Research Output per year
Research Output
2009
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 journal › Article
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 proceeding › Conference 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 journal › Article
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 journal › Article
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 journal › Article
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 journal › Article
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 proceeding › Conference contribution
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 journal › Article
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 journal › Article
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 journal › Article
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 journal › Article
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 journal › Article
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 journal › 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 journal › Article
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 journal › Article
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 journal › Article
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 proceeding › Conference 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 journal › Article
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 journal › Conference 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 journal › Article
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 journal › Article
Treelength optimization for phylogeny estimation
Liu, K. & Warnow, T., Mar 19 2012, In : PloS one. 7, 3, e33104.Research output: Contribution to journal › Article
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 journal › Article
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 journal › Conference 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 journal › Article
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 journal › Conference article
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-i548Research output: Contribution to journal › Article
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 journal › Article
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, , Oct 27 2014, In : GigaScience. 3, 1, 17.Research output: Contribution to journal › Review 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 journal › Article
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 proceeding › Chapter
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 proceeding › Conference 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, , Nov 11 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 45, p. E4859-E4868Research output: Contribution to journal › Article
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 journal › Article
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 journal › Article
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, , Dec 12 2014, In : Science. 346, 6215, p. 1320-1331 12 p.Research output: Contribution to journal › Article
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 journal › Article
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-i52Research output: Contribution to journal › Article
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 journal › Article
Concatenation analyses in the presence of incomplete lineage sorting
Warnow, T., May 22 2015, In : PLoS Currents. 7, TREEOFLIFEResearch output: Contribution to journal › Article
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 journal › Article
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 journal › Article
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 journal › Article
Phylogenomic analyses data of the avian phylogenomics project
The Avian Phylogenomics Consortium, Feb 12 2015, In : GigaScience. 4, 1, 4.Research output: Contribution to journal › Article
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 journal › Article
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 journal › Article
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-bResearch output: Contribution to journal › Comment/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 proceeding › Conference 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 journal › Article
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 journal › Article