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Research Output 1990 2019

Constructing phylogenetic trees efficiently using compatibility criteria

Warnow, T., Jul 1 1993, In : New Zealand Journal of Botany. 31, 3, p. 239-248 10 p.

Research output: Contribution to journalArticle

bioinformatics
phylogenetics
phylogeny

DACTAL: Divide-and-conquer trees (almost) without alignments

Nelesen, S., Liu, K., Wang, L. S., Randal Linder, C. & Warnow, T., Jun 1 2012, In : Bioinformatics. 28, 12, p. i274-i282 bts218.

Research output: Contribution to journalArticle

Divide and conquer
Alignment
Maximum likelihood
Phylogeny
Iteration

Data access for the 1,000 Plants (1KP) project

Matasci, N., Hung, L. H., Yan, Z., Carpenter, E. J., Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Ayyampalayam, S., Barker, M., Burleigh, J. G., Gitzendanner, M. A., Wafula, E., Der, J. P., dePamphilis, C. W., Roure, B., Philippe, H., Ruhfel, B. R., Miles, N. W., Graham, S. W. & 24 others, Mathews, S., Surek, B., Melkonian, M., Soltis, D. E., Soltis, P. S., Rothfels, C., Pokorny, L., Shaw, J. A., DeGironimo, L., Stevenson, D. W., Villarreal, J. C., Chen, T., Kutchan, T. M., Rolf, M., Baucom, R. S., Deyholos, M. K., Samudrala, R., Tian, Z., Wu, X., Sun, X., Zhang, Y., Wang, J., Leebens-Mack, J. & Wong, G. K. S., Oct 27 2014, In : GigaScience. 3, 1, 17.

Research output: Contribution to journalReview article

Viridiplantae
Proteins
Transcriptome
Visualization
Pipelines

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

Determining the evolutionary tree

Kannan, S., Lawler, E. & Warnow, T., Jan 1 1990, Proceedings of the 1st Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 1990. Association for Computing Machinery, p. 475-484 10 p. (Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms).

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

Evolutionary Tree

Determining the Evolutionary Tree Using Experiments

Kannan, S. K., Lawler, E. L. & Warnow, T., Jul 1996, In : Journal of Algorithms. 21, 1, p. 26-50 25 p.

Research output: Contribution to journalArticle

Evolutionary Tree
Experiment
Experiments
Labeled Trees
Models of Computation

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

Phylogenetic Tree
Covering
Markov Model
Leaves
Topology

Disk covering methods improve phylogenomic analyses

Bayzid, M. S., Hunt, T. & Warnow, T., Oct 17 2014, In : BMC genomics. 15, 6, S7.

Research output: Contribution to journalArticle

Expressed Sequence Tags
Computational Biology
Genes
Genome
Growth

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

Engineering in Genomics Combinatorial Optimization in Biology

Warnow, T., Jun 1993, In : IEEE Engineering in Medicine and Biology Magazine. 12, 2, p. 91-92 2 p.

Research output: Contribution to journalArticle

Combinatorial optimization
Genomics

Enhancing searches for optimal trees using SIESTA

Vachaspati, P. & Warnow, T., Jan 1 2017, Comparative Genomics - 15th International Workshop, RECOMB CG 2017, Proceedings. Nakhleh, L. & Meidanis, J. (eds.). Springer-Verlag, p. 232-255 24 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10562 LNBI).

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

Trees (mathematics)
Dynamic programming
Set theory
Data structures
Polynomials

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

Estimating optimal species trees from incomplete gene trees under deep coalescence

Shamsuzzoha Bayzid, M. D. & Warnow, T., Jun 1 2012, In : Journal of Computational Biology. 19, 6, p. 591-605 15 p.

Research output: Contribution to journalArticle

Coalescence
Genes
Gene
Sorting
Alignment

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

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

Evaluating statistical multiple sequence alignment in comparison to other alignment methods on protein data sets

Nute, M., Saleh, E. & Warnow, T., May 1 2019, In : Systematic biology. 68, 3, p. 396-411 16 p.

Research output: Contribution to journalArticle

Open Access
Sequence Alignment
sequence alignment
Benchmarking
Indonesia
protein

Evaluating summarymethods for multilocus species tree estimation in the presence of incomplete lineage sorting

Mirarab, S., Bayzid, M. S. & Warnow, T., Jan 1 2016, In : Systematic biology. 65, 3, p. 366-380 15 p.

Research output: Contribution to journalArticle

sorting
gene
Genes
genes
estimation method

Fast and accurate methods for phylogenomic analyses

Yang, J. & Warnow, T., Oct 5 2011, In : BMC bioinformatics. 12, SUPPL. 9, S4.

Research output: Contribution to journalArticle

Genes
Gene
Sorting
Gene transfer
Biological Phenomena

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

FastRFS: Fast and accurate Robinson-Foulds Supertrees using constrained exact optimization

Vachaspati, P. & Warnow, T., Jan 1 2017, In : Bioinformatics. 33, 5, p. 631-639 9 p.

Research output: Contribution to journalArticle

Constrained optimization
Optimization
Trees (mathematics)
Dynamic programming
Large Data Sets

FASTSP: Linear time calculation of alignment accuracy

Mirarab, S. & Warnow, T., Dec 1 2011, In : Bioinformatics. 27, 23, p. 3250-3258 9 p., btr553.

Research output: Contribution to journalArticle

Linear Time
Alignment
Data storage equipment
Sequence Alignment
Phylogeny

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

Gene tree parsimony for incomplete gene trees

Bayzid, M. S. & Warnow, T., Aug 1 2017, 17th International Workshop on Algorithms in Bioinformatics, WABI 2017. Reinert, K. & Schwartz, R. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 88).

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

Genes
Sampling
Dynamic programming

Gene tree parsimony for incomplete gene trees: Addressing true biological loss

Bayzid, M. S. & Warnow, T., Jan 19 2018, In : Algorithms for Molecular Biology. 13, 1, 1.

Research output: Contribution to journalArticle

Parsimony
Genes
Gene
Incompleteness
Duplication

GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training

GOBLET Consortium, Apr 1 2015, In : PLoS computational biology. 11, 4, e1004143.

Research output: Contribution to journalArticle

bioinformatics
education and training
Bioinformatics
Computational Biology
education

Hen's Teeth and Whale's Feet: Generalized Characters and Their Compatibility

Benham, C., Kannan, S., Paterson, M. & Warnow, T., Jan 1 1995, In : Journal of Computational Biology. 2, 4, p. 515-525 11 p.

Research output: Contribution to journalArticle

Whales
Compatibility
Foot
Molecular Biology
Tooth

High diversity of picornaviruses in rats from different continents revealed by deep sequencing

Hansen, T. A., Mollerup, S., Nguyen, N. P., White, N. E., Coghlan, M., Alquezar-Planas, D. E., Joshi, T., Jensen, R. H., Fridholm, H., Kjartansdóttir, K. R., Mourier, T., Warnow, T., Belsham, G. J., Bunce, M., Willerslev, E., Nielsen, L. P., Vinner, L. & Hansen, A. J., Aug 17 2016, In : Emerging microbes & infections. 5, 8, p. e90

Research output: Contribution to journalArticle

Picornaviridae
High-Throughput Nucleotide Sequencing
Zoonoses
Cardiovirus
Arthropod Vectors

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

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

HIPPI: Highly accurate protein family classification with ensembles of HMMs

Nguyen, N. P., Nute, M., Mirarab, S. & Warnow, T., Nov 11 2016, In : BMC genomics. 17, 765.

Research output: Contribution to journalArticle

Computational Biology
Sequence Alignment
Proteins
Databases
Metagenomics

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

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

Inferring evolutionary history from DNA sequences

Kannan, S. K. & Warnow, T. J., Jan 1 1994, In : SIAM Journal on Computing. 23, 4, p. 713-737 25 p.

Research output: Contribution to journalArticle

DNA sequences
DNA Sequence
Molecular biology
Phylogenetic Tree
Compatibility

Inferring evolutionary history from DNA sequences

Kannan, S. & Warnow, T., Jan 1 1991, In : IEEE Transactions on Industry Applications. 27, 1 pt 1, p. 362-371 10 p.

Research output: Contribution to journalConference article

DNA sequences
Polynomials
Color

Inferring evolutionary trees from polymorphic characters, and an analysis of the Indo-European family of languages

Bonet, M., Phillips, C., Warnow, T. & Yooseph, S., 1997, Mathematical hierarchies and biology (Piscataway, NJ, 1996). Amer. Math. Soc., Providence, RI, Vol. 37. p. 43-55 13 p. (DIMACS Ser. Discrete Math. Theoret. Comput. Sci.).

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

Inferring optimal species trees under gene duplication and loss

Bayzid, M. S., Mirarab, S. & Warnow, T., Jan 1 2013, In : Pacific Symposium on Biocomputing. p. 250-261 12 p.

Research output: Contribution to journalConference article

Gene Duplication
Genes
Dynamic programming
Software
Polynomials

In Memoriam Eugene L. Lawler

Gustfield, D., Shmoys, D., Lenstra, J. K. & Warnow, T., Jan 1 1994, In : Journal of Computational Biology. 1, 4, p. 255-256 2 p.

Research output: Contribution to journalArticle

Kaikoura tree theorems: Computing the maximum agreement subtree

Steel, M. & Warnow, T., Nov 8 1993, In : Information Processing Letters. 48, 2, p. 77-82 6 p.

Research output: Contribution to journalArticle

Computing
Theorem
Binary trees
Leaves
Binary Tree

Large-scale multiple sequence alignment and tree estimation using saté

Liu, K. & Warnow, T., 2014, Multiple Sequence Alignment Methods. Humana Press Inc., p. 219-244 26 p. (Methods in Molecular Biology; vol. 1079).

Research output: Chapter in Book/Report/Conference proceedingChapter

Sequence Alignment
Datasets
Bioinformatics
Computer science
Artificial intelligence
Artificial Intelligence
Computer Science

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

Local quartet splits of a binary tree infer all quartet splits via one dyadic inference rule

ErdH os, P., Steel, M. A., Székely, L. & Warnow, T. J., 1997, In : Computing and Informatics. 16, 2, p. 217-227 11 p.

Research output: Contribution to journalArticle

Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods

Roch, S., Nute, M. & Warnow, T., Mar 1 2019, In : Systematic biology. 68, 2, p. 281-297 17 p.

Research output: Contribution to journalArticle

topology
loci
methodology
gene
genomics

Mathematical approaches to comparative linguistics

Warnow, T., Jun 24 1997, In : Proceedings of the National Academy of Sciences of the United States of America. 94, 13, p. 6585-6590 6 p.

Research output: Contribution to journalArticle

Linguistics
Language
History

Minimizing phylogenetic number to find good evolutionary trees

Goldberg, L. A., Goldberg, P. W., Phillips, C. A., Sweedyk, E. & Warnow, T., Dec 5 1996, In : Discrete Applied Mathematics. 71, 1-3, p. 111-136 26 p.

Research output: Contribution to journalArticle

Evolutionary Tree
Phylogenetics
Topology
Polynomials
Parsimony

Minimizing phylogenetic number to find good evolutionary trees

Goldberg, L. A., Goldberg, P. W., Phillips, C. A., Sweedyk, E. & Warnow, T., Jan 1 1995, Combinatorial Pattern Matching - 6th Annual Symposium, CPM 1995, Proceedings. Galil, Z. & Ukkonen, E. (eds.). Springer-Verlag, p. 102-127 26 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 937).

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

Evolutionary Tree
Phylogenetics
Topology
Polynomials
Parsimony

Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows

Shah, N., Nute, M. G., Warnow, T. & Pop, M., May 1 2019, In : Bioinformatics. 35, 9, p. 1613-1614 2 p.

Research output: Contribution to journalLetter

Workflow
Bioinformatics
Computational Biology
Work Flow
Correctness

MRL and SuperFine+MRL: New supertree methods

Nguyen, N., Mirarab, S. & Warnow, T., Jan 26 2012, In : Algorithms for Molecular Biology. 7, 1, 3.

Research output: Contribution to journalArticle

Matrix Representation
Parsimony
Likelihood
Trinitrotoluene
Heuristics

Multiple sequence alignment: A major challenge to large-scale phylogenetics

Liu, K., Linder, C. R. & Warnow, T., Dec 1 2010, In : PLoS Currents. NOV, ecurrents.RRN1198.

Research output: Contribution to journalArticle

Sequence Alignment
Phylogeny
Benchmarking
Datasets
Research Personnel

Naive binning improves phylogenomic analyses

Bayzid, M. S. & Warnow, T., Sep 15 2013, In : Bioinformatics. 29, 18, p. 2277-2284 8 p.

Research output: Contribution to journalArticle

Binning
Genes
Sorting
Gene
Coalescence