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Spatial normalization of array-CGH data.

Pierre Neuvial , Philippe Hupé , Isabel Brito , Stéphane Liva , Elodie Manié et al.
BMC Bioinformatics, 2006, 7, pp.264. ⟨10.1186/1471-2105-7-264⟩
Journal articles inserm-00089910v1
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Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration

David P A Cohen , Loredana Martignetti , Sylvie Robine , Emmanuel Barillot , Andrei Zinovyev et al.
PLoS Computational Biology, 2015, 11 (11), pp.e1004571. ⟨10.1371/journal.pcbi.1004571⟩
Journal articles inserm-02141625v1

VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles

Philippe La Rosa , Eric Viara , Philippe Hupé , Gaëlle Pierron , Stéphane Liva et al.
Bioinformatics, 2006, 22 (17), pp.2066-2073. ⟨10.1093/bioinformatics/btl359⟩
Journal articles hal-01199867v1

ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis

Adil El Filali , Séverine Lair , Catia Verbeke , Philippe La Rosa , François Radvanyi et al.
Nucleic Acids Research, 2006, 34 (90001), pp.D613-D616. ⟨10.1093/nar/gkj022⟩
Journal articles hal-03225608v1
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CAPweb: a bioinformatics CGH array Analysis Platform

Stéphane Liva , Philippe Hupé , Pierre Neuvial , Isabel Brito , Eric Viara et al.
Nucleic Acids Research, 2006, 34 (W), pp.477-481. ⟨10.1093/nar/gkl215⟩
Journal articles hal-01199870v1
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A comprehensive approach to the molecular determinants of lifespan using a Boolean model of geroconversion

Loic Verlingue , Aurélien Dugourd , Gautier Stoll , Emmanuel Barillot , Laurence Calzone et al.
Aging Cell, 2016, 15 (6), pp.1018-1026. ⟨10.1111/acel.12504⟩
Journal articles hal-01366791v1

Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks

Sylvain Blachon , Gautier Stoll , Carito Guziolowski , Andrei Zinovyev , Emmanuel Barillot et al.
AIAI 2009 Workshop -- Workshop on Biomedical Informatics and Intelligent Approaches in the Support of Genomic Medicine (BMIINT), Apr 2009, Thessalonik, Greece. pp.72-87
Conference papers inria-00429801v1

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

Daria Iakovishina , Isabelle Janoueix-Lerosey , Emmanuel Barillot , Mireille Regnier , Valentina Boeva et al.
Bioinformatics, 2016, 32, pp.984-992. ⟨10.1093/bioinformatics/btv751⟩
Journal articles hal-01253126v1
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Mathematical modelling of cell-fate decision in response to death receptor engagement.

Laurence Calzone , Laurent Tournier , Simon Fourquet , Denis Thieffry , Boris Zhivotovsky et al.
PLoS Computational Biology, 2010, 6 (3), pp.e1000702. ⟨10.1371/journal.pcbi.1000702⟩
Journal articles inserm-00704979v1

LICORN: learning cooperative regulation networks from gene expression data.

Mohamed Elati , Pierre Neuvial , Monique Bolotin-Fukuhara , Emmanuel Barillot , François Radvanyi et al.
Bioinformatics, 2007, 23 (18), pp.2407-14. ⟨10.1093/bioinformatics/btm352⟩
Journal articles hal-00192537v1
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Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation.

Constance Ciaudo , Nicolas Servant , Valérie Cognat , Alexis Sarazin , Emmanuelle Kieffer et al.
PLoS Genetics, 2009, 5 (8), pp.e1000620. ⟨10.1371/journal.pgen.1000620⟩
Journal articles inserm-00438642v1
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Dynamical Boolean Modeling of Immunogenic Cell Death

Andrea Checcoli , Jonathan Pol , Aurelien Naldi , Vincent Noël , Emmanuel Barillot et al.
Frontiers in Physiology, 2020, 11, pp.590479. ⟨10.3389/fphys.2020.590479⟩
Journal articles hal-03050475v1
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WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically

Vincent Noël , Marco Ruscone , Gautier Stoll , Eric Viara , Andrei Zinovyev et al.
Frontiers in Molecular Biosciences, 2021, 8, ⟨10.3389/fmolb.2021.754444⟩
Journal articles hal-03479335v1
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A high-risk retinoblastoma subtype with stemness features, dedifferentiated cone states and neuronal/ganglion cell gene expression

Jing Liu , Daniela Ottaviani , Meriem Sefta , Céline Desbrousses , Elodie Chapeaublanc et al.
Nature Communications, 2021, 12 (1), pp.1-20. ⟨10.1038/s41467-021-25792-0⟩
Journal articles hal-03374490v1
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Spectral analysis of gene expression profiles using gene networks

Franck Rapaport , Andrei Zinovyev , Marie Dutreix , Emmanuel Barillot , Jean-Philippe Vert et al.
Preprints, Working Papers, ... hal-00021785v1

Classification of microarray data using gene networks.

Franck Rapaport , Andrei Zinovyev , Marie Dutreix , Emmanuel Barillot , Jean-Philippe Vert et al.
BMC Bioinformatics, 2007, 8, pp.35. ⟨10.1186/1471-2105-8-35⟩
Journal articles hal-00433577v1

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

Isabel Brito , Philippe Hupé , Pierre Neuvial , Emmanuel Barillot
PLoS ONE, 2012, 8 (12), pp.e81458
Journal articles hal-01201580v1

Classification of gene signatures for their information value and functional redundancy

Laura Cantini , Laurence Calzone , Loredana Martignetti , Mattias Rydenfelt , Nils Blüthgen et al.
npj Systems Biology and Applications, 2018, 4 (1), ⟨10.1038/s41540-017-0038-8⟩
Journal articles hal-02129604v1

Contribution of epigenetic landscapes and transcription factors to X-chromosome reactivation in the inner cell mass

Maud Borensztein , Ikuhiro Okamoto , Laurène Syx , Guillaume Guilbaud , Christel Picard et al.
Nature Communications, 2017, 8 (1), ⟨10.1038/s41467-017-01415-5⟩
Journal articles hal-03437406v1
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Xist-dependent imprinted X inactivation and the early developmental consequences of its failure

Maud Borensztein , Laurène Syx , Katia Ancelin , Patricia Diabangouaya , Christel Picard et al.
Nature Structural and Molecular Biology, 2017, ⟨10.1038/nsmb.3365⟩
Journal articles hal-03021809v1
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Demarcation of Topologically Associating Domains Is Uncoupled from Enriched CTCF Binding in Developing Zebrafish

Yuvia A Perèz Rico , Emmanuel Barillot , Alena Shkumatava
iScience, 2020, 23 (5), pp.101046. ⟨10.1016/j.isci⟩
Journal articles hal-02872297v1
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Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries

Valentina Boeva , Caroline Louis-Brennetot , Agathe Peltier , Simon Durand , Cecile Pierre-Eugene et al.
Nature Genetics, 2017, 49 (9), pp.1408-1413. ⟨10.1038/ng.3921⟩
Journal articles hal-01741718v1

Identification of microRNA clusters cooperatively acting on epithelial to mesenchymal transition in triple negative breast cancer

Laura Cantini , Gloria Bertoli , Claudia Cava , Thierry Dubois , Andrei Zinovyev et al.
Nucleic Acids Research, 2019, 47 (5), pp.2205-2215. ⟨10.1093/nar/gkz016⟩
Journal articles hal-02129600v1

Aberrant ERBB4-SRC Signaling as a Hallmark of Group 4 Medulloblastoma Revealed by Integrative Phosphoproteomic Profiling

Antoine Forget , Loredana Martignetti , Stéphanie Puget , Laurence Calzone , Sebastian Brabetz et al.
Cancer Cell, 2018, 34 (3), pp.379-395.e7. ⟨10.1016/j.ccell.2018.08.002⟩
Journal articles hal-02347170v1
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Live-Cell Chromosome Dynamics and Outcome of X Chromosome Pairing Events during ES Cell Differentiation

Osamu Masui , Isabelle Bonnet , Patricia Le Baccon , Isabel Brito , Tim Pollex et al.
Cell, 2011, 145 (3), pp.447-458. ⟨10.1016/j.cell.2011.03.032⟩
Journal articles hal-02454276v1
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Effective normalization for copy number variation in Hi-C data

Nicolas Servant , Nelle Varoquaux , Edith Heard , Emmanuel Barillot , Jean-Philippe Vert et al.
BMC Bioinformatics, 2018, 19 (1), pp.313. ⟨10.1186/s12859-018-2256-5⟩
Journal articles inserm-02059124v1
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Sequence Profiling of the Saccharomyces cerevisiae Genome Permits Deconvolution of Unique and Multialigned Reads for Variant Detection

Claire Jubin , Alexandre Serero , Sophie Loeillet , Emmanuel Barillot , Alain Nicolas et al.
G3, 2014, 4 (4), pp.707-715. ⟨10.1534/g3.113.009464⟩
Journal articles hal-01324830v1
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Interpreting pathways to discover cancer driver genes with Moonlight

Antonio Colaprico , Catharina Olsen , Matthew Bailey , Gabriel Odom , Thilde Terkelsen et al.
Nature Communications, 2020, 11 (1), ⟨10.1038/s41467-019-13803-0⟩
Journal articles hal-03001026v1
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Search for a gene expression signature of breast cancer local recurrence in young women.

Nicolas Servant , Marc Bollet , Hans Halfwerk , Kevin Bleakley , Bas Kreike et al.
Clinical Cancer Research, 2012, 18 (6), pp.1704-15. ⟨10.1158/1078-0432.CCR-11-1954⟩
Journal articles hal-00756723v1
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Analysis of Somatic Alterations in Cancer Genome: From SNP Arrays to Next Generation Sequencing

Tatiana Popova , Valentina Boeva , Elodie Manié , Yves Rozenholc , Emmanuel Barillot et al.
Genomics I Humans, Animals and Plants, 2013
Book sections hal-01108425v1