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)

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

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

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

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

The design of a nonparametric hierarchical classifier. - Chea-Tin (Tim) Tseng; Bernard M. E. Moret (ICPR (1), 1990)

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

How to Find a Minimum Spanning Tree in Practice. - Bernard M. E. Moret; Henry D. Shapiro (New Results and New Trends in Computer Science, 1991)

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

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

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

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

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

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

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

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

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

The Ice Rink Problem. - Bernard M. E. Moret; Michael J. Collins 003; Jared Saia; Ling Yu (WAE, 1997)

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

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

Improved Lower Bounds for the Link Length of Rectilinear Spanning Paths in Grids. - Michael J. Collins 003; Bernard M. E. Moret (Inf. Process. Lett., 1998)

Towards a discipline of experimental algorithmics. - Bernard M. E. Moret (Data Structures, Near Neighbor Searches, and Methodology, 1999)

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

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

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

Algorithm Engineering for Parallel Computation. - David A. Bader; Bernard M. E. Moret; Peter Sanders 001 (Experimental Algorithmics, 2000)

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

New approaches for reconstructing phylogenies from gene order data. - Bernard M. E. Moret; Li-San Wang; Tandy J. Warnow; Stacia K. Wyman (ISMB (Supplement of Bioinformatics), 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 (Pacific Symposium on Biocomputing, 2001)

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

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

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

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

The Accuracy of Fast Phylogenetic Methods for Large Datasets. - Luay Nakhleh; Bernard M. E. Moret; Usman Roshan; Katherine St. John; Jerry Sun 001; Tandy J. Warnow (Pacific Symposium on Biocomputing, 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 (Pacific Symposium on Biocomputing, 2002)

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

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

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

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

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

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

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

Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. - Luay Nakhleh; Jerry Sun 001; Tandy J. Warnow; C. Randal Linder; Bernard M. E. Moret; Anna Tholse (Pacific Symposium on Biocomputing, 2003)

Phylogenetic Reconstruction from Gene-Rearrangement Data with Unequal Gene Content. - Jijun Tang; Bernard M. E. Moret (WADS, 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 Arbitrary Gene-Order Data. - Jijun Tang; Bernard M. E. Moret; Liying Cui; Claude W. dePamphilis (BIBE, 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 (CSB, 2004)

Reversing Gene Erosion - Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data. - Joel V. Earnest-DeYoung; Emmanuelle Lerat; Bernard M. E. Moret (WABI, 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 001; Ruth E. Timme (IEEE ACM Trans. Comput. Biol. Bioinform., 2004)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Using Phylogenetic Relationships to Improve the Inference of Transcriptional Regulatory Networks. - Xiuwei Zhang; Maryam Zaheri; Bernard M. E. Moret (BMEI (1), 2008)

Estimating true evolutionary distances under the DCJ model. - Yu Lin 001; Bernard M. E. Moret (ISMB, 2008)

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

Hurdles Hardly Have to Be Heeded. - Krister M. Swenson; Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (RECOMB-CG, 2008)

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

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

Sorting Signed Permutations by Inversions in O(nlogn) Time. - Krister M. Swenson; Vaibhav Rajan; Yu Lin 001; Bernard M. E. Moret (RECOMB, 2009)

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

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

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

Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results. - Krister M. Swenson; Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (J. Comput. Biol., 2009)

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

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

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

Estimating true evolutionary distances under rearrangements, duplications, and losses. - Yu Lin 001; Vaibhav Rajan; Krister M. Swenson; Bernard M. E. Moret (BMC Bioinform., 2010)

Heuristics for the inversion median problem. - Vaibhav Rajan; Andrew Wei Xu; Yu Lin 001; Krister M. Swenson; Bernard M. E. Moret (BMC Bioinform., 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)

Sorting Signed Permutations by Inversions in O(nlogn) Time. - Krister M. Swenson; Vaibhav Rajan; Yu Lin 001; Bernard M. E. Moret (J. Comput. Biol., 2010)

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

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

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

A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes. - Yu Lin 001; Bernard M. E. Moret (J. Comput. Biol., 2011)

Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator. - Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (J. Comput. Biol., 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)

Bootstrapping phylogenies inferred from rearrangement data. - Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (Algorithms Mol. Biol., 2012)

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis. - Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (Bioinform., 2012)

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

A Metric for Phylogenetic Trees Based on Matching. - Yu Lin 001; Vaibhav Rajan; Bernard M. E. Moret (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

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

Rearrangements in Phylogenetic Inference: Compare, Model, or Encode? - Bernard M. E. Moret; Yu Lin 001; Jijun Tang (Models and Algorithms for Genome Evolution, 2013)

Maximum Likelihood Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Tree of 68 Eukaryotes. - Yu Lin 001; Fei Hu; Jijun Tang; Bernard M. E. Moret (Pacific Symposium on Biocomputing, 2013)

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

Phylogenetic Analysis of Cell Types Using Histone Modifications. - Nishanth Ulhas Nair; Yu Lin 001; Philipp Bucher; Bernard M. E. Moret (WABI, 2013)

Sorting genomes with rearrangements and segmental duplications through trajectory graphs. - Mingfu Shao; Yu Lin 001; Bernard M. E. Moret (BMC Bioinform., 2013)

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

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

An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes. - Mingfu Shao; Yu Lin 001; Bernard M. E. Moret (RECOMB, 2014)

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

Study of cell differentiation by phylogenetic analysis using histone modification data. - Nishanth Ulhas Nair; Yu Lin 001; Ana Manasovska; Jelena Antic; Paulina Grnarova; Avinash Das Sahu; Philipp Bucher; Bernard M. E. Moret (BMC Bioinform., 2014)

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

An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes. - Mingfu Shao; Yu Lin 001; Bernard M. E. Moret (J. Comput. Biol., 2015)

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

A maximum-likelihood approach for building cell-type trees by lifting. - Nishanth Ulhas Nair; Laura Hunter; Mingfu Shao; Paulina Grnarova; Yu Lin 001; Philipp Bucher; Bernard M. E. Moret (BMC Genom., 2016)

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

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)

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

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