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2020 – today
- 2024
[j70]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): 199 (2024)- [i3]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 abs/2406.18371 (2024) - 2022
- [j69]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): 2963-2964 (2022) - 2021
- [j68]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) - 2020
- [j67]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): 2620-2622 (2020) - [j66]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): 4975 (2020) - [j65]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): 241 (2020) - [j64]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): 296 (2020) - [j63]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) - [i2]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 abs/2007.03788 (2020)
2010 – 2019
- 2019
- [j62]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): 659-670 (2019) - [j61]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): 701-716 (2019) - [j60]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): 1238-1249 (2019) - [j59]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): 1188-1196 (2019) - [j58]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): 4307-4313 (2019) - [j57]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. 20-S(4): 140:1-140:14 (2019) - 2018
- [j56]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: bay036 (2018) - [j55]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): 1808-1816 (2018) - [j54]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): 313:1-313:16 (2018) - [c8]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: 501-513 - [i1]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 abs/1804.07580 (2018) - 2017
- [j53]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: bax026 (2017) - [j52]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): 2226-2228 (2017) - 2016
- [j51]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): 984-992 (2016) - [j50]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): 293 (2016) - 2015
- [j49]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: 46 (2015) - [j48]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): W560-W565 (2015) - [j47]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) - 2014
- [j46]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): 3443-3450 (2014) - 2013
- [j45]Paola Vera-Licona, Eric Bonnet, Emmanuel Barillot, Andrei Yu. Zinovyev:
OCSANA: optimal combinations of interventions from network analysis. Bioinform. 29(12): 1571-1573 (2013) - [j44]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): 2979-2986 (2013) - [j43]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: 18 (2013) - [j42]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: 100 (2013) - [j41]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) - 2012
- [j40]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): 423-425 (2012) - [j39]Valentina Boeva, Alban Lermine, Camille Barette, Christel Guillouf, Emmanuel Barillot:
Nebula - a web-server for advanced ChIP-seq data analysis. Bioinform. 28(19): 2517-2519 (2012) - [j38]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): 2843-2844 (2012) - [j37]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): 3147-3149 (2012) - [j36]Gautier Stoll, Eric Viara, Emmanuel Barillot, Laurence Calzone:
Continuous time boolean modeling for biological signaling: application of Gillespie algorithm. BMC Syst. Biol. 6: 116 (2012) - [j35]Loredana Martignetti, Andrei Yu. Zinovyev, Emmanuel Barillot:
Identification of Shortened 3′ untranslated Regions from Expression Arrays. J. Bioinform. Comput. Biol. 10(2) (2012) - 2011
- [j34]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): 268-269 (2011) - 2010
- [j33]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): 1895-1896 (2010) - [j32]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): 2902-2903 (2010) - [j31]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: 13 (2010) - [j30]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)
2000 – 2009
- 2009
- [c7]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: 72-87 - 2008
- [j29]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): 768-774 (2008) - [j28]Andrei Yu. Zinovyev, Eric Viara, Laurence Calzone, Emmanuel Barillot:
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinform. 24(6): 876-877 (2008) - [j27]Eugene Novikov, Emmanuel Barillot:
Regulatory network reconstruction using an integral additive model with flexible kernel functions. BMC Syst. Biol. 2: 8 (2008) - [c6]Franck Rapaport, Emmanuel Barillot, Jean-Philippe Vert:
Classification of arrayCGH data using fused SVM. ISMB 2008: 375-382 - 2007
- [j26]Eugene Novikov, Emmanuel Barillot:
Software package for automatic microarray image analysis (MAIA). Bioinform. 23(5): 639-640 (2007) - [j25]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): 2407-2414 (2007) - [j24]Franck Rapaport, Andrei Yu. Zinovyev, Marie Dutreix, Emmanuel Barillot, Jean-Philippe Vert:
Classification of microarray data using gene networks. BMC Bioinform. 8 (2007) - 2006
- [j23]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): 849-856 (2006) - [j22]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): 2066-2073 (2006) - [j21]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: 264 (2006) - [j20]Eugene Novikov, Emmanuel Barillot:
A noise-resistant algorithm for grid finding in microarray image analysis. Mach. Vis. Appl. 17(5): 337-345 (2006) - [j19]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): 613-616 (2006) - [j18]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): 477-481 (2006) - 2005
- [j17]Eugene Novikov, Emmanuel Barillot:
An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments. BMC Bioinform. 6: 293 (2005) - [j16]Eugene Novikov, Emmanuel Barillot:
A Robust Algorithm for Ratio Estimation in Two-color Microarray Experiments. J. Bioinform. Comput. Biol. 3(6): 1411-1428 (2005) - 2004
- [j15]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): 3413-3422 (2004) - [c5]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: 86-93 - 2003
- [j14]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): 138-141 (2003) - [j13]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): 179-182 (2003) - 2002
- [c4]Eric Viara, Guy Vaysseix, Emmanuel Barillot:
Distributing CORBA views from an OODBMS. IDEAS 2002: 116-129 - 2001
- [j12]Frédéric Achard, Guy Vaysseix, Emmanuel Barillot:
XML, bioinformatics and data integration. Bioinform. 17(1): 115-125 (2001) - [j11]Frédéric Tores, Emmanuel Barillot:
The art of pedigree drawing: algorithmic aspects. Bioinform. 17(1): 174-179 (2001) - 2000
- [j10]Claude Discala, Xavier Benigni, Emmanuel Barillot, Guy Vaysseix:
DBcat: a catalog of 500 biological databases. Nucleic Acids Res. 28(1): 8-9 (2000) - [c3]Stuart Pook, Eric Lecolinet, Guy Vaysseix, Emmanuel Barillot:
Context and Interaction in Zooable User Interfaces. Advanced Visual Interfaces 2000: 227-231 - [c2]Stuart Pook, Eric Lecolinet, Guy Vaysseix, Emmanuel Barillot:
Control menus: excecution and control in a single interactor. CHI Extended Abstracts 2000: 263-264
1990 – 1999
- 1999
- [j9]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): 157-169 (1999) - [j8]L. Brun-Samarcq, Sophie Gallina, A. Philippi, Florence Demenais, Guy Vaysseix, Emmanuel Barillot:
CoPE: a collaborative pedigree drawing environment. Bioinform. 15(4): 345-346 (1999) - [j7]Claude Discala, Marion Ninnin, Frédéric Achard, Emmanuel Barillot, Guy Vaysseix:
DBcat: a catalog of biological databases. Nucleic Acids Res. 27(1): 10-11 (1999) - [j6]Frédéric Achard, Guy Vaysseix, Philippe Dessen, Emmanuel Barillot:
Virgil database for rich links (1999 update). Nucleic Acids Res. 27(1): 113-114 (1999) - [j5]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): 119-122 (1999) - [c1]Eric Viara, Emmanuel Barillot, Guy Vaysseix:
The EyeDB OODBMS. IDEAS 1999: 390-402 - 1998
- [j4]Frédéric Achard, Christophe Cussat-Blanc, Eric Viara, Emmanuel Barillot:
The new Virgil database: a service of rich links. Bioinform. 14(4): 342-348 (1998) - [j3]Stuart Pook, Guy Vaysseix, Emmanuel Barillot:
Zomit: biological data visualization and browsing. Bioinform. 14(9): 807-814 (1998) - [j2]Frédéric Achard, Emmanuel Barillot:
Virgil: a database of rich links between GDB and GenBank. Nucleic Acids Res. 26(1): 100-101 (1998) - [j1]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): 106-107 (1998)
Coauthor Index
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