Bernard M. E. Moret

ORCID

Publication Activity (10 Years)

Years Active: 1980-2023
Publications (10 Years): 10

Top Venues

Publications

Daniel Doerr, Bernard M. E. Moret
Fast computation of approximate weak common intervals in multiple indeterminate strings. CoRR (2023)
Mingfu Shao, Bernard M. E. Moret
On Computing Breakpoint Distances for Genomes with Duplicate Genes. J. Comput. Biol. 24 (6) (2017)
Daniel Doerr, Luis Antonio Brasil Kowada, Eloi Araujo, Shachi Deshpande, Simone Dantas, Bernard M. E. Moret, Jens Stoye
New Genome Similarity Measures based on Conserved Gene Adjacencies. J. Comput. Biol. 24 (6) (2017)
Mingfu Shao, Bernard M. E. Moret
On Computing Breakpoint Distances for Genomes with Duplicate Genes. RECOMB (2016)
Mingfu Shao, Bernard M. E. Moret
A Fast and Exact Algorithm for the Exemplar Breakpoint Distance. J. Comput. Biol. 23 (5) (2016)
Min Ye, Gabriela C. Racz, Qijia Jiang, Xiuwei Zhang, Bernard M. E. Moret
NEMo: An Evolutionary Model with Modularity for PPI Networks. ISBRA (2016)
Nishanth Ulhas Nair, Laura Hunter, Mingfu Shao, Paulina Grnarova, Yu Lin, Philipp Bucher, Bernard M. E. Moret
A maximum-likelihood approach for building cell-type trees by lifting. BMC Genom. 17 (S-1) (2016)
Mingfu Shao, Bernard M. E. Moret
Comparing genomes with rearrangements and segmental duplications. Bioinform. 31 (12) (2015)
Mingfu Shao, Bernard M. E. Moret
A Fast and Exact Algorithm for the Exemplar Breakpoint Distance. RECOMB (2015)
Mingfu Shao, Yu Lin, Bernard M. E. Moret
An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes. J. Comput. Biol. 22 (5) (2015)
Nishanth Ulhas Nair, Sunil Kumar, Bernard M. E. Moret, Philipp Bucher
Probabilistic partitioning methods to find significant patterns in ChIP-Seq data. Bioinform. 30 (17) (2014)
Nishanth Ulhas Nair, Yu Lin, Ana Manasovska, Jelena Antic, Paulina Grnarova, Avinash Das Sahu, Philipp Bucher, Bernard M. E. Moret
Study of cell differentiation by phylogenetic analysis using histone modification data. BMC Bioinform. 15 (2014)
Cristina G. Ghiurcuta, Bernard M. E. Moret
Evaluating synteny for improved comparative studies. Bioinform. 30 (12) (2014)
Mingfu Shao, Yu Lin, Bernard M. E. Moret
An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes. RECOMB (2014)
Mingfu Shao, Bernard M. E. Moret
On the DCJ Median Problem. CPM (2014)
Yu Lin, Fei Hu, Jijun Tang, Bernard M. E. Moret
Maximum Likelihood Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Tree of 68 Eukaryotes. Pacific Symposium on Biocomputing (2013)
Nishanth Ulhas Nair, Yu Lin, Philipp Bucher, Bernard M. E. Moret
Phylogenetic Analysis of Cell Types Using Histone Modifications. WABI (2013)
Bernard M. E. Moret
Extending the Reach of Phylogenetic Inference. WABI (2013)
Yann Christinat, Bernard M. E. Moret
A Transcript Perspective on Evolution. IEEE ACM Trans. Comput. Biol. Bioinform. 10 (6) (2013)
Mingfu Shao, Yu Lin, Bernard M. E. Moret
Sorting genomes with rearrangements and segmental duplications through trajectory graphs. BMC Bioinform. 14 (S-15) (2013)
Yann Christinat, Bernard M. E. Moret
A Transcript Perspective on Evolution. ISBRA (2012)
Xiuwei Zhang, Bernard M. E. Moret
Refining Regulatory Networks through Phylogenetic Transfer of Information. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (4) (2012)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Bootstrapping phylogenies inferred from rearrangement data. Algorithms Mol. Biol. 7 (2012)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis. Bioinform. 28 (24) (2012)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
A Metric for Phylogenetic Trees Based on Matching. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (4) (2012)
Yann Christinat, Bernard M. E. Moret
Inferring transcript phylogenies. BMC Bioinform. 13 (S-9) (2012)
Nicholas D. Pattengale, Andre J. Aberer, Krister M. Swenson, Alexandros Stamatakis, Bernard M. E. Moret
Uncovering Hidden Phylogenetic Consensus in Large Data Sets. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (4) (2011)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Bootstrapping Phylogenies Inferred from Rearrangement Data. WABI (2011)
Bernard M. E. Moret
Phylogenetic Analysis of Whole Genomes - (Keynote Talk). ISBRA (2011)
Yann Christinat, Bernard M. E. Moret
Inferring Transcript Phylogenies. BIBM (2011)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator. J. Comput. Biol. 18 (9) (2011)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
A Metric for Phylogenetic Trees Based on Matching. ISBRA (2011)
Xiuwei Zhang, Bernard M. E. Moret
ProPhyC: A Probabilistic Phylogenetic Model for Refining Regulatory Networks. ISBRA (2011)
Yu Lin, Bernard M. E. Moret
A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes. J. Comput. Biol. 18 (9) (2011)
Andrew Wei Xu, Bernard M. E. Moret
GASTS: Parsimony Scoring under Rearrangements. WABI (2011)
Yu Lin, Bernard M. E. Moret
A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses That Applies across Eukaryotes and Prokaryotes. RECOMB-CG (2010)
Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M. Swenson, Bernard M. E. Moret
Heuristics for the inversion median problem. BMC Bioinform. 11 (S-1) (2010)
Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator. RECOMB-CG (2010)
Yu Lin, Vaibhav Rajan, Krister M. Swenson, Bernard M. E. Moret
Estimating true evolutionary distances under rearrangements, duplications, and losses. BMC Bioinform. 11 (S-1) (2010)
Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff
Session Introduction. Pacific Symposium on Biocomputing (2010)
Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret
) Time. J. Comput. Biol. 17 (3) (2010)
Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis
How Many Bootstrap Replicates Are Necessary? J. Comput. Biol. 17 (3) (2010)
Nicholas D. Pattengale, Krister M. Swenson, Bernard M. E. Moret
Uncovering Hidden Phylogenetic Consensus. ISBRA (2010)
Xiuwei Zhang, Bernard M. E. Moret
Refining transcriptional regulatory networks using network evolutionary models and gene histories. Algorithms Mol. Biol. 5 (2010)
Alisa Yurovsky, Bernard M. E. Moret
FluRF, an automated flu virus reassortment finder based on phylogenetic trees. BIBM (2010)
Nicholas D. Pattengale, Masoud Alipour, Olaf R. P. Bininda-Emonds, Bernard M. E. Moret, Alexandros Stamatakis
How Many Bootstrap Replicates Are Necessary? RECOMB (2009)
Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results. J. Comput. Biol. 16 (10) (2009)
Krister M. Swenson, Vaibhav Rajan, Yu Lin, Bernard M. E. Moret
Sorting Signed Permutations by Inversions in O(nlogn) Time. RECOMB (2009)
Xiuwei Zhang, Bernard M. E. Moret
Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models. WABI (2009)
Krister M. Swenson, Yokuki To, Jijun Tang, Bernard M. E. Moret
Maximum independent sets of commuting and noninterfering inversions. BMC Bioinform. 10 (S-1) (2009)
Krister M. Swenson, Bernard M. E. Moret
Inversion-based genomic signatures. BMC Bioinform. 10 (S-1) (2009)
Bernard M. E. Moret, Webb Miller, Pavel A. Pevzner, David Sankoff
Session Introduction. Pacific Symposium on Biocomputing (2009)
Michael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy J. Warnow
Session Introduction. Pacific Symposium on Biocomputing (2008)
Krister M. Swenson, Yu Lin, Vaibhav Rajan, Bernard M. E. Moret
Hurdles Hardly Have to Be Heeded. RECOMB-CG (2008)
Yu Lin, Bernard M. E. Moret
Estimating true evolutionary distances under the DCJ model. ISMB (2008)
Xiuwei Zhang, Bernard M. E. Moret
Boosting the Performance of Inference Algorithms for Transcriptional Regulatory Networks Using a Phylogenetic Approach. WABI (2008)
Xiuwei Zhang, Maryam Zaheri, Bernard M. E. Moret
Using Phylogenetic Relationships to Improve the Inference of Transcriptional Regulatory Networks. BMEI (1) (2008)
Krister M. Swenson, Mark Marron, Joel V. Earnest-DeYoung, Bernard M. E. Moret
Approximating the true evolutionary distance between two genomes. ACM J. Exp. Algorithmics 12 (2008)
Krister M. Swenson, William Arndt, Jijun Tang, Bernard M. E. Moret
Phylogenetic Reconstruction from Complete Gene Orders of Whole Genomes. APBC (2008)
Moulik Kothari, Bernard M. E. Moret
An Experimental Evaluation of Inversion-and Transposition-Based Genomic Distances through Simulations. CIBCB (2007)
Nicholas D. Pattengale, Eric J. Gottlieb, Bernard M. E. Moret
Efficiently Computing the Robinson-Foulds Metric. J. Comput. Biol. 14 (6) (2007)
Nicholas D. Pattengale, Bernard M. E. Moret
A Sublinear-Time Randomized Approximation Scheme for the Robinson-Foulds Metric. RECOMB (2006)
M. M. Morin, Bernard M. E. Moret
NetGen: generating phylogenetic networks with diploid hybrids. Bioinform. 22 (15) (2006)
Liying Cui, Feng Yue, Claude W. dePamphilis, Bernard M. E. Moret, Jijun Tang
Inferring Ancestral Chloroplast Genomes with Inverted Repea. BIOCOMP (2006)
Krister M. Swenson, Nicholas D. Pattengale, Bernard M. E. Moret
A Framework for Orthology Assignment from Gene Rearrangement Data. Comparative Genomics (2005)
Nicholas D. Pattengale, Bernard M. E. Moret
Phylogenetic Postprocessing. CSB Workshops (2005)
Mahesh M. Kulkarni, Bernard M. E. Moret
Consensus Methods Using Phylogenetic Databases. CSB Workshops (2005)
Bernard M. E. Moret
Computational Challenges from the Tree of Life. ALENEX/ANALCO (2005)
Tao Liu, Jijun Tang, Bernard M. E. Moret
Quartet-Based Phylogeny Reconstruction from Gene Orders. COCOON (2005)
Krister M. Swenson, Mark Marron, Joel V. Earnest-DeYoung, Bernard M. E. Moret
Approximating the True Evolutionary Distance between Two Genomes. ALENEX/ANALCO (2005)
Jijun Tang, Bernard M. E. Moret
Linear Programming for Phylogenetic Reconstruction Based on Gene Rearrangements. CPM (2005)
Mark Marron, Krister M. Swenson, Bernard M. E. Moret
Genomic Distances under Deletions and Insertions. Theor. Comput. Sci. 325 (3) (2004)
Jijun Tang, Bernard M. E. Moret, Liying Cui, Claude W. dePamphilis
Phylogenetic Reconstruction from Arbitrary Gene-Order Data. BIBE (2004)
Bernard M. E. Moret, Luay Nakhleh, Tandy J. Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun, Ruth E. Timme
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. IEEE ACM Trans. Comput. Biol. Bioinform. 1 (1) (2004)
Usman Roshan, Bernard M. E. Moret, Tandy J. Warnow, Tiffani L. Williams
Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees. CSB (2004)
Joel V. Earnest-DeYoung, Emmanuelle Lerat, Bernard M. E. Moret
Reversing Gene Erosion - Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data. WABI (2004)
Mark Marron, Krister M. Swenson, Bernard M. E. Moret
Genomic Distances under Deletions and Insertions. COCOON (2003)
Tiffani L. Williams, Bernard M. E. Moret
An Investigation of Phylogenetic Likelihood Methods. BIBE (2003)
Katherine St. John, Tandy J. Warnow, Bernard M. E. Moret, Lisa Vawter
Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. J. Algorithms 48 (1) (2003)
Jijun Tang, Bernard M. E. Moret
Phylogenetic Reconstruction from Gene-Rearrangement Data with Unequal Gene Content. WADS (2003)
Luay Nakhleh, Jerry Sun, Tandy J. Warnow, C. Randal Linder, Bernard M. E. Moret, Anna Tholse
Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. Pacific Symposium on Biocomputing (2003)
Jijun Tang, Bernard M. E. Moret
Scaling up accurate phylogenetic reconstruction from gene-order data. ISMB (Supplement of Bioinformatics) (2003)
Bernard M. E. Moret, Li-San Wang, Tandy J. Warnow
Toward New Software for Computational Phylogenetics. Computer 35 (7) (2002)
Bernard M. E. Moret, David A. Bader, Tandy J. Warnow
High-Performance Algorithm Engineering for Computational Phylogenetics. J. Supercomput. 22 (1) (2002)
Bernard M. E. Moret, Usman Roshan, Tandy J. Warnow
Sequence-Length Requirements for Phylogenetic Methods. WABI (2002)
Srinivas Doddi, Madhav V. Marathe, Bernard M. E. Moret
Point Set Labeling with Specified Positions. Int. J. Comput. Geom. Appl. 12 (1-2) (2002)
Bernard M. E. Moret, Adam C. Siepel, Jijun Tang, Tao Liu
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data. WABI (2002)
Bernard M. E. Moret, Jijun Tang, Li-San Wang, Tandy J. Warnow
Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci. 65 (3) (2002)
Li-San Wang, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Tandy J. Warnow
Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study. Pacific Symposium on Biocomputing (2002)
Luay Nakhleh, Bernard M. E. Moret, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow
The Accuracy of Fast Phylogenetic Methods for Large Datasets. Pacific Symposium on Biocomputing (2002)
Katherine St. John, Tandy J. Warnow, Bernard M. E. Moret, Lisa Vawter
Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. SODA (2001)
David A. Bader, Bernard M. E. Moret, Mi Yan
A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study. WADS (2001)
Adam C. Siepel, Bernard M. E. Moret
Finding an Optimal Inversion Median: Experimental Results. WABI (2001)
Bernard M. E. Moret, Stacia K. Wyman, David A. Bader, Tandy J. Warnow, Mi Yan
A New Implmentation and Detailed Study of Breakpoint Analysis. Pacific Symposium on Biocomputing (2001)
David A. Bader, Bernard M. E. Moret, Mi Yan
A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study. J. Comput. Biol. 8 (5) (2001)
Tandy J. Warnow, Bernard M. E. Moret, Katherine St. John
Absolute convergence: true trees from short sequences. SODA (2001)
Bernard M. E. Moret
Foreword. J. Algorithms 38 (1) (2001)
David A. Bader, Ajith K. Illendula, Bernard M. E. Moret, Nina R. Weisse-Bernstein
Using PRAM Algorithms on a Uniform-Memory-Access Shared-Memory Architecture. WAE (2001)
Bernard M. E. Moret, Henry D. Shapiro
Algorithms and Experiments: The New (and Old) Methodology. J. Univers. Comput. Sci. 7 (5) (2001)
Bernard M. E. Moret, David A. Bader, Tandy J. Warnow
High-Performance Algorithm Engineering for Computational Phylogenetics. International Conference on Computational Science (2) (2001)

Bernard M. E. Moret.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Bernard M. E. Moret