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Research Output

2019

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

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

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

New Divide-and-Conquer Techniques for Large-Scale Phylogenetic Estimation

Warnow, T., Jan 1 2019, Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Proceedings. Vega-Rodríguez, M. A., Holmes, I. & Martín-Vide, C. (eds.). Springer-Verlag, p. 3-21 19 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11488 LNBI).

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

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

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

Traction: Fast non-parametric improvement of estimated gene trees

Christensen, S., Molloy, E. K., Vachaspati, P. & Warnow, T., Sep 2019, 19th International Workshop on Algorithms in Bioinformatics, WABI 2019. Huber, K. T. & Gusfield, D. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 4. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 143).

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

TreeMerge: A new method for improving the scalability of species tree estimation methods

Molloy, E. K. & Warnow, T., Jul 15 2019, In : Bioinformatics. 35, 14, p. i417-i426 btz344.

Research output: Contribution to journalArticle

Open Access

Using INC Within Divide-and-Conquer Phylogeny Estimation

Le, T., Sy, A., Molloy, E. K., Zhang, Q. R., Rao, S. & Warnow, T., Jan 1 2019, Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Proceedings. Vega-Rodríguez, M. A., Holmes, I. & Martín-Vide, C. (eds.). Springer-Verlag, p. 167-178 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11488 LNBI).

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

2018

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

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

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

New absolute fast converging phylogeny estimation methods with improved scalability and accuracy

Zhang, Q., Rao, S. & Warnow, T., Aug 1 2018, 18th International Workshop on Algorithms in Bioinformatics, WABI 2018. Parida, L. & Ukkonen, E. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 8. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 113).

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

NJMerge: A Generic technique for scaling phylogeny estimation methods and its application to species trees

Molloy, E. K. & Warnow, T., Jan 1 2018, Comparative Genomics - 16th International Conference, RECOMB-CG 2018, Proceedings. Ouangraoua, A. & Blanchette, M. (eds.). Springer-Verlag, p. 260-276 17 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11183 LNBI).

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

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

PASTA for proteins

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

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 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 performance of coalescent-based species tree estimation methods under models of missing data

Nute, M., Chou, J., Molloy, E. K. & Warnow, T., May 8 2018, In : BMC genomics. 19, 286.

Research output: Contribution to journalArticle

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

Molloy, E. K. & Warnow, T., Mar 1 2018, In : Systematic biology. 67, 2, p. 285-303 19 p.

Research output: Contribution to journalArticle

2017

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

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

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

Optimal completion of incomplete gene trees in polynomial time using OCTAL

Christensen, S., Molloy, E. K., Vachaspati, P. & 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, 27. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 88).

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

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

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

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

2016

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

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

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

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

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

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

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

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

2015

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

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., Jan 1 2015, In : BMC genomics. 16, p. 1-13 13 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

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

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

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

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

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

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds"

Cracraft, J., Houde, P., Ho, S. Y. W., Mindell, D. P., Fjeldså, J., Lindow, B., Edwards, S. V., Rahbek, C., Mirarab, S., Warnow, T., Gilbert, M. T. P., Zhang, G., Braun, E. L. & Jarvis, E. D., Sep 25 2015, In : Science. 349, 6255, p. 1460-b

Research output: Contribution to journalComment/debate