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Author Details

Emmanuel Barillot
Institut Curie, Universite PSL
1991
183
57
Antoine Forget (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37287810Corrigendum to "Modeling signaling pathways in biology with MaBoSS: From one single cell to a dynamic population of heterogeneous interacting cells" [Comput. Struct. Biotechnol. 20 (2022) 5661-5671].Comput Struct Biotechnol J2023
37903760PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks.NPJ Syst Biol Appl2023
37289551Multiscale model of the different modes of cancer cell invasion.Bioinformatics2023
35164900Patient-specific Boolean models of signalling networks guide personalised treatments.Elife2022
35561190BIODICA: a computational environment for Independent Component Analysis of omics data.Bioinformatics2022
35513532A comparison of Sars-Cov-2 vaccine platforms: the CoviCompare project.Nat Med2022
36284705Modeling signaling pathways in biology with MaBoSS: From one single cell to a dynamic population of heterogeneous interacting cells.Comput Struct Biotechnol J2022
35309516UPMaBoSS: A Novel Framework for Dynamic Cell Population Modeling.Front Mol Biosci2022
33368296Gene- and pathway-level analyses of iCOGS variants highlight novel signaling pathways underlying familial breast cancer susceptibility.Int J Cancer2021
33507915Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers.PLoS Comput Biol2021
34939300COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.Mol Syst Biol2021
34439123Network-Based Integration of Multi-Omics Data Identifies the Determinants of miR-491-5p Effects.Cancers (Basel)2021
34552068A high-risk retinoblastoma subtype with stemness features, dedifferentiated cone states and neuronal/ganglion cell gene expression.Nat Commun2021
34664389COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.Mol Syst Biol2021
32371892COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.Sci Data2020
31900418Interpreting pathways to discover cancer driver genes with Moonlight.Nat Commun2020
32049009Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution.Cell Rep2020
32069277Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network.PLoS Comput Biol2020
33281620Dynamical Boolean Modeling of Immunogenic Cell Death.Front Physiol2020
33276543Modelling of Immune Checkpoint Network Explains Synergistic Effects of Combined Immune Checkpoint Inhibitor Therapy and the Impact of Cytokines in Patient Response.Cancers (Basel)2020
33241287Trajectories, bifurcations, and pseudo-time in large clinical datasets: applications to myocardial infarction and diabetes data.Gigascience2020
32678106Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.Sci Data2020
32527218Exact solving and sensitivity analysis of stochastic continuous time Boolean models.BMC Bioinformatics2020
32334414Demarcation of Topologically Associating Domains Is Uncoupled from Enriched CTCF Binding in Developing Zebrafish.iScience2020
29237040Conceptual and computational framework for logical modelling of biological networks deregulated in diseases.Brief Bioinform2019
31641119A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures.Nat Commun2019
31890048Tools and best practices for retrotransposon analysis using high-throughput sequencing data.Mob DNA2019
30169736PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling.Bioinformatics2019
31500324Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets.Int J Mol Sci2019
31247897Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization.Int J Mol Sci2019
30733688Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients.Front Physiol2019
30999838Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer.BMC Bioinformatics2019
30938767Assessing reproducibility of matrix factorization methods in independent transcriptomes.Bioinformatics2019
30657980Identification of microRNA clusters cooperatively acting on epithelial to mesenchymal transition in triple negative breast cancer.Nucleic Acids Res2019
29726961Application of Atlas of Cancer Signalling Network in preclinical studies.Brief Bioinform2019
29688273Community-driven roadmap for integrated disease maps.Brief Bioinform2019
29342233QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction.Bioinformatics2018
30189838Effective normalization for copy number variation in Hi-C data.BMC Bioinformatics2018
30205043Aberrant ERBB4-SRC Signaling as a Hallmark of Group 4 Medulloblastoma Revealed by Integrative Phosphoproteomic Profiling.Cancer Cell2018
29872544Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.NPJ Syst Biol Appl2018
29688383Signalling maps in cancer research: construction and data analysis.Database (Oxford)2018
27559053Drug-Driven Synthetic Lethality: Bypassing Tumor Cell Genetics with a Combination of AsiDNA and PARP Inhibitors.Clin Cancer Res2017
28415074NaviCom: a web application to create interactive molecular network portraits using multi-level omics data.Database (Oxford)2017
28410145A review of computational approaches detecting microRNAs involved in cancer.Front Biosci (Landmark Ed)2017
28134930Xist-dependent imprinted X inactivation and the early developmental consequences of its failure.Nat Struct Mol Biol2017
29101321Contribution of epigenetic landscapes and transcription factors to X-chromosome reactivation in the inner cell mass.Nat Commun2017
28947736Genetic and epigenetic features direct differential efficiency of Xist-mediated silencing at X-chromosomal and autosomal locations.Nat Commun2017
29263798Classification of gene signatures for their information value and functional redundancy.NPJ Syst Biol Appl2017
28881959MaBoSS 2.0: an environment for stochastic Boolean modeling.Bioinformatics2017
28740262Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries.Nat Genet2017
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Collaborators

Andrei Zinovyev
INSERM U, Institut Curie, PSL Research University
Co-authored papers 56
Laurence Calzone
Institut Curie, Universite PSL
Co-authored papers 36
Olivier Delattre
PSL Research University, Institut Curie Research Center, INSERM U, Institut Curie
Co-authored papers 18
Edith Heard
Institut Curie, PSL Research University, CNRS UMR 5, INSERM U934
Co-authored papers 18
Loredana Martignetti
Institut Curie, PSL Research University
Co-authored papers 12
Laura Cantini
Institut Pasteur, Universite Paris Cite, CNRS UMR 3738
Co-authored papers 9
Arnau Montagud
Institut Curie, PSL Research University
Co-authored papers 9
St??phane Liva
Institut Curie, France PSL Research University, France Inserm
Co-authored papers 7
Ga??lle Pierron
Institut Curie Hospital
Co-authored papers 7
Charles Auffray
European Institute for Systems Biology and Medicine
Co-authored papers 7
Alfonso Valencia
Josep Carreras Leukaemia Research Institute (IJC)
Co-authored papers 7
Gudrun Schleiermacher
Institut Curie
Co-authored papers 6
Reinhard Schneider
Co-authored papers 6
Nicolas Stransky
Co-authored papers 5
Aur??lien Naldi
Institut de Biologie de l'Ecole Normale Superieure, Inserm, CNRS, Universite PSL
Co-authored papers 5
Franck Tirode
Cancer Center of Lyon
Co-authored papers 5
Denis Thieffry
Institut de Biologie de l'Ecole Normale Superieure, Inserm, CNRS, Universite PSL
Co-authored papers 4
Emek Demir
Knight Cancer Institute, Oregon Health & Science University
Co-authored papers 4
Henning Hermjakob
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 4
Chris T Evelo
Maastricht University
Co-authored papers 4
Hiroaki Kitano
Co-authored papers 4
Alexander R Pico
Institute of Data Science and Biotechnology, Gladstone Institutes
Co-authored papers 4
Marc Gillespie
Ontario Institute for Cancer Research
Co-authored papers 4
Aurelien Dugourd
Institute of Experimental Medicine and Systems Biology, RWTH Aachen University
Co-authored papers 4
Didier Surdez
Balgrist University Hospital, University of Zurich (UZH)
Co-authored papers 4
Chris Sander
Broad Institute of MIT and Harvard
Co-authored papers 3
Damarys Loew
Institut Curie, PSL Research University
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Bertrand De Meulder
European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM
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Patrick Poullet
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Job Dekker
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Release 1.2