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Research Output 1990 2019

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 comparative study of SVDquartets and other coalescent-based species tree estimation methods

Chou, J., Gupta, A., Yaduvanshi, S., Davidson, R., Nute, M., Mirarab, S. & Warnow, T., Jan 1 2015, In : BMC genomics. 16, p. 1-11 11 p.

Research output: Contribution to journalArticle

Genes
Sequence Alignment
Genetic Recombination

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

A fast algorithm for the computation and enumeration of perfect phylogenies

Kannan, S. & Warnow, T., Dec 1997, In : SIAM Journal on Computing. 26, 6, p. 1749-1763 15 p.

Research output: Contribution to journalArticle

Phylogeny
Enumeration
Fast Algorithm
Polynomials
Biology

A fast algorithm for the computation and enumeration of perfect phylogenies when the number of character states is fixed

Kannan, S. & Warnow, T., 1995, Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithms (San Francisco, CA, 1995). ACM, New York, p. 595-603 9 p.

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

A fast algorithm for the computation and enumeration of perfect phylogenies when the number of character states is fixed

Kannan, S. & Warnow, T., Jan 22 1995, Proceedings of the 6th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 1995. Association for Computing Machinery, p. 595-603 9 p. (Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms).

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

Phylogeny
Enumeration
Fast Algorithm
Polynomials
Biology

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

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

Algorithms for MDC-based multi-locus phylogeny inference

Yu, Y., Warnow, T. & Nakhleh, L., Apr 4 2011, Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. p. 531-545 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6577 LNBI).

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

Phylogeny
Locus
Genes
Gene
Binary trees

Algorithms for MDC-based multi-locus phylogeny inference: Beyond rooted binary gene trees on single alleles

Yu, Y., Warnow, T. & Nakhleh, L., Nov 1 2011, In : Journal of Computational Biology. 18, 11, p. 1543-1559 17 p.

Research output: Contribution to journalArticle

Phylogeny
Coalescence
Locus
Genes
Alleles

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

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

Uricchio, L. H., Warnow, T. & Rosenberg, N. A., Nov 11 2016, In : BMC bioinformatics. 17, 417.

Research output: Contribution to journalArticle

Locus
Genes
Upper bound
Gene
Topology

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

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

An experimental study comparing linguistic phylogenetic reconstruction methods

Barbancon, F., Evans, S. N., Nakhleh, L., Ringe, D. & Warnow, T., Jul 11 2013, In : Diachronica. 30, 2, p. 143-170 28 p.

Research output: Contribution to journalArticle

reconstruction
linguistics
phylogeny
weighting
simulation

An experimental study of quartets MaxCut and other supertree methods

Swenson, M. S., Suri, R., Linder, C. R. & Warnow, T., Nov 10 2010, Algorithms in Bioinformatics - 10th International Workshop, WABI 2010, Proceedings. p. 288-299 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6293 LNBI).

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

Max-cut
Experimental Study
Parsimony
Matrix Representation
Evaluate

An experimental study of Quartets MaxCut and other supertree methods

Swenson, M. S., Suri, R., Linder, C. R. & Warnow, T., Apr 19 2011, In : Algorithms for Molecular Biology. 6, 1, 7.

Research output: Contribution to journalArticle

Max-cut
Experimental Study
Sampling
Scalability
Parsimony

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

Nguyen, N. P., Warnow, T., Pop, M. & White, B., Apr 20 2016, In : npj Biofilms and Microbiomes. 2, 16004.

Research output: Contribution to journalReview article

Cluster Analysis
Sequence Alignment
Microbiota

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee)

Welch, L., Brooksbank, C., Schwartz, R., Morgan, S. L., Gaeta, B., Kilpatrick, A. M., Mietchen, D., Moore, B. L., Mulder, N., Pauley, M., Pearson, W., Radivojac, P., Rosenberg, N., Rosenwald, A., Rustici, G. & Warnow, T., May 2016, In : PLoS computational biology. 12, 5, e1004943.

Research output: Contribution to journalArticle

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

Are Profile Hidden Markov Models Identifiable?

Pattabiraman, S. & Warnow, T., Aug 15 2018, ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 448-456 9 p. (ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics).

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

Hidden Markov models
Computational Biology
Sequence Alignment
Statistical Models
Bioinformatics

A roadmap for global synthesis of the plant tree of life

Eiserhardt, W. L., Antonelli, A., Bennett, D. J., Botigué, L. R., Burleigh, J. G., Dodsworth, S., Enquist, B. J., Forest, F., Kim, J. T., Kozlov, A. M., Leitch, I. J., Maitner, B. S., Mirarab, S., Piel, W. H., Pérez-Escobar, O. A., Pokorny, L., Rahbek, C., Sandel, B., Smith, S. A., Stamatakis, A. & 3 others, Vos, R. A., Warnow, T. & Baker, W. J., Mar 2018, In : American journal of botany. 105, 3, p. 614-622 9 p.

Research output: Contribution to journalArticle

synthesis
phylogeny
phylogenetics
informatics
botanists

A robust model for finding optimal evolutionary trees

Farach, M., Kannan, S. & Warnow, T., Feb 1 1995, In : Algorithmica. 13, 1-2, p. 155-179 25 p.

Research output: Contribution to journalArticle

Evolutionary Tree
Distance Matrix
Model
Polynomial-time Algorithm
Upper and Lower Bounds

A robust model for finding optimal evolutionary trees extended abstract

Farach, M., Kannan, S. & Warnow, T., Jun 1 1993, Proceedings of the 25th Annual ACM Symposium on Theory of Computing, STOC 1993. Association for Computing Machinery, p. 137-145 9 p. (Proceedings of the Annual ACM Symposium on Theory of Computing; vol. Part F129585).

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

Polynomials
Computational complexity

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

A simulation study comparing supertree and combined analysis methods using SMIDGen

Swenson, M. S., Barbançon, F., Warnow, T. & Linder, C. R., Jan 4 2010, In : Algorithms for Molecular Biology. 5, 1, 8.

Research output: Contribution to journalArticle

Parsimony
Matrix Representation
Simulation Study
Maximum Likelihood
Maximum likelihood

ASTRAL: Genome-scale coalescent-based species tree estimation

Mirarab, S., Reaz, R., Bayzid, M. S., Zimmermann, T., S. Swenson, M. & Warnow, T., Sep 1 2014, In : Bioinformatics. 30, 17

Research output: Contribution to journalArticle

Genome
Genes
Gene
Sorting
Biodiversity

ASTRAL-II: Coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

Mirarab, S. & Warnow, T., Jun 15 2015, In : Bioinformatics. 31, 12, p. i44-i52

Research output: Contribution to journalArticle

Genes
Gene
Locus
Sorting
Search Space

ASTRID: Accurate species TRees from internode distances

Vachaspati, P. & Warnow, T., Jan 1 2015, In : BMC genomics. 16, p. 1-13 13 p.

Research output: Contribution to journalArticle

Datasets
Genes

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

BBCA: Improving the scalability of *BEAST using random binning

Zimmermann, T., Mirarab, S. & Warnow, T., Oct 17 2014, In : BMC genomics. 15, 6, S11.

Research output: Contribution to journalArticle

Genes
Bayes Theorem
Sequence Alignment
Expressed Sequence Tags
Population Density

Benchmark datasets and software for developing and testing methods for large-scale multiple sequence alignment and phylogenetic inference

Linder, C. R., Suri, R., Liu, K. & Warnow, T., Dec 1 2010, In : PLoS Currents. NOV, ecurrents.RRN1195.

Research output: Contribution to journalArticle

Benchmarking
Sequence Alignment
Software
Datasets
Social Planning

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

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

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

Chemical phylogenetics of histone deacetylases

Bradner, J. E., West, N., Grachan, M. L., Greenberg, E. F., Haggarty, S. J., Warnow, T. & Mazitschek, R., Mar 2010, In : Nature chemical biology. 6, 3, p. 238-243 6 p.

Research output: Contribution to journalArticle

Histone Deacetylases
Libraries
Protein Isoforms
Medicine
Computer science
Students
Computational methods
Statistics
Phylogeny

Computing the local consensus of trees

Kannan, S., Warnow, T. & Yooseph, S., Jan 22 1995, Proceedings of the 6th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 1995. Association for Computing Machinery, p. 68-77 10 p. (Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms).

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

Computing
Linguistics
Polynomials
Evolutionary Tree
Tie

Computing the local consensus of trees

Kannan, S., Warnow, T. & Yooseph, S., Dec 1998, In : SIAM Journal on Computing. 27, 6, p. 1695-1724 30 p.

Research output: Contribution to journalArticle

Computing
Linguistics
Polynomials
Evolutionary Tree
Tie

Concatenation analyses in the presence of incomplete lineage sorting

Warnow, T., May 22 2015, In : PLoS Currents. 7, TREEOFLIFE

Research output: Contribution to journalArticle

Steel
Genome
Genes
Surveys and Questionnaires
Phylogeny
Joining
Scalability
Large Data Sets
Polynomials

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

Henzinger, M. R., King, V. & Warnow, T., Jan 28 1996, Proceedings of the 7th Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 1996. Association for Computing Machinery, p. 333-340 8 p. (Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms; vol. Part F129447).

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

Homeomorphic
Biology
Deterministic Algorithm
Batch
Linear Space

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 big trees from short sequences

Erdős, P. L., Steel, M. A., Székely, L. A. & Warnow, T. J., Jan 1 1997, Automata, Languages and Programming - 24th International Colloquium, ICALP 1997, Proceedings. Degano, P., Gorrieri, R. & Marchetti-Spaccamela, A. (eds.). Springer-Verlag, p. 827-837 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 1256).

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

Evolutionary Tree
Topology
Polynomials
Trees (mathematics)
Approximation algorithms

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

Constructing evolutionary trees in the presence of polymorphic characters

Bonet, M., Phillips, C., Warnow, T. & Yooseph, S., Jul 1 1996, Proceedings of the 28th Annual ACM Symposium on Theory of Computing, STOC 1996. Association for Computing Machinery, p. 220-229 10 p. (Proceedings of the Annual ACM Symposium on Theory of Computing; vol. Part F129452).

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

Polymorphism
Linguistics
Phylogeny