Spring 2025
Teaching awards
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.
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M. Canby, S.N. Evans, D. Ringe,and T. Warnow (2024)
Addressing polymorphism in linguistic phylogenetics.
Transactions on the Philological Society, 2024
(HTML)
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Y. Tabatabaee, K. Sarkar, and T. Warnow (2022) Quintet Rooting: Rooting Species Trees under the Multi-Species Coalescent Mode. ISMB (Intelligent Systems for Molecular Biology) 2022 (also Bioinformatics, the special issue for ISMB 2022).
(HTML)
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P. Dibaiena, S. Tabe Bordhbar, and T. Warnow (2021).
FASTRAL: Improving scalability of phylogenomic analysis.
Bioinformatics, btab093.
(HTML)
(supplementary materials).
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P. Zaharias, M. Grosshauser, and T. Warnow (2021).
Re-evaluating deep neural networks for phylogeny estimation:
The issue of taxon sampling.
Journal of Computational Biology (2022),
special issue for RECOMB 2021.
(HTML)
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J. Willson, M.S. Ruddur, and T. Warnow (2021).
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)
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E. Koning, M. Phillips, and T. Warnow (2021). pplacerDC: a New Scalable Phylogenetic Placement Method. ACM-BCB 2021.
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E. Wedell, Y. Cai, and T. Warnow (2021).
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
(HTML)
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M. Gupta, P. Zaharias, and T. Warnow (2021).
Accurate Large-scale Phylogeny-Aware Alignment using BAli-Phy.
Bioinformatics 2021.
(HTML)
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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.
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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)
This was subsequently written up into a journal version,
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)
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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)
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R. Davidson, P. Vachaspati, S. Mirarab, and T. Warnow (2015).
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.
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J. Chou, A. Gupta, S. Yaduvanshi, R. Davidson, M. Nute, S. Mirarab and
T. Warnow (2015).
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.
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Md S. Bayzid, T. Hunt, and T. Warnow (2014).
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
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T. Zimmermann, S. Mirarab and T. Warnow (2014).
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.
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S. Mirarab, R. Reaz, Md S. Bayzid, T. Zimmermann, M.S. Swenson,
and T. Warnow (2014).
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)
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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).
Prior Courses taught at UIUC
2022-2023
2021-2022
2020-2021:
2019-2020:
2018-2019:
2017-2018:
2016-2017
2015-2016
2014-2015
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CS 598: Algorithmic Genomic Biology