Fast computation of approximate weak common intervals in multiple indeterminate strings. - Doerr, Daniel; Moret, Bernard M. E. (CoRR, 2023)

On Computing Breakpoint Distances for Genomes with Duplicate Genes. - Shao, Mingfu; Moret, Bernard M. E. (J. Comput. Biol., 2017)

New Genome Similarity Measures based on Conserved Gene Adjacencies. - Doerr, Daniel; Kowada, Luis Antonio Brasil; Araujo, Eloi; Deshpande, Shachi; Dantas, Simone; Moret, Bernard M. E.; Stoye, Jens (J. Comput. Biol., 2017)

A maximum-likelihood approach for building cell-type trees by lifting. - Nair, Nishanth Ulhas; Hunter, Laura; Shao, Mingfu; Grnarova, Paulina; Lin, Yu; Bucher, Philipp; Moret, Bernard M. E. (BMC Genom., 2016)

A Fast and Exact Algorithm for the Exemplar Breakpoint Distance. - Shao, Mingfu; Moret, Bernard M. E. (J. Comput. Biol., 2016)

NEMo: An Evolutionary Model with Modularity for PPI Networks. - Ye, Min; Racz, Gabriela C.; Jiang, Qijia; Zhang, Xiuwei; Moret, Bernard M. E. (2016)

On Computing Breakpoint Distances for Genomes with Duplicate Genes. - Shao, Mingfu; Moret, Bernard M. E. (2016)

Comparing genomes with rearrangements and segmental duplications. - Shao, Mingfu; Moret, Bernard M. E. (Bioinform., 2015)

An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes. - Shao, Mingfu; Lin, Yu; Moret, Bernard M. E. (J. Comput. Biol., 2015)

A Fast and Exact Algorithm for the Exemplar Breakpoint Distance. - Shao, Mingfu; Moret, Bernard M. E. (2015)

Evaluating synteny for improved comparative studies. - Ghiurcuta, Cristina G.; Moret, Bernard M. E. (Bioinform., 2014)

Probabilistic partitioning methods to find significant patterns in ChIP-Seq data. - Nair, Nishanth Ulhas; Kumar, Sunil; Moret, Bernard M. E.; Bucher, Philipp (Bioinform., 2014)

Study of cell differentiation by phylogenetic analysis using histone modification data. - Nair, Nishanth Ulhas; Lin, Yu; Manasovska, Ana; Antic, Jelena; Grnarova, Paulina; Sahu, Avinash Das; Bucher, Philipp; Moret, Bernard M. E. (BMC Bioinform., 2014)

On the DCJ Median Problem. - Shao, Mingfu; Moret, Bernard M. E. (2014)

An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes. - Shao, Mingfu; Lin, Yu; Moret, Bernard M. E. (2014)

Sorting genomes with rearrangements and segmental duplications through trajectory graphs. - Shao, Mingfu; Lin, Yu; Moret, Bernard M. E. (BMC Bioinform., 2013)

A Transcript Perspective on Evolution. - Christinat, Yann; Moret, Bernard M. E. (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Maximum Likelihood Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Tree of 68 Eukaryotes. - Lin, Yu; Hu, Fei; Tang, Jijun; Moret, Bernard M. E. (2013)

Extending the Reach of Phylogenetic Inference. - Moret, Bernard M. E. (2013)

Phylogenetic Analysis of Cell Types Using Histone Modifications. - Nair, Nishanth Ulhas; Lin, Yu; Bucher, Philipp; Moret, Bernard M. E. (2013)

Rearrangements in Phylogenetic Inference: Compare, Model, or Encode? - Moret, Bernard M. E.; Lin, Yu; Tang, Jijun (2013)

Bootstrapping phylogenies inferred from rearrangement data. - Lin, Yu; Rajan, Vaibhav; Moret, Bernard M. E. (Algorithms Mol. Biol., 2012)

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis. - Lin, Yu; Rajan, Vaibhav; Moret, Bernard M. E. (Bioinform., 2012)

Inferring transcript phylogenies. - Christinat, Yann; Moret, Bernard M. E. (BMC Bioinform., 2012)

A Metric for Phylogenetic Trees Based on Matching. - Lin, Yu; Rajan, Vaibhav; Moret, Bernard M. E. (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Refining Regulatory Networks through Phylogenetic Transfer of Information. - Zhang, Xiuwei; Moret, Bernard M. E. (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

A Transcript Perspective on Evolution. - Christinat, Yann; Moret, Bernard M. E. (2012)

A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes. - Lin, Yu; Moret, Bernard M. E. (J. Comput. Biol., 2011)

Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator. - Lin, Yu; Rajan, Vaibhav; Moret, Bernard M. E. (J. Comput. Biol., 2011)

Uncovering Hidden Phylogenetic Consensus in Large Data Sets. - Pattengale, Nicholas D.; Aberer, Andre J.; Swenson, Krister M.; Stamatakis, Alexandros; Moret, Bernard M. E. (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Inferring Transcript Phylogenies. - Christinat, Yann; Moret, Bernard M. E. (2011)

Phylogenetic Analysis of Whole Genomes - (Keynote Talk). - Moret, Bernard M. E. (2011)

A Metric for Phylogenetic Trees Based on Matching. - Lin, Yu; Rajan, Vaibhav; Moret, Bernard M. E. (2011)

ProPhyC: A Probabilistic Phylogenetic Model for Refining Regulatory Networks. - Zhang, Xiuwei; Moret, Bernard M. E. (2011)

Bootstrapping Phylogenies Inferred from Rearrangement Data. - Lin, Yu; Rajan, Vaibhav; Moret, Bernard M. E. (2011)

GASTS: Parsimony Scoring under Rearrangements. - Xu, Andrew Wei; Moret, Bernard M. E. (2011)

Refining transcriptional regulatory networks using network evolutionary models and gene histories. - Zhang, Xiuwei; Moret, Bernard M. E. (Algorithms Mol. Biol., 2010)

Heuristics for the inversion median problem. - Rajan, Vaibhav; Xu, Andrew Wei; Lin, Yu; Swenson, Krister M.; Moret, Bernard M. E. (BMC Bioinform., 2010)

Estimating true evolutionary distances under rearrangements, duplications, and losses. - Lin, Yu; Rajan, Vaibhav; Swenson, Krister M.; Moret, Bernard M. E. (BMC Bioinform., 2010)

How Many Bootstrap Replicates Are Necessary? - Pattengale, Nicholas D.; Alipour, Masoud; Bininda-Emonds, Olaf R. P.; Moret, Bernard M. E.; Stamatakis, Alexandros (J. Comput. Biol., 2010)

Sorting Signed Permutations by Inversions in O(nlogn) Time. - Swenson, Krister M.; Rajan, Vaibhav; Lin, Yu; Moret, Bernard M. E. (J. Comput. Biol., 2010)

FluRF, an automated flu virus reassortment finder based on phylogenetic trees. - Yurovsky, Alisa; Moret, Bernard M. E. (2010)

Uncovering Hidden Phylogenetic Consensus. - Pattengale, Nicholas D.; Swenson, Krister M.; Moret, Bernard M. E. (2010)

Session Introduction. - Moret, Bernard M. E.; Miller, Webb; Pevzner, Pavel A.; Sankoff, David (2010)

Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator. - Lin, Yu; Rajan, Vaibhav; Moret, Bernard M. E. (2010)

A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses That Applies across Eukaryotes and Prokaryotes. - Lin, Yu; Moret, Bernard M. E. (2010)

Inversion-based genomic signatures. - Swenson, Krister M.; Moret, Bernard M. E. (BMC Bioinform., 2009)

Maximum independent sets of commuting and noninterfering inversions. - Swenson, Krister M.; To, Yokuki; Tang, Jijun; Moret, Bernard M. E. (BMC Bioinform., 2009)

Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results. - Swenson, Krister M.; Lin, Yu; Rajan, Vaibhav; Moret, Bernard M. E. (J. Comput. Biol., 2009)

Session Introduction. - Moret, Bernard M. E.; Miller, Webb; Pevzner, Pavel A.; Sankoff, David (2009)

How Many Bootstrap Replicates Are Necessary? - Pattengale, Nicholas D.; Alipour, Masoud; Bininda-Emonds, Olaf R. P.; Moret, Bernard M. E.; Stamatakis, Alexandros (2009)

Sorting Signed Permutations by Inversions in O(nlogn) Time. - Swenson, Krister M.; Rajan, Vaibhav; Lin, Yu; Moret, Bernard M. E. (2009)

Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models. - Zhang, Xiuwei; Moret, Bernard M. E. (2009)

Approximating the true evolutionary distance between two genomes. - Swenson, Krister M.; Marron, Mark; Earnest-DeYoung, Joel V.; Moret, Bernard M. E. (ACM J. Exp. Algorithmics, 2008)

Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes. - Swenson, Krister M.; Arndt, William; Tang, Jijun; Moret, Bernard M. E. (2008)

Using Phylogenetic Relationships to Improve the Inference of Transcriptional Regulatory Networks. - Zhang, Xiuwei; Zaheri, Maryam; Moret, Bernard M. E. (2008)

Estimating true evolutionary distances under the DCJ model. - Lin, Yu; Moret, Bernard M. E. (2008)

Session Introduction. - Brudno, Michael; Moret, Bernard M. E.; Linder, C. Randal; Warnow, Tandy J. (2008)

Hurdles Hardly Have to Be Heeded. - Swenson, Krister M.; Lin, Yu; Rajan, Vaibhav; Moret, Bernard M. E. (2008)

Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach. - Zhang, Xiuwei; Moret, Bernard M. E. (2008)

Efficiently Computing the Robinson-Foulds Metric. - Pattengale, Nicholas D.; Gottlieb, Eric J.; Moret, Bernard M. E. (J. Comput. Biol., 2007)

An Experimental Evaluation of Inversion-and Transposition-Based Genomic Distances through Simulations. - Kothari, Moulik; Moret, Bernard M. E. (2007)

Reconstructing phylogenies from gene-content and gene-order data. - Moret, Bernard M. E.; Tang, Jijun; Warnow, Tandy J. (2007)

NetGen: generating phylogenetic networks with diploid hybrids. - Morin, M. M.; Moret, Bernard M. E. (Bioinform., 2006)

Inferring Ancestral Chloroplast Genomes with Inverted Repea. - Cui, Liying; Yue, Feng; dePamphilis, Claude W.; Moret, Bernard M. E.; Tang, Jijun (2006)

A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric. - Pattengale, Nicholas D.; Moret, Bernard M. E. (2006)

Algorithms in Bioinformatics, 6th International Workshop, WABI 2006, Zurich, Switzerland, September 11-13, 2006, Proceedings (Springer, 2006)

Computational Challenges from the Tree of Life. - Moret, Bernard M. E. (2005)

Approximating the True Evolutionary Distance between Two Genomes. - Swenson, Krister M.; Marron, Mark; Earnest-DeYoung, Joel V.; Moret, Bernard M. E. (2005)

Quartet-Based Phylogeny Reconstruction from Gene Orders. - Liu, Tao; Tang, Jijun; Moret, Bernard M. E. (2005)

Linear Programming for Phylogenetic Reconstruction Based on Gene Rearrangements. - Tang, Jijun; Moret, Bernard M. E. (2005)

Phylogenetic Postprocessing. - Pattengale, Nicholas D.; Moret, Bernard M. E. (2005)

Consensus Methods Using Phylogenetic Databases. - Kulkarni, Mahesh M.; Moret, Bernard M. E. (2005)

A Framework for Orthology Assignment from Gene Rearrangement Data. - Swenson, Krister M.; Pattengale, Nicholas D.; Moret, Bernard M. E. (2005)

Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. - Moret, Bernard M. E.; Nakhleh, Luay; Warnow, Tandy J.; Linder, C. Randal; Tholse, Anna; Padolina, Anneke; Sun, Jerry; Timme, Ruth E. (IEEE ACM Trans. Comput. Biol. Bioinform., 2004)

Genomic Distances under Deletions and Insertions. - Marron, Mark; Swenson, Krister M.; Moret, Bernard M. E. (Theor. Comput. Sci., 2004)

Phylogenetic Reconstruction from Arbitrary Gene-Order Data. - Tang, Jijun; Moret, Bernard M. E.; Cui, Liying; dePamphilis, Claude W. (2004)

Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees. - Roshan, Usman; Moret, Bernard M. E.; Warnow, Tandy J.; Williams, Tiffani L. (2004)

Reversing Gene Erosion - Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data. - Earnest-DeYoung, Joel V.; Lerat, Emmanuelle; Moret, Bernard M. E. (2004)

Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. - John, Katherine St.; Warnow, Tandy J.; Moret, Bernard M. E.; Vawter, Lisa (J. Algorithms, 2003)

An Investigation of Phylogenetic Likelihood Methods. - Williams, Tiffani L.; Moret, Bernard M. E. (2003)

Genomic Distances under Deletions and Insertions. - Marron, Mark; Swenson, Krister M.; Moret, Bernard M. E. (2003)

Scaling up accurate phylogenetic reconstruction from gene-order data. - Tang, Jijun; Moret, Bernard M. E. (2003)

Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. - Nakhleh, Luay; Sun, Jerry; Warnow, Tandy J.; Linder, C. Randal; Moret, Bernard M. E.; Tholse, Anna (2003)

Phylogenetic Reconstruction from Gene-Rearrangement Data with Unequal Gene Content. - Tang, Jijun; Moret, Bernard M. E. (2003)

Toward New Software for Computational Phylogenetics. - Moret, Bernard M. E.; Wang, Li-San; Warnow, Tandy J. (Computer, 2002)

Point Set Labeling with Specified Positions. - Doddi, Srinivas; Marathe, Madhav V.; Moret, Bernard M. E. (Int. J. Comput. Geom. Appl., 2002)

Steps toward accurate reconstructions of phylogenies from gene-order data. - Moret, Bernard M. E.; Tang, Jijun; Wang, Li-San; Warnow, Tandy J. (J. Comput. Syst. Sci., 2002)

High-Performance Algorithm Engineering for Computational Phylogenetics. - Moret, Bernard M. E.; Bader, David A.; Warnow, Tandy J. (J. Supercomput., 2002)

The Accuracy of Fast Phylogenetic Methods for Large Datasets. - Nakhleh, Luay; Moret, Bernard M. E.; Roshan, Usman; John, Katherine St.; Sun, Jerry; Warnow, Tandy J. (2002)

Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study. - Wang, Li-San; Jansen, Robert K.; Moret, Bernard M. E.; Raubeson, Linda A.; Warnow, Tandy J. (2002)

Sequence-Length Requirements for Phylogenetic Methods. - Moret, Bernard M. E.; Roshan, Usman; Warnow, Tandy J. (2002)

Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data. - Moret, Bernard M. E.; Siepel, Adam C.; Tang, Jijun; Liu, Tao (2002)

Experimental Algorithmics, From Algorithm Design to Robust and Efficient Software [Dagstuhl seminar, September 2000] (Springer, 2002)

Foreword. - Moret, Bernard M. E. (J. Algorithms, 2001)

A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study. - Bader, David A.; Moret, Bernard M. E.; Yan, Mi (J. Comput. Biol., 2001)

Algorithms and Experiments: The New (and Old) Methodology. - Moret, Bernard M. E.; Shapiro, Henry D. (J. Univers. Comput. Sci., 2001)

High-Performance Algorithm Engineering for Computational Phylogenetics. - Moret, Bernard M. E.; Bader, David A.; Warnow, Tandy J. (2001)

New approaches for reconstructing phylogenies from gene order data. - Moret, Bernard M. E.; Wang, Li-San; Warnow, Tandy J.; Wyman, Stacia K. (2001)

A New Implmentation and Detailed Study of Breakpoint Analysis. - Moret, Bernard M. E.; Wyman, Stacia K.; Bader, David A.; Warnow, Tandy J.; Yan, Mi (2001)

Absolute convergence: true trees from short sequences. - Warnow, Tandy J.; Moret, Bernard M. E.; John, Katherine St. (2001)

Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. - John, Katherine St.; Warnow, Tandy J.; Moret, Bernard M. E.; Vawter, Lisa (2001)

Finding an Optimal Inversion Median: Experimental Results. - Siepel, Adam C.; Moret, Bernard M. E. (2001)

A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study. - Bader, David A.; Moret, Bernard M. E.; Yan, Mi (2001)

Using PRAM Algorithms on a Uniform-Memory-Access Shared-Memory Architecture. - Bader, David A.; Illendula, Ajith K.; Moret, Bernard M. E.; Weisse-Bernstein, Nina R. (2001)

Algorithms in Bioinformatics, First International Workshop, WABI 2001, Aarhus, Denmark, August 28-31, 2001, Proceedings (Springer, 2001)

Point set labeling with specified positions. - Doddi, Srinivas; Marathe, Madhav V.; Moret, Bernard M. E. (2000)

Algorithm Engineering for Parallel Computation. - Bader, David A.; Moret, Bernard M. E.; Sanders, Peter (2000)

Reconstructing Optimal Phylogenetic Trees: A Challenge in Experimental Algorithmics. - Moret, Bernard M. E.; Warnow, Tandy J. (2000)

A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data. - Cosner, Mary E.; Jansen, Robert K.; Moret, Bernard M. E.; Raubeson, Linda A.; Wang, Li-San; Warnow, Tandy J.; Wyman, Stacia K. (2000)

How to present a paper on experimental work with algorithms. - McGeoch, Catherine C.; Moret, Bernard M. E. (SIGACT News, 1999)

Towards a discipline of experimental algorithmics. - Moret, Bernard M. E. (1999)

Combinatorial Algorithms Test Sets [CATS]: The ACM/EATCS Platform for Experimental Research. - Goldberg, Andrew V.; Moret, Bernard M. E. (1999)

Dynamical System Representation of Open Address Hash Functions. - Heileman, Gregory L.; Abdallah, Chaouki T.; Moret, Bernard M. E.; Smith, Bradley J. (1999)

Theory of computation. - Moret, Bernard M. E. (Addison-Wesley-Longman, 1998)

Improved Lower Bounds for the Link Length of Rectilinear Spanning Paths in Grids. - Collins, Michael J.; Moret, Bernard M. E. (Inf. Process. Lett., 1998)

Workshop on algorithm engineering: a report. - Moret, Bernard M. E. (SIGACT News, 1997)

Map Labeling and Its Generalizations. - Doddi, Srinivas; Marathe, Madhav V.; Mirzaian, Andy; Moret, Bernard M. E.; Zhu, Binhai (1997)

The Ice Rink Problem. - Moret, Bernard M. E.; Collins, Michael J.; Saia, Jared; Yu, Ling (1997)

Folding a Simple Polygon: A Paradigm for Computational Geometry. - Kooshesh, Ali A.; Moret, Bernard M. E. (1995)

Network Routing Models Applied to Aircraft Routing Problems. - Chen, Zhiqiang; Holle, Andrew T.; Moret, Bernard M. E.; Saia, Jared; Boroujerdi, Ali (1995)

An Exact Characterization of Greedy Structures. - Helman, Paul; Moret, Bernard M. E.; Shapiro, Henry D. (SIAM J. Discret. Math., 1993)

Three-coloring the vertices of a triangulated simple polygon. - Kooshesh, Ali A.; Moret, Bernard M. E. (Pattern Recognit., 1992)

An Empirical Assessment of Algorithms for Constructing a Minimum Spanning Tree. - Moret, Bernard M. E.; Shapiro, Henry D. (1992)

An Exact Characterization of Greedy Structures. - Helman, Paul; Moret, Bernard M. E.; Shapiro, Henry D. (1992)

Constructive complexity. - Abrahamson, Karl R.; Fellows, Michael R.; Langston, Michael A.; Moret, Bernard M. E. (Discret. Appl. Math., 1991)

How to Find a Minimum Spanning Tree in Practice. - Moret, Bernard M. E.; Shapiro, Henry D. (1991)

Folding a Triangulated Simple Polygon: Structural and Algorithmic Results. - Kooshesh, Ali A.; Moret, Bernard M. E. (1991)

An Emperical Analysis of Algorithms for Constructing a Minimum Spanning Tree. - Moret, Bernard M. E.; Shapiro, Henry D. (1991)

A new method for one-dimensional linear feature transformations. - Tseng, Chea-Tin (Tim); Moret, Bernard M. E. (Pattern Recognit., 1990)

The design of a nonparametric hierarchical classifier. - Tseng, Chea-Tin (Tim); Moret, Bernard M. E. (1990)

Planar NAE3SAT is in P. - Moret, Bernard M. E. (SIGACT News, 1988)

The Computational Metaphor and Quantum Physics. - Mathey, Michael J.; Moret, Bernard M. E. (Commun. ACM, 1983)

Symmetric and Threshold Boolean Functions Are Exhaustive. - Moret, Bernard M. E.; Thomason, Michael G.; González, Rafael C. (IEEE Trans. Computers, 1983)

Decision Trees and Diagrams. - Moret, Bernard M. E. (ACM Comput. Surv., 1982)

The Activity of a Variable and Its Relation to Decision Trees. - Moret, Bernard M. E.; Thomason, Michael G.; González, Rafael C. (ACM Trans. Program. Lang. Syst., 1980)