directory

Tandy Warnow

Education

  • BA Mathematics, The University of California at Berkeley, 1984
  • PhD Mathematics, The University of California at Berkeley, 1991

Academic Positions

  • The University of Illinois at Urbana-Champaign, Founder Professor of Computer Science, 2014-present. Special Advisor to Department Head 2019-present;  Associate Chair for Computer Science 2017-2018. Affiliate in the departments of Mathematics, Electrical and Computer Engineering, Bioengineering, Statistics, Plant Biology, Animal Biology, and Entomology. Affiliate in the National Center for Supercomputing Applications (NCSA), Coordinated Sciences Laboratory (CSL), and member of the Carl R. Woese Institute for Genomic Biology (IGB). Affiliate in the PEEC program.
  • The University of Texas at Austin, David Bruton Jr. Professor of Computer Science, 2003-2014
  • The University of Texas at Austin, Associate Professor of Computer Science, 1999-2003
  • The University of Pennsylvania, Associate Professor of Computer and Information Sciences, 1998-1999
  • The University of Pennsylvania, Assistant Professor of Computer and Information Sciences, 1993-1998

For more information

Research Interests

  • Computational Historical Linguistics
  • Metagenomics
  • Multiple sequence alignment
  • Phylogenomics
  • Phylogenetic tree estimation
  • Big Data
  • Discrete and graph-theoretic algorithms

Research Statement

My research combines mathematics, computer science, probability, and statistics, in order to develop algorithms with improved accuracy for large-scale and complex estimation problems in phylogenomics and metagenomics. My major interests include multiple sequence alignment and phylogeny estimation (both gene trees and species trees) and metagenomic analysis, but I also work in Historical Linguistics. My current work aims to develop methods for ultra-large datasets (anywhere from 10,000 to 1,000,000 sequences), including datasets that are highly fragmentary and present other real world challenges. We use real data and perform massive simulations to evaluate the performance of methods that we develop, and also collaborate closely with biologists and linguists in data analysis.

Books Authored or Co-Authored (Original Editions)

  • Computational Phylogenetics: An introduction to designing methods for phylogeny estimation 2018, Cambridge University Press

Selected Articles in Journals

  • P. Vachaspati and T. Warnow (2016). FastRFS: Fast and Accurate Robinson-Foulds Supertrees using Constrained Exact Optimization Bioinformatics 2016; doi: 10.1093/bioinformatics/btw600. (Special issue for papers from RECOMB-CG)
  • L. Uricchio, T. Warnow, and N. Rosenberg (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. BMC Bioinformatics, 17 (Suppl 14): 1266, special issue for RECOMB-CG.
  • M. Nute and T. Warnow (2016). Scaling statistical multiple sequence alignment to large datasets. BMC Genomics 17(Suppl 10): 764, special issue for RECOMB-CG.
  • N. Nguyen, M. Nute, S. Mirarab, and T. Warnow (2016). HIPPI: Highly accurate protein family classification with ensembles of HMMs. BMC Genomics 17 (Suppl 10):765, special issue for RECOMB-CG.
  • T. Hansen, S. Mollerup, N. Nguyen, L. Vinner, N. White, M. Coghlan, D. Alquezar-Planas, T. Joshi, R. Jensen, H. Fridholm, K. Kjaransdottir, T. Mourier, T. Warnow, G. Belsham, T. Gilbert, L. Orlando, M. Bunce, E. Willerslev, L. Nielsen, and A. Hansen (2016). High diversity of picornaviruses in rats from different continents revealed by deep sequencing, Emerging Microbes & Infections 5, e90, doi:doi:10.1038/emi.2016.90.
  • N. Nguyen, T. Warnow, M. Pop, and B. White. A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity. npj Biofilms and Microbiomes 2, Article number 16004 (2016), doi:10.1038/npjbiofilms.2016.4.
  • J.E. Tarver, M. d. Reis, S. Mirarab, R. J. Moran, S. Parker, J.E. O'Reilly, B.L. King, M.J. O'Connell, R.J. Asher, T. Warnow, K. J. Peterson, P.C.J. Donoghue, and D. Pisani. The interrelationships of placental mammals and the limits of phylogenetic inference. Genome Biology and Evolution, doi:10.1093/gbe/evv261.
  • S. Mirarab, Md. S. Bayzid, B. Boussau, and T. Warnow. Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree". Science, 2015, volume 350, number 6257, p. 171, DOI: 10.1126/science.aaa7719.
  • P. Vachaspati and T. Warnow. ASTRID: Accurate Species TRees from Internode Distances. BMC Genomics, 2015, 16 (Suppl 10): S3.
  • J. Chou, A. Gupta, S. Yaduvanshi, R. Davidson, M. Nute, S. Mirarab and T. Warnow. A comparative study of SVDquartets and other coalescent-based species tree estimation methods. BMC Genomics, 2015., 2015, 16 (Suppl 10): S2.
  • R. Davidson, P. Vachaspati, S. Mirarab, and T. Warnow. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer.  BMC Genomics, 2015, Preliminary version at (PDF), 2015, 16 (Suppl 10): S1.
  • T. Warnow. "Concatenation analyses in the presence of incomplete lineage sorting", PLOS Currents: Tree of Life 2015 May 22. Edition 1. doi: 10.1371/currents.tol.8d41ac0f13d1abedf4c4a59f5d17b1f7 (HTML)
  • S. Roch and T. Warnow. "On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods", Systematic Biology, 64(4):663-676, 2015, (PDF)
  • S. Mirarab and T. Warnow. "ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes", Proceedings Intelligent Systems for Molecular Biology (ISMB) 2015, and Bioinformatics 2015 31 (12): i44-i52 doi: 10.1093/bioinformatics/btv234
  • M. S. Bayzid, S. Mirarab, B. Boussau, and T. Warnow. "Weighted Statistical Binning: enabling statistically consistent genome-scale phylogenetic analyses", PLOS One, 2015, DOI: 10.1371/journal.pone.0129183.
  • N. Nguyen, S. Mirarab, K. Kumar, and T. Warnow, "Ultra-large alignments using phylogeny aware profiles". Genome Biology (2015) 16:124 doi: 10.1186/s13059-015-0688-z
  • E. D. Jarvis, S. Mirarab, A. J. Aberer, B. Li, P. Houde, C. Li, S. Y. W. Ho, B. C. Faircloth, B. Nabholz, J. T. Howard, A. Suh, C. C. Weber, R. R. da Fonseca, J. Li, F. Zhang, H. Li, L. Zhou, N. Narula, L. Liu, G. Ganapathy, B. Boussau, Md. S. Bayzid, V. Zavidovych, S. Subramanian, T. Gabaldon, S. Capella-Gutierrez, J. Huerta-Cepas, B. Rekepalli, K. Munch, M. Schierup, B. Lindow, W. C. Warren, D. Ray, R. E. Green, M. W. Bruford, X. Zhan, A. Dixon, S. Li, N. Li, Y. Huang, E. P. Derryberry, M. F. Bertelsen, F. H. Sheldon, R. T. Brumfield, C. V. Mello, P. V. Lovell, M. Wirthlin, M. P. C. Schneider, F. Prosdocimi, J. A. Samaniego, A. M. V. Velazquez, A. Alfaro-Nunez, P. F. Campos, B. Petersen, T. Sicheritz-Ponten, A. Pas, T. Bailey, P. Scofield, M. Bunce, D. M. Lambert, Q. Zhou, P. Perelman, A. C. Driskell, B. Shapiro, Z. Xiong, Y. Zeng, S. Liu, Z. Li, B. Liu, K. Wu, J. Xiao, X. Yinqi, Q. Zheng, Y. Zhang, H. Yang, J. Wang, L. Smeds, F. E. Rheindt, M. Braun, J. Fjeldsa, L. Orlando, F. K. Barker, K. A. Jonsson, W. Johnson, K.-P. Koepfli, S. O'Brien, D. Haussler, O. A. Ryder, C. Rahbek, E. Willerslev, G. R. Graves, T. C. Glenn, J. McCormack, D. Burt, H. Ellegren, P. Alstrom, S. V. Edwards, A. Stamatakis, D. P. Mindell, J. Cracraft, E. L. Braun, T. Warnow, W. Jun, M. T. P. Gilbert, and G. Zhang. "Whole-genome analyses resolve early branches in the tree of life of modern birds." Science 12 December 2014: 1320-1331
  • S. Mirarab, Md. S. Bayzid, B. Boussau, and T. Warnow. "Statistical binning enables an accurate coalescent-based estimation of the avian tree". Science, 12 December 2014: 1250463. Science
  • S. Mirarab, N. Nguyen, S. Guo, L.-S. Wang, J. Kim, and T. Warnow ``PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences." Journal of Computational Biology. December 2014 (ahead of print)
  • N. Nguyen, S. Mirarab, B. Liu, M. Pop, and T. Warnow "TIPP:Taxonomic Identification and Phylogenetic Profiling." Bioinformatics, 2014; doi: 10.1093/bioinformatics/btu721
  • N. Wickett, S. Mirarab, N. Nguyen, T. Warnow, et al. (37 authors). ``Phylotranscriptomic analysis of the origin and diversification of land plants." Proceedings of the National Academy of Sciences (PNAS), doi: 10.1073/pnas.1323926111
  • S. Mirarab, Md S. Bayzid, and T. Warnow. "Evaluating summary methods for multi-locus species tree estimation in the presence of incomplete lineage sorting". Systematic Biology, doi =10.1093/sysbio/syu063
  • T. Zimmermann, S. Mirarab and T. Warnow. "BBCA: Improving the scalability of *BEAST using random binning". BMC Genomics 2014, 15(Suppl 6): S11
  • Md S. Bayzid, T. Hunt, and T. Warnow. "Disk Covering Methods Improve Phylogenomic Analyses". BMC Genomics 2014, 15(Suppl 6): S7
  • S. Mirarab, R. Reaz, Md. S. Bayzid, T. Zimmermann, M.S. Swenson, and T. Warnow. "ASTRAL: Genome-Scale Coalescent-Based Species Tree Estimation." Bioinformatics 2014 30 (17): i541-i548. doi: 10.1093/bioinformatics/btu462.

Journal Editorships

  • Associate Editor, Journal Graph Algorithms and Applications (to 2019)

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