| 2016 | RECOMB | On Computing Breakpoint Distances for Genomes with Duplicate Genes. | Mingfu Shao, Bernard M. E. Moret |
| 2015 | RECOMB | A Fast and Exact Algorithm for the Exemplar Breakpoint Distance. | Mingfu Shao, Bernard M. E. Moret |
| 2014 | CPM | On the DCJ Median Problem. | Mingfu Shao, Bernard M. E. Moret |
| 2014 | RECOMB | An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes. | Mingfu Shao, Yu Lin, Bernard M. E. Moret |
| 2013 | PSB | Maximum Likelihood Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Tree of 68 Eukaryotes. | Yu Lin, Fei Hu, Jijun Tang, Bernard M. E. Moret |
| 2013 | WABI | Extending the Reach of Phylogenetic Inference. | Bernard M. E. Moret |
| 2013 | WABI | Phylogenetic Analysis of Cell Types Using Histone Modifications. | Nishanth Ulhas Nair, Yu Lin, Philipp Bucher, Bernard M. E. Moret |
| 2011 | WABI | Bootstrapping Phylogenies Inferred from Rearrangement Data. | Yu Lin, Vaibhav Rajan, Bernard M. E. Moret |
| 2011 | WABI | GASTS: Parsimony Scoring under Rearrangements. | Andrew Wei Xu, Bernard M. E. Moret |
| 2010 | PSB | Session Introduction. | Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff |
| 2010 | RECOMB | A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses That Applies across Eukaryotes and Prokaryotes. | Yu Lin, Bernard M. E. Moret |
| 2010 | RECOMB | Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator. | Yu Lin, Vaibhav Rajan, Bernard M. E. Moret |
| 2009 | PSB | Session Introduction. | Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff |
| 2009 | RECOMB | How Many Bootstrap Replicates Are Necessary? | Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis |
| 2009 | RECOMB | Sorting Signed Permutations by Inversions in O(nlogn) Time. | Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret |
| 2009 | WABI | Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models. | Xiuwei Zhang, Bernard M. E. Moret |
| 2008 | APBC | Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes. | Krister M. Swenson, William Arndt, Jijun Tang, Bernard M. E. Moret |
| 2008 | ISMB | Estimating true evolutionary distances under the DCJ model. | Yu Lin, Bernard M. E. Moret |
| 2008 | PSB | Session Introduction. | Michael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy J. Warnow |
| 2008 | RECOMB | Hurdles Hardly Have to Be Heeded. | Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret |
| 2008 | WABI | Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach. | Xiuwei Zhang, Bernard M. E. Moret |
| 2007 | CIBCB | An Experimental Evaluation of Inversion-and Transposition-Based Genomic Distances through Simulations. | Moulik Kothari, Bernard M. E. Moret |
| 2006 | RECOMB | A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric. | Nicholas D. Pattengale, Bernard M. E. Moret |
| 2005 | ALENEX | Computational Challenges from the Tree of Life. | Bernard M. E. Moret |
| 2005 | ALENEX | Approximating the True Evolutionary Distance between Two Genomes. | Krister M. Swenson, Mark Marron, Joel V. Earnest-DeYoung, Bernard M. E. Moret |
| 2005 | COCOON | Quartet-Based Phylogeny Reconstruction from Gene Orders. | Tao Liu, Jijun Tang, Bernard M. E. Moret |
| 2005 | CPM | Linear Programming for Phylogenetic Reconstruction Based on Gene Rearrangements. | Jijun Tang, Bernard M. E. Moret |
| 2005 | RECOMB | A Framework for Orthology Assignment from Gene Rearrangement Data. | Krister M. Swenson, Nicholas D. Pattengale, Bernard M. E. Moret |
| 2004 | BIBE | Phylogenetic Reconstruction from Arbitrary Gene-Order Data. | Jijun Tang, Bernard M. E. Moret, Liying Cui, Claude W. dePamphilis |
| 2004 | WABI | Reversing Gene Erosion - Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data. | Joel V. Earnest-DeYoung, Emmanuelle Lerat, Bernard M. E. Moret |
| 2003 | BIBE | An Investigation of Phylogenetic Likelihood Methods. | Tiffani L. Williams, Bernard M. E. Moret |
| 2003 | COCOON | Genomic Distances under Deletions and Insertions. | Mark Marron, Krister M. Swenson, Bernard M. E. Moret |
| 2003 | ISMB | Scaling up accurate phylogenetic reconstruction from gene-order data. | Jijun Tang, Bernard M. E. Moret |
| 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 | WADS | Phylogenetic Reconstruction from Gene-Rearrangement Data with Unequal Gene Content. | Jijun Tang, Bernard M. E. Moret |
| 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 | Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data. | Bernard M. E. Moret, Adam C. Siepel, Jijun Tang, Tao Liu |
| 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 | 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 | WABI | Finding an Optimal Inversion Median: Experimental Results. | Adam C. Siepel, Bernard M. E. Moret |
| 2001 | WADS | A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study. | David A. Bader, Bernard M. E. Moret, Mi Yan |
| 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 | SODA | Combinatorial Algorithms Test Sets [CATS]: The ACM/EATCS Platform for Experimental Research. | Andrew V. Goldberg, Bernard M. E. Moret |
| 1999 | SODA | Dynamical System Representation of Open Address Hash Functions. | Gregory L. Heileman, Chaouki T. Abdallah, Bernard M. E. Moret, Bradley J. Smith |
| 1997 | SODA | Map Labeling and Its Generalizations. | Srinivas Doddi, Madhav V. Marathe, Andy Mirzaian, Bernard M. E. Moret, Binhai Zhu |
| 1995 | WSC | Network Routing Models Applied to Aircraft Routing Problems. | Zhiqiang Chen, Andrew T. Holle, Bernard M. E. Moret, Jared Saia, Ali Boroujerdi |
| 1992 | IPCO | An Exact Characterization of Greedy Structures. | Paul Helman, Bernard M. E. Moret, Henry D. Shapiro |
| 1991 | ICCI | Folding a Triangulated Simple Polygon: Structural and Algorithmic Results. | Ali A. Kooshesh, Bernard M. E. Moret |
| 1991 | WADS | An Emperical Analysis of Algorithms for Constructing a Minimum Spanning Tree. | Bernard M. E. Moret, Henry D. Shapiro |
| 1990 | ICPR | The design of a nonparametric hierarchical classifier. | Chea-Tin (Tim) Tseng, Bernard M. E. Moret |