Emmanuel Barillot

85 papers A 1B 1C 2Journal 77Unranked 4
YearRankTypeTitle / Venue / Authors
2026 J jnl
LEMON: a foundation model for nuclear morphology in Computational Pathology.
CoRR
Loïc Chadoutaud, Alice Blondel, Hana Feki, Jacqueline Fontugne, Emmanuel Barillot, Thomas Walter
2025 J jnl
NeKo: A tool for automatic network construction from prior knowledge.
PLoS Comput. Biol.
Marco Ruscone, Eirini Tsirvouli, Andrea Checcoli, Dénes Türei, Emmanuel Barillot, Julio Saez-Rodriguez, Loredana Martignetti, Åsmund Flobak, Laurence Calzone
2024 J jnl
Building multiscale models with PhysiBoSS, an agent-based modeling tool.
Briefings Bioinform.
Marco Ruscone, Andrea Checcoli, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Laurence Calzone, Vincent Noël
2024 J jnl
Building multiscale models with PhysiBoSS, an agent-based modeling tool.
CoRR
Marco Ruscone, Andrea Checcoli, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Laurence Calzone, Vincent Noël
2024 J jnl
Maboss for HPC environments: implementations of the continuous time Boolean model simulator for large CPU clusters and GPU accelerators.
BMC Bioinform.
Adam Smelko, Miroslav Kratochvíl, Emmanuel Barillot, Vincent Noël
2023 J jnl
Multiscale model of the different modes of cancer cell invasion.
Bioinform.
Marco Ruscone, Arnau Montagud, Philippe Chavrier, Olivier Destaing, Isabelle Bonnet, Andrei Yu. Zinovyev, Emmanuel Barillot, Vincent Noël, Laurence Calzone
2022 J jnl
BIODICA: a computational environment for Independent Component Analysis of omics data.
Bioinform.
Nicolas Captier, Jane Merlevede, Askhat Molkenov, Ainur Seisenova, Altynbek Zhubanchaliyev, Petr V. Nazarov, Emmanuel Barillot, Ulykbek Kairov, Andrei Yu. Zinovyev
2021 J jnl
Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers.
PLoS Comput. Biol.
Jonas Béal, Lorenzo Pantolini, Vincent Noël, Emmanuel Barillot, Laurence Calzone
2020 J jnl
Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network.
PLoS Comput. Biol.
Andrei Yu. Zinovyev, Urszula Czerwinska, Laura Cantini, Emmanuel Barillot, Klaus M. Frahm, Dima L. Shepelyansky
2020 J jnl
Exact solving and sensitivity analysis of stochastic continuous time Boolean models.
BMC Bioinform.
Mihály Koltai, Vincent Noel, Andrei Yu. Zinovyev, Laurence Calzone, Emmanuel Barillot
2020 J jnl
Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph.
Entropy
Luca Albergante, Evgeny M. Mirkes, Jonathan Bac, Huidong Chen, Alexis Martin, Louis Faure, Emmanuel Barillot, Luca Pinello, Alexander N. Gorban, Andrei Yu. Zinovyev
2020 J jnl
Trajectories, bifurcations and pseudotime in large clinical datasets: applications to myocardial infarction and diabetes data.
CoRR
Sergey E. Golovenkin, Jonathan Bac, Alexander Chervov, Evgeny M. Mirkes, Yuliya V. Orlova, Emmanuel Barillot, Alexander N. Gorban, Andrei Yu. Zinovyev
2020 J jnl
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats.
Bioinform.
Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev
2020 J jnl
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats.
Bioinform.
Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev
2019 J jnl
Application of Atlas of Cancer Signalling Network in preclinical studies.
Briefings Bioinform.
L. Cristobal Monraz Gomez, Maria Kondratova, Jean-Marie Ravel, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein
2019 J jnl
Assessing reproducibility of matrix factorization methods in independent transcriptomes.
Bioinform.
Laura Cantini, Ulykbek Kairov, Aurélien de Reyniès, Emmanuel Barillot, François Radvanyi, Andrei Yu. Zinovyev
2019 J jnl
Community-driven roadmap for integrated disease maps.
Briefings Bioinform.
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
2019 J jnl
Conceptual and computational framework for logical modelling of biological networks deregulated in diseases.
Briefings Bioinform.
Arnau Montagud, Pauline Traynard, Loredana Martignetti, Eric Bonnet, Emmanuel Barillot, Andrei Yu. Zinovyev, Laurence Calzone
2019 J jnl
Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer.
BMC Bioinform.
Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M. T. Fleming, Andrei Yu. Zinovyev, Inna Kuperstein
2019 J jnl
PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling.
Bioinform.
Gaëlle Letort, Arnau Montagud, Gautier Stoll, Randy W. Heiland, Emmanuel Barillot, Paul Macklin, Andrei Yu. Zinovyev, Laurence Calzone
2018 — conf
Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific and Reproducible Immune-Related Signals.
LVA/ICA
Urszula Czerwinska, Laura Cantini, Ulykbek Kairov, Emmanuel Barillot, Andrei Yu. Zinovyev
2018 J jnl
Effective normalization for copy number variation in Hi-C data.
BMC Bioinform.
Nicolas Servant, Nelle Varoquaux, Edith Heard, Emmanuel Barillot, Jean-Philippe Vert
2018 J jnl
QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction.
Bioinform.
Paul Deveau, Leo Colmet Daage, Derek Oldridge, Virginie Bernard, Angela Bellini, Mathieu Chicard, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-François Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre, John M. Maris, Gudrun Schleiermacher, Valentina Boeva
2018 J jnl
Robust and scalable learning of data manifolds with complex topologies via ElPiGraph.
CoRR
Luca Albergante, Evgeny M. Mirkes, Huidong Chen, Alexis Martin, Louis Faure, Emmanuel Barillot, Luca Pinello, Alexander N. Gorban, Andrei Yu. Zinovyev
2018 J jnl
Signalling maps in cancer research: construction and data analysis.
Database J. Biol. Databases Curation
Maria Kondratova, Nicolas Sompairac, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein
2017 J jnl
MaBoSS 2.0: an environment for stochastic Boolean modeling.
Bioinform.
Gautier Stoll, Barthélémy Caron, Eric Viara, Aurélien Dugourd, Andrei Yu. Zinovyev, Aurélien Naldi, Guido Kroemer, Emmanuel Barillot, Laurence Calzone
2017 J jnl
NaviCom: a web application to create interactive molecular network portraits using multi-level omics data.
Database J. Biol. Databases Curation
Mathurin Dorel, Eric Viara, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein
2016 J jnl
Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages.
R J.
Paul Deveau, Emmanuel Barillot, Valentina Boeva, Andrei Yu. Zinovyev, Eric Bonnet
2016 J jnl
SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability.
Bioinform.
Daria Iakovishina, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Mireille Régnier, Valentina Boeva
2015 J jnl
DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts.
BMC Syst. Biol.
Urszula Czerwinska, Laurence Calzone, Emmanuel Barillot, Andrei Yu. Zinovyev
2015 J jnl
Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration.
PLoS Comput. Biol.
David P. A. Cohen, Loredana Martignetti, Sylvie Robine, Emmanuel Barillot, Andrei Yu. Zinovyev, Laurence Calzone
2015 J jnl
NaviCell Web Service for network-based data visualization.
Nucleic Acids Res.
Eric Bonnet, Eric Viara, Inna Kuperstein, Laurence Calzone, David P. A. Cohen, Emmanuel Barillot, Andrei Yu. Zinovyev
2014 J jnl
Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data.
Bioinform.
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
2013 J jnl
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.
BMC Syst. Biol.
Eric Bonnet, Laurence Calzone, Daniel Rovera, Gautier Stoll, Emmanuel Barillot, Andrei Yu. Zinovyev
2013 J jnl
HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.
Bioinform.
Haitham Ashoor, Aurélie Hérault, Aurélie Kamoun, François Radvanyi, Vladimir B. Bajic, Emmanuel Barillot, Valentina Boeva
2013 J jnl
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.
BMC Syst. Biol.
Inna Kuperstein, David P. A. Cohen, Stuart Pook, Eric Viara, Laurence Calzone, Emmanuel Barillot, Andrei Yu. Zinovyev
2013 J jnl
OCSANA: optimal combinations of interventions from network analysis.
Bioinform.
Paola Vera-Licona, Eric Bonnet, Emmanuel Barillot, Andrei Yu. Zinovyev
2013 J jnl
Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps.
PLoS Comput. Biol.
Andrei Yu. Zinovyev, Inna Kuperstein, Emmanuel Barillot, Wolf-Dietrich Heyer
2012 J jnl
Continuous time boolean modeling for biological signaling: application of Gillespie algorithm.
BMC Syst. Biol.
Gautier Stoll, Eric Viara, Emmanuel Barillot, Laurence Calzone
2012 J jnl
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data.
Bioinform.
Valentina Boeva, Tatiana G. Popova, Kevin Bleakley, Pierre Chiche, Julie Cappo, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot
2012 J jnl
HiTC: exploration of high-throughput 'C' experiments.
Bioinform.
Nicolas Servant, Bryan R. Lajoie, Elphège P. Nora, Luca Giorgetti, Chong-Jian Chen, Edith Heard, Job Dekker, Emmanuel Barillot
2012 J jnl
Identification of Shortened 3′ untranslated Regions from Expression Arrays.
J. Bioinform. Comput. Biol.
Loredana Martignetti, Andrei Yu. Zinovyev, Emmanuel Barillot
2012 J jnl
Nebula - a web-server for advanced ChIP-seq data analysis.
Bioinform.
Valentina Boeva, Alban Lermine, Camille Barette, Christel Guillouf, Emmanuel Barillot
2012 J jnl
ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data.
Bioinform.
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
2011 J jnl
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization.
Bioinform.
Valentina Boeva, Andrei Yu. Zinovyev, Kevin Bleakley, Jean-Philippe Vert, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot
2010 J jnl
Dynamical modeling of microRNA action on the protein translation process.
BMC Syst. Biol.
Andrei Yu. Zinovyev, Nadya Morozova, Nora Nonne, Emmanuel Barillot, Annick Harel-Bellan, Alexander N. Gorban
2010 J jnl
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement.
PLoS Comput. Biol.
Laurence Calzone, Laurent Tournier, Simon Fourquet, Denis Thieffry, Boris Zhivotovsky, Emmanuel Barillot, Andrei Yu. Zinovyev
2010 J jnl
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.
Bioinform.
Bruno Zeitouni, Valentina Boeva, Isabelle Janoueix-Lerosey, Sophie Loeillet, Patricia Legoix-né, Alain Nicolas, Olivier Delattre, Emmanuel Barillot
2010 J jnl
girafe - an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads.
Bioinform.
Joern Toedling, Constance Ciaudo, Olivier Voinnet, Edith Heard, Emmanuel Barillot
2009 — conf
Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks.
AIAI (Workshops)
Sylvain Blachon, Gautier Stoll, Carito Guziolowski, Andrei Yu. Zinovyev, Emmanuel Barillot, Anne Siegel, Ovidiu Radulescu
2008 J jnl
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks.
Bioinform.
Andrei Yu. Zinovyev, Eric Viara, Laurence Calzone, Emmanuel Barillot
2008 A conf
Classification of arrayCGH data using fused SVM.
ISMB
Franck Rapaport, Emmanuel Barillot, Jean-Philippe Vert
2008 J jnl
ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays.
Bioinform.
Guillem Rigaill, Philippe Hupé, Anna Almeida, Philippe La Rosa, Jean-Philippe Meyniel, Charles Decraene, Emmanuel Barillot
2008 J jnl
Regulatory network reconstruction using an integral additive model with flexible kernel functions.
BMC Syst. Biol.
Eugene Novikov, Emmanuel Barillot
2007 J jnl
Classification of microarray data using gene networks.
BMC Bioinform.
Franck Rapaport, Andrei Yu. Zinovyev, Marie Dutreix, Emmanuel Barillot, Jean-Philippe Vert
2007 J jnl
LICORN: learning cooperative regulation networks from gene expression data.
Bioinform.
Mohamed Elati, Pierre Neuvial, Monique Bolotin-Fukuhara, Emmanuel Barillot, François Radvanyi, Céline Rouveirol
2007 J jnl
Software package for automatic microarray image analysis (MAIA).
Bioinform.
Eugene Novikov, Emmanuel Barillot
2006 J jnl
A noise-resistant algorithm for grid finding in microarray image analysis.
Mach. Vis. Appl.
Eugene Novikov, Emmanuel Barillot
2006 J jnl
CAPweb: a bioinformatics CGH array Analysis Platform.
Nucleic Acids Res.
Stéphane Liva, Philippe Hupé, Pierre Neuvial, Isabel Brito, Eric Viara, Philippe La Rosa, Emmanuel Barillot
2006 J jnl
Computation of recurrent minimal genomic alterations from array-CGH data.
Bioinform.
Céline Rouveirol, Nicolas Stransky, Philippe Hupé, Philippe La Rosa, Eric Viara, Emmanuel Barillot, François Radvanyi
2006 J jnl
ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis.
Nucleic Acids Res.
Adil Elfilali, Séverine Lair, Catia Verbeke, Philippe La Rosa, François Radvanyi, Emmanuel Barillot
2006 J jnl
Spatial normalization of array-CGH data.
BMC Bioinform.
Pierre Neuvial, Philippe Hupé, Isabel Brito, Stéphane Liva, Elodie Manié, Caroline Brennetot, François Radvanyi, Alain Aurias, Emmanuel Barillot
2006 J jnl
VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles.
Bioinform.
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
2005 J jnl
A Robust Algorithm for Ratio Estimation in Two-color Microarray Experiments.
J. Bioinform. Comput. Biol.
Eugene Novikov, Emmanuel Barillot
2005 J jnl
An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments.
BMC Bioinform.
Eugene Novikov, Emmanuel Barillot
2004 J jnl
Analysis of array CGH data: from signal ratio to gain and loss of DNA regions.
Bioinform.
Philippe Hupé, Nicolas Stransky, Jean-Paul Thiery, François Radvanyi, Emmanuel Barillot
2004 — conf
Selecting biomedical data sources according to user preferences.
ISMB/ECCB (Supplement of Bioinformatics)
Sarah Cohen Boulakia, Séverine Lair, Nicolas Stransky, Stéphane Graziani, François Radvanyi, Emmanuel Barillot, Christine Froidevaux
2003 J jnl
GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics.
Nucleic Acids Res.
Delphine Samson, Fabrice Legeai, Emmanuelle Karsenty, Sébastien Reboux, Jean-Baptiste Veyrieras, Jeremy Just, Emmanuel Barillot
2003 J jnl
The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa).
Nucleic Acids Res.
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
2002 C conf
Distributing CORBA views from an OODBMS.
IDEAS
Eric Viara, Guy Vaysseix, Emmanuel Barillot
2001 J jnl
The art of pedigree drawing: algorithmic aspects.
Bioinform.
Frédéric Tores, Emmanuel Barillot
2001 J jnl
XML, bioinformatics and data integration.
Bioinform.
Frédéric Achard, Guy Vaysseix, Emmanuel Barillot
2000 B conf
Context and Interaction in Zooable User Interfaces.
Advanced Visual Interfaces
Stuart Pook, Eric Lecolinet, Guy Vaysseix, Emmanuel Barillot
2000 — conf
Control menus: excecution and control in a single interactor.
CHI Extended Abstracts
Stuart Pook, Eric Lecolinet, Guy Vaysseix, Emmanuel Barillot
2000 J jnl
DBcat: a catalog of 500 biological databases.
Nucleic Acids Res.
Claude Discala, Xavier Benigni, Emmanuel Barillot, Guy Vaysseix
1999 J jnl
A proposal for a standard CORBA interface for genome maps.
Bioinform.
Emmanuel Barillot, Ulf Leser, Philip Lijnzaad, Christophe Cussat-Blanc, Kim Jungfer, Frédéric Guyon, Guy Vaysseix, Carsten Helgesen, Patricia Rodriguez-Tomé
1999 J jnl
CoPE: a collaborative pedigree drawing environment.
Bioinform.
L. Brun-Samarcq, Sophie Gallina, A. Philippi, Florence Demenais, Guy Vaysseix, Emmanuel Barillot
1999 J jnl
DBcat: a catalog of biological databases.
Nucleic Acids Res.
Claude Discala, Marion Ninnin, Frédéric Achard, Emmanuel Barillot, Guy Vaysseix
1999 C conf
The EyeDB OODBMS.
IDEAS
Eric Viara, Emmanuel Barillot, Guy Vaysseix
1999 J jnl
The HuGeMap Database: interconnection and visualization of human genome maps.
Nucleic Acids Res.
Emmanuel Barillot, Stuart Pook, Frédéric Guyon, Christophe Cussat-Blanc, Eric Viara, Guy Vaysseix
1999 J jnl
Virgil database for rich links (1999 update).
Nucleic Acids Res.
Frédéric Achard, Guy Vaysseix, Philippe Dessen, Emmanuel Barillot
1998 J jnl
HuGeMap: a distributed and integrated Human Genome Map database.
Nucleic Acids Res.
Emmanuel Barillot, Frédéric Guyon, Christophe Cussat-Blanc, Eric Viara, Guy Vaysseix
1998 J jnl
The new Virgil database: a service of rich links.
Bioinform.
Frédéric Achard, Christophe Cussat-Blanc, Eric Viara, Emmanuel Barillot
1998 J jnl
Virgil: a database of rich links between GDB and GenBank.
Nucleic Acids Res.
Frédéric Achard, Emmanuel Barillot
1998 J jnl
Zomit: biological data visualization and browsing.
Bioinform.
Stuart Pook, Guy Vaysseix, Emmanuel Barillot