Emmanuel Barillot

Publication Activity (10 Years)

Years Active: 1998-2024
Publications (10 Years): 25

Top Topics

Factorization Methods

Collective Intelligence

Top Venues

Briefings Bioinform.

Publications

Marco Ruscone, Andrea Checcoli, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Laurence Calzone, Vincent Noël
Building multiscale models with PhysiBoSS, an agent-based modeling tool. CoRR (2024)
Adam Smelko, Miroslav Kratochvíl, Emmanuel Barillot, Vincent Noël
Maboss for HPC environments: implementations of the continuous time Boolean model simulator for large CPU clusters and GPU accelerators. BMC Bioinform. 25 (1) (2024)
Nicolas Captier, Jane Merlevede, Askhat Molkenov, Ainur Seisenova, Altynbek Zhubanchaliyev, Petr V. Nazarov, Emmanuel Barillot, Ulykbek Kairov, Andrei Yu. Zinovyev
BIODICA: a computational environment for Independent Component Analysis of omics data. Bioinform. 38 (10) (2022)
Jonas Béal, Lorenzo Pantolini, Vincent Noël, Emmanuel Barillot, Laurence Calzone
Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers. PLoS Comput. Biol. 17 (1) (2021)
Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. Bioinform. 36 (19) (2020)
Luca Albergante, Evgeny M. Mirkes, Jonathan Bac, Huidong Chen, Alexis Martin, Louis Faure, Emmanuel Barillot, Luca Pinello, Alexander N. Gorban, Andrei Yu. Zinovyev
Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph. Entropy 22 (3) (2020)
Andrei Yu. Zinovyev, Urszula Czerwinska, Laura Cantini, Emmanuel Barillot, Klaus M. Frahm, Dima L. Shepelyansky
Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network. PLoS Comput. Biol. 16 (2) (2020)
Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. Bioinform. 36 (8) (2020)
Mihály Koltai, Vincent Noel, Andrei Yu. Zinovyev, Laurence Calzone, Emmanuel Barillot
Exact solving and sensitivity analysis of stochastic continuous time Boolean models. BMC Bioinform. 21 (1) (2020)
Sergey E. Golovenkin, Jonathan Bac, Alexander Chervov, Evgeny M. Mirkes, Yuliya V. Orlova, Emmanuel Barillot, Alexander N. Gorban, Andrei Yu. Zinovyev
Trajectories, bifurcations and pseudotime in large clinical datasets: applications to myocardial infarction and diabetes data. CoRR (2020)
Arnau Montagud, Pauline Traynard, Loredana Martignetti, Eric Bonnet, Emmanuel Barillot, Andrei Yu. Zinovyev, Laurence Calzone
Conceptual and computational framework for logical modelling of biological networks deregulated in diseases. Briefings Bioinform. 20 (4) (2019)
Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M. T. Fleming, Andrei Yu. Zinovyev, Inna Kuperstein
Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer. BMC Bioinform. (4) (2019)
Laura Cantini, Ulykbek Kairov, Aurélien de Reyniès, Emmanuel Barillot, François Radvanyi, Andrei Yu. Zinovyev
Assessing reproducibility of matrix factorization methods in independent transcriptomes. Bioinform. 35 (21) (2019)
Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Yu. Zinovyev, Ugur Dogrusoz, Jan Hasenauer, Ronan M. T. Fleming, Nicolas Le Novère, Piotr Gawron, Thomas S. Ligon, Anna Niarakis, David P. Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider
Community-driven roadmap for integrated disease maps. Briefings Bioinform. 20 (2) (2019)
Gaëlle Letort, Arnau Montagud, Gautier Stoll, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Andrei Yu. Zinovyev, Laurence Calzone
PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. Bioinform. 35 (7) (2019)
L. Cristobal Monraz Gomez, Maria Kondratova, Jean-Marie Ravel, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein
Application of Atlas of Cancer Signalling Network in preclinical studies. Briefings Bioinform. 20 (2) (2019)
Urszula Czerwinska, Laura Cantini, Ulykbek Kairov, Emmanuel Barillot, Andrei Yu. Zinovyev
Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific and Reproducible Immune-Related Signals. LVA/ICA (2018)
Paul Deveau, Leo Colmet Daage, Derek Oldridge, Virginie Bernard, Angela Bellini, Mathieu Chicard, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-Francois Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre, John M. Maris, Gudrun Schleiermacher, Valentina Boeva
QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction. Bioinform. 34 (11) (2018)
Luca Albergante, Evgeny M. Mirkes, Huidong Chen, Alexis Martin, Louis Faure, Emmanuel Barillot, Luca Pinello, Alexander N. Gorban, Andrei Yu. Zinovyev
Robust and scalable learning of data manifolds with complex topologies via ElPiGraph. CoRR (2018)
Nicolas Servant, Nelle Varoquaux, Edith Heard, Emmanuel Barillot, Jean-Philippe Vert
Effective normalization for copy number variation in Hi-C data. BMC Bioinform. 19 (1) (2018)
Maria Kondratova, Nicolas Sompairac, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein
Signalling maps in cancer research: construction and data analysis. Database J. Biol. Databases Curation 2018 (2018)
Gautier Stoll, Barthélémy Caron, Eric Viara, Aurélien Dugourd, Andrei Yu. Zinovyev, Aurélien Naldi, Guido Kroemer, Emmanuel Barillot, Laurence Calzone
MaBoSS 2.0: an environment for stochastic Boolean modeling. Bioinform. 33 (14) (2017)
Mathurin Dorel, Eric Viara, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein
NaviCom: a web application to create interactive molecular network portraits using multi-level omics data. Database J. Biol. Databases Curation 2017 (2017)
Daria Iakovishina, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Mireille Régnier, Valentina Boeva
SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability. Bioinform. 32 (7) (2016)
Paul Deveau, Emmanuel Barillot, Valentina Boeva, Andrei Yu. Zinovyev, Eric Bonnet
Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages. R J. 8 (2) (2016)
Urszula Czerwinska, Laurence Calzone, Emmanuel Barillot, Andrei Yu. Zinovyev
DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. BMC Syst. Biol. 9 (2015)
David P. A. Cohen, Loredana Martignetti, Sylvie Robine, Emmanuel Barillot, Andrei Yu. Zinovyev, Laurence Calzone
Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration. PLoS Comput. Biol. 11 (11) (2015)
Eric Bonnet, Eric Viara, Inna Kuperstein, Laurence Calzone, David P. A. Cohen, Emmanuel Barillot, Andrei Yu. Zinovyev
NaviCell Web Service for network-based data visualization. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Valentina Boeva, Tatiana G. Popova, Maxime Lienard, Sebastien Toffoli, Maud Kamal, Christophe Le Tourneau, David Gentien, Nicolas Servant, Pierre Gestraud, Thomas Rio Frio, Philippe Hupé, Emmanuel Barillot, Jean-François Laes
Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data. Bioinform. 30 (24) (2014)
Haitham Ashoor, Aurélie Hérault, Aurélie Kamoun, François Radvanyi, Vladimir B. Bajic, Emmanuel Barillot, Valentina Boeva
HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data. Bioinform. 29 (23) (2013)
Inna Kuperstein, David P. A. Cohen, Stuart Pook, Eric Viara, Laurence Calzone, Emmanuel Barillot, Andrei Yu. Zinovyev
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Syst. Biol. 7 (2013)
Andrei Yu. Zinovyev, Inna Kuperstein, Emmanuel Barillot, Wolf-Dietrich Heyer
Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps. PLoS Comput. Biol. 9 (4) (2013)
Paola Vera-Licona, Eric Bonnet, Emmanuel Barillot, Andrei Yu. Zinovyev
OCSANA: optimal combinations of interventions from network analysis. Bioinform. 29 (12) (2013)
Eric Bonnet, Laurence Calzone, Daniel Rovera, Gautier Stoll, Emmanuel Barillot, Andrei Yu. Zinovyev
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. BMC Syst. Biol. 7 (2013)
Loredana Martignetti, Andrei Yu. Zinovyev, Emmanuel Barillot
Identification of Shortened 3′ untranslated Regions from Expression Arrays. J. Bioinform. Comput. Biol. 10 (2) (2012)
Valentina Boeva, Alban Lermine, Camille Barette, Christel Guillouf, Emmanuel Barillot
Nebula - a web-server for advanced ChIP-seq data analysis. Bioinform. 28 (19) (2012)
Gautier Stoll, Eric Viara, Emmanuel Barillot, Laurence Calzone
Continuous time boolean modeling for biological signaling: application of Gillespie algorithm. BMC Syst. Biol. 6 (2012)
Valentina Boeva, Tatiana G. Popova, Kevin Bleakley, Pierre Chiche, Julie Cappo, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinform. 28 (3) (2012)
Nicolas Servant, Bryan R. Lajoie, Elphège P. Nora, Luca Giorgetti, Chong-Jian Chen, Edith Heard, Job Dekker, Emmanuel Barillot
HiTC: exploration of high-throughput 'C' experiments. Bioinform. 28 (21) (2012)
Chong-Jian Chen, Nicolas Servant, Joern Toedling, Alexis Sarazin, Antonin Marchais, Evelyne Duvernois-Berthet, Valérie Cognat, Vincent Colot, Olivier Voinnet, Edith Heard, Constance Ciaudo, Emmanuel Barillot
ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data. Bioinform. 28 (23) (2012)
Valentina Boeva, Andrei Yu. Zinovyev, Kevin Bleakley, Jean-Philippe Vert, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinform. 27 (2) (2011)
Laurence Calzone, Laurent Tournier, Simon Fourquet, Denis Thieffry, Boris Zhivotovsky, Emmanuel Barillot, Andrei Yu. Zinovyev
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement. PLoS Comput. Biol. 6 (3) (2010)
Bruno Zeitouni, Valentina Boeva, Isabelle Janoueix-Lerosey, Sophie Loeillet, Patricia Legoix-né, Alain Nicolas, Olivier Delattre, Emmanuel Barillot
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. Bioinform. 26 (15) (2010)
Joern Toedling, Constance Ciaudo, Olivier Voinnet, Edith Heard, Emmanuel Barillot
girafe - an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads. Bioinform. 26 (22) (2010)
Andrei Yu. Zinovyev, Nadya Morozova, Nora Nonne, Emmanuel Barillot, Annick Harel-Bellan, Alexander N. Gorban
Dynamical modeling of microRNA action on the protein translation process. BMC Syst. Biol. 4 (2010)
Sylvain Blachon, Gautier Stoll, Carito Guziolowski, Andrei Yu. Zinovyev, Emmanuel Barillot, Anne Siegel, Ovidiu Radulescu
Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks. AIAI Workshops (2009)
Guillem Rigaill, Philippe Hupé, Anna Almeida, Philippe La Rosa, Jean-Philippe Meyniel, Charles Decraene, Emmanuel Barillot
ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays. Bioinform. 24 (6) (2008)
Andrei Yu. Zinovyev, Eric Viara, Laurence Calzone, Emmanuel Barillot
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinform. 24 (6) (2008)
Franck Rapaport, Emmanuel Barillot, Jean-Philippe Vert
Classification of arrayCGH data using fused SVM. ISMB (2008)
Eugene Novikov, Emmanuel Barillot
Regulatory network reconstruction using an integral additive model with flexible kernel functions. BMC Syst. Biol. 2 (2008)
Eugene Novikov, Emmanuel Barillot
Software package for automatic microarray image analysis (MAIA). Bioinform. 23 (5) (2007)
Mohamed Elati, Pierre Neuvial, Monique Bolotin-Fukuhara, Emmanuel Barillot, François Radvanyi, Céline Rouveirol
LICORN: learning cooperative regulation networks from gene expression data. Bioinform. 23 (18) (2007)
Franck Rapaport, Andrei Yu. Zinovyev, Marie Dutreix, Emmanuel Barillot, Jean-Philippe Vert
Classification of microarray data using gene networks. BMC Bioinform. 8 (2007)
Pierre Neuvial, Philippe Hupé, Isabel Brito, Stéphane Liva, Elodie Manié, Caroline Brennetot, François Radvanyi, Alain Aurias, Emmanuel Barillot
Spatial normalization of array-CGH data. BMC Bioinform. 7 (2006)
Philippe La Rosa, Eric Viara, Philippe Hupé, Gaëlle Pierron, Stéphane Liva, Pierre Neuvial, Isabel Brito, Séverine Lair, Nicolas Servant, Nicolas Robine, Elodie Manié, Caroline Brennetot, Isabelle Janoueix-Lerosey, Virginie Raynal, Nadège Gruel, Céline Rouveirol, Nicolas Stransky, Marc-Henri Stern, Olivier Delattre, Alain Aurias, François Radvanyi, Emmanuel Barillot
VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles. Bioinform. 22 (17) (2006)
Adil Elfilali, Séverine Lair, Catia Verbeke, Philippe La Rosa, François Radvanyi, Emmanuel Barillot
ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. Nucleic Acids Res. 34 (Database-Issue) (2006)
Céline Rouveirol, Nicolas Stransky, Philippe Hupé, Philippe La Rosa, Eric Viara, Emmanuel Barillot, François Radvanyi
Computation of recurrent minimal genomic alterations from array-CGH data. Bioinform. 22 (7) (2006)
Eugene Novikov, Emmanuel Barillot
A noise-resistant algorithm for grid finding in microarray image analysis. Mach. Vis. Appl. 17 (5) (2006)
Stéphane Liva, Philippe Hupé, Pierre Neuvial, Isabel Brito, Eric Viara, Philippe La Rosa, Emmanuel Barillot
CAPweb: a bioinformatics CGH array Analysis Platform. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Eugene Novikov, Emmanuel Barillot
An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments. BMC Bioinform. 6 (2005)
Eugene Novikov, Emmanuel Barillot
A Robust Algorithm for Ratio Estimation in Two-color Microarray Experiments. J. Bioinform. Comput. Biol. 3 (6) (2005)
Sarah Cohen Boulakia, Séverine Lair, Nicolas Stransky, Stéphane Graziani, François Radvanyi, Emmanuel Barillot, Christine Froidevaux
Selecting biomedical data sources according to user preferences. ISMB/ECCB (Supplement of Bioinformatics) (2004)
Philippe Hupé, Nicolas Stransky, Jean-Paul Thiery, François Radvanyi, Emmanuel Barillot
Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinform. 20 (18) (2004)
Emmanuelle Karsenty, Emmanuel Barillot, Gwenola Tosser-Klopp, Yvette Lahbib-Mansais, Denis Milan, Francois Hatey, Susanna Cirera, Milena Sawera, Claus B. Jørgensen, Bhanu Chowdhary, Merete Fredholm, Klaus Wimmers, Siriluck Ponsuksili, Roberta Davoli, Luca Fontanesi, Silvia Braglia, Paolo Zambonelli, Daniele Bigi, Stefan Neuenschwander, Joël Gellin
The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa). Nucleic Acids Res. 31 (1) (2003)
Delphine Samson, Fabrice Legeai, Emmanuelle Karsenty, Sébastien Reboux, Jean-Baptiste Veyrieras, Jeremy Just, Emmanuel Barillot
GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics. Nucleic Acids Res. 31 (1) (2003)
Eric Viara, Guy Vaysseix, Emmanuel Barillot
Distributing CORBA views from an OODBMS. IDEAS (2002)
Frédéric Tores, Emmanuel Barillot
The art of pedigree drawing: algorithmic aspects. Bioinform. 17 (1) (2001)
Frédéric Achard, Guy Vaysseix, Emmanuel Barillot
XML, bioinformatics and data integration. Bioinform. 17 (1) (2001)
Stuart Pook, Eric Lecolinet, Guy Vaysseix, Emmanuel Barillot
Control menus: excecution and control in a single interactor. CHI Extended Abstracts (2000)
Claude Discala, Xavier Benigni, Emmanuel Barillot, Guy Vaysseix
DBcat: a catalog of 500 biological databases. Nucleic Acids Res. 28 (1) (2000)
Stuart Pook, Eric Lecolinet, Guy Vaysseix, Emmanuel Barillot
Context and Interaction in Zooable User Interfaces. Advanced Visual Interfaces (2000)
Emmanuel Barillot, Stuart Pook, Frédéric Guyon, Christophe Cussat-Blanc, Eric Viara, Guy Vaysseix
The HuGeMap Database: interconnection and visualization of human genome maps. Nucleic Acids Res. 27 (1) (1999)
Claude Discala, Marion Ninnin, Frédéric Achard, Emmanuel Barillot, Guy Vaysseix
DBcat: a catalog of biological databases. Nucleic Acids Res. 27 (1) (1999)
Eric Viara, Emmanuel Barillot, Guy Vaysseix
The EyeDB OODBMS. IDEAS (1999)
Emmanuel Barillot, Ulf Leser, Philip Lijnzaad, Christophe Cussat-Blanc, Kim Jungfer, Frédéric Guyon, Guy Vaysseix, Carsten Helgesen, Patricia Rodriguez-Tomé
A proposal for a standard CORBA interface for genome maps. Bioinform. 15 (2) (1999)
L. Brun-Samarcq, Sophie Gallina, A. Philippi, Florence Demenais, Guy Vaysseix, Emmanuel Barillot
CoPE: a collaborative pedigree drawing environment. Bioinform. 15 (4) (1999)
Frédéric Achard, Guy Vaysseix, Philippe Dessen, Emmanuel Barillot
Virgil database for rich links (1999 update). Nucleic Acids Res. 27 (1) (1999)
Frédéric Achard, Christophe Cussat-Blanc, Eric Viara, Emmanuel Barillot
The new Virgil database: a service of rich links. Bioinform. 14 (4) (1998)
Emmanuel Barillot, Frédéric Guyon, Christophe Cussat-Blanc, Eric Viara, Guy Vaysseix
HuGeMap: a distributed and integrated Human Genome Map database. Nucleic Acids Res. 26 (1) (1998)
Frédéric Achard, Emmanuel Barillot
Virgil: a database of rich links between GDB and GenBank. Nucleic Acids Res. 26 (1) (1998)
Stuart Pook, Guy Vaysseix, Emmanuel Barillot
Zomit: biological data visualization and browsing. Bioinform. 14 (9) (1998)