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Research Output

2015

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

Ultra-large alignments using ensembles of hidden Markov models

Nguyen, N. P., Mirarab, S., Kumar, K. & Warnow, T., Jan 1 2015, Research in Computational Molecular Biology - 19th Annual International Conference, RECOMB 2015, Proceedings. Przytycka, T. M. (ed.). Springer-Verlag Berlin Heidelberg, p. 259-260 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9029).

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

Ultra-large alignments using phylogeny-aware profiles

Nguyen, N. P. D., Mirarab, S., Kumar, K. & Warnow, T., Jun 16 2015, In : Genome biology. 16, 1, 124.

Research output: Contribution to journalArticle

Weighted statistical binning: Enabling statistically consistent genome-scale phylogenetic analyses

Bayzid, M. S., Mirarab, S., Boussau, B. & Warnow, T., Jun 18 2015, In : PloS one. 10, 6, e0129183.

Research output: Contribution to journalArticle

2014

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

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

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

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

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

PASTA: Ultra-large multiple sequence alignment

Mirarab, S., Nguyen, N. & Warnow, T., Jan 1 2014, Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Proceedings. Springer-Verlag, p. 177-191 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8394 LNBI).

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

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

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

TIPP: Taxonomic identification and phylogenetic profiling

Nguyen, N. P., Mirarab, S., Liu, B., Pop, M. & Warnow, T., Dec 15 2014, In : Bioinformatics. 30, 24, p. 3548-3555 8 p.

Research output: Contribution to journalArticle

Whole-genome analyses resolve early branches in the tree of life of modern birds

Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., Suh, A., Weber, C. C., Da Fonseca, R. R., Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L., Ganapathy, G. & 85 others, Boussau, B., Bayzid, M. S., Zavidovych, V., Subramanian, S., Gabaldón, T., Capella-Gutiérrez, S., Huerta-Cepas, J., Rekepalli, B., Munch, K., Schierup, M., Lindow, B., Warren, W. C., Ray, D., Green, R. E., Bruford, M. W., Zhan, X., Dixon, A., Li, S., Li, N., Huang, Y., Derryberry, E. P., Bertelsen, M. F., Sheldon, F. H., Brumfield, R. T., Mello, C. V., Lovell, P. V., Wirthlin, M., Schneider, M. P. C., Prosdocimi, F., Samaniego, J. A., Velazquez, A. M. V., Alfaro-Núñez, A., Campos, P. F., Petersen, B., Sicheritz-Ponten, T., Pas, A., Bailey, T., Scofield, P., Bunce, M., Lambert, D. M., Zhou, Q., Perelman, P., Driskell, A. C., Shapiro, B., Xiong, Z., Zeng, Y., Liu, S., Li, Z., Liu, B., Wu, K., Xiao, J., Yinqi, X., Zheng, Q., Zhang, Y., Yang, H., Wang, J., Smeds, L., Rheindt, F. E., Braun, M., Fjeldsa, J., Orlando, L., Barker, F. K., Jønsson, K. A., Johnson, W., Koepfli, K. P., O'Brien, S., Haussler, D., Ryder, O. A., Rahbek, C., Willerslev, E., Graves, G. R., Glenn, T. C., McCormack, J., Burt, D., Ellegren, H., Alström, P., Edwards, S. V., Stamatakis, A., Mindell, D. P., Cracraft, J., Braun, E. L., Warnow, T., Jun, W., Gilbert, M. T. P. & Zhang, G., Dec 12 2014, In : Science. 346, 6215, p. 1320-1331 12 p.

Research output: Contribution to journalArticle

2013

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

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

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

Phylogenomics and population genomics: Moddels, algorithms, and analytical tools

Nakhleh, L. K., Rosenberg, N. A. & Warnow, T., Jan 1 2013, In : Pacific Symposium on Biocomputing.

Research output: Contribution to journalConference article

2012

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

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

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

Parallelizing SuperFine

Neves, D. T., Warnow, T., Sobral, J. L. & Pingali, K., Jul 12 2012, 27th Annual ACM Symposium on Applied Computing, SAC 2012. p. 1361-1367 7 p. (Proceedings of the ACM Symposium on Applied Computing).

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

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

SEPP: SATé-enabled phylogenetic placement

Mirarab, S., Nguyen, N. & Warnow, T., Jan 1 2012, In : Pacific Symposium on Biocomputing. p. 247-258 12 p.

Research output: Contribution to journalConference article

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

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

Treelength optimization for phylogeny estimation

Liu, K. & Warnow, T., Mar 19 2012, In : PloS one. 7, 3, e33104.

Research output: Contribution to journalArticle

2011

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

Algorithms for MDC-based multi-locus phylogeny inference

Yu, Y., Warnow, T. & Nakhleh, L., Apr 4 2011, Research in Computational Molecular Biology - 15th Annual International Conference, RECOMB 2011, Proceedings. p. 531-545 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6577 LNBI).

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

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

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

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

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

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

2010

An experimental study of quartets MaxCut and other supertree methods

Swenson, M. S., Suri, R., Linder, C. R. & Warnow, T., Nov 10 2010, Algorithms in Bioinformatics - 10th International Workshop, WABI 2010, Proceedings. p. 288-299 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6293 LNBI).

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

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

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

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

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

2009

A simulation study comparing supertree and combined analysis methods using SMIDGen

Swenson, M. S., Barbançon, F., Linder, C. R. & Warnow, T., Nov 2 2009, Algorithms in Bioinformatics - 9th International Workshop, WABI 2009, Proceedings. p. 333-344 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5724 LNBI).

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

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

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

2008

Beyond gap models: Reconstructing alignments and phylogenies under genomic-scale events

Brudno, M., Moret, B., Linder, R. & Warnow, T., 2008, Pacific Symposium on Biocomputing 2008, PSB 2008. p. 1-2 2 p.

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

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

The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses

Nelesen, S., Liu, K., Zhao, D., Linder, C. R. & Warnow, T., Dec 1 2008, Pacific Symposium on Biocomputing 2008, PSB 2008. p. 25-36 12 p. (Pacific Symposium on Biocomputing 2008, PSB 2008).

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

Tutorial on computational linguistic phylogeny

Nichols, J. & Warnow, T., Jan 1 2008, In : Linguistics and Language Compass. 2, 5, p. 760-820 61 p.

Research output: Contribution to journalArticle

2006

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

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

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