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Research Output

Article

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

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

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

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

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

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

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

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

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

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

OCTAL: Optimal Completion of gene trees in polynomial time

Christensen, S., Molloy, E. K., Vachaspati, P. & Warnow, T., Mar 15 2018, In : Algorithms for Molecular Biology. 13, 1, 6.

Research output: Contribution to journalArticle

One thousand plant transcriptomes and the phylogenomics of green plants

One Thousand Plant Transcriptomes Initiative, Oct 31 2019, In : Nature. 574, 7780, p. 679-685 7 p.

Research output: Contribution to journalArticle

Open Access

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

Roch, S. & Warnow, T., Jul 1 2015, In : Systematic biology. 64, 4, p. 663-676 14 p.

Research output: Contribution to journalArticle

PASTA: Ultra-large multiple sequence alignment for nucleotide and amino-acid sequences

Mirarab, S., Nguyen, N., Guo, S., Wang, L. S., Kim, J. & Warnow, T., May 1 2015, In : Journal of Computational Biology. 22, 5, p. 377-386 10 p.

Research output: Contribution to journalArticle

PASTA for proteins

Collins, K. & Warnow, T., Nov 15 2018, In : Bioinformatics. 34, 22, p. 3939-3941 3 p.

Research output: Contribution to journalArticle

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

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

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

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

Phylogenomic analyses data of the avian phylogenomics project

The Avian Phylogenomics Consortium, Feb 12 2015, In : GigaScience. 4, 1, 4.

Research output: Contribution to journalArticle

Phylogenomics from whole genome sequences using aTRAM

Allen, J. M., Boyd, B., Nguyen, N. P., Vachaspati, P., Warnow, T., Huang, D. I., Grady, P. G. S., Bell, K. C., Cronk, Q. C. B., Mugisha, L., Pittendrigh, B. R., Leonardi, M. S., Reed, D. L. & Johnson, K. P., Sep 1 2017, In : Systematic biology. 66, 5, p. 786-798 13 p.

Research output: Contribution to journalArticle

Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

Davidson, R., Vachaspati, P., Mirarab, S. & Warnow, T., Jan 1 2015, In : BMC genomics. 16, p. 1-12 12 p.

Research output: Contribution to journalArticle

Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola)

Boyd, B. M., Allen, J. M., Nguyen, N. P., Sweet, A. D., Warnow, T., Shapiro, M. D., Villa, S. M., Bush, S. E., Clayton, D. H. & Johnson, K. P., Nov 1 2017, In : Systematic biology. 66, 6, p. 896-911 16 p.

Research output: Contribution to journalArticle

Phylotranscriptomic analysis of the origin and early diversification of land plants

Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, M. S., Burleigh, J. G., Gitzendanner, M. A., Ruhfel, B. R., Wafula, E., Der, J. P., Graham, S. W., Mathews, S., Melkonian, M., Soltis, D. E., Soltis, P. S., Miles, N. W., Rothfels, C. J. & 22 others, Pokorny, L., Shaw, A. J., De Gironimo, L., Stevenson, D. W., Surek, B., Villarreal, J. C., Roure, B., Philippe, H., De Pamphilis, C. W., Chen, T., Deyholos, M. K., Baucom, R. S., Kutchan, T. M., Augustin, M. M., Wang, J., Zhang, Y., Tian, Z., Yan, Z., Wu, X., Sun, X., Wong, G. K. S. & Leebens-Mack, J., Nov 11 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 45, p. E4859-E4868

Research output: Contribution to journalArticle

Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice

Boyd, B. M., Allen, J. M., Nguyen, N. P., Vachaspati, P., Quicksall, Z. S., Warnow, T., Mugisha, L., Johnson, K. P. & Reed, D. L., Jul 1 2017, In : Molecular biology and evolution. 34, 7, p. 1743-1757 15 p.

Research output: Contribution to journalArticle

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees

Liu, K., Raghavan, S., Nelesen, S., Linder, C. R. & Warnow, T., Jun 19 2009, In : Science. 324, 5934, p. 1561-1564 4 p.

Research output: Contribution to journalArticle

RAxML and FastTree: Comparing two methods for large-scale maximum likelihood phylogeny estimation

Liu, K., Linder, C. R. & Warnow, T., Nov 21 2011, In : PloS one. 6, 11, e27731.

Research output: Contribution to journalArticle

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

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

Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree"

Mirarab, S., Bayzid, M. S., Boussau, B. & Warnow, T., Oct 9 2015, In : Science. 350, 6257, 171.

Research output: Contribution to journalArticle

SATé-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees

Liu, K., Warnow, T. J., Holder, M. T., Nelesen, S. M., Yu, J., Stamatakis, A. P. & Randal Linder, C., Jan 1 2012, In : Systematic biology. 61, 1, p. 90-106 17 p.

Research output: Contribution to journalArticle

Scaling statistical multiple sequence alignment to large datasets

Nute, M. & Warnow, T., Nov 11 2016, In : BMC genomics. 17, 764.

Research output: Contribution to journalArticle

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

SIESTA: Enhancing searches for optimal supertrees and species trees

Vachaspati, P. & Warnow, T., May 8 2018, In : BMC genomics. 19, 252.

Research output: Contribution to journalArticle

Simultaneous radiation of bird and mammal lice following the K-Pg boundary

Johnson, K. P., Nguyen, N. P., Sweet, A. D., Boyd, B. M., Warnow, T. & Allen, J. M., Jan 1 2018, In : Biology Letters. 14, 5, 20180141.

Research output: Contribution to journalArticle

Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent

Warnow, T., Oct 19 2012, In : PLoS Currents. ecurrents.RRN1308.

Research output: Contribution to journalArticle

Statistical binning enables an accurate coalescent-based estimation of the avian tree

Mirarab, S., Bayzid, M. S., Boussau, B. & Warnow, T., Dec 12 2014, In : Science. 346, 6215, 1250463.

Research output: Contribution to journalArticle

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

Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge

Molloy, E. K. & Warnow, T., Jul 19 2019, In : Algorithms for Molecular Biology. 14, 1, 30 p., 14.

Research output: Contribution to journalArticle

Open Access

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

SuperFine: Fast and accurate supertree estimation

Swenson, M. S., Suri, R., Linder, C. R. & Warnow, T., Mar 1 2012, In : Systematic biology. 61, 2, p. 214-227 14 p.

Research output: Contribution to journalArticle

SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space

Vachaspati, P. & Warnow, T., Jul 2018, In : Molecular Phylogenetics and Evolution. 124, p. 122-136 15 p.

Research output: Contribution to journalArticle

The asymmetric median tree - A new model for building consensus trees

Phillips, C. & Warnow, T., Dec 5 1996, In : Discrete Applied Mathematics. 71, 1-3, p. 311-335 25 p.

Research output: Contribution to journalArticle

The development and application of bioinformatics core competencies to improve bioinformatics training and education

Mulder, N., Schwartz, R., Brazas, M. D., Brooksbank, C., Gaeta, B., Morgan, S. L., Pauley, M. A., Rosenwald, A., Rustici, G., Sierk, M., Warnow, T. & Welch, L., Feb 2018, In : PLoS computational biology. 14, 2, e1005772.

Research output: Contribution to journalArticle

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. J., Aug 6 2000, In : Theoretical Computer Science. 244, 1-2, p. 167-188 22 p.

Research output: Contribution to journalArticle

The impact of multiple protein sequence alignment on phylogenetic estimation

Wang, L. S., Leebens-Mack, J., Wall, P. K., Beckmann, K., Depamphilis, C. W. & Warnow, T., Mar 22 2011, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8, 4, p. 1108-1119 12 p., 5235137.

Research output: Contribution to journalArticle

The interrelationships of placental mammals and the limits of phylogenetic inference

Tarver, J. E., Dos Reis, M., Mirarab, S., Moran, R. J., Parker, S., O'Reilly, J. E., King, B. L., O'Connell, M. J., Asher, R. J., Warnow, T., Peterson, K. J., Donoghue, P. C. J. & Pisani, D., Jan 1 2016, In : Genome biology and evolution. 8, 2, p. 330-344 15 p.

Research output: Contribution to journalArticle