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List of works by Emmanuel Barillot

A comprehensive approach to the molecular determinants of lifespan using a Boolean model of geroconversion.

scientific article

A comprehensive modular map of molecular interactions in RB/E2F pathway

scientific article published on 4 March 2008

A critical function for transforming growth factor-β, interleukin 23 and proinflammatory cytokines in driving and modulating human TH-17 responses

article

A high-risk retinoblastoma subtype with stemness features, dedifferentiated cone states and neuronal/ganglion cell gene expression

scientific article published on 22 September 2021

A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures

scientific article published on 22 October 2019

A review of computational approaches detecting microRNAs involved in cancer

scientific article

A robust algorithm for ratio estimation in two-color microarray experiments

scientific article published in December 2005

ACTuDB, a new database for the integrated analysis of array-CGH and clinical data for tumors.

scientific article

APC inactivation associates with abnormal mitosis completion and concomitant BUB1B/MAD2L1 up-regulation

scientific article

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

scientific article published on 01 September 2018

Advanced spot quality analysis in two-colour microarray experiments

scientific article

An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments

scientific article

Analysis of array CGH data: from signal ratio to gain and loss of DNA regions

scientific article

Antagonism pattern detection between microRNA and target expression in Ewing's sarcoma

scientific article

Application of Atlas of Cancer Signalling Network in preclinical studies

scientific article published on 01 March 2019

Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific and Reproducible Immune-Related Signals

Asf1b, the necessary Asf1 isoform for proliferation, is predictive of outcome in breast cancer

scientific article

Assessing reproducibility of matrix factorization methods in independent transcriptomes

scientific article published on 01 November 2019

Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps

scientific article

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 17 July 2020

BAC array CGH distinguishes mutually exclusive alterations that define clinicogenetic subtypes of gliomas.

scientific article

Beta-catenin status in paediatric medulloblastomas: correlation of immunohistochemical expression with mutational status, genetic profiles, and clinical characteristics

scientific article published in May 2009

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats

scientific article

BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks

scientific article published on 16 November 2007

Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial

scientific article

Biologie des systèmes appliqués aux cancers

scientific article published on 01 June 2009

Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis

scientific article

CAPweb: a bioinformatics CGH array Analysis Platform

scientific article

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 05 May 2020

CSIG-15. PROTEOMIC AND PHOSPHOPROTEOMIC ANALYSIS OF HUMAN MEDULLOBLASTOMA REVEALS DISTINCT ACTIVATED PATHWAYS BETWEEN SUBGROUPS

Cell death and life in cancer: mathematical modeling of cell fate decisions

scientific article published in January 2012

Characterization of rearrangements involving the ALK gene reveals a novel truncated form associated with tumor aggressiveness in neuroblastoma

scientific article

Classification of arrayCGH data using fused SVM.

scientific article

Classification of gene signatures for their information value and functional redundancy

scientific article published on 19 December 2017

Classification of microarray data using gene networks

scientific article

Clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction

Collective intelligence defines biological functions in Wikipedia as communities in the hidden protein connection network

scientific article published on 18 February 2020

Combinatorial code governing cellular responses to complex stimuli

scientific article published on 21 April 2015

Community-driven roadmap for integrated disease maps

scientific article published on 23 April 2018

Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes.

scientific article published on 13 December 2016

Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases

scientific article published on 17 April 2020

Conceptual and computational framework for logical modelling of biological networks deregulated in diseases

scientific article published on 8 December 2017

Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut.

scientific article

Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm

scientific article

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

scientific article

Contribution to high-resolution mapping in pigs with 101 type I markers and progress in comparative map between humans and pigs

scientific article published in April 2003

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

scientific article

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

scientific article

Correction: RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells

scientific article published on 14 May 2015

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis.

scientific article

DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts

scientific article

Deep-sequencing protocols influence the results obtained in small-RNA sequencing

scientific article (publication date: 2012)

Demarcation of Topologically Associating Domains Is Uncoupled from Enriched CTCF Binding in Developing Zebrafish

scientific article published on 10 April 2020

Detection of miRNA regulatory effect on triple negative breast cancer transcriptome

scientific article published on June 2015

Determining the optimal number of independent components for reproducible transcriptomic data analysis

scientific article

Developmental dynamics and disease potential of random monoallelic gene expression

scientific article published on February 2014

Drug-Driven Synthetic Lethality: Bypassing Tumor Cell Genetics with a Combination of AsiDNA and PARP Inhibitors

scientific article

Dynamical Boolean Modeling of Immunogenic Cell Death

scientific article published on 12 November 2020

Dynamical modeling of microRNA action on the protein translation process

scientific article

EMA - A R package for Easy Microarray data analysis

scientific article

Effective normalization for copy number variation in Hi-C data

scientific article published on 06 September 2018

Establishment and characterization of a panel of human uveal melanoma xenografts derived from primary and/or metastatic tumors.

scientific article published on 6 April 2010

Exact solving and sensitivity analysis of stochastic continuous time Boolean models

scientific article published on 11 June 2020

Frequent PTEN genomic alterations and activated phosphatidylinositol 3-kinase pathway in basal-like breast cancer cells

scientific article published on 03 December 2008

Frequent genomic structural alterations at HPV insertion sites in cervical carcinoma

scientific article

From a biological hypothesis to the construction of a mathematical model

scientific article published in January 2013

Gene and pathway level analyses of iCOGS variants highlight novel signalling pathways underlying familial breast cancer susceptibility

scientific article published on 24 December 2020

Genetic and epigenetic features direct differential efficiency of Xist-mediated silencing at X-chromosomal and autosomal locations

scientific article published on 25 September 2017

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays

scientific article

Genome-wide redistribution of meiotic double-strand breaks in Saccharomyces cerevisiae

scientific article published on 22 December 2006

Genomic profiling and identification of high-risk uveal melanoma by array CGH analysis of primary tumors and liver metastases

scientific article

Germline BAP1 mutations predispose to renal cell carcinomas

scientific article published on 16 May 2013

Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads

scientific article published on 21 September 2010

GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics

scientific article published on January 2003

HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.

scientific article

Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries.

scientific article

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

scientific article

HiTC: exploration of high-throughput 'C' experiments

scientific article published on 24 August 2012

High PTP4A3 Phosphatase Expression Correlates with Metastatic Risk in Uveal Melanoma Patients

scientific article published on 06 December 2010

High-Resolution Mapping of DNA Breakpoints to Define True Recurrences Among Ipsilateral Breast Cancers

scientific article published on 25 December 2007

Highly dynamic and sex-specific expression of microRNAs during early ES cell differentiation

scientific article

How Cell Decides Between Life and Death: Mathematical Modeling of Epigenetic Landscapes of Cellular Fates

ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays

scientific article published on 5 February 2008

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

scientific article

Identification of microRNA clusters cooperatively acting on Epithelial to Mesenchymal Transition in Triple Negative Breast Cancer

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

scientific article published on 01 March 2019

Identification of shortened 3' untranslated regions from expression arrays ⬇️

scientific article published on April 1, 2012

Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets

scientific article published on 07 September 2019

Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes

scientific article published on 13 November 2014

Independent transcriptional reprogramming and apoptosis induction by cisplatin

scientific article

Integrated genomic and transcriptomic analysis of ductal carcinoma in situ of the breast

scientific article

Interpreting pathways to discover cancer driver genes with Moonlight

scientific article published on 03 January 2020

Isolation of chromosome 21-specific yeast artificial chromosomes from a total human genome library

scientific article published on June 1, 1992

LICORN: learning cooperative regulation networks from gene expression data

scientific article

LINE-1 Activity in Facultative Heterochromatin Formation during X Chromosome Inactivation

scientific article published in July 2016

LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation

scientific article published on June 2010

Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation

scientific article

MaBoSS 2.0: an environment for stochastic Boolean modeling

scientific article published in July 2017

Maternal LSD1/KDM1A is an essential regulator of chromatin and transcription landscapes during zygotic genome activation

scientific article

Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration

scientific article published on 3 November 2015

Mathematical modelling of cell-fate decision in response to death receptor engagement

scientific article

Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

Model selection in the reconstruction of regulatory networks from time-series data

scientific article

Modelling of Immune Checkpoint Network Explains Synergistic Effects of Combined Immune Checkpoint Inhibitor Therapy and the Impact of Cytokines in Patient Response

scientific article published on 02 December 2020

Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization

scientific article published on 26 June 2019

Moonlight: a tool for biological interpretation and driver genes discovery

article

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data

scientific article

Multiparametric analysis of cytokine-driven human Th17 differentiation reveals a differential regulation of IL-17 and IL-22 production.

scientific article

Multiple-checkpoint inhibition of thymic stromal lymphopoietin-induced TH2 response by TH17-related cytokines

scientific article

NaviCell Web Service for network-based data visualization

scientific article

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

scientific article

NaviCom: a web application to create interactive molecular network portraits using multi-level omics data

scientific article

Nebula--a web-server for advanced ChIP-seq data analysis

scientific article

Network-based approaches for drug response prediction and targeted therapy development in cancer

scientific article published on 15 June 2015

NormaCurve: a SuperCurve-based method that simultaneously quantifies and normalizes reverse phase protein array data

scientific article

OCSANA: optimal combinations of interventions from network analysis

article

Patient-derived xenografts recapitulate molecular features of human uveal melanomas

scientific article

Patient-specific Boolean models of signalling networks guide personalised treatments

scientific article published in 2022

Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients

article

PhysiBoSS: a multi-scale agent based modelling framework integrating physical dimension and cell signalling

PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling.

scientific article

Polo-like kinase 1: a potential therapeutic option in combination with conventional chemotherapy for the management of patients with triple-negative breast cancer

scientific article

Practical use of BiNoM: a biological network manager software

scientific article published in January 2013

Predicting genetic interactions from Boolean models of biological networks

scientific article published on 11 May 2015

Preferential occurrence of chromosome breakpoints within early replicating regions in neuroblastoma

scientific article published on 14 December 2005

Prognostic Impact of Vitamin B6 Metabolism in Lung Cancer

article

Prognostic Impact of Vitamin B6 Metabolism in Lung Cancer

QuantumClone: Clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction

scientific article published on 12 January 2018

RNAi-dependent and independent control of LINE1 accumulation and mobility in mouse embryonic stem cells

scientific article

ROMA: Representation and Quantification of Module Activity from Target Expression Data

scientific article

Regulatory network reconstruction using an integral additive model with flexible kernel functions

scientific article

Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008)

scientific article

Retraction: RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells

article

Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph

scientific article published on 04 March 2020

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

scientific article published on 6 January 2016

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

scientific article

Search for a gene expression signature of breast cancer local recurrence in young women

scientific article published on 23 January 2012

Selecting biomedical data sources according to user preferences

scientific article

Sequence profiling of the Saccharomyces cerevisiae genome permits deconvolution of unique and multialigned reads for variant detection

scientific article

Signalling maps in cancer research: construction and data analysis

scientific article published in January 2018

Software package for automatic microarray image analysis (MAIA).

scientific article published on 19 January 2007

Spatial normalization of array-CGH data

scientific article

Spatial partitioning of the regulatory landscape of the X-inactivation centre ⬇️

scientific article (publication date: 11 April 2012)

Spi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia

scientific article

Spi-1/PU.1 oncogene accelerates DNA replication fork elongation and promotes genetic instability in the absence of DNA breakage

scientific article published on 21 July 2010

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

scientific article

Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model

scientific article

Synthetic lethality between gene defects affecting a single non-essential molecular pathway with reversible steps

scientific article

Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis

scientific article published on 08 August 2013

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.

scientific article published on 2 June 2018

TTK/hMPS1 is an attractive therapeutic target for triple-negative breast cancer

scientific article

The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa).

scientific article published on January 2003

The HuGeMap Database: interconnection and visualization of human genome maps

scientific article published on January 1999

The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function

scientific article

The shortest path is not the one you know: application of biological network resources in precision oncology research

scientific article

Tools and best practices for retrotransposon analysis using high-throughput sequencing data

scientific article published on 29 December 2019

Trajectories, bifurcations, and pseudo-time in large clinical datasets: applications to myocardial infarction and diabetes data

scientific article published on 01 November 2020

Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution

scientific article published on 01 February 2020

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

scientific article

Xist-dependent imprinted X inactivation and the early developmental consequences of its failure

scientific article published on 30 January 2017

[Biological network modelling and precision medicine in oncology]

scientific article published on 01 June 2014

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

scientific article published on 06 January 2020

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

scientific article published on 31 October 2020

miR-181a and miR-630 regulate cisplatin-induced cancer cell death

scientific article

myProMS, a web server for management and validation of mass spectrometry-based proteomic data

scientific article

ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data

scientific article

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