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Research Output 1990 2019

2015

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

sequence alignment
Phylogeny
Sequence Alignment
phylogeny
amino acid sequences

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

Genes
Genome
genome
phylogeny
genes
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

Research output: Contribution to journalArticle

Genome
Genes
Gene
Sorting
Biodiversity

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

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

Viridiplantae
Proteins
Transcriptome
Visualization
Pipelines

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

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

Sequence Alignment
Datasets

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

Multiple Sequence Alignment
Alignment
Large Data Sets
Data storage equipment

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

Embryophyta
Hepatophyta
Plant Genome
Bryophyta
Chlorophyta

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

Genes
Expressed Sequence Tags
Genome

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

Metagenomics
Phylogenetics
Profiling
Genes
Genome

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

Birds
Genome
Biological Extinction
Modern 1601-history
Columbidae
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

reconstruction
linguistics
phylogeny
weighting
simulation

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

Gene Duplication
Genes
Dynamic programming
Software
Polynomials

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

Binning
Genes
Sorting
Gene
Coalescence

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

Genomics
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, bts218.

Research output: Contribution to journalArticle

Divide and conquer
Alignment
Maximum likelihood
Phylogeny
Iteration

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

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

Matrix Representation
Parsimony
Likelihood
Trinitrotoluene
Heuristics

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

Binary trees
Scaffolds
Computational complexity

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

Sequence Alignment
sequence alignment
phylogenetics
phylogeny
alignment

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

Sequence Alignment
Software
Metagenomics
Genes
Association reactions

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

Phylogeny
Sequence Alignment
Research

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

phylogenetics
phylogeny
estimation method
methodology
method

Treelength optimization for phylogeny estimation

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

Research output: Contribution to journalArticle

Phylogeny
phylogeny
Maximum likelihood
Sequence Alignment
sequence alignment
2011

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

Phylogeny
Locus
Genes
Gene
Binary trees

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

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

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

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

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

Maximum likelihood estimation
Phylogeny
Maximum likelihood
phylogeny
Sequence Alignment

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

Sequence Alignment
Phylogenetics
Protein Sequence
Alignment
Proteins
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

Max-cut
Experimental Study
Parsimony
Matrix Representation
Evaluate

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

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

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

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

Sequence Alignment
Phylogeny
Benchmarking
Datasets
Research Personnel
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

Parsimony
Simulation Study
Matrix Representation
Subset
Maximum likelihood

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
Bioinformatics
Computer science
Artificial intelligence
Artificial Intelligence
Computer Science

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

Sequence Alignment
Molecular Sequence Data
DNA
Datasets
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

Phylogeny

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

Phylogeny
Reconstruction Algorithm
Joining
Maximum likelihood
Maximum Parsimony

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

Sequence Alignment
Phylogeny
Muscle
Muscles

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

computational linguistics
phylogeny
biology
linguistics
methodology
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

Phylogeny
phylogeny
genome
Genes
Genome

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

biogeography
Identification Problem
Linear-time Algorithm
Formalization
Efficient Algorithms

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

Chromosomes
Chromosome
Transposition
Genes
Genome Rearrangement

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA)

Leebens-Mack, J., Vision, T., Brenner, E., Bowers, J. E., Cannon, S., Clement, M. J., Cunningham, C. W., DePamphilis, C., DeSalle, R., Doyle, J. J., Eisen, J. A., Gu, X., Harshman, J., Jansen, R. K., Kellogg, E. A., Koonin, E. V., Mishler, B. D., Philippe, H., Pires, J. C., Qiu, Y. L. & 8 others, Rhee, S. Y., Sjölander, K., Soltis, D. E., Soltis, P. S., Stevenson, D. W., Wall, K., Warnow, T. & Zmasek, C., Sep 4 2006, In : OMICS A Journal of Integrative Biology. 10, 2, p. 231-237 7 p.

Research output: Contribution to journalReview article

Phylogeny
Genes
Genome
Microarrays
Genomics
2005

A comparison of phylogenetic reconstruction methods on an Indo-European dataset

Nakhleh, L., Warnow, T., Ringe, D. & Evans, S. N., Aug 1 2005, In : Transactions of the Philological Society. 103, 2, p. 171-192 22 p.

Research output: Contribution to journalReview article

phylogeny
reconstruction
estimation procedure
language
linguistics