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Research Output 1990 2019

1999

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

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
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

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, p. S190-S198

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, p. S165-S173

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
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, p. S285-S293

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
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

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

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
Datasets
Heuristics

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
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

phylogeny
reconstruction
estimation procedure
language
linguistics

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
2006

Distance-based genome rearrangement phylogeny

Wang, L. S., Warnow, T., Moret, B. M. E., Jansen, R. K. & Raubeson, L. A., Oct 1 2006, In : Journal of Molecular Evolution. 63, 4, p. 473-483 11 p.

Research output: Contribution to journalArticle

Phylogeny
phylogeny
genome
Genes
Genome

Pattern identification in biogeography

Ganapathy, G., Goodson, B., Jansen, R., Le, H. S., Ramachandran, V. & Warnow, T., Oct 1 2006, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 3, 4, p. 334-346 13 p.

Research output: Contribution to journalArticle

biogeography
Identification Problem
Linear-time Algorithm
Formalization
Efficient Algorithms

Reconstructing chromosomal evolution

Wang, L. S. & Warnow, T., Dec 1 2006, In : SIAM Journal on Computing. 36, 1, p. 99-131 33 p.

Research output: Contribution to journalArticle

Chromosomes
Chromosome
Transposition
Genes
Genome Rearrangement

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)

Leebens-Mack, J., Vision, T., Brenner, E., Bowers, J. E., Cannon, S., Clement, M. J., Cunningham, C. W., DePamphilis, C., DeSalle, R., Doyle, J. J., Eisen, J. A., Gu, X., Harshman, J., Jansen, R. K., Kellogg, E. A., Koonin, E. V., Mishler, B. D., Philippe, H., Pires, J. C., Qiu, Y. L. & 8 others, Rhee, S. Y., Sjölander, K., Soltis, D. E., Soltis, P. S., Stevenson, D. W., Wall, K., Warnow, T. & Zmasek, C., Sep 4 2006, In : OMICS A Journal of Integrative Biology. 10, 2, p. 231-237 7 p.

Research output: Contribution to journalReview article

Phylogeny
Genes
Genome
Microarrays
Genomics
2008

Beyond gap models: Reconstructing alignments and phylogenies under genomic-scale events

Brudno, M., Moret, B., Linder, R. & Warnow, T., 2008, Pacific Symposium on Biocomputing 2008, PSB 2008. p. 1-2 2 p.

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

Phylogeny

Short Quartet Puzzling: A new quartet-based phylogeny reconstruction algorithm

Snir, S., Warnow, T. & Rao, S., Jan 1 2008, In : Journal of Computational Biology. 15, 1, p. 91-103 13 p.

Research output: Contribution to journalArticle

Phylogeny
Reconstruction Algorithm
Joining
Maximum likelihood
Maximum Parsimony

The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses

Nelesen, S., Liu, K., Zhao, D., Linder, C. R. & Warnow, T., Dec 1 2008, Pacific Symposium on Biocomputing 2008, PSB 2008. p. 25-36 12 p. (Pacific Symposium on Biocomputing 2008, PSB 2008).

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

Sequence Alignment
Phylogeny
Muscle
Muscles

Tutorial on computational linguistic phylogeny

Nichols, J. & Warnow, T., Jan 1 2008, In : Linguistics and Language Compass. 2, 5, p. 760-820 61 p.

Research output: Contribution to journalArticle

computational linguistics
phylogeny
biology
linguistics
methodology
2009

A simulation study comparing supertree and combined analysis methods using SMIDGen

Swenson, M. S., Barbançon, F., Linder, C. R. & Warnow, T., Nov 2 2009, Algorithms in Bioinformatics - 9th International Workshop, WABI 2009, Proceedings. p. 333-344 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5724 LNBI).

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

Parsimony
Simulation Study
Matrix Representation
Subset
Maximum likelihood

Barking up the wrong treelength: The impact of gap penalty on alignment and tree accuracy

Liu, K., Nelesen, S., Raghavan, S., Linder, C. R. & Warnow, T., Jan 1 2009, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 6, 1, p. 7-21 15 p., 4547425.

Research output: Contribution to journalArticle

Penalty
Alignment
Simultaneous Estimation
Simulation Study
Maximum Parsimony