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Research Output 1990 2019

Article

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

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 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

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

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., Apr 19 2011, In : Algorithms for Molecular Biology. 6, 1, 7.

Research output: Contribution to journalArticle

Max-cut
Experimental Study
Sampling
Scalability
Parsimony

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

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 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

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

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., 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

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, bts218.

Research output: Contribution to journalArticle

Divide and conquer
Alignment
Maximum likelihood
Phylogeny
Iteration

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

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., 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

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

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

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

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

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