Warnow's courses

Fall 2023

CS 581: Algorithmic Genomic Biology

Teaching awards

I have been on the list of Teachers Ranked As Excellent by their Students five times -- for Spring 2017, Spring 2018, Fall 2018, Fall 2020, and Fall 2021. (Spring 2017 is for CS 466 and the others are for CS 581.)

Papers based on student course projects

Several student course projects for my graduate courses (CS 581 or its precursors here and at UT-Austin) have been the basis for subsequent papers that have been published in strong journals and conferences. Here is a partial list.

Y. Tabatabaee, K. Sarkar, and T. Warnow. Quintet Rooting: Rooting Species Trees under the Multi-Species Coalescent Mode. To appear, ISMB (Intelligent Systems for Molecular Biology), 2022. (Will also appear in Bioinformatics, the special issue for ISMB 2022).
J. Willson, M.S. Ruddur, and T. Warnow. Comparing Methods for Species Tree Estimation With Gene Duplication and Loss. In: Martin-Vide C., Vega-Rodriguez M.A., Wheeler T. (eds) Algorithms for Computational Biology. AlCoB 2021. Lecture Notes in Computer Science, vol 12715. Springer, Cham. DOI: https://doi.org/10.1007/978-3-030-74432-8_8 (HTML)
E. Koning, M. Phillips, and T. Warnow. pplacerDC: a New Scalable Phylogenetic Placement Method. ACM-BCB 2021.
E. Wedell, Y. Cai, and T. Warnow. Scalable and Accurate Phylogenetic Placement using pplacer-XR. In: Martin-Vide C., Vega-Rodriguez M.A., Wheeler T. (eds) Algorithms for Computational Biology. AlCoB 2021. Lecture Notes in Computer Science, vol 12715. Springer, Cham. DOI: https://doi.org/10.1007/978-3-030-74432-8_7 (HTML) An extended version of this paper has been accepted to the IEEE/ACM Transactions on Computational Biology and Bioinformatics.
P. Dibaiena, S. Tabe Bordhbar, and T. Warnow (2021). FASTRAL: Improving scalability of phylogenomic analysis. Bioinformatics, btab093. (HTML)
M. Gupta, P. Zaharias, and T. Warnow. Accurate Large-scale Phylogeny-Aware Alignment using BAli-Phy. Bioinformatics 2021. (HTML)
P. Zaharias, M. Grosshauser, and T. Warnow (2021). Re-evaluating deep neural networks for phylogeny estimation: The issue of taxon sampling. RECOMB 2021 and J. Computational Biology 2022.
S. Pattabiraman and T. Warnow (2018). Are Profile Hidden Markov Models Identifiable? Proceedings of ACM-BCB 2018, pages 448-456, DOI: 10.1145/3233547.3233563. (HTML)
S. Pattabiraman and T. Warnow (2019). Profile Hidden Markov Models are not Identifiable. IEEE/ACM Transactions on Computational Biology, Vol. 18, No. 1, Jan/Feb 2021. DOI 10.1109/TCBB.2019.2933821. (PDF)
S. Christensen, E. Molloy, P. Vachaspati, and T. Warnow (2018). OCTAL: Optimal Completion of Gene Trees in Polynomial Time. Algorithms for Molecular Biology, 13:6, DOI: 10.1186/s13015-018-0124-5. (HTML)
R. Davidson, P. Vachaspati, S. Mirarab, and T. Warnow. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. RECOMB-Comparative Genomics, and BMC Genomics, 2015, Preliminary version at (PDF), 2015, 16 (Suppl 10): S1.
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. RECOMB-Comparative Genomics and BMC Genomics, 2015., 2015, 16 (Suppl 10): S2.
Md S. Bayzid, T. Hunt, and T. Warnow. Disk Covering Methods Improve Phylogenomic Analyses. Proceedings of RECOMB-CG (Comparative Genomics), 2014, and BMC Genomics 2014, 15(Suppl 6): S7. (PDF) and Supplementary materials
T. Zimmermann, S. Mirarab and T. Warnow. BBCA: Improving the scalability of *BEAST using random binning. Proceedings of RECOMB-CG (Comparative Genomics), 2014, and BMC Genomics 2014, 15(Suppl 6): S11. (PDF) and Supplementary materials.
S. Mirarab, R. Reaz, Md S. Bayzid, T. Zimmermann, M.S. Swenson, and T. Warnow. ASTRAL: Genome-Scale Coalescent-Based Species Tree Estimation. Proceedings, ECCB (European Conference on Computational Biology), 2014. Also, Bioinformatics 2014 30 (17): i541-i548. doi: 10.1093/bioinformatics/btu462. (PDF)
J. Yang and T. Warnow "Fast and accurate methods for phylogenomic analyses." RECOMB Comparative Genomics 2011, and BMC Bioinformatics 12(Suppl 9): S4 (5 October 2011).