Bernard M. E. Moret

According to our database, Bernard M. E. Moret authored at least 116 papers between 1980 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Fast computation of approximate weak common intervals in multiple indeterminate strings.

Daniel Doerr, Bernard M. E. Moret

CoRR, 2023

2017

On Computing Breakpoint Distances for Genomes with Duplicate Genes.

Mingfu Shao, Bernard M. E. Moret

J. Comput. Biol., 2017

New Genome Similarity Measures based on Conserved Gene Adjacencies.

Daniel Doerr, Luis Antonio Brasil Kowada, Eloi Araujo, Shachi Deshpande, Simone Dantas, Bernard M. E. Moret, Jens Stoye

J. Comput. Biol., 2017

2016

A Fast and Exact Algorithm for the Exemplar Breakpoint Distance.

Mingfu Shao, Bernard M. E. Moret

J. Comput. Biol., 2016

A maximum-likelihood approach for building cell-type trees by lifting.

Nishanth Ulhas Nair, Laura Hunter, Mingfu Shao, Paulina Grnarova, Yu Lin, Philipp Bucher, Bernard M. E. Moret

BMC Genom., 2016

NEMo: An Evolutionary Model with Modularity for PPI Networks.

Min Ye, Gabriela C. Racz, Qijia Jiang, Xiuwei Zhang, Bernard M. E. Moret

Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016

2015

An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes.

Mingfu Shao, Yu Lin, Bernard M. E. Moret

J. Comput. Biol., 2015

Comparing genomes with rearrangements and segmental duplications.

Mingfu Shao, Bernard M. E. Moret

Bioinform., 2015

2014

Study of cell differentiation by phylogenetic analysis using histone modification data.

Nishanth Ulhas Nair, Yu Lin, Ana Manasovska, Jelena Antic, Paulina Grnarova, Avinash Das Sahu, Philipp Bucher, Bernard M. E. Moret

BMC Bioinform., 2014

Probabilistic partitioning methods to find significant patterns in ChIP-Seq data.

Nishanth Ulhas Nair, Sunil Kumar, Bernard M. E. Moret, Philipp Bucher

Bioinform., 2014

Evaluating synteny for improved comparative studies.

Cristina G. Ghiurcuta, Bernard M. E. Moret

Bioinform., 2014

An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes.

Mingfu Shao, Yu Lin, Bernard M. E. Moret

Proceedings of the Research in Computational Molecular Biology, 2014

On the DCJ Median Problem.

Mingfu Shao, Bernard M. E. Moret

Proceedings of the Combinatorial Pattern Matching - 25th Annual Symposium, 2014

2013

A Transcript Perspective on Evolution.

Yann Christinat, Bernard M. E. Moret

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Sorting genomes with rearrangements and segmental duplications through trajectory graphs.

Mingfu Shao, Yu Lin, Bernard M. E. Moret

BMC Bioinform., 2013

Phylogenetic Analysis of Cell Types Using Histone Modifications.

Nishanth Ulhas Nair, Yu Lin, Philipp Bucher, Bernard M. E. Moret

Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

Extending the Reach of Phylogenetic Inference.

Bernard M. E. Moret

Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

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

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Rearrangements in Phylogenetic Inference: Compare, Model, or Encode?

Bernard M. E. Moret, Yu Lin, Jijun Tang

Proceedings of the Models and Algorithms for Genome Evolution, 2013

2012

Refining Regulatory Networks through Phylogenetic Transfer of Information.

Xiuwei Zhang, Bernard M. E. Moret

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

A Metric for Phylogenetic Trees Based on Matching.

Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Inferring transcript phylogenies.

Yann Christinat, Bernard M. E. Moret

BMC Bioinform., 2012

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis.

Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

Bioinform., 2012

Bootstrapping phylogenies inferred from rearrangement data.

Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

Algorithms Mol. Biol., 2012

2011

Uncovering Hidden Phylogenetic Consensus in Large Data Sets.

Nicholas D. Pattengale, Andre J. Aberer, Krister M. Swenson, Alexandros Stamatakis, Bernard M. E. Moret

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator.

Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

J. Comput. Biol., 2011

A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes.

Yu Lin, Bernard M. E. Moret

J. Comput. Biol., 2011

GASTS: Parsimony Scoring under Rearrangements.

Andrew Wei Xu, Bernard M. E. Moret

Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

ProPhyC: A Probabilistic Phylogenetic Model for Refining Regulatory Networks.

Xiuwei Zhang, Bernard M. E. Moret

Proceedings of the Bioinformatics Research and Applications - 7th International Symposium, 2011

Phylogenetic Analysis of Whole Genomes - (Keynote Talk).

Bernard M. E. Moret

Proceedings of the Bioinformatics Research and Applications - 7th International Symposium, 2011

2010

Sorting Signed Permutations by Inversions in <i>O</i>(<i>n</i>log<i>n</i>) Time.

Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret

J. Comput. Biol., 2010

How Many Bootstrap Replicates Are Necessary?

Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis

J. Comput. Biol., 2010

Heuristics for the inversion median problem.

Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M. Swenson, Bernard M. E. Moret

BMC Bioinform., 2010

Estimating true evolutionary distances under rearrangements, duplications, and losses.

Yu Lin, Vaibhav Rajan, Krister M. Swenson, Bernard M. E. Moret

BMC Bioinform., 2010

Refining transcriptional regulatory networks using network evolutionary models and gene histories.

Xiuwei Zhang, Bernard M. E. Moret

Algorithms Mol. Biol., 2010

Uncovering Hidden Phylogenetic Consensus.

Nicholas D. Pattengale, Krister M. Swenson, Bernard M. E. Moret

Proceedings of the Bioinformatics Research and Applications, 6th International Symposium, 2010

FluRF, an automated flu virus reassortment finder based on phylogenetic trees.

Alisa Yurovsky, Bernard M. E. Moret

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

2009

Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results.

Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

J. Comput. Biol., 2009

Maximum independent sets of commuting and noninterfering inversions.

Krister M. Swenson, Yokuki To, Jijun Tang, Bernard M. E. Moret

BMC Bioinform., 2009

Inversion-based genomic signatures.

Krister M. Swenson, Bernard M. E. Moret

BMC Bioinform., 2009

Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models.

Xiuwei Zhang, Bernard M. E. Moret

Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

Sorting Signed Permutations by Inversions in O(nlogn) Time.

Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret

Proceedings of the Research in Computational Molecular Biology, 2009

Session Introduction.

Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff

Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

2008

Approximating the true evolutionary distance between two genomes.

Krister M. Swenson, Mark Marron, Joel V. Earnest-DeYoung, Bernard M. E. Moret

ACM J. Exp. Algorithmics, 2008

Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach.

Xiuwei Zhang, Bernard M. E. Moret

Proceedings of the Algorithms in Bioinformatics, 8th International Workshop, 2008

Hurdles Hardly Have to Be Heeded.

Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret

Proceedings of the Comparative Genomics, International Workshop, 2008

Session Introduction.

Michael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy J. Warnow

Proceedings of the Biocomputing 2008, 2008

Estimating true evolutionary distances under the DCJ model.

Yu Lin, Bernard M. E. Moret

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

Using Phylogenetic Relationships to Improve the Inference of Transcriptional Regulatory Networks.

Xiuwei Zhang, Maryam Zaheri, Bernard M. E. Moret

Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics, 2008

Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes.

Krister M. Swenson, William Arndt, Jijun Tang, Bernard M. E. Moret

Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

2007

Efficiently Computing the Robinson-Foulds Metric.

Nicholas D. Pattengale, Eric J. Gottlieb, Bernard M. E. Moret

J. Comput. Biol., 2007

An Experimental Evaluation of Inversion-and Transposition-Based Genomic Distances through Simulations.

Moulik Kothari, Bernard M. E. Moret

Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2007

Reconstructing phylogenies from gene-content and gene-order data.

Bernard M. E. Moret, Jijun Tang, Tandy J. Warnow

Proceedings of the Mathematics of Evolution and Phylogeny., 2007

2006

NetGen: generating phylogenetic networks with diploid hybrids.

M. M. Morin, Bernard M. E. Moret

Bioinform., 2006

A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric.

Nicholas D. Pattengale, Bernard M. E. Moret

Proceedings of the Research in Computational Molecular Biology, 2006

Inferring Ancestral Chloroplast Genomes with Inverted Repea.

Liying Cui, Feng Yue, Claude W. dePamphilis, Bernard M. E. Moret, Jijun Tang

Proceedings of the 2006 International Conference on Bioinformatics & Computational Biology, 2006

2005

A Framework for Orthology Assignment from Gene Rearrangement Data.

Krister M. Swenson, Nicholas D. Pattengale, Bernard M. E. Moret

Proceedings of the Comparative Genomics, 2005

Phylogenetic Postprocessing.

Nicholas D. Pattengale, Bernard M. E. Moret

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005

Consensus Methods Using Phylogenetic Databases.

Mahesh M. Kulkarni, Bernard M. E. Moret

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference Workshops & Poster Abstracts, 2005

Linear Programming for Phylogenetic Reconstruction Based on Gene Rearrangements.

Jijun Tang, Bernard M. E. Moret

Proceedings of the Combinatorial Pattern Matching, 16th Annual Symposium, 2005

Quartet-Based Phylogeny Reconstruction from Gene Orders.

Tao Liu, Jijun Tang, Bernard M. E. Moret

Proceedings of the Computing and Combinatorics, 11th Annual International Conference, 2005

Computational Challenges from the Tree of Life.

Bernard M. E. Moret

Proceedings of the Seventh Workshop on Algorithm Engineering and Experiments and the Second Workshop on Analytic Algorithmics and Combinatorics, 2005

2004

Genomic Distances under Deletions and Insertions.

Mark Marron, Krister M. Swenson, Bernard M. E. Moret

Theor. Comput. Sci., 2004

Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy.

Bernard M. E. Moret, Luay Nakhleh, Tandy J. Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun, Ruth E. Timme

IEEE ACM Trans. Comput. Biol. Bioinform., 2004

Reversing Gene Erosion - Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data.

Joel V. Earnest-DeYoung, Emmanuelle Lerat, Bernard M. E. Moret

Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees.

Usman Roshan, Bernard M. E. Moret, Tandy J. Warnow, Tiffani L. Williams

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

Phylogenetic Reconstruction from Arbitrary Gene-Order Data.

Jijun Tang, Bernard M. E. Moret, Liying Cui, Claude W. dePamphilis

Proceedings of the 4th IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2004), 2004

2003

Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining.

Katherine St. John, Tandy J. Warnow, Bernard M. E. Moret, Lisa Vawter

J. Algorithms, 2003

Phylogenetic Reconstruction from Gene-Rearrangement Data with Unequal Gene Content.

Jijun Tang, Bernard M. E. Moret

Proceedings of the Algorithms and Data Structures, 8th International Workshop, 2003

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

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

Scaling up accurate phylogenetic reconstruction from gene-order data.

Jijun Tang, Bernard M. E. Moret

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

An Investigation of Phylogenetic Likelihood Methods.

Tiffani L. Williams, Bernard M. E. Moret

Proceedings of the 3rd IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2003), 2003

2002

High-Performance Algorithm Engineering for Computational Phylogenetics.

Bernard M. E. Moret, David A. Bader, Tandy J. Warnow

J. Supercomput., 2002

Steps toward accurate reconstructions of phylogenies from gene-order data.

Bernard M. E. Moret, Jijun Tang, Li-San Wang, Tandy J. Warnow

J. Comput. Syst. Sci., 2002

Point Set Labeling with Specified Positions.

Srinivas Doddi, Madhav V. Marathe, Bernard M. E. Moret

Int. J. Comput. Geom. Appl., 2002

Toward New Software for Computational Phylogenetics.

Bernard M. E. Moret, Li-San Wang, Tandy J. Warnow

Computer, 2002

Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data.

Bernard M. E. Moret, Adam C. Siepel, Jijun Tang, Tao Liu

Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002

Sequence-Length Requirements for Phylogenetic Methods.

Bernard M. E. Moret, Usman Roshan, Tandy J. Warnow

Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002

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

Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

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

Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

2001

Algorithms and Experiments: The New (and Old) Methodology.

Bernard M. E. Moret, Henry D. Shapiro

J. Univers. Comput. Sci., 2001

A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study.

David A. Bader, Bernard M. E. Moret, Mi Yan

J. Comput. Biol., 2001

Foreword.

Bernard M. E. Moret

J. Algorithms, 2001

Using PRAM Algorithms on a Uniform-Memory-Access Shared-Memory Architecture.

David A. Bader, Ajith K. Illendula, Bernard M. E. Moret, Nina R. Weisse-Bernstein

Proceedings of the Algorithm Engineering, 2001

Finding an Optimal Inversion Median: Experimental Results.

Adam C. Siepel, Bernard M. E. Moret

Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001

Absolute convergence: true trees from short sequences.

Tandy J. Warnow, Bernard M. E. Moret, Katherine St. John

Proceedings of the Twelfth Annual Symposium on Discrete Algorithms, 2001

A New Implmentation and Detailed Study of Breakpoint Analysis.

Bernard M. E. Moret, Stacia K. Wyman, David A. Bader, Tandy J. Warnow, Mi Yan

Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

New approaches for reconstructing phylogenies from gene order data.

Bernard M. E. Moret, Li-San Wang, Tandy J. Warnow, Stacia K. Wyman

Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001

2000

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

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000

Reconstructing Optimal Phylogenetic Trees: A Challenge in Experimental Algorithmics.

Bernard M. E. Moret, Tandy J. Warnow

Proceedings of the Experimental Algorithmics, 2000

Algorithm Engineering for Parallel Computation.

David A. Bader, Bernard M. E. Moret, Peter Sanders

Proceedings of the Experimental Algorithmics, 2000

1999

How to present a paper on experimental work with algorithms.

Catherine C. McGeoch, Bernard M. E. Moret

SIGACT News, 1999

Dynamical System Representation of Open Address Hash Functions.

Gregory L. Heileman, Chaouki T. Abdallah, Bernard M. E. Moret, Bradley J. Smith

Proceedings of the Tenth Annual ACM-SIAM Symposium on Discrete Algorithms, 1999

Combinatorial Algorithms Test Sets [CATS]: The ACM/EATCS Platform for Experimental Research.

Andrew V. Goldberg, Bernard M. E. Moret

Proceedings of the Tenth Annual ACM-SIAM Symposium on Discrete Algorithms, 1999

Towards a discipline of experimental algorithmics.

Bernard M. E. Moret

Proceedings of the Data Structures, 1999

1998

Improved Lower Bounds for the Link Length of Rectilinear Spanning Paths in Grids.

Michael J. Collins, Bernard M. E. Moret

Inf. Process. Lett., 1998

Theory of computation.

Bernard M. E. Moret

Addison-Wesley-Longman, ISBN: 978-0-201-25828-8, 1998

1997

Workshop on algorithm engineering: a report.

Bernard M. E. Moret

SIGACT News, 1997

The Ice Rink Problem.

Bernard M. E. Moret, Michael J. Collins, Jared Saia, Ling Yu

Proceedings of the Workshop on Algorithm Engineering, 1997

Map Labeling and Its Generalizations.

Srinivas Doddi, Madhav V. Marathe, Andy Mirzaian, Bernard M. E. Moret, Binhai Zhu

Proceedings of the Eighth Annual ACM-SIAM Symposium on Discrete Algorithms, 1997

1995

Network Routing Models Applied to Aircraft Routing Problems.

Zhiqiang Chen, Andrew T. Holle, Bernard M. E. Moret, Jared Saia, Ali Boroujerdi

Proceedings of the 27th conference on Winter simulation, 1995

Folding a Simple Polygon: A Paradigm for Computational Geometry.

Ali A. Kooshesh, Bernard M. E. Moret

Proceedings of the 1995 ACM 23rd Annual Conference on Computer Science, CSC '95, Nashville, TN, USA, February 28, 1995

1993

An Exact Characterization of Greedy Structures.

Paul Helman, Bernard M. E. Moret, Henry D. Shapiro

SIAM J. Discret. Math., 1993

1992

Three-coloring the vertices of a triangulated simple polygon.

Ali A. Kooshesh, Bernard M. E. Moret

Pattern Recognit., 1992

An Empirical Assessment of Algorithms for Constructing a Minimum Spanning Tree.

Bernard M. E. Moret, Henry D. Shapiro

Proceedings of the Computational Support for Discrete Mathematics, 1992

1991

Constructive complexity.

Karl R. Abrahamson, Michael R. Fellows, Michael A. Langston, Bernard M. E. Moret

Discret. Appl. Math., 1991

An Emperical Analysis of Algorithms for Constructing a Minimum Spanning Tree.

Bernard M. E. Moret, Henry D. Shapiro

Proceedings of the Algorithms and Data Structures, 1991

Folding a Triangulated Simple Polygon: Structural and Algorithmic Results.

Ali A. Kooshesh, Bernard M. E. Moret

Proceedings of the Advances in Computing and Information, 1991

How to Find a Minimum Spanning Tree in Practice.

Bernard M. E. Moret, Henry D. Shapiro

Proceedings of the New Results and New Trends in Computer Science, 1991

1990

A new method for one-dimensional linear feature transformations.

Chea-Tin (Tim) Tseng, Bernard M. E. Moret

Pattern Recognit., 1990

The design of a nonparametric hierarchical classifier.

Chea-Tin (Tim) Tseng, Bernard M. E. Moret

Proceedings of the 10th IAPR International Conference on Pattern Recognition, 1990

1988

Planar NAE3SAT is in P.

Bernard M. E. Moret

SIGACT News, 1988

1983

Symmetric and Threshold Boolean Functions Are Exhaustive.

Bernard M. E. Moret, Michael G. Thomason, Rafael C. González

IEEE Trans. Computers, 1983

The Computational Metaphor and Quantum Physics.

Michael J. Mathey, Bernard M. E. Moret

Commun. ACM, 1983

1982

Decision Trees and Diagrams.

Bernard M. E. Moret

ACM Comput. Surv., 1982

1980

The Activity of a Variable and Its Relation to Decision Trees.

Bernard M. E. Moret, Michael G. Thomason, Rafael C. González

ACM Trans. Program. Lang. Syst., 1980