The new Virgil database: a service of rich links. - Frédéric Achard; Christophe Cussat-Blanc; Eric Viara; Emmanuel Barillot (Bioinform., 1998)

Zomit: biological data visualization and browsing. - Stuart Pook; Guy Vaysseix; Emmanuel Barillot (Bioinform., 1998)

Virgil: a database of rich links between GDB and GenBank. - Frédéric Achard; Emmanuel Barillot (Nucleic Acids Res., 1998)

HuGeMap: a distributed and integrated Human Genome Map database. - Emmanuel Barillot; Frédéric Guyon; Christophe Cussat-Blanc; Eric Viara; Guy Vaysseix (Nucleic Acids Res., 1998)

The EyeDB OODBMS. - Eric Viara; Emmanuel Barillot; Guy Vaysseix (IDEAS, 1999)

A proposal for a standard CORBA interface for genome maps. - Emmanuel Barillot; Ulf Leser; Philip Lijnzaad; Christophe Cussat-Blanc; Kim Jungfer; Frédéric Guyon; Guy Vaysseix; Carsten Helgesen; Patricia Rodriguez-Tomé (Bioinform., 1999)

CoPE: a collaborative pedigree drawing environment. - L. Brun-Samarcq; Sophie Gallina; A. Philippi; Florence Demenais; Guy Vaysseix; Emmanuel Barillot (Bioinform., 1999)

Virgil database for rich links (1999 update). - Frédéric Achard; Guy Vaysseix; Philippe Dessen; Emmanuel Barillot (Nucleic Acids Res., 1999)

The HuGeMap Database: interconnection and visualization of human genome maps. - Emmanuel Barillot; Stuart Pook; Frédéric Guyon; Christophe Cussat-Blanc; Eric Viara; Guy Vaysseix (Nucleic Acids Res., 1999)

DBcat: a catalog of biological databases. - Claude Discala; Marion Ninnin; Frédéric Achard; Emmanuel Barillot; Guy Vaysseix (Nucleic Acids Res., 1999)

Context and Interaction in Zooable User Interfaces. - Stuart Pook; Eric Lecolinet; Guy Vaysseix; Emmanuel Barillot (Advanced Visual Interfaces, 2000)

Control menus: excecution and control in a single interactor. - Stuart Pook; Eric Lecolinet; Guy Vaysseix; Emmanuel Barillot (CHI Extended Abstracts, 2000)

DBcat: a catalog of 500 biological databases. - Claude Discala; Xavier Benigni; Emmanuel Barillot; Guy Vaysseix (Nucleic Acids Res., 2000)

XML, bioinformatics and data integration. - Frédéric Achard; Guy Vaysseix; Emmanuel Barillot (Bioinform., 2001)

The art of pedigree drawing: algorithmic aspects. - Frédéric Tores; Emmanuel Barillot (Bioinform., 2001)

Distributing CORBA views from an OODBMS. - Eric Viara; Guy Vaysseix; Emmanuel Barillot (IDEAS, 2002)

The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa). - 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; et al. (Nucleic Acids Res., 2003)

GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics. - Delphine Samson; Fabrice Legeai; Emmanuelle Karsenty; Sébastien Reboux; Jean-Baptiste Veyrieras; Jeremy Just; Emmanuel Barillot (Nucleic Acids Res., 2003)

Selecting biomedical data sources according to user preferences. - Sarah Cohen Boulakia; Séverine Lair; Nicolas Stransky; Stéphane Graziani; François Radvanyi; Emmanuel Barillot; Christine Froidevaux (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. - Philippe Hupé; Nicolas Stransky; Jean-Paul Thiery; François Radvanyi; Emmanuel Barillot (Bioinform., 2004)

An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments. - Eugene Novikov; Emmanuel Barillot (BMC Bioinform., 2005)

A Robust Algorithm for Ratio Estimation in Two-color Microarray Experiments. - Eugene Novikov; Emmanuel Barillot (J. Bioinform. Comput. Biol., 2005)

VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles. - Philippe La Rosa; Eric Viara; Philippe Hupé; Gaëlle Pierron; Stéphane Liva; Pierre Neuvial; Isabel Brito 002; Séverine Lair; Nicolas Servant; Nicolas Robine; Elodie Manié; Caroline Brennetot; et al. (Bioinform., 2006)

Computation of recurrent minimal genomic alterations from array-CGH data. - Céline Rouveirol; Nicolas Stransky; Philippe Hupé; Philippe La Rosa; Eric Viara; Emmanuel Barillot; François Radvanyi (Bioinform., 2006)

Spatial normalization of array-CGH data. - Pierre Neuvial; Philippe Hupé; Isabel Brito 002; Stéphane Liva; Elodie Manié; Caroline Brennetot; François Radvanyi; Alain Aurias; Emmanuel Barillot (BMC Bioinform., 2006)

A noise-resistant algorithm for grid finding in microarray image analysis. - Eugene Novikov; Emmanuel Barillot (Mach. Vis. Appl., 2006)

ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. - Adil Elfilali; Séverine Lair; Catia Verbeke; Philippe La Rosa; François Radvanyi; Emmanuel Barillot (Nucleic Acids Res., 2006)

CAPweb: a bioinformatics CGH array Analysis Platform. - Stéphane Liva; Philippe Hupé; Pierre Neuvial; Isabel Brito 002; Eric Viara; Philippe La Rosa; Emmanuel Barillot (Nucleic Acids Res., 2006)

LICORN: learning cooperative regulation networks from gene expression data. - Mohamed Elati; Pierre Neuvial; Monique Bolotin-Fukuhara; Emmanuel Barillot; François Radvanyi; Céline Rouveirol (Bioinform., 2007)

Software package for automatic microarray image analysis (MAIA). - Eugene Novikov; Emmanuel Barillot (Bioinform., 2007)

Classification of microarray data using gene networks. - Franck Rapaport; Andrei Yu. Zinovyev; Marie Dutreix; Emmanuel Barillot; Jean-Philippe Vert (BMC Bioinform., 2007)

Classification of arrayCGH data using fused SVM. - Franck Rapaport; Emmanuel Barillot; Jean-Philippe Vert (ISMB, 2008)

ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays. - Guillem Rigaill; Philippe Hupé; Anna Almeida; Philippe La Rosa; Jean-Philippe Meyniel; Charles Decraene; Emmanuel Barillot (Bioinform., 2008)

BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. - Andrei Yu. Zinovyev; Eric Viara; Laurence Calzone; Emmanuel Barillot (Bioinform., 2008)

Regulatory network reconstruction using an integral additive model with flexible kernel functions. - Eugene Novikov; Emmanuel Barillot (BMC Syst. Biol., 2008)

Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks. - Sylvain Blachon; Gautier Stoll; Carito Guziolowski; Andrei Yu. Zinovyev; Emmanuel Barillot; Anne Siegel; Ovidiu Radulescu (AIAI (Workshops), 2009)

girafe - an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads. - Joern Toedling; Constance Ciaudo; Olivier Voinnet; Edith Heard; Emmanuel Barillot (Bioinform., 2010)

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data. - Bruno Zeitouni; Valentina Boeva; Isabelle Janoueix-Lerosey; Sophie Loeillet; Patricia Legoix-né; Alain Nicolas; Olivier Delattre; Emmanuel Barillot (Bioinform., 2010)

Dynamical modeling of microRNA action on the protein translation process. - Andrei Yu. Zinovyev; Nadya Morozova; Nora Nonne; Emmanuel Barillot; Annick Harel-Bellan; Alexander N. Gorban (BMC Syst. Biol., 2010)

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement. - Laurence Calzone; Laurent Tournier; Simon Fourquet; Denis Thieffry; Boris Zhivotovsky; Emmanuel Barillot; Andrei Yu. Zinovyev (PLoS Comput. Biol., 2010)

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. - Valentina Boeva; Andrei Yu. Zinovyev; Kevin Bleakley; Jean-Philippe Vert; Isabelle Janoueix-Lerosey; Olivier Delattre; Emmanuel Barillot (Bioinform., 2011)

Nebula - a web-server for advanced ChIP-seq data analysis. - Valentina Boeva; Alban Lermine; Camille Barette; Christel Guillouf; Emmanuel Barillot (Bioinform., 2012)

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. - Valentina Boeva; Tatiana G. Popova; Kevin Bleakley; Pierre Chiche; Julie Cappo; Gudrun Schleiermacher; Isabelle Janoueix-Lerosey; Olivier Delattre; Emmanuel Barillot (Bioinform., 2012)

ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data. - 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 (Bioinform., 2012)

HiTC: exploration of high-throughput 'C' experiments. - Nicolas Servant; Bryan R. Lajoie; Elphège P. Nora; Luca Giorgetti; Chong-Jian Chen; Edith Heard; Job Dekker; Emmanuel Barillot (Bioinform., 2012)

Continuous time boolean modeling for biological signaling: application of Gillespie algorithm. - Gautier Stoll; Eric Viara; Emmanuel Barillot; Laurence Calzone (BMC Syst. Biol., 2012)

Identification of Shortened 3′ untranslated Regions from Expression Arrays. - Loredana Martignetti; Andrei Yu. Zinovyev; Emmanuel Barillot (J. Bioinform. Comput. Biol., 2012)

HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data. - Haitham Ashoor; Aurélie Hérault; Aurélie Kamoun; François Radvanyi; Vladimir B. Bajic; Emmanuel Barillot; Valentina Boeva (Bioinform., 2013)

OCSANA: optimal combinations of interventions from network analysis. - Paola Vera-Licona; Eric Bonnet; Emmanuel Barillot; Andrei Yu. Zinovyev (Bioinform., 2013)

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. - Eric Bonnet; Laurence Calzone; Daniel Rovera; Gautier Stoll; Emmanuel Barillot; Andrei Yu. Zinovyev (BMC Syst. Biol., 2013)

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. - Inna Kuperstein; David P. A. Cohen; Stuart Pook; Eric Viara; Laurence Calzone; Emmanuel Barillot; Andrei Yu. Zinovyev (BMC Syst. Biol., 2013)

Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps. - Andrei Yu. Zinovyev; Inna Kuperstein; Emmanuel Barillot; Wolf-Dietrich Heyer (PLoS Comput. Biol., 2013)

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data. - 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; et al. (Bioinform., 2014)

DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. - Urszula Czerwinska; Laurence Calzone; Emmanuel Barillot; Andrei Yu. Zinovyev (BMC Syst. Biol., 2015)

NaviCell Web Service for network-based data visualization. - Eric Bonnet; Eric Viara; Inna Kuperstein; Laurence Calzone; David P. A. Cohen; Emmanuel Barillot; Andrei Yu. Zinovyev (Nucleic Acids Res., 2015)

Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration. - David P. A. Cohen; Loredana Martignetti; Sylvie Robine; Emmanuel Barillot; Andrei Yu. Zinovyev; Laurence Calzone (PLoS Comput. Biol., 2015)

SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability. - Daria Iakovishina; Isabelle Janoueix-Lerosey; Emmanuel Barillot; Mireille Régnier; Valentina Boeva (Bioinform., 2016)

Calculating Biological Module Enrichment or Depletion and Visualizing Data on Large-scale Molecular Maps with ACSNMineR and RNaviCell Packages. - Paul Deveau; Emmanuel Barillot; Valentina Boeva; Andrei Yu. Zinovyev; Eric Bonnet (R J., 2016)

NaviCom: a web application to create interactive molecular network portraits using multi-level omics data. - Mathurin Dorel; Eric Viara; Emmanuel Barillot; Andrei Yu. Zinovyev; Inna Kuperstein (Database J. Biol. Databases Curation, 2017)

MaBoSS 2.0: an environment for stochastic Boolean modeling. - Gautier Stoll; Barthélémy Caron; Eric Viara; Aurélien Dugourd; Andrei Yu. Zinovyev; Aurélien Naldi; Guido Kroemer; Emmanuel Barillot; Laurence Calzone (Bioinform., 2017)

Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific and Reproducible Immune-Related Signals. - Urszula Czerwinska; Laura Cantini; Ulykbek Kairov; Emmanuel Barillot; Andrei Yu. Zinovyev (LVA/ICA, 2018)

Signalling maps in cancer research: construction and data analysis. - Maria Kondratova; Nicolas Sompairac; Emmanuel Barillot; Andrei Yu. Zinovyev; Inna Kuperstein (Database J. Biol. Databases Curation, 2018)

QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction. - 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; et al. (Bioinform., 2018)

Effective normalization for copy number variation in Hi-C data. - Nicolas Servant; Nelle Varoquaux; Edith Heard; Emmanuel Barillot; Jean-Philippe Vert (BMC Bioinform., 2018)

Robust and scalable learning of data manifolds with complex topologies via ElPiGraph. - Luca Albergante; Evgeny M. Mirkes; Huidong Chen; Alexis Martin; Louis Faure; Emmanuel Barillot; Luca Pinello; Alexander N. Gorban; Andrei Yu. Zinovyev (CoRR, 2018)

Application of Atlas of Cancer Signalling Network in preclinical studies. - L. Cristobal Monraz Gomez; Maria Kondratova; Jean-Marie Ravel; Emmanuel Barillot; Andrei Yu. Zinovyev; Inna Kuperstein (Briefings Bioinform., 2019)

Conceptual and computational framework for logical modelling of biological networks deregulated in diseases. - Arnau Montagud; Pauline Traynard; Loredana Martignetti; Eric Bonnet; Emmanuel Barillot; Andrei Yu. Zinovyev; Laurence Calzone (Briefings Bioinform., 2019)

Community-driven roadmap for integrated disease maps. - 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; et al. (Briefings Bioinform., 2019)

Assessing reproducibility of matrix factorization methods in independent transcriptomes. - Laura Cantini; Ulykbek Kairov; Aurélien de Reyniès; Emmanuel Barillot; François Radvanyi; Andrei Yu. Zinovyev (Bioinform., 2019)

PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. - Gaëlle Letort; Arnau Montagud; Gautier Stoll; Randy W. Heiland; Emmanuel Barillot; Paul Macklin; Andrei Yu. Zinovyev; Laurence Calzone (Bioinform., 2019)

Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer. - Nicolas Sompairac; Jennifer Modamio; Emmanuel Barillot; Ronan M. T. Fleming; Andrei Yu. Zinovyev; Inna Kuperstein (BMC Bioinform., 2019)

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. - Irina Balaur; Ludovic Roy; Alexander Mazein; S. Gökberk Karaca; Ugur Dogrusoz; Emmanuel Barillot; Andrei Yu. Zinovyev (Bioinform., 2020)

Exact solving and sensitivity analysis of stochastic continuous time Boolean models. - Mihály Koltai; Vincent Noel; Andrei Yu. Zinovyev; Laurence Calzone; Emmanuel Barillot (BMC Bioinform., 2020)

Trajectories, bifurcations and pseudotime in large clinical datasets: applications to myocardial infarction and diabetes data. - Sergey E. Golovenkin; Jonathan Bac; Alexander Chervov; Evgeny M. Mirkes; Yuliya V. Orlova; Emmanuel Barillot; Alexander N. Gorban; Andrei Yu. Zinovyev (CoRR, 2020)

Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph. - Luca Albergante; Evgeny M. Mirkes; Jonathan Bac; Huidong Chen; Alexis Martin; Louis Faure; Emmanuel Barillot; Luca Pinello; Alexander N. Gorban; Andrei Yu. Zinovyev (Entropy, 2020)

Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network. - Andrei Yu. Zinovyev; Urszula Czerwinska; Laura Cantini; Emmanuel Barillot; Klaus M. Frahm; Dima L. Shepelyansky (PLoS Comput. Biol., 2020)

Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers. - Jonas Béal; Lorenzo Pantolini; Vincent Noël; Emmanuel Barillot; Laurence Calzone (PLoS Comput. Biol., 2021)

BIODICA: a computational environment for Independent Component Analysis of omics data. - Nicolas Captier; Jane Merlevede; Askhat Molkenov; Ainur Seisenova; Altynbek Zhubanchaliyev; Petr V. Nazarov; Emmanuel Barillot; Ulykbek Kairov; Andrei Yu. Zinovyev (Bioinform., 2022)

Building multiscale models with PhysiBoSS, an agent-based modeling tool. - Marco Ruscone; Andrea Checcoli; Randy W. Heiland; Emmanuel Barillot; Paul Macklin; Laurence Calzone; Vincent Noël (Briefings Bioinform., 2024)

Maboss for HPC environments: implementations of the continuous time Boolean model simulator for large CPU clusters and GPU accelerators. - Adam Smelko; Miroslav Kratochvíl; Emmanuel Barillot; Vincent Noël (BMC Bioinform., 2024)