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Research Output 1990 2019

2005

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

Gene Order
Phylogeny
Genes
Genome
Chromosomes

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.

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

Bioinformatics
Computer science
Artificial intelligence
Artificial Intelligence
Computer Science

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

Distance Metric
Polynomials
Polynomial-time Algorithm
Leaves
Metric

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

methodology
history
language
contact
candidacy

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

Genes
Polynomials
Polynomial-time Algorithm
Phylogenetic Network
Gene
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 Tree
Contraction
Refinement
Bisection
Maximum Parsimony

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

Phylogenetic Network
Network Modeling
Horizontal Gene Transfer
phylogeny
Gene transfer
Datasets
Heuristics

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

Maximum likelihood

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

Genes
Polynomials
Gene Regulatory Networks

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

Scale factor
Divergence
Trees (mathematics)
Unknown
Clocks
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

Canterbury Tales
Manuscripts
Stemma
Gene
Geoffrey Chaucer

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

Parsimony
Hill Climbing
Data structures
Maximum Parsimony
Evolutionary Tree

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

Phylogenetics
Joining
Cleaning
Experiments
Sample space

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

K-tree
Approximation algorithms
Leaves
Complement
Binary trees

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

Stretch
Clocks
Deviation
Polynomials
Maximum likelihood

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

Genome
Gene Order
Computer Simulation
Mutation

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

Algorithm Engineering
Phylogeny
Phylogenetics
High Performance
Computational Biology

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

phylogeny
methodology
experiment
Methodology
Cladistics

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

Phylogenetics
Joining
Deviation
Requirements
Experiments

Statistically based postprocessing of phylogenetic analysis by clustering

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

Research output: Contribution to journalArticle

Phylogenetic Analysis
Post-processing
Cluster Analysis
Clustering
Clustering algorithms

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

Phylogeny
Speedup
Genes
Gene
Joining

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

Genome
Datasets
History
Parturition

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

Data visualization
DNA sequences
Genes
Polynomials
Phylogeny
2001

Absolute convergence: True trees from short sequences

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

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

Absolute convergence
Polynomials
Phylogenetic Tree
Unknown Parameters
Demonstrate

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

Phylogeny
Gene Order
Datasets
Direction compound

Designing fast converging phylogenetic methods

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

Research output: Contribution to journalArticle

Phylogenetics
Polynomials
Joining
Polynomial time
Leaves

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

Genes
Joining

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

Polynomial time
Polynomials
K-tree
Rooted Trees
Maximum Degree

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

Algorithm Engineering
Phylogenetics
High Performance
Phylogeny
Computational Biology

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

Research output: Contribution to journalArticle

Gene Order
Campanulaceae
Genes
Genome
Chloroplast Genome

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

Human Factors
Phylogenetics
Human engineering
Joining
Experimentation

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

Phylogenetics
Joining
Empirical Study
Convergence Rate
Rate of Convergence
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

Phylogeny
Campanulaceae
Gene Order
Genes
Heuristics

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., Aug 6 2000, In : Theoretical Computer Science. 244, 1-2, p. 167-188 22 p.

Research output: Contribution to journalArticle

Colored Graph
Phylogeny
Coloring
Hardness
DNA
1999

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

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

Research output: Contribution to journalArticle

Joining
Computer science
Computational complexity
Topology
Polynomials

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

Mutation
Polynomials
Evolutionary Tree
Labeled Trees
Phylogenetic Tree

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

Homeomorphic
Biology
Deterministic Algorithm
Batch
Linear Space

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

Evolutionary Tree
Polymorphism
Linguistics
Monomorphism
Phylogeny

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

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

Research output: Contribution to journalArticle

Phylogenetic Tree
Covering
Markov Model
Leaves
Topology

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

Phylogenetics
Polynomials
Evolutionary Tree
Phylogenetic Tree
Random Sequence

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

Joining
Topology
Polynomials
Nucleotides
Computer science

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

Datasets

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

Parsimony
Linguistics
Compatibility
Polynomials
Computational complexity

Better methods for solving parsimony and compatibility

Bonet, M., Steel, M., Warnow, T. & Yooseph, S., 1998, Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB. Anon (ed.). ACM, p. 40-49 10 p.

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

Linguistics
Polynomials
Computational complexity
Hardness
Topology