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Research Output

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., 2015, In : BMC genomics. 16, p. 1-11 11 p.

Research output: Contribution to journalArticle

Advances in phylogeny reconstruction from gene order and content data

Moret, B. M. E. & Warnow, T., 2005, In : Methods in enzymology. 395, p. 673-700 28 p.

Research output: Contribution to journalArticle

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

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

Erdos, P. L., Steel, M. A., Székely, L. A. & Warnow, T. J., Jun 28 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. 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. J., Mar 1999, In : Random Structures and Algorithms. 14, 2, p. 153-184 32 p.

Research output: Contribution to journalArticle

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

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

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

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

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

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

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

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

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, p. i541-i548

Research output: Contribution to journalArticle

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

ASTRID: Accurate species TRees from internode distances

Vachaspati, P. & Warnow, T., 2015, In : BMC genomics. 16, p. 1-13 13 p., S3.

Research output: Contribution to journalArticle

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

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

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., 2010, In : PLoS Currents. NOV, ecurrents.RRN1195.

Research output: Contribution to journalArticle

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

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

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

Concatenation analyses in the presence of incomplete lineage sorting

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

Research output: Contribution to journalArticle

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

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

Constructing phylogenetic trees efficiently using compatibility criteria

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

Research output: Contribution to journalArticle

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

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

Research output: Contribution to journalArticle

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

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

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

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

Distance-based genome rearrangement phylogeny

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

Research output: Contribution to journalArticle

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

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

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

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

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

FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models

Molloy, E. K. & Warnow, T., Jul 1 2020, In : Bioinformatics (Oxford, England). 36, 1, p. i57-i65

Research output: Contribution to journalArticle

Open Access

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

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

Research output: Contribution to journalArticle

FASTSP: Linear time calculation of alignment accuracy

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

Research output: Contribution to journalArticle

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

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

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

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

Research output: Contribution to journalArticle

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

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

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