Publications by authors named "Emmanuel Barillot"

100Publications

Exact solving and sensitivity analysis of stochastic continuous time Boolean models.

BMC Bioinformatics 2020 Jun 11;21(1):241. Epub 2020 Jun 11.

Institut Curie, PSL Research University, Paris, F-75005, France.

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http://dx.doi.org/10.1186/s12859-020-03548-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7291460PMC
June 2020

Demarcation of Topologically Associating Domains Is Uncoupled from Enriched CTCF Binding in Developing Zebrafish.

iScience 2020 May 10;23(5):101046. Epub 2020 Apr 10.

Institut Curie PSL Research University, INSERM U934, CNRS UMR 3215 75005, Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2020.101046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182764PMC
May 2020

Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network.

PLoS Comput Biol 2020 02 18;16(2):e1007652. Epub 2020 Feb 18.

Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France.

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http://dx.doi.org/10.1371/journal.pcbi.1007652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048313PMC
February 2020

Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution.

Cell Rep 2020 02;30(6):1767-1779.e6

INSERM U900, 75005 Paris, France; Mines ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 75006 Paris, France; Institut Curie, PSL Research University, 75005 Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.01.049DOI Listing
February 2020

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats.

Bioinformatics 2020 04;36(8):2620-2622

Institut National de la Santé et de la Recherche Médicale (INSERM), U900, F-75005 Paris, France.

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http://dx.doi.org/10.1093/bioinformatics/btz969DOI Listing
April 2020

Interpreting pathways to discover cancer driver genes with Moonlight.

Nat Commun 2020 01 3;11(1):69. Epub 2020 Jan 3.

Computational Biology Laboratory, and Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark.

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http://dx.doi.org/10.1038/s41467-019-13803-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6941958PMC
January 2020

Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients.

Front Physiol 2018 24;9:1965. Epub 2019 Jan 24.

Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, Paris, France.

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http://dx.doi.org/10.3389/fphys.2018.01965DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6353844PMC
January 2019

Effective normalization for copy number variation in Hi-C data.

BMC Bioinformatics 2018 Sep 6;19(1):313. Epub 2018 Sep 6.

Institut Curie, PSL Research University, Paris, F-75005, France.

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http://dx.doi.org/10.1186/s12859-018-2256-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6127909PMC
September 2018

Application of Atlas of Cancer Signalling Network in preclinical studies.

Brief Bioinform 2019 03;20(2):701-716

Institut Curie, PSL Research University, F-75005 Paris, France, INSERM, U900, F-75005 Paris, France and MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006 Paris, France.

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https://academic.oup.com/bib/advance-article/doi/10.1093/bib
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http://dx.doi.org/10.1093/bib/bby031DOI Listing
March 2019

Signalling maps in cancer research: construction and data analysis.

Database (Oxford) 2018 01;2018

Institut Curie, PSL Research University, F-75005 Paris, France.

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http://dx.doi.org/10.1093/database/bay036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5890450PMC
January 2018

Classification of gene signatures for their information value and functional redundancy.

NPJ Syst Biol Appl 2018 19;4. Epub 2017 Dec 19.

Institut Curie, PSL Research University, INSERM U900, Mines ParisTech, 26, rue d'Ulm, F-75248 Paris, France.

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http://www.nature.com/articles/s41540-017-0038-8
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http://dx.doi.org/10.1038/s41540-017-0038-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736638PMC
December 2017

Determining the optimal number of independent components for reproducible transcriptomic data analysis.

BMC Genomics 2017 Sep 11;18(1):712. Epub 2017 Sep 11.

Institut Curie, PSL Research University, INSERM U900, Mines ParisTech, Paris, France.

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http://dx.doi.org/10.1186/s12864-017-4112-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5594474PMC
September 2017

MaBoSS 2.0: an environment for stochastic Boolean modeling.

Bioinformatics 2017 Jul;33(14):2226-2228

Institut Curie, PSL Research University, INSERM, U900, Mines Paris Tech, Paris, France.

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http://dx.doi.org/10.1093/bioinformatics/btx123DOI Listing
July 2017

A review of computational approaches detecting microRNAs involved in cancer.

Front Biosci (Landmark Ed) 2017 06 1;22:1774-1791. Epub 2017 Jun 1.

Institut Curie, INSERM U900, PSL Research University, Mines ParisTech, 26, rue d'Ulm, F-75248 Paris, France.

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http://dx.doi.org/10.2741/4571DOI Listing
June 2017

Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes.

Genome Res 2017 02 13;27(2):259-268. Epub 2016 Dec 13.

Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France.

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http://dx.doi.org/10.1101/gr.203679.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5287231PMC
February 2017

A comprehensive approach to the molecular determinants of lifespan using a Boolean model of geroconversion.

Aging Cell 2016 Dec 9;15(6):1018-1026. Epub 2016 Sep 9.

Institut Curie, CNRS, UMR3244, Telomere and Cancer Laboratory, PSL Research University, 75005, Paris, France.

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http://dx.doi.org/10.1111/acel.12504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6398530PMC
December 2016

ROMA: Representation and Quantification of Module Activity from Target Expression Data.

Front Genet 2016 19;7:18. Epub 2016 Feb 19.

Computational and Systems Biology of Cancer, Institut CurieParis, France; PSL Research UniversityParis, France; Institut National de la Santé et de la Recherche Médicale U900Paris, France; Mines ParisTechParis, France.

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http://dx.doi.org/10.3389/fgene.2016.00018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760130PMC
February 2016

SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability.

Bioinformatics 2016 04 6;32(7):984-92. Epub 2016 Jan 6.

Institut Curie, Centre De Recherche, Paris Inserm, Department of Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, U900, Paris, France Mines ParisTech, Centre for Computational Biology, Fontainebleau, France PSL Research University, Paris, France.

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http://dx.doi.org/10.1093/bioinformatics/btv751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896370PMC
April 2016

Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration.

PLoS Comput Biol 2015 Nov 3;11(11):e1004571. Epub 2015 Nov 3.

Institut Curie, Paris, France; INSERM, U900, Paris, France; Mines ParisTech, Fontainebleau, Paris, France.

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http://dx.doi.org/10.1371/journal.pcbi.1004571DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631357PMC
November 2015

Network-based approaches for drug response prediction and targeted therapy development in cancer.

Biochem Biophys Res Commun 2015 Aug 15;464(2):386-91. Epub 2015 Jun 15.

Institut Curie, 26 rue d'Ulm, F-75248 Paris France; INSERM, U900, Paris, F-75248 France; Mines ParisTech, Fontainebleau, F-77300 France. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2015.06.094DOI Listing
August 2015

Predicting genetic interactions from Boolean models of biological networks.

Integr Biol (Camb) 2015 Aug 11;7(8):921-9. Epub 2015 May 11.

Institut Curie, 26 rue d'Ulm, Paris, France.

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http://dx.doi.org/10.1039/c5ib00029gDOI Listing
August 2015

NaviCell Web Service for network-based data visualization.

Nucleic Acids Res 2015 Jul 9;43(W1):W560-5. Epub 2015 May 9.

Institut Curie, 26 rue d'Ulm, 75248 Paris, France INSERM, U900, 75248 Paris, France Mines ParisTech, 77300 Fontainebleau, France

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http://dx.doi.org/10.1093/nar/gkv450DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489283PMC
July 2015

The shortest path is not the one you know: application of biological network resources in precision oncology research.

Mutagenesis 2015 Mar;30(2):191-204

Institut Curie, 26 rue d'Ulm, Paris F-75248, France, INSERM, U900, Paris F-75248, France, Mines ParisTech, Fontainebleau F-77300, France,

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http://dx.doi.org/10.1093/mutage/geu078DOI Listing
March 2015

Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes.

Cell Rep 2014 Nov 13;9(4):1235-45. Epub 2014 Nov 13.

Institut Curie, Centre de Recherche, 75248 cedex 05 Paris, France; CNRS, UMR 144, Oncologie Moléculaire, Equipe Labellisée Ligue Contre le Cancer, Institut Curie, 75248 cedex 05 Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.10.035DOI Listing
November 2014

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data.

Bioinformatics 2014 Dec 12;30(24):3443-50. Epub 2014 Jul 12.

Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.

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http://dx.doi.org/10.1093/bioinformatics/btu436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253825PMC
December 2014

[Biological network modelling and precision medicine in oncology].

Bull Cancer 2014 Jun;101 Suppl 1:S18-21

Institut Curie, 26 rue d'Ulm, 75248 Paris, France, INSERM U900, 75248 Paris, France, Mines ParisTech, 77300 Fontainebleau, France.

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http://dx.doi.org/10.1684/bdc.2014.1973DOI Listing
June 2014

Developmental dynamics and disease potential of random monoallelic gene expression.

Dev Cell 2014 Feb;28(4):366-80

Institut Curie, 26 rue d'Ulm, Paris 75248, France; Genetics and Developmental Biology Unit, INSERM U934/CNRS UMR3215, Paris 75248, France. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2014.01.016DOI Listing
February 2014

Sequence profiling of the Saccharomyces cerevisiae genome permits deconvolution of unique and multialigned reads for variant detection.

G3 (Bethesda) 2014 Apr 16;4(4):707-15. Epub 2014 Apr 16.

Institut Curie Centre de Recherche, UMR3244 CNRS, Université Pierre et Marie Curie, 75248 Paris Cedex 05.

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http://dx.doi.org/10.1534/g3.113.009464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4059241PMC
April 2014

Stability-based comparison of class discovery methods for DNA copy number profiles.

PLoS One 2013 5;8(12):e81458. Epub 2013 Dec 5.

Institut Curie, Paris, France ; INSERM, U900, Paris, France ; Mines ParisTech, Fontainebleau, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081458PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3855312PMC
March 2015

RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells.

PLoS Genet 2013 11 7;9(11):e1003791. Epub 2013 Nov 7.

Swiss Federal Institute of Technology Zurich, Department of Biology, Chair of RNA biology, Zurich, Switzerland ; Institut Curie, CNRS UMR3215, Paris, France.

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http://dx.plos.org/10.1371/journal.pgen.1003791
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http://dx.doi.org/10.1371/journal.pgen.1003791DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820764PMC
November 2013

HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.

Bioinformatics 2013 Dec 9;29(23):2979-86. Epub 2013 Sep 9.

Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia, Institut Curie, 75248 Paris Cedex 05, France, INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Mines ParisTech, Fontainebleau 77300, France and UMR 144 CNRS, Subcellular Structure and Cellular Dynamics.

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http://dx.doi.org/10.1093/bioinformatics/btt524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3834794PMC
December 2013

Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model.

Eur J Hum Genet 2014 Apr 14;22(4):535-41. Epub 2013 Aug 14.

1] Service de Génétique Oncologique, Institut Curie, Paris, France [2] INSERM U830, Centre de Recherche de l'Institut Curie, Paris, France [3] Université Paris Descartes, Sorbonne Paris Cité, Paris, France.

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http://dx.doi.org/10.1038/ejhg.2013.181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3953907PMC
April 2014

Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis.

Nucleic Acids Res 2013 Oct 8;41(19):8853-71. Epub 2013 Aug 8.

Institut Curie, 26 rue d'Ulm, 75248 Paris cedex 05, France, INSERM U900, Bioinformatique, biostatistique et épidémiologie d'un système complexe, Paris, France, Mines ParisTech, Fontainebleau, France, INSERM U830, Unité de Génétique et Biologie des Cancers, Paris, France and Institut Curie, Unité de génétique somatique, Paris, France.

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http://dx.doi.org/10.1093/nar/gkt678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799442PMC
October 2013

Practical use of BiNoM: a biological network manager software.

Methods Mol Biol 2013 ;1021:127-46

Institut Curie, Paris, France.

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http://dx.doi.org/10.1007/978-1-62703-450-0_7DOI Listing
December 2013

From a biological hypothesis to the construction of a mathematical model.

Methods Mol Biol 2013 ;1021:107-25

Institut Curie, Paris, France.

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http://dx.doi.org/10.1007/978-1-62703-450-0_6DOI Listing
December 2013

OCSANA: optimal combinations of interventions from network analysis.

Bioinformatics 2013 Jun 26;29(12):1571-3. Epub 2013 Apr 26.

Institut Curie, Paris F-75248, France, INSERM, U900, Paris F-75248, France.

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http://dx.doi.org/10.1093/bioinformatics/btt195DOI Listing
June 2013

Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm.

BMC Syst Biol 2012 Aug 29;6:116. Epub 2012 Aug 29.

Institut Curie, 26 rue d'Ulm, Paris, F-75248 France.

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http://dx.doi.org/10.1186/1752-0509-6-116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3517402PMC
August 2012

Nebula--a web-server for advanced ChIP-seq data analysis.

Bioinformatics 2012 Oct 24;28(19):2517-9. Epub 2012 Jul 24.

Institut Curie, Paris 75248, France.

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http://dx.doi.org/10.1093/bioinformatics/bts463DOI Listing
October 2012

Identification of shortened 3' untranslated regions from expression arrays.

J Bioinform Comput Biol 2012 Apr;10(2):1241001

Institut Curie, 26 rue d'Ulm, Paris, F-75248, France.

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http://dx.doi.org/10.1142/S0219720012410016DOI Listing
April 2012

Cell death and life in cancer: mathematical modeling of cell fate decisions.

Adv Exp Med Biol 2012 ;736:261-74

U900 INSERM/Institut Curie/Ecole de Mines, Institut Curie, 26 rue d'Ulm, Paris 75005, France.

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http://dx.doi.org/10.1007/978-1-4419-7210-1_15DOI Listing
January 2013