| 2023 | RECOMB | Statistically Consistent Rooting of Species Trees Under the Multispecies Coalescent Model. | Yasamin Tabatabaee, Sbastien Roch, Tandy J. Warnow |
| 2023 | WABI | EMMA: Adding Sequences into a Constraint Alignment with High Accuracy and Scalability (Abstract). | Chengze Shen, Baqiao Liu, Kelly P. Williams, Tandy J. Warnow |
| 2023 | WABI | BATCH-SCAMPP: Scaling Phylogenetic Placement Methods to Place Many Sequences (Abstract). | Eleanor Wedell, Chengze Shen, Tandy J. Warnow |
| 2022 | WABI | Fast and Accurate Species Trees from Weighted Internode Distances. | Baqiao Liu, Tandy J. Warnow |
| 2020 | RECOMB | Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. | Brandon Legried, Erin K. Molloy, Tandy J. Warnow, Sbastien Roch |
| 2020 | WABI | Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees. | Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy, Tandy J. Warnow |
| 2019 | WABI | TRACTION: Fast Non-Parametric Improvement of Estimated Gene Trees. | Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy J. Warnow |
| 2018 | RECOMB | NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees. | Erin K. Molloy, Tandy J. Warnow |
| 2018 | WABI | New Absolute Fast Converging Phylogeny Estimation Methods with Improved Scalability and Accuracy. | Qiuyi (Richard) Zhang, Satish Rao, Tandy J. Warnow |
| 2017 | RECOMB | Enhancing Searches for Optimal Trees Using SIESTA. | Pranjal Vachaspati, Tandy J. Warnow |
| 2017 | WABI | Gene Tree Parsimony for Incomplete Gene Trees. | Md. Shamsuzzoha Bayzid, Tandy J. Warnow |
| 2017 | WABI | Optimal Completion of Incomplete Gene Trees in Polynomial Time Using OCTAL. | Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy J. Warnow |
| 2015 | RECOMB | Ultra-Large Alignments Using Ensembles of Hidden Markov Models. | Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow |
| 2014 | RECOMB | PASTA: Ultra-Large Multiple Sequence Alignment. | Siavash Mirarab, Nam-phuong Nguyen, Tandy J. Warnow |
| 2013 | PSB | Inferring Optimal Species Trees Under Gene Duplication and Loss. | Md. Shamsuzzoha Bayzid, Siavash Mirarab, Tandy J. Warnow |
| 2013 | PSB | Session introduction. | Luay Nakhleh, Noah A. Rosenberg, Tandy J. Warnow |
| 2012 | PSB | SEPP: SATe -Enabled Phylogenetic Placement. | Siavash Mirarab, Nam Nguyen, Tandy J. Warnow |
| 2012 | SAC | Parallelizing SuperFine. | Diogo Telmo Neves, Tandy J. Warnow, Joo Lus Sobral, Keshav Pingali |
| 2011 | RECOMB | Algorithms for MDC-Based Multi-locus Phylogeny Inference. | Yun Yu, Tandy J. Warnow, Luay Nakhleh |
| 2010 | WABI | An Experimental Study of Quartets MaxCut and Other Supertree Methods. | M. Shel Swenson, Rahul Suri, C. Randal Linder, Tandy J. Warnow |
| 2009 | WABI | A Simulation Study Comparing Supertree and Combined Analysis Methods Using SMIDGen. | M. Shel Swenson, Franois Barbanon, C. Randal Linder, Tandy J. Warnow |
| 2008 | PSB | Session Introduction. | Michael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy J. Warnow |
| 2008 | PSB | The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analysis. | Serita M. Nelesen, Kevin Liu, D. Zhao, C. Randal Linder, Tandy J. Warnow |
| 2005 | WABI | Pattern Identification in Biogeography. | Ganeshkumar Ganapathy, Barbara Goodson, Robert K. Jansen, Vijaya Ramachandran, Tandy J. Warnow |
| 2004 | RECOMB | Reconstructing reticulate evolution in species: theory and practice. | Luay Nakhleh, Tandy J. Warnow, C. Randal Linder |
| 2004 | SODA | On contract-and-refine transformations between phylogenetic trees. | Ganeshkumar Ganapathy, Vijaya Ramachandran, Tandy J. Warnow |
| 2003 | PSB | Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. | Luay Nakhleh, Jerry Sun, Tandy J. Warnow, C. Randal Linder, Bernard M. E. Moret, Anna Tholse |
| 2003 | WABI | Better Hill-Climbing Searches for Parsimony. | Ganeshkumar Ganapathy, Vijaya Ramachandran, Tandy J. Warnow |
| 2002 | ISMB | Statistically based postprocessing of phylogenetic analysis by clustering. | Cara Stockham, Li-San Wang, Tandy J. Warnow |
| 2002 | PSB | The Accuracy of Fast Phylogenetic Methods for Large Datasets. | Luay Nakhleh, Bernard M. E. Moret, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow |
| 2002 | PSB | Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study. | Li-San Wang, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Tandy J. Warnow |
| 2002 | WABI | Sequence-Length Requirements for Phylogenetic Methods. | Bernard M. E. Moret, Usman Roshan, Tandy J. Warnow |
| 2002 | WABI | Estimating the Deviation from a Molecular Clock. | Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy J. Warnow |
| 2001 | ICCS | High-Performance Algorithm Engineering for Computational Phylogenetics. | Bernard M. E. Moret, David A. Bader, Tandy J. Warnow |
| 2001 | ISMB | New approaches for reconstructing phylogenies from gene order data. | Bernard M. E. Moret, Li-San Wang, Tandy J. Warnow, Stacia K. Wyman |
| 2001 | ISMB | Designing fast converging phylogenetic methods. | Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow |
| 2001 | PSB | A New Implmentation and Detailed Study of Breakpoint Analysis. | Bernard M. E. Moret, Stacia K. Wyman, David A. Bader, Tandy J. Warnow, Mi Yan |
| 2001 | SODA | Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. | Katherine St. John, Tandy J. Warnow, Bernard M. E. Moret, Lisa Vawter |
| 2001 | SODA | Absolute convergence: true trees from short sequences. | Tandy J. Warnow, Bernard M. E. Moret, Katherine St. John |
| 2001 | STOC | Estimating true evolutionary distances between genomes. | Li-San Wang, Tandy J. Warnow |
| 2001 | WABI | Finding a Maximum Compatible Tree for a Bounded Number of Trees with Bounded Degree Is Solvable in Polynomial Time. | Ganeshkumar Ganapathysaravanabavan, Tandy J. Warnow |
| 2001 | WABI | The Performance of Phylogenetic Methods on Trees of Bounded Diameter. | Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow |
| 2000 | ISMB | A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data. | Mary E. Cosner, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Li-San Wang, Tandy J. Warnow, Stacia K. Wyman |
| 1999 | ISMB | Solving Large Scale Phylogenetic Problems using DCM2. | Daniel H. Huson, Lisa Vawter, Tandy J. Warnow |
| 1999 | RECOMB | Obtaining highly accurate topology estimates of evolutionary trees from very short sequences. | Daniel H. Huson, Scott Nettles, Tandy J. Warnow |
| 1998 | RECOMB | Better methods for solving parsimony and compatibility. | Maria Luisa Bonet, Mike A. Steel, Tandy J. Warnow, Shibu Yooseph |
| 1997 | COCOON | Parsimony is Hard to Beat. | Kenneth Rice, Tandy J. Warnow |
| 1997 | ICALP | Constructing Big Trees from Short Sequences. | Pter L. Erds, Mike A. Steel, Lszl A. Szkely, Tandy J. Warnow |
| 1996 | CPM | The Asymmetric Median Tree - A New model for Building Consensus Trees. | Cynthia A. Phillips, Tandy J. Warnow |
| 1996 | SODA | Constructing a Tree from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology. | Monika Rauch Henzinger, Valerie King, Tandy J. Warnow |
| 1996 | SODA | Reconstructing the Evolutionary History of Natural Languages. | Tandy J. Warnow, Donald Ringe, Ann Taylor |
| 1996 | STOC | Constructing Evolutionary Trees in the Presence of Polymorphic Characters. | Maria Luisa Bonet, Cynthia A. Phillips, Tandy J. Warnow, Shibu Yooseph |
| 1995 | CPM | Of Chicken Teeth and Mouse Eyes, or Generalized Character Compatibility. | Craig J. Benham, Sampath Kannan, Tandy J. Warnow |
| 1995 | CPM | Minimizing Phylogenetic Number to find Good Evolutionary Trees. | Leslie Ann Goldberg, Paul W. Goldberg, Cynthia A. Phillips, Elizabeth Sweedyk, Tandy J. Warnow |
| 1995 | SODA | A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies when the Number of Character States is Fixed. | Sampath Kannan, Tandy J. Warnow |
| 1995 | SODA | Computing the Local Consensus of Trees. | Sampath Kannan, Tandy J. Warnow, Shibu Yooseph |
| 1993 | SODA | Triangulating Vertex Colored Graphs. | Fred R. McMorris, Tandy J. Warnow, Thomas Wimer |
| 1993 | SODA | Tree Compatibility and Inferring Evoluationary History. | Tandy J. Warnow |
| 1993 | STOC | A robust model for finding optimal evolutionary trees. | Martin Farach, Sampath Kannan, Tandy J. Warnow |
| 1993 | WADS | Tree Reconstruction from Partial Orders. | Sampath Kannan, Tandy J. Warnow |
| 1992 | ICALP | Two Strikes Against Perfect Phylogeny. | Hans L. Bodlaender, Michael R. Fellows, Tandy J. Warnow |
| 1991 | SODA | Triangulating Three-Colored Graphs. | Sampath Kannan, Tandy J. Warnow |
| 1990 | FOCS | Inferring Evolutionary History from DNA Sequences (Extended Abstract) | Sampath Kannan, Tandy J. Warnow |
| 1990 | SODA | Determining the Evolutionary Tree. | Sampath Kannan, Eugene L. Lawler, Tandy J. Warnow |