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Research Output

2005

A comparison of phylogenetic reconstruction methods on an Indo-European dataset

Nakhleh, L., Warnow, T., Ringe, D. & Evans, S. N., Aug 1 2005, In : Transactions of the Philological Society. 103, 2, p. 171-192 22 p.

Research output: Contribution to journalReview article

Advances in phylogeny reconstruction from gene order and content data

Moret, B. M. E. & Warnow, T., Jan 1 2005, In : Methods in enzymology. 395, p. 673-700 28 p.

Research output: Contribution to journalArticle

Alenex workshop preface

Applegate, D., Brandes, U., Demetrescu, C., Gabow, H., Maheshwari, A., Pettie, S., Pruhs, K., Tamassia, R., Teillaud, M., Warnow, T., Arge, L., Battiti, R., Buchsbaum, A., Goldberg, A. V., Goodrich, M. T., Italiano, G. F., Johnson, D. S., Ladner, R. E., McGeoch, C. C., Moret, B. M. E. & 3 others, Mount, D., Snoeyink, J. & Stein, C., Dec 1 2005, In : Proceedings of the Seventh Workshop on Algorithm Engineering and Experiments and the Second Workshop on Analytic Algorithms and Combinatorics. p. vii

Research output: Contribution to journalEditorial

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface

Agarwal, P. K., Akutsu, T., Amihood, A., Apostolico, A., Benham, C., Benson, G., Blanchette, M., El-Mabrouk, N., Gascuel, O., Giancarlo, R., Guigo, R., Hallet, M., Huson, D., Kucherov, G., Lacey, M., Lagergren, J., Lancia, G., Landau, G. M., Lecroq, T., Moret, B. & 22 others, Morishita, S., Mossel, E., Moulton, V., Pachter, L., Reinert, K., Rigoutsos, I., Sagot, M. F., Sankoff, D., Schbath, S., Segal, E., Semple, C., Setubal, J. C., Sharan, R., Skiena, S., Stoye, J., Ukkonen, E., Vawter, L., Valencia, A., Warnow, T., Wang, L., Casadio, R. & Myers, G., Dec 1 2005, In : Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3692 LNBI

Research output: Contribution to journalEditorial

Pattern identification in biogeography

Ganapathy, G., Goodson, B., Jansen, R., Ramachandran, V. & Warnow, T., Dec 1 2005, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). p. 116-127 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3692 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Perfect phylogenetic networks: A new methodology for reconstructing the evolutionary history of natural languages

Nakhleh, L., Ringe, D. & Warnow, T., Jun 1 2005, In : Language. 81, 2, p. 382-420 39 p.

Research output: Contribution to journalArticle

Reconstructing reticulate evolution in species - Theory and practice

Nakhleh, L., Warnow, T., Linder, C. R. & St. John, K., Jul 1 2005, In : Journal of Computational Biology. 12, 6, p. 796-811 16 p.

Research output: Contribution to journalArticle

2004

On Contract-and-Refine Transformations Between Phylogenetic Trees

Ganapathy, G., Ramachandran, V. & Warnow, T., 2004, Proceedings of the Fifteenth Annual ACM-SIAM Symposium on Discrete Algorithms. Vol. 15. p. 893-902 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Phylogenetic networks: Modeling, reconstructibility, and accuracy

Moret, B. M. E., Nakhleh, L., Warnow, T., Linder, C. R., Tholse, A., Padolina, A., Sun, J. & Timme, R., Jan 1 2004, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 1, 1, p. 13-23 11 p.

Research output: Contribution to journalArticle

Rec-I-DCM3: A fast algorithmic technique for reconstructing large phylogenetic trees

Roshan, U. W., Warnow, T., Moret, B. M. E. & Williams, T. L., Jan 1 2004, Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. IEEE Computer Society, p. 98-109 12 p. (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Reconstructing reticulate evolution in species - Theory and practice

Nakhleh, L., Warnow, T. & Linder, C. R., 2004, RECOMB 2004 - Proceedings of the Eight Annual International Conference on Research in Computational Molecular Biology. Vol. 8. p. 337-346 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Unidentifiable divergence times in rates-across-sites models

Evans, S. N. & Warnow, T., Jul 1 2004, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 1, 3, p. 130-134 5 p.

Research output: Contribution to journalArticle

2003

Analyzing the order of items in manuscripts of the canterbury tales

Spencer, M., Bordalejo, B., Wang, L. I. S., Barbrook, A. C., Mooney, L. R., Robinson, P., Warnow, T. & Howe, C. J., Dec 1 2003, In : Computers and the Humanities. 37, 1, p. 97-109 13 p.

Research output: Contribution to journalArticle

Better hill-climbing searches for parsimony

Ganapathy, G., Ramachandran, V. & Warnow, T., Dec 1 2003, In : Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2812, p. 245-258 14 p.

Research output: Contribution to journalArticle

Performance study of phylogenetic methods: (Unweighted) quartet methods and neighbor-joining

St. John, K., Warnow, T., Moret, B. M. E. & Vawter, L., Aug 2003, In : Journal of Algorithms. 48, 1, p. 173-193 21 p.

Research output: Contribution to journalArticle

Towards the development of computational tools for evaluating phylogenetic network reconstruction methods.

Nakhleh, L., Sun, J., Warnow, T., Linder, C. R., Moret, B. M. E. & Tholse, A., Aug 18 2003, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. p. 315-326 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2002

Approximating the complement of the maximum compatible subset of leaves of k trees

Ganapathy, G. & Warnow, T., Jan 1 2002, Approximation Algorithms for Combinatorial Optimization - 5th International Workshop, APPROX 2002, Proceedings. Leonardi, S., Jansen, K. & Vazirani, V. (eds.). Springer-Verlag, p. 122-134 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 2462).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Estimating the deviation from a molecular clock

Nakhleh, L., Roshan, U., Vawter, L. & Warnow, T., Jan 1 2002, Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. Guigo, R. & Gusfield, D. (eds.). Springer-Verlag, p. 287-299 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 2452).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Fast phylogenetic methods for the analysis of genome rearrangement data: an empirical study.

Wang, L. S., Jansen, R. K., Moret, B. M. E., Raubeson, L. A. & Warnow, T., Apr 3 2002, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. p. 524-535 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

High-performance algorithm engineering for computational phylogenetics

Moret, B. M. E., Bader, D. A. & Warnow, T., May 2002, In : Journal of Supercomputing. 22, 1, p. 99-111 13 p., 397940.

Research output: Contribution to journalArticle

Indo-European and computational cladistics

Ringe, D., Warnow, T. & Taylor, A., Jan 1 2002, In : Transactions of the Philological Society. 100, 1, p. 59-129 71 p.

Research output: Contribution to journalArticle

Sequence-length requirements for phylogenetic methods

Moret, B. M. E., Roshan, U. & Warnow, T., Jan 1 2002, Algorithms in Bioinformatics - 2nd International Workshop,WABI 2002, Proceedings. Guigo, R. & Gusfield, D. (eds.). Springer-Verlag, p. 343-356 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 2452).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Statistically based postprocessing of phylogenetic analysis by clustering

Stockham, C., Wang, L. S. & Warnow, T., Jan 1 2002, In : Bioinformatics. 18, SUPPL. 1, p. S285-S293

Research output: Contribution to journalArticle

Steps toward accurate reconstructions of phylogenies from gene-order data

Moret, B. M. E., Tang, J., Wang, L. S. & Warnow, T., Nov 2002, In : Journal of Computer and System Sciences. 65, 3, p. 508-525 18 p.

Research output: Contribution to journalArticle

The accuracy of fast phylogenetic methods for large datasets.

Nakhleh, L., Moret, B. M. E., Roshan, U., St John, K., Sun, J. & Warnow, T., Apr 3 2002, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. p. 211-222 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Toward new software for computational phylogenetics

Moret, B. M. E., Wang, L. S. & Warnow, T., Jul 1 2002, In : Computer. 35, 7

Research output: Contribution to journalArticle

2001

Absolute convergence: True trees from short sequences

Warnow, T., Moret, B. M. E. & John, K. S., Dec 1 2001, Proceedings of the 12th Annual ACM-SIAM Symposium on Discrete Algorithms. p. 186-195 10 p. (Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

A new implementation and detailed study of breakpoint analysis.

Moret, B. M., Wyman, S., Bader, D. A., Warnow, T. & Yan, M., Mar 23 2001, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. p. 583-594 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Designing fast converging phylogenetic methods

Nakhleh, L., Roshan, U., John, K. S., Sun, J. & Warnow, T., Jan 1 2001, In : Bioinformatics. 17, SUPPL. 1, p. S190-S198

Research output: Contribution to journalArticle

Estimating true evolutionary distances between genomes

Wang, L. S. & Warnow, T., Sep 29 2001, In : Conference Proceedings of the Annual ACM Symposium on Theory of Computing. p. 637-646 10 p.

Research output: Contribution to journalConference article

Finding a maximum compatible tree for a bounded number of trees with bounded degree is solvable in polynomial time

Ganapathysaravanabavan, G. & Warnow, T., Jan 1 2001, Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings. Moret, B. M. E. & Gascuel, O. (eds.). Springer-Verlag, p. 156-163 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 2149).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

High-performance algorithm engineering for computational phylogenetics

Moret, B. M. E., Bader, D. A. & Warnow, T., Jan 1 2001, Computational Science – ICCS 2001 - International Conference, Proceedings. Alexandrov, V. N., Dongarra, J. J., Juliano, B. A., Renner, R. S. & Kenneth Tan, C. J. (eds.). Springer-Verlag, p. 1012-1021 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 2074).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

New approaches for reconstructing phytogenies from gene order data

Moret, B. M. E., Wang, L. S., Warnow, T. & Wyman, S. K., Jan 1 2001, In : Bioinformatics. 17, SUPPL. 1, p. S165-S173

Research output: Contribution to journalArticle

Performance study of phylogenetic methods: (Unweighted) quartet methods and neighbor-joining

Warnow, T., Moret, B. M. E. & John, K. S., Dec 1 2001, Proceedings of the 12th Annual ACM-SIAM Symposium on Discrete Algorithms. p. 196-205 10 p. (Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

The performance of phylogenetic methods on trees of bounded diameter

Nakhleh, L., Roshan, U., St. John, K., Sun, J. & Warnow, T., Jan 1 2001, Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings. Moret, B. M. E. & Gascuel, O. (eds.). Springer-Verlag, p. 214-226 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 2149).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2000

A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data.

Cosner, M. E., Jansen, R. K., Moret, B. M., Raubeson, L. A., Wang, L. S., Warnow, T. & Wyman, S., Dec 1 2000, Proceedings / . International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology. Vol. 8. p. 104-115 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs

Bodlaender, H. L., Fellows, M. R., Hallett, M. T., Wareham, H. T. & Warnow, T. J., Aug 6 2000, In : Theoretical Computer Science. 244, 1-2, p. 167-188 22 p.

Research output: Contribution to journalArticle

1999

A few logs suffice to build (almost) all trees: Part II

Erdos, P. L., Steel, M. A., Székely, L. A. & Warnow, T. J., Jun 28 1999, In : Theoretical Computer Science. 221, 1-2, p. 77-118 42 p.

Research output: Contribution to journalArticle

A few logs suffice to build (almost) all trees. II

ErdH os, P. L., Steel, M. A., Székely, L. A. & Warnow, T. J., 1999, In : Theoretical Computer Science. 221, 1-2, p. 77-118 42 p.

Research output: Contribution to journalArticle

A few logs suffice to build (almost) all trees (I)

Erdos, P. L., Steel, M. A., Székely, L. A. & Warnow, T., Mar 1999, In : Random Structures and Algorithms. 14, 2, p. 153-184 32 p.

Research output: Contribution to journalArticle

Constructing a tree from homeomorphic subtrees, with applications to computational evolutionary biology

Henzinger, M. R., King, V. & Warnow, T., May 1999, In : Algorithmica (New York). 24, 1, p. 1-13 13 p.

Research output: Contribution to journalArticle

Constructing evolutionary trees in the presence of polymorphic characters

Bonet, M., Phillips, C., Warnow, T. & Yooseph, S., Sep 1999, In : SIAM Journal on Computing. 29, 1, p. 103-131 29 p.

Research output: Contribution to journalArticle

Disk-covering, a fast-converging method for phylogenetic tree reconstruction

Huson, D. H., Nettles, S. M. & Warnow, T. J., Sep 1 1999, In : Journal of Computational Biology. 6, 3-4, p. 369-386 18 p.

Research output: Contribution to journalArticle

Estimating large distances in phylogenetic reconstruction

Huson, D. H., Ann Smith, K. & Warnow, T., 1999, Algorithm Engineering - 3rd International Workshop, WAE 1999, Proceedings. Springer Verlag, Vol. 1668. p. 271-285 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 1668).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hybrid tree reconstruction methods

Huson, D., Nettles, S., Rice, K., Warnow, T. & Yooseph, S., 1999, In : Journal of Experimental Algorithmics. 4, p. 21 1 p.

Research output: Contribution to journalArticle

Obtaining highly accurate topology estimates of evolutionary trees from very short sequences

Huson, D. H., Nettles, S. & Warnow, T., Jan 1 1999, Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB. New York, NY, United States: ACM, p. 198-207 10 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Solving large scale phylogenetic problems using DCM2.

Huson, D. H., Vawter, L. & Warnow, T., Dec 1 1999, Proceedings / . International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology. p. 118-129 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Some combinatorial optimization problems in phylogenetics

Warnow, T., 1999, Graph theory and combinatorial biology (Balatonlelle, 1996). János Bolyai Math. Soc., Budapest, Vol. 7. p. 363-413 51 p. (Bolyai Soc. Math. Stud.).

Research output: Chapter in Book/Report/Conference proceedingOther chapter contribution

1998

Better methods for solving parsimony and compatibility

Bonet, M., Steel, M., Warnow, T. & Yooseph, S., Jan 1 1998, In : Journal of Computational Biology. 5, 3, p. 391-407 17 p.

Research output: Contribution to journalArticle