Bernard M Moret

Bernard M E Moret

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Bernard M Moret

Bernard M E Moret

Publications by authors named "Bernard M E Moret"

39Publications

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1PubMed Central Citations

Sequence-Based Synteny Analysis of Multiple Large Genomes.

Methods Mol Biol 2018 ;1704:317-329

School of Computer and Communication Sciences, EPFL, Lausanne, Switzerland.

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http://dx.doi.org/10.1007/978-1-4939-7463-4_11DOI Listing
December 2018

On Computing Breakpoint Distances for Genomes with Duplicate Genes.

J Comput Biol 2017 Jun 27;24(6):571-580. Epub 2016 Oct 27.

1 Laboratory for Computational Biology and Bioinformatics, School of Computer and Communication Sciences , École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland .

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http://dx.doi.org/10.1089/cmb.2016.0149DOI Listing
June 2017

New Genome Similarity Measures based on Conserved Gene Adjacencies.

J Comput Biol 2017 Jun;24(6):616-634

2 Universidade Federal Fluminense , Niterói, Brazil .

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http://dx.doi.org/10.1089/cmb.2017.0065DOI Listing
June 2017

NEMo: An Evolutionary Model With Modularity for PPI Networks.

IEEE Trans Nanobioscience 2017 03 19;16(2):131-139. Epub 2017 Jan 19.

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http://dx.doi.org/10.1109/TNB.2017.2656058DOI Listing
March 2017

A Fast and Exact Algorithm for the Exemplar Breakpoint Distance.

J Comput Biol 2016 05 8;23(5):337-46. Epub 2016 Mar 8.

Laboratory for Computational Biology and Bioinformatics, School of Computer and Communication Sciences , École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland .

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http://dx.doi.org/10.1089/cmb.2015.0193DOI Listing
May 2016

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

BMC Genomics 2016 Jan 11;17 Suppl 1:14. Epub 2016 Jan 11.

School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, Lausanne, CH-1015, Switzerland.

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http://dx.doi.org/10.1186/s12864-015-2297-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895258PMC
January 2016

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

J Comput Biol 2015 May 17;22(5):425-35. Epub 2014 Dec 17.

1 Laboratory for Computational Biology and Bioinformatics, École Polytechnique Fédérale de Lausanne (EPFL) , Lausanne, Switzerland .

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http://lcbb.epfl.ch/papers/Shao-RECOMB14.pdf
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http://link.springer.com/content/pdf/10.1007%2F978-3-319-052
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http://online.liebertpub.com/doi/10.1089/cmb.2014.0096
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http://dx.doi.org/10.1089/cmb.2014.0096DOI Listing
May 2015

A transcript perspective on evolution.

IEEE/ACM Trans Comput Biol Bioinform 2013 Nov-Dec;10(6):1403-11

Ecole Polytechnique Federale de Lausanne, Lausanne.

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http://dx.doi.org/10.1109/TCBB.2012.145DOI Listing
September 2014

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

Bioinformatics 2014 Sep 7;30(17):2406-13. Epub 2014 May 7.

Laboratory for Computational Biology and Bioinformatics, School of Computer and Communication Sciences, Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne and Swiss Institute for Bioinformatics, 1015 Lausanne, Switzerland Laboratory for Computational Biology and Bioinformatics, School of Computer and Communication Sciences, Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne and Swiss Institute for Bioinformatics, 1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btu318DOI Listing
September 2014

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

BMC Bioinformatics 2014 Aug 8;15:269. Epub 2014 Aug 8.

School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne (EPFL), EPFL IC IIF LCBB, INJ 211 (Batiment INJ), Station 14, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1186/1471-2105-15-269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138389PMC
August 2014

Evaluating synteny for improved comparative studies.

Bioinformatics 2014 Jun;30(12):i9-18

Laboratory for Computational Biology and Bioinformatics, EPFL-IC-LCBB INJ 230, Station 14, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btu259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058928PMC
June 2014

Maximum likelihood phylogenetic reconstruction from high-resolution whole-genome data and a tree of 68 eukaryotes.

Pac Symp Biocomput 2013 :285-96

Laboratory for Computational Biology and Bioinformatics, EPFL, Lausanne VD, CH-1015, Switzerland.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712796PMC
December 2013

ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries.

PLoS One 2012 3;7(8):e39573. Epub 2012 Aug 3.

Laboratory for Computational Biology and Bioinformatics, School of Computer and Communication Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0039573PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411705PMC
February 2013

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

Bioinformatics 2012 Dec 11;28(24):3324-5. Epub 2012 Oct 11.

Laboratory for Computational Biology and Bioinformatics, EPFL, EPFL-IC-LCBB INJ 230, Station 14, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/bts603DOI Listing
December 2012

A metric for phylogenetic trees based on matching.

IEEE/ACM Trans Comput Biol Bioinform 2012 Jul-Aug;9(4):1014-22

Laboratory for Computational Biology and Bioinformatics, School of Computer and Communication Sciences, Swiss Federal Institute of Technology-EPFL, INJ 211, Station 14, Lausanne CH-1015, Switzerland.

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http://dx.doi.org/10.1109/TCBB.2011.157DOI Listing
October 2012

Refining regulatory networks through phylogenetic transfer of information.

IEEE/ACM Trans Comput Biol Bioinform 2012 Jul-Aug;9(4):1032-45

Laboratory for Computational Biology and Bioinformatics, Ecole Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, EPFL IC IIF LCBB INJ211, Lausanne CH-1015, Switzerland.

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http://lcbb.epfl.ch/papers/tcbb12-prophyc.pdf
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https://www.computer.org/csdl/trans/tb/2012/04/06193091.pdf
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http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumbe
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http://dx.doi.org/10.1109/TCBB.2012.62DOI Listing
October 2012

Inferring transcript phylogenies.

BMC Bioinformatics 2012 Jun 11;13 Suppl 9:S1. Epub 2012 Jun 11.

Laboratory of Computational Biology and Bioinformatics, EPFL, 1015 Lausanne, Switzerland.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372451PMC
http://dx.doi.org/10.1186/1471-2105-13-s9-s1DOI Listing
June 2012

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

BMC Genomics 2011 27;12 Suppl 2:S3. Epub 2011 Jul 27.

Department of Computer Science, EPFL (Swiss Federal Institute of Technology), Lausanne, CH-1015, Switzerland.

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http://dx.doi.org/10.1186/1471-2164-12-S2-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194234PMC
January 2012

Uncovering hidden phylogenetic consensus in large data sets.

IEEE/ACM Trans Comput Biol Bioinform 2011 Jul-Aug;8(4):902-11

Sandia National Laboratories, PO Box 5800, Albuquerque, NM 87185, USA.

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http://dx.doi.org/10.1109/TCBB.2011.28DOI Listing
September 2011

A new genomic evolutionary model for rearrangements, duplications, and losses that applies across eukaryotes and prokaryotes.

J Comput Biol 2011 Sep;18(9):1055-64

Laboratory for Computational Biology and Bioinformatics, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.

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http://dx.doi.org/10.1089/cmb.2011.0098DOI Listing
September 2011

Sorting signed permutations by inversions in O(nlogn) time.

J Comput Biol 2010 Mar;17(3):489-501

Laboratory for Computational Biology and Bioinformatics, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland.

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http://dx.doi.org/10.1089/cmb.2009.0184DOI Listing
March 2010

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

Algorithms Mol Biol 2010 Jan 4;5. Epub 2010 Jan 4.

Laboratory for Computational Biology and Bioinformatics, Ecole Polytechnique Fédérale de Lausanne, EPFL-IC-LCBB, INJ230, Station 14, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1186/1748-7188-5-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2823753PMC
January 2010

Heuristics for the inversion median problem.

BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S30. Epub 2010 Jan 18.

Laboratory for Computational Biology and Bioinformatics, EPFL, CH-1015 Lausanne, Switzerland.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-11-S1-S30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009502PMC
January 2010

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

BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S54. Epub 2010 Jan 18.

Laboratory for Computational Biology and Bioinformatics, Swiss Federal Institute of Technology (EPFL), EPFL-IIS-LCBB, INJ 230, Station 14, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1186/1471-2105-11-S1-S54DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009527PMC
January 2010

Hurdles and sorting by inversions: combinatorial, statistical, and experimental results.

J Comput Biol 2009 Oct;16(10):1339-51

Laboratory for Computational Biology and Bioinformatics, EPFL (Ecole Polytechnique Fédérale de Lausanne), and Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://www.liebertpub.com/doi/10.1089/cmb.2009.0156
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http://dx.doi.org/10.1089/cmb.2009.0156DOI Listing
October 2009

Maximum independent sets of commuting and noninterfering inversions.

BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S6. Epub 2009 Jan 30.

Laboratory for Computational Biology and Bioinformatics, School of Computer and Communication Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland.

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http://www.biomedcentral.com/1471-2105/10/S1/S6
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http://dx.doi.org/10.1186/1471-2105-10-S1-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648783PMC
January 2009

Inversion-based genomic signatures.

BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S7. Epub 2009 Jan 30.

Laboratory for Computational Biology and Bioinformatics, EPFL (Swiss Federal Institute of Technology), EPFL-IC-LCBB, INJ 230, Station 14, CH-1014 Lausanne, Switzerland.

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http://dx.doi.org/10.1186/1471-2105-10-S1-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648787PMC
January 2009

Estimating true evolutionary distances under the DCJ model.

Bioinformatics 2008 Jul;24(13):i114-22

Laboratory for Computational Biology and Bioinformatics, Swiss Federal Institute of Technology (EPFL), EPFL-IIS-LCBB, INJ 230, Station 14, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btn148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718626PMC
July 2008

Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat.

BMC Genomics 2008 ;9 Suppl 1:S25

Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA.

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http://dx.doi.org/10.1186/1471-2164-9-S1-S25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2386067PMC
June 2008

Efficiently computing the Robinson-Foulds metric.

J Comput Biol 2007 Jul-Aug;14(6):724-35

Department of Computer Science, University of New Mexico, Albuquerque, NM, USA.

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http://dx.doi.org/10.1089/cmb.2007.R012DOI Listing
September 2007

Phylogenetic networks: modeling, reconstructibility, and accuracy.

IEEE/ACM Trans Comput Biol Bioinform 2004 Jan-Mar;1(1):13-23

Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA.

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http://dx.doi.org/10.1109/TCBB.2004.10DOI Listing
November 2006

Distance-based genome rearrangement phylogeny.

J Mol Evol 2006 Oct 4;63(4):473-83. Epub 2006 Oct 4.

Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1007/s00239-005-0216-yDOI Listing
October 2006

Advances in phylogeny reconstruction from gene order and content data.

Methods Enzymol 2005 ;395:673-700

Department of Computer Sciences, University of New Mexico, Albuquerque, New Mexico 87131, USA.

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http://dx.doi.org/10.1016/S0076-6879(05)95035-0DOI Listing
August 2005

Scaling up accurate phylogenetic reconstruction from gene-order data.

Bioinformatics 2003 ;19 Suppl 1:i305-12

Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg1042DOI Listing
October 2004

Towards the development of computational tools for evaluating phylogenetic network reconstruction methods.

Pac Symp Biocomput 2003 :315-26

Dept. of Computer Sciences, U of Texas, Austin, TX 78712, USA.

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August 2003

The accuracy of fast phylogenetic methods for large datasets.

Pac Symp Biocomput 2002 :211-22

Dept. of Computer Sciences, University of Texas, Austin, TX 78712, USA.

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October 2002

Fast phylogenetic methods for the analysis of genome rearrangement data: an empirical study.

Pac Symp Biocomput 2002 :524-35

Dept. of Computer Sciences, University of Texas, Austin, TX 78712, USA.

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October 2002