1. T. Warnow. Computational Phylogenetics: An Introduction to Designing Methods for Phylogeny Estimation. Cambridge University Press. (HTML)
1. Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, Edited by Tandy Warnow, Springer 2019, DOI: 10.1007/978-3-030-10837-3 (HTML)
1. Proceedings of the Tenth Annual ACM-SIAM Symposium on Discrete Algorithms, 17-19 January 1999, Baltimore, Maryland, USA. Robert Endre Tarjan and Tandy J. Warnow, eds. ACM/SIAM 1999, ISBN 0-89871-434-6.
2. Computing and Combinatorics: Proceedings of the 9th Annual International Conference, COCOON 2003, Big Sky, MT, USA, July 25-28, 2003. Binhui Zhu and Tandy Warnow, eds. Lecture Notes in Computer Science DOI: 10.1007/3-540-45071-8.
3. Algorithms in Bioinformatics, Proceedings of the 9th International Workshop, WABI 2009, Philadelphia, PA, USA, September 12-13, 2009. Steven Salzberg and Tandy Warnow, eds. Lecture Notes in Computer Science 5724, Springer 2009, ISBN 978-3-642-04240-9
4. Next Generation Sequencing (Dagstuhl Seminar 16351), 2016. DOI: 10.4230/DagRep.6.8.91. Eugene Myers, Mihai Pop, Knut Reinert, and Tandy Warnow, editors. (PDF)
1. S. Kannan, E. Lawler, and T. Warnow, 1990. Determining the Evolutionary Tree. Proceedings of the First ACM-SIAM Symposium on Discrete Algorithms (SODA) 1990, pp. 475-484.
2. S. Kannan and T. Warnow, 1990. Inferring Evolutionary History from DNA Sequences. Proceedings of the Foundations of Computer Science (FOCS) 1990, pp. 362-371.
3. 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 SODA 1991.)
4. H. Bodlaender, M. Fellows, and T. Warnow, 1992. Two strikes against perfect phylogeny, Proceedings, International Colloquium on Automata, Languages and Programming (ICALP). Springer-Verlag Lecture Notes in Computer Science, volume 623, pp. 273-283.
5. M. Steel and T. Warnow, 1993. Kaikoura Tree Theorems: The Maximum Agreement Subtree Problem. Information Processing Letters, 48, pp. 77-82.
6. M. Farach, S. Kannan, and T. Warnow, 1993. A robust model for finding optimal evolutionary trees. Proceedings of the Symposium on the Theory of Computing (STOC) 1993.
7. T. Warnow, 1993. Tree Compatibility and Inferring Evolutionary History. Proceedings, ACM-SIAM Symposium on Discrete Algorithms (SODA) 1993.
8. 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)
9. S. Kannan and T. Warnow, 1994. Inferring Evolutionary History from DNA Sequences. SIAM J. on Computing, Vol. 23, No. 4, pp. 713-737. (This is an extended version of a paper that appeared in the Proceedings of FOCS 1990, pp. 362-371.)
10. 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.)
11. 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.)
12. 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.)
13. 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.)
14. 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).
15. S. Kannan, T. Warnow, and S. Yooseph, 1998. Computing the local consensus of trees. Proceedings of the 1995 ACM-SIAM Symposium on Discrete Algorithms (SODA), pp. 68-77.
16. T. Warnow, D. Ringe, and A. Taylor. Reconstructing the evolutionary history of natural languages. Proceedings of the 1996 ACM-SIAM Symposium on Discrete Algorithms (SODA), pp. 314-322.
17. M. Bonet, C.A. Phillips, T. Warnow, and S. Yooseph, 1999. Constructing evolutionary trees in the presence of polymorphic characters. Proceedings, ACM Symposium on the Theory of Computing (STOC), 1996.
18. 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)
19. 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, pp. 102-127.)
20. 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.)
21. M. Henzinger, V. King, and T. Warnow, 1996. Constructing a tree from homeomorphic subtrees, with applications to computational molecular biology. SODA 1996, pp. 333-340.
22. S. Kannan, E. Lawler, and T. Warnow, 1996. Determining the evolutionary tree using experiments. Journal of Algorithms, 21(1): 26-50. (A preliminary version of this paper appeared at SODA 1990, pp. 475-484.)
23. D. Ringe, T. Warnow, A. Taylor, A. Michailov, and L. Levison, 1997. Computational cladistics and the position of Tocharian. In V. Mair (Ed.), The Bronze Age and Early Iron Age Peoples of Eastern Central Asia, a special volume of the Journal of Indoeuropean Studies.
24. 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)
25. T. Warnow, 1997. Mathematical approaches to comparative linguistics. Proceedings of the National Academy of Sciences, Vol. 94, pp. 6585-6590, 1997. (PDF)
26. S. Kannan and T. Warnow, 1997. A fast algorithm for the computation and enumeration of perfect phylogenies. SIAM J. Computing, Vol. 26, No. 6, pp. 1749-1763. (A preliminary version appeared in SODA 1995.)
27. 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.
28. 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.)
29. 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)
30. 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.
31. 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 SODA 1995, pp. 68-77.)
32. 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.
33. 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)
34. 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.
35. 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)
36. 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.)
37. 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 SODA 1996, pp. 333-340.)
38. D. Huson, S. Nettles, and T. Warnow. Obtaining highly accurate topology estimates of evolutionary trees from very short sequences. Proceedings of RECOMB 1999.
39. 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)
40. 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).
41. 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.
42. J. Kim and T. Warnow. 1999. Tutorial on Phylogenetic Tree Estimation. Intelligent Systems for Molecular Biology, Heidelberg 1999. (PS) (PDF)
43. 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)
44. 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)
45. 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.
46. 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.
47. 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.)
48. 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, Vol. 7, No. 09, pp. 186-195. (PDF)
49. 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).
50. 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)
51. 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)
52. 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)
53. 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)
54. 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)
55. 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)
56. 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)
57. 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.)
58. 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)
59. 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)
60. 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)
61. 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)
62. 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)
63. 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)
64. 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)
65. 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)
66. 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)
67. 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.
68. 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.
69. 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)
70. 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)
71. 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.)
72. 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.
73. 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)
74. 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)
75. 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)
76. 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)
77. L. Nakhleh, T. Warnow, and C. R. Linder 2004. "Reconstructing reticulate evolution in species - theory and practice." Journal of Computational Biology 2005, Vol. 12, No. 6, pp. 796-811, selected papers from RECOMB 2004. (J. Computational Biology and RECOMB 2004)
78. 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)
79. 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)
80. 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)
81. 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).
82. L.-S. Wang and T. Warnow, 2006. "Reconstructing Chromosomal Evolution." SIAM J. Computing, Vol. 36, Issue 2, 99-131, 2006.
83. 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)
84. 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, (PDF) Vol 3, No. 4, pp. 334-346, 2006
85. 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.
86. J. Nichols and T. Warnow, 2008. "Tutorial on computational linguistic phylogeny." Linguistics and Language Compass, Vol. 2, Issue 5, September 2008, pages 760-820.
87. 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, volume 13, pages 25-36. (PDF)
88. 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.
90. K. Liu, 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. (Recommended by F1000)
91. M.S. Swenson, 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.
92. J.E. Bradner, 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. (Recommended by F1000)
93. M.S. Swenson, 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 (16 pages), special issue of selected papers from WABI 2009.
94. M.S. Swenson, 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.
95. C.R. Linder, 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.
96. K. Liu, 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.
97. M.S. Swenson, 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.
98. 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.
99. Y. Yu, T. Warnow, and L. Nakhleh. "Algorithms for MDC-based Multi-locus Phylogeny Inference." Proceedings of RECOMB 2011 (PDF).
100. Y. Yu, T. Warnow, and L. Nakhleh. ``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 (extended version of a paper that appeared in RECOMB 2011).
101. J. Yang and T. Warnow "Fast and accurate methods for phylogenomic analyses." RECOMB Comparative Genomics 2011, and BMC Bioinformatics 12(Suppl 9): S4 (5 October 2011).
102. S. Mirarab and T. Warnow. "FastSP: Linear-time calculation of alignment accuracy." Bioinformatics (2011) 27(23):3250-3258.
103. K. Liu, C.R. 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
104. K. Liu, 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,
105. M.S. Swenson, R. Suri, C.R. Linder, and T. Warnow. "SuperFine: fast and accurate supertree estimation." Systematic Biology (2012) 61(2):214-227.
106. S. Mirarab, N. Nguyen, and T. Warnow. "SEPP: SATe-Enabled Phylogenetic Placement." Proceedings of the 2012 Pacific Symposium on Biocomputing (PSB 2012), 17:247-258.
107. 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.
108. 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).
109. N. Nguyen, S. Mirarab, and T. Warnow. "MRL and SuperFine+MRL: new supertree methods." Journal Algorithms for Molecular Biology 7:3, 2012.
110. K. Liu and T. Warnow. "Treelength optimization for phylogeny estimation." PLoS One, 7(3):e33104. doi:10.1371/journal.pone.0033104, 2012.
111. 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.
112. S. Nelesen, 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 (special issue for ISMB 2012)
113. 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.
114. 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).
115. Md S. Bayzid and T. Warnow. "Naive binning improves phylogenomic analyses". Bioinformatics 2013, vol. 29, no. 18, pages 2277-2284. (PDF), supplementary materials
116. S. Mirarab, N. Nguyen, and T. Warnow. "PASTA: ultra-large multiple sequence alignment". Proceedings RECOMB 2014 (PDF). Supplementary materials at figshare -- (PDF)
117. 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)
118. 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
119. 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.
120. 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), 11, 2014 111 (45) E4859-E4868; doi: 10.1073/pnas.1323926111. (PDF).
121. N. Nguyen, S. Mirarab, B. Liu, M. Pop, and T. Warnow TIPP:Taxonomic Identification and Phylogenetic Profiling. Bioinformatics (2014) 30(24):3548-3555. HTML.
122. 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)
123. 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
124. 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)
125. 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.
126. 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) Supplementary Materials: (PDF)
127. 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)
128. 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)
129. 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)
130. 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)
131. 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.
132. 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.
133. P. Vachaspati and T. Warnow. ASTRID: Accurate Species TRees from Internode Distances. RECOMB-Comparative Genomics and BMC Genomics, 2015, 16 (Suppl 10): S3.
134. 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.
135. 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.
136. 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)
137. 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 (2016). The interrelationships of placental mammals and the limits of phylogenetic inference. Genome Biology and Evolution, Vol. 8, Issue 2, pp. 330-344, doi:10.1093/gbe/evv261. (PDF). (Recommended by F1000)
138. 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).
139. 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)
140. 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).
141. 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)
142. 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)
143. 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)
144. 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)
145. 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 Volume 66, Issue 6, Nov 2017, pp. 896-911, doi: 10.1093/sysbio/syx027. (HTML)
146. 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, Volume 66, Issue 5, September 2017, pages 786-798, doi:10.1093/sysbio/syw105. (HTML)
147. 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)
148. 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)
149. 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)
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. E. Molloy and T. Warnow. To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods. Systematic Biology, Volume 67, Issue 2, 1 March 2018, pages 285-303 (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 (extended versions of selected papers that appeared in WABI 2017). DOI: 10.1186/s13015-017-0120-1. (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, DOI: 10.1002/ajb2.1041, 2018. (HTML)
154. S. Christensen, E. Molloy, P. Vachaspati, and T. Warnow (2018). OCTAL: Optimal Completion of Gene Trees in Polynomial Time. Algorithms for Molecular Biology, 13:6, DOI: 10.1186/s13015-018-0124-5. (HTML)
155. P. Vachaspati and T. Warnow (2018). SIESTA: Enhancing searches for optimal supertrees and species trees. BMC Genomics, 19(Suppl 5):252, DOI: 10.1186/s12864-018-4621-1 Special issue for selected papers from RECOMB-CG, 2017. (HTML)
156. M. Nute, J. Chou, E.K. Molloy, and T. Warnow (2018) The Performance of Coalescent-Based Species Tree Estimation Methods under Models of Missing Data. BMC Genomics, 19(Suppl 5):286, DOI: 10.1186/s12864-018-4619-8. Special issue for selected papers from RECOMB-CG, 2017. (HTML)
157. P. Vachaspati and T. Warnow (2018). SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space. Molecular Phylogenetics and Evolution, Vol. 124, pp. 122-136, DOI: 10.1016/j.ympev.2018.03.006. (HTML)
158. K.P. Johnson, N. Nguyen, A.D. Sweet, B.M. Boyd, T. Warnow, and J.M. Allen (2018). Simultaneous radiation of bird and mammal lice following the K-Pg boundary. Biology Letters, Vol. 14, page 20180141, DOI: 10.1098/rsbl.2018.0141. (HTML)
159. R. Zhang, S. Rao, and T. Warnow (2018). New absolute fast converging phylogeny estimation methods with improved scalability and accuracy. Proceedings of WABI (Workshop on Algorithms for Bioinformatics) 2018 DOI: 10.4230/LIPIcs.WABI.2018. (PDF)
160. S. Pattabiraman and T. Warnow (2018). Are Profile Hidden Markov Models Identifiable? Proceedings of ACM-BCB 2018, pages 448-456, DOI: 10.1145/3233547.3233563. (HTML)
161. K. Collins and T. Warnow. PASTA for proteins. Bioinformatics, Volume 34, Issue 22, 15 Nov 2018, pp. 3939-3941 doi: 10.1093/bioinformatics/bty495 (2018) (HTML)
162. E. Molloy and T. Warnow. NJMerge: A generic technique for scaling phylogeny estimation methods and its application to species trees. In: Blanchette M., Ouangraoua A. (eds) Comparative Genomics. RECOMB-CG 2018. Lecture Notes in Computer Science, vol 11183. Springer, Cham. (HTML). Selected papers from RECOMB-CG (Satellite conference for Comparative Genomics), see also (HTML)
163. S. Roch, M. Nute, and T. Warnow. Long-branch attraction in species tree estimation: inconsistency of partitioned likelihood and topology-based summary methods. Systematic Biology, Volume 68, Issue 2, March 2019, Pages 281-297, (HTML)
164. M.G. Nute, E. Saleh, and T. Warnow. Evaluating statistical multiple sequence alignment in comparison to other alignment methods on protein data sets. Systematic Biology, Volume 68, Issue 3, May 2019, Pages 396-411, https://doi.org/10.1093/sysbio/syy068 Systematic Biology
165. N. Shah, M. Nute, T. Warnow, and M. Pop. Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows. Bioinformatics, 35(9), 2019, 1613-1614, https://doi.org/10.1093/bioinformatics/bty833 (HTML)
166. Q. Zhang, S. Rao, and T. Warnow. Constrained incremental tree building: new absolute fast converging phylogeny estimation methods with improved scalability and accuracy. Algorithms for Molecular Biology, 14(2), 2019. (HTML)
167. T. Le, A. Sy, E. Molloy, Q. Zhang, S. Rao and T. Warnow. Using INC within Divide-and-Conquer Phylogeny Estimation. To appear, Algorithms for Computational Biology, Sixth International Conference, Berkeley, CA, May 28-30, 2019; LNCS/LNBI, Chapter 12, DOI:10.1007/978-3-030-18174-1_12. (HTML).
168. E. Molloy and T. Warnow. TreeMerge: A new method for improving the scalability of species tree estimation methods. Bioinformatics, special issue for Intelligent Systems for Molecular Biology (ISMB) 2019, Volume 35, Issue 14, July 2019, Pages i417--i426, (HTML)
169. E. Molloy and T. Warnow. Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. Algorithms for Molecular Biology (2019) 14:14, doi: 10.1186/s13015-019-0151-x (special issue of extended abstracts of selected papers from RECOMB-CG 2018). A preliminary version of this paper appears in bioRxiv at https://www.biorxiv.org/content/10.1101/469130v3. (HTML)
170. S. Christensen, E. Molloy, P. Vachaspati, and T. Warnow. TRACTION: Fast non-parametric improvement of estimated gene trees. (HTML). Accepted, WABI 2019, LIPICS volume 143, pages 4:1-4:16, 2019 (PDF)
171. J. Bradley, S. Devarakonda, A. Davey, D. Korobskiy, S. Liu, D. Lakhdar-Hamina,T. Warnow, and G. Chacko. Co-citations in context: disciplinary heterogeneity is relevant. In press, Quantitative Science Sciences (MIT Press), https://doi.org/10.1162/qss_a_00007. Pre-print version at MIT press
172. S. Pattabiraman and T. Warnow (2019). Profile Hidden Markov Models are not Identifiable. IEEE/ACM Transactions on Computational Biology, Vol. 18, No. 1, Jan/Feb 2021. DOI 10.1109/TCBB.2019.2933821. (PDF)
173. J. Leebens-Mack et al. One thousand plant transcriptomes and the phylogenomics of green plants, Nature, https://doi.org/10.1038/s41586-019-1693-2. (PDF)
174. S.A. Christensen, E.K. Molloy, P. Vachaspati, A. Yammanuru, and T. Warnow (2020). Non-parametric correction of estimated gene trees using TRACTION. Algorithms for Molecular Biology, 15 (1). (HTML)
175. V. Smirnov and T. Warnow (2020). Unblended Disjoint Tree Merging using GTM improves species tree estimation. BMC Genomics (special issue of selected papers from RECOMB-CG), Volume 21 (Suppl 2): 235, https://doi.org/10.1186/s12864-020-6605-1 (HTML)
176. B. Legried, E.K. Molloy, T. Warnow, and S. Roch (2020). Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss. RECOMB 2020, pp. 120-135, (HTML) The extended version of the paper appears in the Journal of Computational Biology, special issue for RECOMB 2020, 15 Dec 2020, https://doi.org/10.1089/cmb.2020.0424 (JCB)
177. E.K. Molloy and T. Warnow (2020). FastMulRFS: Fast and accurate species tree estimation under generic gene duplication and loss models. ISMB 2020 and Bioinformatics, Vol. 36, pages i57-i65, doi:10.1093/bioinformatics/btaa444 (HTML)
178. T. Le, A. Sy, E. K. Molloy, Q. Zhang, S. Rao, and T. Warnow (2020). "Using Constrained-INC for Large-scale Gene Tree and Species Tree Estimation." IEEE/ACM Transactions on Computational Biology and Bioinformatics. (HTML), doi: 10.1109/TCBB.2020.2990867
179. X. Yu, T. Le, S. Christensen, E. Molloy, and T. Warnow (2020). "Advancing Divide-and-Conquer Phylogeny Estimation using Robinson-Foulds Supertrees." Accepted to WABI 2020. Available as biorxiv 2020.05.16.099895. (HTML)
180. S. Devarakonda, D. Korobskiy, T. Warnow, and G. Chacko (2020). Viewing computer science through citation analysis: Salton and Bergmark Redux. Scientometrics (2020). https://doi.org/10.1007/s11192-020-03624-0. (HTML)
181. S. Devarakonda, J. Bradley, D. Korobskiy, T. Warnow, and G. Chacko (2020). Frequently Co-cited Publications: Features and Kinetics, Quantitative Science Studies (MIT Press), 1(1), 264-276, doi:10.1162/qss_a_00075 (HTML)
182. S. Chandrasekharan, M. Zaka, S. Gallo, W. Zhao, D. Korobskiy, T. Warnow, & G. Chacko (2020). Finding Scientific Communities in Citation Graphs. In Press, Quantitative Science Studies (MIT Press), Dec 3, 2020. (HTML). Also available in preprint form at arXiv.
183. V. Smirnov and T. Warnow (2020). MAGUS: Multiple Sequence Alignment using Graph Clustering. Bioinformatics, Volume 37, Issue 12, 15 June 2021, Pages 1666-1672, https://doi.org/10.1093/bioinformatics/btaa992 (HTML)
184. V. Smirnov and T. Warnow (2021). Phylogeny Estimation Given Sequence Length Heterogeneity. Systematic Biology, Volume 70, Issue 2, March 2021, Pages 268--282, https://doi.org/10.1093/sysbio/syaa058 (HTML) Supplementary materials at (PDF). Datasets available at Dryad.
185. P. Zaharias, M. Grosshauser, and T. Warnow (2021). Re-evaluating deep neural networks for phylogeny estimation: The issue of taxon sampling. Journal of Computational Biology (2022), special issue for RECOMB 2021. (HTML)
186. N. Shah, E.K. Molloy, M. Pop, and T. Warnow (2021) TIPP2: metagenomic taxonomic profiling using phylogenetic markers. Bioinformatics, btab023 (HTML)
187. P. Dibaiena, S. Tabe Bordhbar, and T. Warnow (2021). FASTRAL: Improving scalability of phylogenomic analysis. Bioinformatics, btab093. (HTML) (supplementary materials).
188. P. Zaharias, V. Smirnov, and T. Warnow (2021). The Maximum Weight Trace Alignment Merging Problem. In: Martin-Vide C., Vega-Rodriguez M.A., Wheeler T. (eds) Algorithms for Computational Biology. AlCoB 2021. Lecture Notes in Computer Science, vol 12715. Springer, Cham. DOI: https://doi.org/10.1007/978-3-030-74432-8_12 (HTML)
189. E. Wedell, Y. Cai, and T. Warnow. Scalable and Accurate Phylogenetic Placement using pplacer-XR. In: Martin-Vide C., Vega-Rodriguez M.A., Wheeler T. (eds) Algorithms for Computational Biology. AlCoB 2021. Lecture Notes in Computer Science, vol 12715. Springer, Cham. DOI: https://doi.org/10.1007/978-3-030-74432-8_7 (HTML)
190. J. Willson, M.S. Ruddur, and T. Warnow. Comparing Methods for Species Tree Estimation With Gene Duplication and Loss. In: Martin-Vide C., Vega-Rodriguez M.A., Wheeler T. (eds) Algorithms for Computational Biology. AlCoB 2021. Lecture Notes in Computer Science, vol 12715. Springer, Cham. DOI: https://doi.org/10.1007/978-3-030-74432-8_8 (HTML)
191. A. Rhie, S.A. McCarthy, O. Fedrigo, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature 592, 737-746 (2021). (HTML)
192. M. Park, P. Zaharias, and T. Warnow. Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation. Algorithms 2021, 14(5), 148. Special issue on Algorithms for Computational Biology. (HTML)
193. E. Koning, M. Phillips, and T. Warnow. pplacerDC: a New Scalable Phylogenetic Placement Method. To appear, ACM-BCB 2021. BCB '21: Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. August 2021 Article No.: 3. Pages 1-9. (HTML)
194. M. Gupta, P. Zaharias, and T. Warnow. Accurate Large-scale Phylogeny-Aware Alignment using BAli-Phy. Bioinformatics 2021. (HTML)
195. S. Mirarab, L. Nakhleh, and T. Warnow. Multispecies Coalescent: Theory and Applications in Phylogenetics Annual Review of Ecology, Evolution, and Systematics 2021. 52:247-68. (PDF)
196. J. Willson, M. Roddur, B. Liu, P. Zaharias, and T. Warnow. DISCO: Species Tree Inference using Multi-Copy Gene-Family Tree Decomposition. Systematic Biology, syab070, 2021. (HTML) (supplementary materials)
197. C. Shen, P. Zaharias, and T. Warnow. MAGUS+eHMMs: Improved Multiple Sequence Alignment Accuracy for Fragmentary Sequences. Bioinformatics 2021, (HTML)
198. X. Yu, T. Le, S.A. Christensen, E.K. Molloy, and T. Warnow. Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation. Algorithms Mol Biol 16, 12 (2021). (HTML)
199. B. Liu and T. Warnow. Scalable Species Tree Inference with External Constraints. Journal of Computational Biology, special issue in honor of Michael Waterman, (HTML). Preprint version available on BiorXiv at (HTML)
200. P. Zaharias and T. Warnow. Recent Progress on Methods for Estimating and Updating Large Phylogenies. The Philosophical Transactions of the Royal Society, Vol. 377, Issue 1861 (Discussion meeting issue for "Genomic population structures of microbial pathogens"). Article available at HTML. Extended preprint version (not identical to the accepted version) available at Preprints 2021, 2021100258, DOI: 10.20944/preprints202110.0258.v2 (HTML)
201. M. Blaxter et al. Why sequence all eukaryotes? Proc. National Academy Sciences 119(4):e2115636118. (HTML)
202. E. Wedell, M. Park, D. Korobskiy, T. Warnow, and G. Chacko (2022) Center-Periphery Structure in Communities: Extracellular Vesicles. Quantitative Science Studies 3 (1):289-314. (HTML). Preprint version at arXiv 2111.07418
203. C. Shen, M. Park, and T. Warnow (2022). WITCH: Improved Multiple Sequence Alignment through Weighted Consensus HMM alignment. J. Computational Biology, Vol. 29, issue 8, pages:782--801. special issue for Mike Waterman. (HTML).
204. Y. Tabatabaee, K. Sarkar, and T. Warnow (2022). Quintet Rooting: Rooting Species Trees under the Multi-Species Coalescent Model. Bioinformatics, Volume 38, Supplement 1, pages i109-i117, Special issue for ISMB (Intelligent Systems for Molecular Biology), 2022. (HTML)
205. E. Wedell, Y. Cai, and T. Warnow (2022). SCAMPP: Scaling alignment-based phylogenetic placement methods to large trees". IEEE/ACM Transactions on Computational Biology and Bioinformatics. (HTML)
206. B. Liu and T. Warnow (2022). Fast and Accurate Species Trees from Weighted Internode Distances. 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), 8:1--8:24, Leibniz International Proceedings in Informatics (LIPIcs), DOI: 10.4230/LIPIcs.WABI.2022.8 (PDF)
207. P. Zaharias, V. Smirnov, and T. Warnow (2022). Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2022. (HTML)
208. A. Jakatdar, B. Liu, T. Warnow, and G. Chacko (2022). AOC: Assembling Overlapping Communities. Quantitative Science Studies (QSS), published by MIT Press, online Nov 21, 2022 (HTML)
209. Y. Tabatabaee, S. Roch, and T. Warnow (2022). Statistically Consistent Rooting of Species Trees under the Multi-Species Coalescent Model. In: Tang, H. (eds) Research in Computational Molecular Biology. RECOMB 2023. Lecture Notes in Computer Science(), vol 13976. Springer, Cham. (Proceedings HTML). Preprint available at bioRxiv (HTML)
210. M. Park, S. Ivanovic, G. Chu, C. Shen, and T. Warnow (2023) UPP2: Fast and Accurate Alignment Estimation of Datasets with Fragmentary Sequences. Bioinformatics, Volume 39, Issue 1, January 2023, btad007, (HTML)
211. G. Chu and T. Warnow. SCAMPP+FastTree: Improving Scalability for Likelihood-based Phylogenetic Placement. Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad008, special issue for ISCB-LA (HTML). (HTML)
212. J. Willson, Y. Tabatabaee, B. Liu, and T. Warnow. DISCO+QR: Rooting Species Trees in the Presence of GDL and ILS. Bioinformatics Advances, Volume 3, Issue 1, vbad015, special issue for ISCB-LA 2022. (HTML) (HTML)
213. B. Liu and T. Warnow. WITCH-NG: Efficient and Accurate Alignment of Datasets with Sequence Length Heterogeneity. Bioinformatics Advances, special issue for ISCB-LA 2022 (HTML) (HTML) (HTML)
214. Y. Tabatabaee, C. Zhang, T. Warnow, and S. Mirarab. Phylogenomic branch length estimation using quartets. ISMB 2023, in Bioinformatics (special issue for ISMB 2023) (HTML)
215. M. Park and T. Warnow. HMMerge: an Ensemble Method for Improving Multiple Sequence Alignment. Bioinformatics Advances, special issue for ISCB-LA 2022. (HTML). (HTML)
216. C. Shen, B. Liu, K.P. Williams, and T. Warnow. EMMA: Adding sequences into a constraint alignment with high accuracy and scalability. WABI 2023. (Preprint of full version available on bioRxiv (HTML)) Journal version: Algorithms for Molecular Biology, DOI: 10.1186/s13015-023-00247-x. (HTML)
217. E. Wedell, C. Shen, and T. Warnow. BATCH-SCAMPP: Scaling phylogenetic placement methods to place many sequences. WABI 2023. (Preprint of full version available on bioRxiv (HTML))
218. Y. Tabatabaee, C. Zhang, T. Warnow, S. Mirarab. Phylogenomic branch length estimation using quartets. Bioinformatics, Vol. 39, Issue Supplement_1, pages i185-i193, (HTML) (special issue for ISMB 2023)
219. B. Liu and T. Warnow. Weighed ASTRID: fast and accurate species trees from weighted internode distances. ALgorithms for Molecular Biology 18(6), 2023. special issue for selected papers from WABI 2022. (HTML)
220. Y. Tabatabaee, S. Roch, and T. Warnow (2023). QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent. Journal of Computational Biology, 30(11), 1146-1181. (Special issue for RECOMB 2023)
221. V. Ramavarapu, F. Ayres, M. Park, V. Pallodi, J. Larry, T. Warnow, and G. Chacko (2024). CM++ - A Meta-method for Well-Connected Community Detection. Journal of Open Source Software, 9(93), 6073, (HTML)
222. M. Park, Y. Tabatabaee, B. Liu, V. Kamath Pailodi, V. Ramavarapu, R. Ramachandran, D. Korobskiy, F. Ayres, G. Chacko, T. Warnow. Identifying Well-Connected Communities in Real-World and Synthetic Networks. Proceedings of Complex Networks and Their Applications XII, (HTML)
223. T. Warnow, Y. Tabatabaee, and S.N. Evans. Statistically Consistent Estimation of Rooted and Unrooted Level-1 Phylogenetic Networks from SNP data. To appear, Proceedings of RECOMB Comparative Genomics (RECOMB-CG), 2024.
224. M. Canby, S.N. Evans, D. Ringe,and T. Warnow. Addressing polymorphism in linguistic phylogenetics. Transactions on the Philological Society, 2024 (HTML)
225. J. Stiller, S. Feng, AA Chowdhury, et al. Complexity of avian evolution revealed by family-level genomes. Nature (2024). (PDF)
1. 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. https://doi.org/10.1371/journal.pcbi.1004943 (HTML)
1. 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, December 2005. (PDF)
2. 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, December 2005. (PDF)
3. B.M.E. Moret, J. Tang, and T. Warnow (2005). "Reconstructing phylogenies from gene-content and gene-order data." Book chapter, In Mathematics of Evolution and Phylogeny, pp. 321-352, O. Gascuel, ed., Oxford Univ. Press. (PDF)
4. B.M.E. Moret and T. Warnow (2005). "Advances in phylogeny reconstruction from gene order and content data," Book chapter, in Molecular Evolution: Producing the Biochemical Data, Part B, E.A. Zimmer and E.H. Roalson, eds., Vol. 395 of Methods in Enzymology, Elsevier (PDF)
5. S.N. Evans, D. Ringe, and T. Warnow (2006). "Inference of divergence times as a statistical inverse problem." Book chapter in Phylogenetic Methods and the Prehistory of Languages, pp. 119-129. Edited by Peter Forster and Colin Renfrew. Edited for the Institute by Chris Scarre (Series Editor) and Dora A. Kemp (Production Editor). Publisher: McDonald Institute for Archaeological Research/University of Cambridge, 2006. (PDF)
6. T. Warnow, S. N. Evans, D. Ringe, and L. Nakhleh (2006). "A stochastic model of language evolution that incorporates homoplasy and borrowing." Book chapter in Phylogenetic methods and the prehistory of languages, pp.75-87. Edited by Peter Forster and Colin Renfrew. Edited for the Institute by Chris Scarre (Series Editor) and Dora A. Kemp (Production Editor). Publisher: McDonald Institute for Archaeological Research/University of Cambridge. (PDF)
7. D. Ringe and T. Warnow (2008). "Linguistic History and Computational Cladistics." Book chapter (pages 257-271) in Origin and Evolution of Languages: Approaches, Models, Paradigms. Edited by Bernard Laks, pp. 75-87. Equinox Publishing.
8. T. Warnow (2013). "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,
9. T. Warnow (2019). "Divide-and-Conquer Tree Estimation: Opportunities and Challenges." Book chapter in Bioinformatics and Phylogenetics, (T. Warnow, ed.), pp. 121-150, Springer. (PDF)
10. T. Warnow (2021). Revisiting Evaluation of Multiple Sequence Alignment Methods. In: Katoh K. (eds) Multiple Sequence Alignment. Methods in Molecular Biology, vol 2231. Humana, New York, NY. (HTML)
11. T. Warnow and S. Mirarab (2021). Multiple Sequence Alignment for Large Heterogeneous Datasets Using SATé, PASTA, and UPP. In: Katoh K. (eds) Multiple Sequence Alignment. Methods in Molecular Biology, vol 2231. Humana, New York, NY. (HTML)
12. E.K. Molloy and T. Warnow (2022). Large-scale Species Tree Estimation. In: Lacey Knowles and Laura Kubatko (eds). Species Tree Inference: A Guide to Methods and Applications, Princeton University Press. Preprint at (HTML)
T. Warnow. Supertree Construction: Opportunities and challenges. arXiv:1805.03530. (HTML)
J. Rhodes, M.G. Nute, and T. Warnow. NJst and ASTRID are not statistically consistent under a random model of missing data. Available at arXiv:2001.07844. (HTML)
Q. Yang and T. Warnow. An improved mode of running PASTA. Available at bioRxiv (HTML)
C. Shen, B. Liu, and T. Warnow. eMAFFTadd: scaling MAFFT-linsi-add to large datasets. BioRxiv doi: https://doi.org/10.1101/2022.05.23.493139 (HTML)
E. Wedell, C. Shen, and T. Warnow. BATCH-SCAMPP: Scaling phylogenetic placement methods to place many sequences. Preprint available at biorXiv (HTML)
M. Park, Y. Tabatabaee, B. Liu, V. Kamath Pailodi, V. Ramavarapu, R. Ramachandran, D. Korobskiy, F. Ayres, G. Chacko, T. Warnow. Well-Connected Communities in Real-World Networks. Preprint available on arXiv. (HTML)
T. Warnow, S.N. Evans, and L. Nakhleh. Progress on Conxstructing Phylogenetic Networks for Languages. Preprint available on arXiv. (HTML)