (PDF)

69. B.M.E. Moret, J. Tang, and T. Warnow. "Reconstructing phylogenies from gene-content and gene-order data." In Mathematics of Evolution and Phylogeny, pp. 321-352, O. Gascuel, ed., Oxford Univ. Press. (PDF)

70. B.M.E. Moret and T. Warnow, "Advances in phylogeny reconstruction from gene order and content data," in Molecular Evolution: Producing the Biochemical Data, Part B, E.A. Zimmer and E.H. Roalson, eds., Vol. 395 of Methods in Enzymology, Elsevier (to appear April 2005). (PDF)

71. L. Nakhleh, D. Ringe, and T. Warnow, "Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages." Language (Journal of the Linguistic Society of America), 81(2):382-420, 2005. (PDF)

72. L. Nakhleh, T. Warnow, C. R. Linder, and K. St. John. 2005. "Reconstructing reticulate evolution in species - theory and practice." The Journal of Computational Biology, 12(6-7), 796-811, 2005; special issue for selected papers from RECOMB 2004. (PDF)

73. L. Nakhleh, T. Warnow, D. Ringe, and S.N. Evans, "A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset." The Transactions of the Philological Society, 103(2): 171-192, 2005. (PDF)

74. G. Ganapathy, G., B. Goodson, R. Jansen, V. Ramachandran, and T. Warnow, 2005. "Pattern identification in biogeography: metrics and algorithms for comparing area cladograms." Proceedings of the Fifth International Workshop on Algorithms for Bioinformatics (WABI), pp. 116-127, 2005. (PDF).

75. T. Warnow, 2005. "Large-scale phylogenetic reconstruction." Book chapter, in S. Aluru (editor), Handbook of Computational Biology, Chapman & Hall, CRC Computer and Information Science Series, 2005. (PDF)

76. C.R. Linder, and T. Warnow, 2005. "Overview of phylogeny reconstruction." Book chapter, in S. Aluru (editor), Handbook of Computational Biology, Chapman & Hall, CRC Computer and Information Science Series, 2005. (PDF)

77. S.N. Evans, Don Ringe, and Tandy Warnow, "Inference of divergence times as a statistical inverse problem." Invited paper, Phylogenetic Methods and the Prehistory of Languages, MacDonald Institute Press, University of Cambridge (PDF), 2006.

78. T. Warnow, S.N. Evans, D. Ringe, and L. Nakhleh, "A stochastic model of language evolution that incorporates homoplasy and borrowing." Invited paper, Phylogenetic Methods and the Prehistory of Languages, MacDonald Institute Press, University of Cambridge (PDF), 2006.

79. L.-S. Wang and T. Warnow, 2006. "Reconstructing Chromosomal Evolution." SIAM J. Computing, Vol. 36, Issue 2, 99-131, 2006.

80. L.-S. Wang, T. Warnow, B.M.E. Moret, R.K. Jansen, and L.A. Raubeson, 2006. "Distance-based Genome Rearrangement Phylogeny." Journal of Molecular Evolution, 63(4):473-83, 2006. (PDF)

81. G. Ganapathy, Goodson B., Jansen R., Le H., Ramachandran, V., and Warnow, T., "Pattern Identification in Biogeography". IEEE/ACM Transactions on Computational Biology and Bioinformatics, (IEEE-TCBB), Vol 3, No. 4, pp. 334-346, 2006

82. J.H. Leebens-Mack, T. Vision, E. Brenner, J.E. Bowers, S. Cannon, M.J. Clement, C.W. Cunningham, C. dePamphilis, R. Desalle, J.J. Doyle, J.A. Eisen, X. Gu, J. Harshman, R.K. Jansen, E.A. Kellogg, E.V. Koonin, B.D. Mishler, H. Philippe, J.C. Pires, Y-L. Qiu, S.Y. Rhee, K. Sjolander, D.E. Soltis, P.S. Soltis, D.W. Stevenson, K. Wall, T. Warnow, C. Zmasek. 2006. "Taking the First Steps towards a Standard for Reporting on Phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)." OMICS 10(2):231-237, 2006.

83. Nelesen, S., K. Liu, D. Zhao, R. Linder, and T. Warnow, 2008. "The effect of the guide tree on multiple sequence alignment and subsequent phylogenetic analyses", Proceedings of the 2008 Pacific Symposium on Biocomputing PSB online. (PSB 2008), pages 25-36.

84. S. Snir, T. Warnow and S. Rao, "Short Quartet Puzzling: A New Quartet-based Phylogeny Reconstruction Algorithm". Journal of Computational Biology, Vol. 15, No. 1, January 2008, pp. 91-103.

85. D. Ringe and T. Warnow. "Linguistic History and Computational Cladistics", book chapter in Origin and Evolution of Languages: Approaches, Models, Paradigms. Edited by Bernard Laks. Equinox Publishing. March, 2008.

86. Nichols, J. and T. Warnow, 2008. "Tutorial on computational linguistic phylogeny." Linguistics and Language Compass, Vol. 2, Issue 5, September 2008, pages 760-820.

88. Liu, K., S. Raghavan, S. Nelesen, C. R. Linder, T. Warnow, 2009. "Rapid and accurate largescale coestimation of sequence alignments and phylogenetic trees." Science, vol. 324, no. 5934, pp. 1561-1564, 19 June 2009, doi: 10.1126/science.1171243. (Corresponding author)

89. Swenson, M.S., F. Barbancon, R. Linder, and T. Warnow. "A simulation study comparing supertree and combined analysis methods using SMIDGen." Proceedings of WABI (Workshop on Algorithms for Bioinformatics) 2009.

90. Bradner, J.E., N. West, M.L. Grachan, E. Greenberg, S.J. Haggarty, T. Warnow and R. Mazitschek. "Chemical phylogenetics of histone deacetylases", 2010. Nature Chemical Biology, 6, pp. 238-243; published online 7 February 2010.

91. Swenson, M.S., F. Barbancon, C.R. Linder, and T. Warnow. "A simulation study comparing supertree and combined analysis methods using SMIDGen." Algorithms for Molecular Biology, 5:8 (4 January 2010), https://doi.org/10.1186/1748-7188-5-8, special issue of selected papers from WABI 2009.

92. Swenson, M.S., R. Suri, C.R. Linder and T. Warnow. "An experimental study of Quartets MaxCut and other supertree methods." Proceedings of Workshop on Algorithms for Bioinformatics (WABI 2010) 2010.

93. Linder, C.R., R. Suri, K. Liu, and T. Warnow. "Benchmark datasets and software for developing and testing methods for large-scale multiple sequence alignment and phylogenetic inference." PLoS Currents: Tree of Life, 2010 Nov 18 doi: 10.1371/currents.RRN1195.

94. Liu, K., C.R. Linder, and T. Warnow. "Multiple sequence alignment: a major challenge for large-scale phylogenetics." PLoS Currents: Tree of Life, 2010 Nov 18 doi:10.1371/currents.RRN1198.

95. Swenson, M.S., R. Suri, C.R. Linder, and T. Warnow. "An experimental study of Quartets MaxCut and other supertree methods." Journal of Algorithms for Molecular Biology 2011, 6(7), special issue of selected papers from WABI 2010.

96. L.-S. Wang, J. Leebens-Mack, P.K. Wall, K. Beckmann, C.W. dePamphilis, and T. Warnow. "The impact of multiple protein sequence alignment on phylogenetic estimation." IEEE Transactions on Computational Biology and Bioinformatics (IEEE-TCBB), Vol 8, pp. 1108-1119, 2011.

97. Yu, Y., T. Warnow, and L. Nakhleh. "Algorithms for MDC-based Multi-locus Phylogeny Inference." Proceedings of RECOMB 2011 (PDF). The full paper has additional results: ``Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles," J. Computational Biology November 2011, Vol. 18, No. 11, pp 1543-1559.

98. Yang, J. and T. Warnow "Fast and accurate methods for phylogenomic analyses." RECOMB Comparative Genomics 2011, and BMC Bioinformatics 12(Suppl 9): S4 (5 October 2011).

99. Mirarab, S. and T. Warnow. "FastSP: Linear-time calculation of alignment accuracy." Bioinformatics (2011) 27(23):3250-3258.

100. Liu, K., C. Randal Linder, and T. Warnow. "RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation" 2012. PLoS ONE 6(11): e27731. doi:10.1371/journal.pone.0027731

101. Liu, K., T.J. Warnow, M.T. Holder, S. Nelesen, J. Yu, A. Stamatakis, and C.R. Linder. "SATe-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees." Systematic Biology (2012) 61(1):90-106.

102. Swenson, M.S., R. Suri, C.R. Linder, and T. Warnow. "SuperFine: fast and accurate supertree estimation." Systematic Biology (2012) 61(2):214-227.

103. Mirarab, S., N. Nguyen, and T. Warnow. "SEPP: SATe-Enabled Phylogenetic Placement." Proceedings of the 2012 Pacific Symposium on Biocomputing (PSB 2012), 17:247-258.

104. D.T. Neves, T. Warnow, J. L. Sobral and K. Pingali. ``Parallelizing SuperFine." 27th Symposium on Applied Computing (ACM-SAC), Bioinformatics, 2012, pages 1361--1367, doi = 10.1145/2231936.2231992.

105. Md S. Bayzid and T. Warnow. "Estimating Optimal Species Trees from Incomplete Gene Trees under Deep Coalescence." Journal of Computational Biology, June 2012, Vol. 19, No. 6: 591-605, special issue for Simon Tavare and Michael Waterman. (HTML). (Corresponding author)

106. Nguyen, N., S. Mirarab, and T. Warnow. "MRL and SuperFine+MRL: new supertree methods." Journal Algorithms for Molecular Biology 7:3, 2012. (Corresponding author)

107. Liu, K. and T. Warnow. "Treelength optimization for phylogeny estimation." PLoS One, 7(3):e33104. doi:10.1371/journal.pone.0033104, 2012. (Corresponding author)

108. T. Warnow. "Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent." PLoS Currents: Tree of Life, 2012 March 12 doi:10.1371/currents.RRN1308. See also PMC.

109. Nelesen, S., K. Liu, L.-S. Wang, C. R. Linder, and T. Warnow. "DACTAL: divide-and-conquer trees (almost) without alignments." (html) Bioinformatics, Vol 28, Issue 12, pages i274-i282. (Corresponding author)

110. F. Barbancon, S. Evans, L. Nakhleh, D. Ringe, and T. Warnow. "An experimental study comparing linguistic phylogenetic reconstruction methods." Diachronica, 2013, 30(2):143-170, with supplementary materials. A preliminary version of this was presented at the conference Languages and Genes, organized by Bernard Comrie and held at UC Santa Barbara in 2007; this version is available as Technical Report 732, Department of Statistics, University of California at Berkeley. (Corresponding author)

111. Md S. Bayzid, S. Mirarab, and T. Warnow. "Inferring optimal species trees under gene duplication and loss." Pacific Symposium on Biocomputing, 18:250-261 (2013). (PDF). (Corresponding author)

112. Md S. Bayzid and T. Warnow. "Naive binning improves phylogenomic analyses". Bioinformatics 2013, vol. 29, no. 18, pages 2277-2284. (PDF), supplementary materials (Corresponding author)

113. T. Warnow. "Large-scale multiple sequence alignment and phylogeny estimation" Chapter 6 in "Models and Algorithms for Genome Evolution", edited by Cedric Chauve, Nadia El-Mabrouk and Eric Tannier, Springer series on "Computational Biology". For a preprint (not in final form) of this chapter, see this PDF,

114. S. Mirarab, N. Nguyen, and T. Warnow. "PASTA: ultra-large multiple sequence alignment". Proceedings RECOMB 2014 (PDF). Supplementary materials at figshare -- (PDF) (Corresponding author)

115. S. Mirarab, R. Reaz, Md S. Bayzid, T. Zimmermann, M.S. Swenson, and T. Warnow. "ASTRAL: Genome-Scale Coalescent-Based Species Tree Estimation." Proceedings, ECCB (European Conference on Computational Biology), 2014. Also, Bioinformatics 2014 30 (17): i541-i548. doi: 10.1093/bioinformatics/btu462. (PDF) (Corresponding author)

116. Md S. Bayzid, T. Hunt, and T. Warnow. "Disk Covering Methods Improve Phylogenomic Analyses". Proceedings of RECOMB-CG (Comparative Genomics), 2014, and BMC Genomics 2014, 15(Suppl 6): S7. (PDF) and Supplementary materials (Corresponding author)

117. T. Zimmermann, S. Mirarab and T. Warnow. "BBCA: Improving the scalability of *BEAST using random binning". Proceedings of RECOMB-CG (Comparative Genomics), 2014, and BMC Genomics 2014, 15(Suppl 6): S11. (PDF) and Supplementary materials. (Corresponding author)

118. S. Mirarab, Md S. Bayzid, and T. Warnow. "Evaluating summary methods for multi-locus species tree estimation in the presence of incomplete lineage sorting". Systematic Biology (2016) 65(3):366-380. doi = {10.1093/sysbio/syu063}, (First published online August 26, 2014.) (PDF) (Corresponding author)

119. N. Wickett, S. Mirarab, N. Nguyen, T. Warnow, et al. (37 authors). ``Phylotranscriptomic analysis of the origin and diversification of land plants." Proceedings of the National Academy of Sciences (PNAS), doi: 10.1073/pnas.1323926111. (PDF).

120. N. Nguyen, S. Mirarab, B. Liu, M. Pop, and T. Warnow "TIPP:Taxonomic Identification and Phylogenetic Profiling." Bioinformatics (2014) 30(24):3548-3555. HTML. (Corresponding author)

121. S. Mirarab, N. Nguyen, S. Guo, L.-S. Wang, J. Kim, and T. Warnow ``PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences." Journal of Computational Biology (2014), 22(5):377-386. (ahead of print). (Special issue for RECOMB 2014, expanded version of the RECOMB paper to include analyses of amino acid sequences.) Supplementary materials (PDF)

122. S. Mirarab, Md S. Bayzid, B. Boussau, and T. Warnow. "Statistical binning enables an accurate coalescent-based estimation of the avian tree". Science, 12 December 2014: 1250463. Science (Corresponding author)

123. E. D. Jarvis, S. Mirarab, A. J. Aberer, B. Li, P. Houde, C. Li, S. Y. W. Ho, B. C. Faircloth, B. Nabholz, J. T. Howard, A. Suh, C. C. Weber, R. R. da Fonseca, J. Li, F. Zhang, H. Li, L. Zhou, N. Narula, L. Liu, G. Ganapathy, B. Boussau, Md S. Bayzid, V. Zavidovych, S. Subramanian, T. Gabaldon, S. Capella-Gutierrez, J. Huerta-Cepas, B. Rekepalli, K. Munch, M. Schierup, B. Lindow, W. C. Warren, D. Ray, R. E. Green, M. W. Bruford, X. Zhan, A. Dixon, S. Li, N. Li, Y. Huang, E. P. Derryberry, M. F. Bertelsen, F. H. Sheldon, R. T. Brumfield, C. V. Mello, P. V. Lovell, M. Wirthlin, M. P. C. Schneider, F. Prosdocimi, J. A. Samaniego, A. M. V. Velazquez, A. Alfaro-Nunez, P. F. Campos, B. Petersen, T. Sicheritz-Ponten, A. Pas, T. Bailey, P. Scofield, M. Bunce, D. M. Lambert, Q. Zhou, P. Perelman, A. C. Driskell, B. Shapiro, Z. Xiong, Y. Zeng, S. Liu, Z. Li, B. Liu, K. Wu, J. Xiao, X. Yinqi, Q. Zheng, Y. Zhang, H. Yang, J. Wang, L. Smeds, F. E. Rheindt, M. Braun, J. Fjeldsa, L. Orlando, F. K. Barker, K. A. Jonsson, W. Johnson, K.-P. Koepfli, S. O'Brien, D. Haussler, O. A. Ryder, C. Rahbek, E. Willerslev, G. R. Graves, T. C. Glenn, J. McCormack, D. Burt, H. Ellegren, P. Alstrom, S. V. Edwards, A. Stamatakis, D. P. Mindell, J. Cracraft, E. L. Braun, T. Warnow, W. Jun, M. T. P. Gilbert, and G. Zhang. "Whole-genome analyses resolve early branches in the tree of life of modern birds." Science 12 December 2014: 1320-1331. (Co-corresponding author)

124. N. Matasci, L.-H. Hung, Z. Yan, E. Carpenter, N. J. Wickett, S. Mirarab, N. Nguyen, T. Warnow, S. Ayyampalayam, M. Barker, J. G. Burleigh, M. A. Gitzendanner, E. Wafula, J. P. Der, C. dePamphilis, B. Roure, H. Philippe, B. Ruhfel, N. Miles, S. Graham, S. Mathews, B. Surek, M. Melkonian, D. Soltis, P. Soltis, C. Rothfels, L. Pokorny, J. Shaw, L. DeGironimo, D. Stevenson, J. Villarreal, T. Chen, T. Kutchan, M. Rolf, R. Baucom, M. Deyholos, R. Samudrala, Z. Tian, X. Wu, X. Sun, Y. Zhang, J. Wang, J. Leebens-Mack, and G. K-S. Wang. Data access for the 1,000 Plants (1KP) project. GigaScience 2014 3:17, DOI: 10.1186/2047-217X-3-17. HTML. (Review)

125. N. Nguyen, S. Mirarab, K. Kumar, and T. Warnow,
"Ultra-large alignments using phylogeny aware profiles".
Proceedings RECOMB 2015 and
Genome Biology (2015) 16:124
doi: 10.1186/s13059-015-0688-z
**Highly accessed**
(PDF)
(html)

126. Md S. Bayzid, S. Mirarab, B. Boussau, and T. Warnow. "Weighted Statistical Binning: enabling statistically consistent genome-scale phylogenetic analyses", PLOS One, 2015, DOI: 10.1371/journal.pone.0129183. (html) (PDF)

127. S. Mirarab and T. Warnow. "ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes", Proceedings ISMB 2015, and Bioinformatics 2015 31 (12): i44-i52 doi: 10.1093/bioinformatics/btv234 (PDF)

128. S. Roch and T. Warnow. "On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods", Systematic Biology, 64(4):663-676, 2015, (PDF)

129. T. Warnow. "Concatenation analyses in the presence of incomplete lineage sorting", PLOS Currents: Tree of Life 2015 May 22. Edition 1. doi: 10.1371/currents.tol.8d41ac0f13d1abedf4c4a59f5d17b1f7 (HTML)

130. R. Davidson, P. Vachaspati, S. Mirarab, and T. Warnow. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. RECOMB-Comparative Genomics, and BMC Genomics, 2015, Preliminary version at (PDF), 2015, 16 (Suppl 10): S1.

131. J. Chou, A. Gupta, S. Yaduvanshi, R. Davidson, M. Nute, S. Mirarab and T. Warnow. A comparative study of SVDquartets and other coalescent-based species tree estimation methods. RECOMB-Comparative Genomics and BMC Genomics, 2015., 2015, 16 (Suppl 10): S2.

132. P. Vachaspati and T. Warnow. ASTRID: Accurate Species TRees from Internode Distances. RECOMB-Comparative Genomics and BMC Genomics, 2015, 16 (Suppl 10): S3.

133. J. Cracraft, P. Houde, S.Y.W. Ho, D.P. Mindell, J. Fjeldsa, B. Lindow, S.V. Edwards, C. Rahbek, S. Mirarab, T. Warnow, M.T.P. Gilbert, G. Zhang, E.L. Braun, and E.D. Jarvis. Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds". Science, 2015, volume 349, number 6255, doi = 10.1126/science.aab1578.

134. S. Mirarab, Md S. Bayzid, B. Boussau, and T. Warnow. Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree". Science, 2015, volume 350, number 6257, p. 171, DOI: 10.1126/science.aaa7719.

135. E.D. Jarvis, S. Mirarab, A.A. Aberer, B. Li, P. Houde, C. Li, S. Ho, B. Faircloth, B. Nabholz, J. T. Howard, A. Suh, C. C. Weber, R. R. da Fonseca, A. Alfaro-Nunez, N. Narula, L. Liu, D. Burt, H. Ellegren, S. Edwards, A. Stamatakis, D. Mindell, J. Cracraft, E. Braun, T. Warnow, W. Jun, M.T.P. Gilbert, G. Zhang, and The Avian Phylogenomics Consortium. Phylogenomic analyses data of the avian phylogenomics project. GigaScience 2015, 4:4, DOI:10.1186/s13742-014-0038-1. HTML. (Data Note)

136. J.E. Tarver, M. d. Reis, S. Mirarab, R. J. Moran, S. Parker, J.E. O'Reilly, B.L. King, M.J. O'Connell, R.J. Asher, T. Warnow, K. J. Peterson, P.C.J. Donoghue, and D. Pisani. The interrelationships of placental mammals and the limits of phylogenetic inference. Genome Biology and Evolution, doi:10.1093/gbe/evv261. (PDF).

137.
N. Nguyen, T. Warnow, M. Pop, and B. White.
A perspective on 16S rRNA operational taxonomic
unit clustering using sequence similarity.
npj Biofilms and Microbiomes **2**,
Article number 16004 (2016), doi:10.1038/npjbiofilms.2016.4.
(HTML).

138.
T. Hansen, S. Mollerup, N. Nguyen, L. Vinner, N. White, M. Coghlan,
D. Alquezar-Planas, T. Joshi, R. Jensen, H. Fridholm, K. Kjaransdottir,
T. Mourier, T. Warnow, G. Belsham, T. Gilbert, L. Orlando, M. Bunce,
E. Willerslev, L. Nielsen, and A. Hansen (2016).
High diversity of picornaviruses in rats from different continents revealed by deep sequencing,
Emerging Microbes & Infections **5**,
e90, doi:doi:10.1038/emi.2016.90.
(HTML).

139. N. Nguyen, M. Nute, S. Mirarab, and T. Warnow (2016). HIPPI: Highly accurate protein family classification with ensembles of HMMs. BMC Genomics 17 (Suppl 10):765, special issue for RECOMB-CG. (HTML) (supplement)

140. M. Nute and T. Warnow (2016). Scaling statistical multiple sequence alignment to large datasets. BMC Genomics 17(Suppl 10): 764, special issue for RECOMB-CG. (HTML)

141. L. Uricchio, T. Warnow, and N. Rosenberg (2016). 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. BMC Bioinformatics, 17 (Suppl 14): 1266, special issue for RECOMB-CG. (HTML)

142. P. Vachaspati and T. Warnow (2016). FastRFS: Fast and Accurate Robinson-Foulds Supertrees using Constrained Exact Optimization Bioinformatics 2016; doi: 10.1093/bioinformatics/btw600. (Special issue for papers from RECOMB-CG) (PDF)

143. L. Welch, C. Brooksbank, R. Schwartz, S.L. Morgan, B. Gaeta, A.M. Kilpatrick, D. Mietchen, B.L. Moore, N. Mulder, M. Pauley, W. Pearson, P. Radivojac, N. Rosenberg, A. Rosenwald, G. Rustici, and T. Warnow (2016). Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee). PLoS Comput Biol 12(5): e1004943, 2016. (HTML)

144. B.M. Boyd, J.M. Allen, N. Nguyen, A.D. Sweet, T. Warnow, M.D. Shapiro, S.M. Villa, S.E. Bush, D.H. Clayton, and K.P. Johnson. Phylogenomics using Target-restricted Assembly Resolves Intra-generic Relationships of Parasitic Lice (Phthiraptera: Columbicola). Systematic Biology 2017, doi: 10.1093/sysbio/syx027.

145. J.M. Allen, B. Boyd, N.P. Nguyen, P. Vachaspati, T. Warnow, D.I. Huang, P.G. Grady, K.C. Bell, Q.C. Cronk, L. Mugisha, B.R. Pittendrigh, L.M. Soledad, D.L. Reed, and K.P. Johnson. Phylogenomics from Whole Genome Sequences Using aTRAM. Systematic Biology 2017, doi:10.1093/sysbio/syw105.

146. B. Boyd, J.M. Allen, N. Nguyen, P. Vachaspati, Z.S. Quicksall, T. Warnow, L. Mugisha, K.P. Johnson, and D.L. Reed. Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice. Molecular Biology and Evolution 2017; 34 (7): 1743-1757. doi: 10.1093/molbev/msx117 (HTML)

147. S. Christensen, E. Molloy, P. Vachaspati, and T. Warnow. Optimal Completion of Incomplete Gene Trees in Polynomial Time. 17th International Workshop on Algorithms for Bioinformatics (WABI) 2017. Lecture Notes in Computer Science (LNCS), Springer. (PDF)

148. Md S. Bayzid and T. Warnow. Gene Tree Parsimony for Incomplete Gene Trees. 17th International Workshop on Algorithms for Bioinformatics (WABI) 2017. Lecture Notes in Computer Science (LNCS), Springer. (PDF)

149. E. Molloy and T. Warnow. To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods. Systematic Biology, syx077, https://doi.org/10.1093/sysbio/syx077 (2017). (HTML)

150. P. Vachaspati and T. Warnow. Enhancing searches for optimal trees using SIESTA. Proceedings RECOMB-CG (RECOMB International Workshop on Comparative Genomics) 2017, Lecture Notes in Computer Science book series (LNCS, volume 10562), pages 232-255. (HTML).

151. T. Warnow. Computational Phylogenetics: An Introduction to Designing Methods for Phylogeny Estimation. Cambridge University Press. (html)

152. Md S. Bayzid and T. Warnow. Gene tree parsimony for incomplete gene trees: addressing true biological loss. Algorithms for Molecular Biology, 13:1. (html)

153. W. Eiserhardt, A. Antonelli, D.J. Bennett, L.R. Botigue, J.G. Burleigh, S. Dodsworth, B.J. Enquist, F. Forest, J.T. Kim, A.M. Kozlov, I.J. Leitch, B.S. Maitner, S. Mirarab, W.H. Piel, O.A. Perez-Escobar, L. Pokorny, C. Rahbek, B. Sandel, S.A. Smith, A. Stamatakis, R.A. Vos, T. Warnow, W.J. Baker. A roadmap for global synthesis of the plant tree of life. American Journal of Botany, to appear.