Evolution, Ecology, and Behavior

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  • 2025

    FastEnsemble: A New Scalable Ensemble Clustering Method

    Tabatabaee, Y., Wedell, E., Park, M. & Warnow, T., 2025, Complex Networks and Their Applications XIII - Proceedings of The 13th International Conference on Complex Networks and Their Applications: COMPLEX NETWORKS 2024 - Volume 3. Cherifi, H., Donduran, M., Rocha, L. M., Cherifi, C. & Varol, O. (eds.). Springer, p. 57-70 14 p. (Studies in Computational Intelligence; vol. 1189 SCI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Improved Community Detection Using Stochastic Block Models

    Park, M., Feng, D. W., Digra, S., Vu-Le, T. A., Chacko, G. & Warnow, T., 2025, Complex Networks and Their Applications XIII - Proceedings of The 13th International Conference on Complex Networks and Their Applications: COMPLEX NETWORKS 2024 - Volume 3. Cherifi, H., Donduran, M., Rocha, L. M., Cherifi, C. & Varol, O. (eds.). Springer, p. 103-114 12 p. (Studies in Computational Intelligence; vol. 1189 SCI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Synthetic Networks That Preserve Edge Connectivity

    Anne, L., Vu-Le, T. A., Park, M., Warnow, T. & Chacko, G., 2025, Complex Networks and Their Applications XIII - Proceedings of The 13th International Conference on Complex Networks and Their Applications: COMPLEX NETWORKS 2024 - Volume 3. Cherifi, H., Donduran, M., Rocha, L. M., Cherifi, C. & Varol, O. (eds.). Springer, p. 166-177 12 p. (Studies in Computational Intelligence; vol. 1189 SCI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2024

    Identifying Well-Connected Communities in Real-World and Synthetic Networks

    Park, M., Tabatabaee, Y., Ramavarapu, V., Liu, B., Pailodi, V. K., Ramachandran, R., Korobskiy, D., Ayres, F., Chacko, G. & Warnow, T., 2024, Complex Networks and Their Applications XII - Proceedings of The 12th International Conference on Complex Networks and their Applications: COMPLEX NETWORKS 2023. Cherifi, H., Rocha, L. M., Cherifi, C. & Donduran, M. (eds.). Springer, p. 3-14 12 p. (Studies in Computational Intelligence; vol. 1142 SCI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Statistically Consistent Estimation of Rooted and Unrooted Level-1 Phylogenetic Networks from SNP Data

    Warnow, T., Tabatabaee, Y. & Evans, S. N., 2024, Comparative Genomics - 21st International Conference, RECOMB-CG 2024, Proceedings. Scornavacca, C. & Hernández-Rosales, M. (eds.). Springer, p. 3-23 21 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14616 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2023

    Statistically Consistent Rooting of Species Trees Under the Multispecies Coalescent Model

    Tabatabaee, Y., Roch, S. & Warnow, T., 2023, Research in Computational Molecular Biology - 27th Annual International Conference, RECOMB 2023, Proceedings. Tang, H. (ed.). Springer, p. 41-57 17 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13976 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access
  • 2022

    Fast and Accurate Species Trees from Weighted Internode Distances

    Liu, B. & Warnow, T., Sep 1 2022, 22nd International Workshop on Algorithms in Bioinformatics, WABI 2022. Boucher, C. & Rahmann, S. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 8. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 242).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2021

    Comparing Methods for Species Tree Estimation with Gene Duplication and Loss

    Willson, J., Roddur, M. S. & Warnow, T., 2021, Algorithms for Computational Biology - 8th International Conference, AlCoB 2021, Proceedings. Martín-Vide, C., Vega-Rodríguez, M. A. & Wheeler, T. (eds.). Springer, p. 106-117 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12715 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • PpIacerDC: A new scalable phylogenetic placement method

    Koning, E., Phillips, M. & Warnow, T., Jan 18 2021, Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2021. Association for Computing Machinery, (Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2021).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access

  • Scalable and Accurate Phylogenetic Placement Using pplacer-XR

    Wedell, E., Cai, Y. & Warnow, T., 2021, Algorithms for Computational Biology - 8th International Conference, AlCoB 2021, Proceedings. Martín-Vide, C., Vega-Rodríguez, M. A. & Wheeler, T. (eds.). Springer, p. 94-105 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12715 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • The Maximum Weight Trace Alignment Merging Problem

    Zaharias, P., Smirnov, V. & Warnow, T., 2021, Algorithms for Computational Biology - 8th International Conference, AlCoB 2021, Proceedings. Martín-Vide, C., Vega-Rodríguez, M. A. & Wheeler, T. (eds.). Springer, p. 159-171 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12715 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2020

    Advancing divide-and-conquer phylogeny estimation using robinson-foulds supertrees

    Yu, X., Le, T., Christensen, S., Molloy, E. K. & Warnow, T., Aug 1 2020, 20th International Workshop on Algorithms in Bioinformatics, WABI 2020. Kingsford, C. & Pisanti, N. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 15. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 172).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Polynomial-time statistical estimation of species trees under gene duplication and loss

    Legried, B., Molloy, E. K., Warnow, T. & Roch, S., 2020, Research in Computational Molecular Biology - 24th Annual International Conference, RECOMB 2020, Proceedings. Schwartz, R. (ed.). Springer, p. 120-135 16 p. (Lecture Notes in Computer Science; vol. 12074 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2019

    New Divide-and-Conquer Techniques for Large-Scale Phylogenetic Estimation

    Warnow, T., 2019, Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Proceedings. Vega-Rodríguez, M. A., Holmes, I. & Martín-Vide, C. (eds.). Springer, p. 3-21 19 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11488 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Traction: Fast non-parametric improvement of estimated gene trees

    Christensen, S., Molloy, E. K., Vachaspati, P. & Warnow, T., Sep 2019, 19th International Workshop on Algorithms in Bioinformatics, WABI 2019. Huber, K. T. & Gusfield, D. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 4. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 143).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Using INC Within Divide-and-Conquer Phylogeny Estimation

    Le, T., Sy, A., Molloy, E. K., Zhang, Q., Rao, S. & Warnow, T., 2019, Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Proceedings. Martín-Vide, C., Holmes, I. & Vega-Rodríguez, M. A. (eds.). Springer, p. 167-178 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11488 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2018

    Are Profile Hidden Markov Models Identifiable?

    Pattabiraman, S. & Warnow, T., Aug 15 2018, ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, p. 448-456 9 p. (ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    Open Access

  • New absolute fast converging phylogeny estimation methods with improved scalability and accuracy

    Zhang, Q., Rao, S. & Warnow, T., Aug 1 2018, 18th International Workshop on Algorithms in Bioinformatics, WABI 2018. Parida, L. & Ukkonen, E. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 8. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 113).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • NJMerge: A Generic technique for scaling phylogeny estimation methods and its application to species trees

    Molloy, E. K. & Warnow, T., 2018, Comparative Genomics - 16th International Conference, RECOMB-CG 2018, Proceedings. Ouangraoua, A. & Blanchette, M. (eds.). Springer, p. 260-276 17 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11183 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2017

    Enhancing searches for optimal trees using SIESTA

    Vachaspati, P. & Warnow, T., 2017, Comparative Genomics - 15th International Workshop, RECOMB CG 2017, Proceedings. Nakhleh, L. & Meidanis, J. (eds.). Springer, p. 232-255 24 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10562 LNBI).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Gene tree parsimony for incomplete gene trees

    Bayzid, M. S. & Warnow, T., Aug 1 2017, 17th International Workshop on Algorithms in Bioinformatics, WABI 2017. Reinert, K. & Schwartz, R. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 88).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Optimal completion of incomplete gene trees in polynomial time using OCTAL

    Christensen, S., Molloy, E. K., Vachaspati, P. & Warnow, T., Aug 1 2017, 17th International Workshop on Algorithms in Bioinformatics, WABI 2017. Reinert, K. & Schwartz, R. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 27. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 88).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2015

    Evaluating the prevalence and effects of within-nest colonies of the odorous house ant (Tapinoma sessile) on nestling survivorship and success in five species of midwestern birds

    Gibson, J., Merrill, L., Suarez, A., Benson, T. J. & Chiavacci, S. J., 2015, Entomology 2015.

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Ultra-large alignments using ensembles of hidden Markov models

    Nguyen, N. P., Mirarab, S., Kumar, K. & Warnow, T., 2015, Research in Computational Molecular Biology - 19th Annual International Conference, RECOMB 2015, Proceedings. Przytycka, T. M. (ed.). Springer, 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

  • 2014

    Effect of larval competition on the extrinsic incubation period and vectorial capacity of Aedes albopictus for Dengue virus

    Bara, J. J., Rapti, Z., Caceres, C. & Muturi, E. J., 2014, Entomology 2014.

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • The Genetic Legacy of the Mississippians

    Marshall, C., Millward, G. G., Lindo, J., Carbaugh, A., Hedman, K. M., Emerson, T. E., Kaestle, F. A., Cook, D. C. & Malhi, R. S., 2014, MAC 2014 Abstracts. p. 81 1 p.

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 2013

    Ancient DNA Analysis of Late Woodland Dogs from Janey B. Goode

    Witt, K. & Malhi, R. S., 2013, MAC, Midwest Archaeological Conference.

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Mitochondrial genetic variation among American Bottom Mississippians: preliminary results from the Janey B. Goode and East St. Louis Sites [presentation]

    Marshall, C., Hedman, K. M., Carbaugh, A. & Malhi, R. S., 2013, MAC, Midwest Archaeological Conference. p. 77-78

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 1997

    Inferring evolutionary trees from polymorphic characters, and an analysis of the Indo-European family of languages

    Bonet, M., Phillips, C., Warnow, T. & Yooseph, S., 1997, Mathematical Hierarchies and Biology. Mirkin, B., McMorris, F. R., Roberts, F. S. & Rzhetsky, A. (eds.). American Mathematical Society, p. 43-55 13 p. (DIMACS Series in Discrete Mathematics and Theoretical Computer Science; vol. 37).

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 1995

    A fast algorithm for the computation and enumeration of perfect phylogenies when the number of character states is fixed

    Kannan, S. & Warnow, T., 1995, Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithms (San Francisco, CA, 1995). ACM, New York, p. 595-603 9 p.

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • 1991

    Triangulating three-colored graphs

    Kannan, S. K. & Warnow, T. J., 1991, Proceedings of the Second Annual ACM-SIAM Symposium on Discrete Algorithms (San Francisco, CA, 1991). ACM, New York, p. 337-343 7 p.

    Research output: Chapter in Book/Report/Conference proceeding › Conference contribution