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

Kondratova M, Czerwinska U, Sompairac N, Amigorena SD, Soumelis V, Barillot E, Zinovyev A, Kuperstein I.

Nat Commun. 2019 Oct 22;10(1):4808. doi: 10.1038/s41467-019-12270-x.


Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets.

Sompairac N, Nazarov PV, Czerwinska U, Cantini L, Biton A, Molkenov A, Zhumadilov Z, Barillot E, Radvanyi F, Gorban A, Kairov U, Zinovyev A.

Int J Mol Sci. 2019 Sep 7;20(18). pii: E4414. doi: 10.3390/ijms20184414. Review.


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

Greco A, Sanchez Valle J, Pancaldi V, Baudot A, Barillot E, Caselle M, Valencia A, Zinovyev A, Cantini L.

Int J Mol Sci. 2019 Jun 26;20(13). pii: E3114. doi: 10.3390/ijms20133114.


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

Sompairac N, Modamio J, Barillot E, Fleming RMT, Zinovyev A, Kuperstein I.

BMC Bioinformatics. 2019 Apr 18;20(Suppl 4):140. doi: 10.1186/s12859-019-2682-z.


Assessing reproducibility of matrix factorization methods in independent transcriptomes.

Cantini L, Kairov U, de Reyniès A, Barillot E, Radvanyi F, Zinovyev A.

Bioinformatics. 2019 Nov 1;35(21):4307-4313. doi: 10.1093/bioinformatics/btz225.


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

Béal J, Montagud A, Traynard P, Barillot E, Calzone L.

Front Physiol. 2019 Jan 24;9:1965. doi: 10.3389/fphys.2018.01965. eCollection 2018.


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

Cantini L, Bertoli G, Cava C, Dubois T, Zinovyev A, Caselle M, Castiglioni I, Barillot E, Martignetti L.

Nucleic Acids Res. 2019 Mar 18;47(5):2205-2215. doi: 10.1093/nar/gkz016.


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

Forget A, Martignetti L, Puget S, Calzone L, Brabetz S, Picard D, Montagud A, Liva S, Sta A, Dingli F, Arras G, Rivera J, Loew D, Besnard A, Lacombe J, Pagès M, Varlet P, Dufour C, Yu H, Mercier AL, Indersie E, Chivet A, Leboucher S, Sieber L, Beccaria K, Gombert M, Meyer FD, Qin N, Bartl J, Chavez L, Okonechnikov K, Sharma T, Thatikonda V, Bourdeaut F, Pouponnot C, Ramaswamy V, Korshunov A, Borkhardt A, Reifenberger G, Poullet P, Taylor MD, Kool M, Pfister SM, Kawauchi D, Barillot E, Remke M, Ayrault O.

Cancer Cell. 2018 Sep 10;34(3):379-395.e7. doi: 10.1016/j.ccell.2018.08.002.


Effective normalization for copy number variation in Hi-C data.

Servant N, Varoquaux N, Heard E, Barillot E, Vert JP.

BMC Bioinformatics. 2018 Sep 6;19(1):313. doi: 10.1186/s12859-018-2256-5.


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

Letort G, Montagud A, Stoll G, Heiland R, Barillot E, Macklin P, Zinovyev A, Calzone L.

Bioinformatics. 2019 Apr 1;35(7):1188-1196. doi: 10.1093/bioinformatics/bty766.


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

Mazein A, Ostaszewski M, Kuperstein I, Watterson S, Le Novère N, Lefaudeux D, De Meulder B, Pellet J, Balaur I, Saqi M, Nogueira MM, He F, Parton A, Lemonnier N, Gawron P, Gebel S, Hainaut P, Ollert M, Dogrusoz U, Barillot E, Zinovyev A, Schneider R, Balling R, Auffray C.

NPJ Syst Biol Appl. 2018 Jun 2;4:21. doi: 10.1038/s41540-018-0059-y. eCollection 2018.


Application of Atlas of Cancer Signalling Network in preclinical studies.

Monraz Gomez LC, Kondratova M, Ravel JM, Barillot E, Zinovyev A, Kuperstein I.

Brief Bioinform. 2019 Mar 25;20(2):701-716. doi: 10.1093/bib/bby031.


Signalling maps in cancer research: construction and data analysis.

Kondratova M, Sompairac N, Barillot E, Zinovyev A, Kuperstein I.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay036.


Community-driven roadmap for integrated disease maps.

Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming RMT, Le Novère N, Gawron P, Ligon T, Niarakis A, Nickerson D, Weindl D, Balling R, Barillot E, Auffray C, Schneider R.

Brief Bioinform. 2019 Mar 25;20(2):659-670. doi: 10.1093/bib/bby024.


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

Deveau P, Colmet Daage L, Oldridge D, Bernard V, Bellini A, Chicard M, Clement N, Lapouble E, Combaret V, Boland A, Meyer V, Deleuze JF, Janoueix-Lerosey I, Barillot E, Delattre O, Maris JM, Schleiermacher G, Boeva V.

Bioinformatics. 2018 Jun 1;34(11):1808-1816. doi: 10.1093/bioinformatics/bty016.


Classification of gene signatures for their information value and functional redundancy.

Cantini L, Calzone L, Martignetti L, Rydenfelt M, Blüthgen N, Barillot E, Zinovyev A.

NPJ Syst Biol Appl. 2017 Dec 19;4:2. doi: 10.1038/s41540-017-0038-8. eCollection 2018.


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

Montagud A, Traynard P, Martignetti L, Bonnet E, Barillot E, Zinovyev A, Calzone L.

Brief Bioinform. 2019 Jul 19;20(4):1238-1249. doi: 10.1093/bib/bbx163.


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

Borensztein M, Okamoto I, Syx L, Guilbaud G, Picard C, Ancelin K, Galupa R, Diabangouaya P, Servant N, Barillot E, Surani A, Saitou M, Chen CJ, Anastassiadis K, Heard E.

Nat Commun. 2017 Nov 3;8(1):1297. doi: 10.1038/s41467-017-01415-5.


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

Loda A, Brandsma JH, Vassilev I, Servant N, Loos F, Amirnasr A, Splinter E, Barillot E, Poot RA, Heard E, Gribnau J.

Nat Commun. 2017 Sep 25;8(1):690. doi: 10.1038/s41467-017-00528-1.


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

Kairov U, Cantini L, Greco A, Molkenov A, Czerwinska U, Barillot E, Zinovyev A.

BMC Genomics. 2017 Sep 11;18(1):712. doi: 10.1186/s12864-017-4112-9.


MaBoSS 2.0: an environment for stochastic Boolean modeling.

Stoll G, Caron B, Viara E, Dugourd A, Zinovyev A, Naldi A, Kroemer G, Barillot E, Calzone L.

Bioinformatics. 2017 Jul 15;33(14):2226-2228. doi: 10.1093/bioinformatics/btx123.


Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries.

Boeva V, Louis-Brennetot C, Peltier A, Durand S, Pierre-Eugène C, Raynal V, Etchevers HC, Thomas S, Lermine A, Daudigeos-Dubus E, Geoerger B, Orth MF, Grünewald TGP, Diaz E, Ducos B, Surdez D, Carcaboso AM, Medvedeva I, Deller T, Combaret V, Lapouble E, Pierron G, Grossetête-Lalami S, Baulande S, Schleiermacher G, Barillot E, Rohrer H, Delattre O, Janoueix-Lerosey I.

Nat Genet. 2017 Sep;49(9):1408-1413. doi: 10.1038/ng.3921. Epub 2017 Jul 24.


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

Dorel M, Viara E, Barillot E, Zinovyev A, Kuperstein I.

Database (Oxford). 2017 Jan 1;2017(1). doi: 10.1093/database/bax026.


A review of computational approaches detecting microRNAs involved in cancer.

Cantini L, Caselle M, Forget A, Zinovyev A, Barillot E, Martignetti L.

Front Biosci (Landmark Ed). 2017 Jun 1;22:1774-1791. Review.


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

Borensztein M, Syx L, Ancelin K, Diabangouaya P, Picard C, Liu T, Liang JB, Vassilev I, Galupa R, Servant N, Barillot E, Surani A, Chen CJ, Heard E.

Nat Struct Mol Biol. 2017 Mar;24(3):226-233. doi: 10.1038/nsmb.3365. Epub 2017 Jan 30.


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

Pérez-Rico YA, Boeva V, Mallory AC, Bitetti A, Majello S, Barillot E, Shkumatava A.

Genome Res. 2017 Feb;27(2):259-268. doi: 10.1101/gr.203679.115. Epub 2016 Dec 13.


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

Verlingue L, Dugourd A, Stoll G, Barillot E, Calzone L, Londoño-Vallejo A.

Aging Cell. 2016 Dec;15(6):1018-1026. doi: 10.1111/acel.12504. Epub 2016 Sep 9.


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

Jdey W, Thierry S, Russo C, Devun F, Al Abo M, Noguiez-Hellin P, Sun JS, Barillot E, Zinovyev A, Kuperstein I, Pommier Y, Dutreix M.

Clin Cancer Res. 2017 Feb 15;23(4):1001-1011. doi: 10.1158/1078-0432.CCR-16-1193. Epub 2016 Aug 24.


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

Chow JC, Ciaudo C, Fazzari MJ, Mise N, Servant N, Glass JL, Attreed M, Avner P, Wutz A, Barillot E, Greally JM, Voinnet O, Heard E.

Cell. 2016 Jul 28;166(3):782. doi: 10.1016/j.cell.2016.07.013. No abstract available.


Cytonuclear interactions affect adaptive traits of the annual plant Arabidopsis thaliana in the field.

Roux F, Mary-Huard T, Barillot E, Wenes E, Botran L, Durand S, Villoutreix R, Martin-Magniette ML, Camilleri C, Budar F.

Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):3687-92. doi: 10.1073/pnas.1520687113. Epub 2016 Mar 15.


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

Martignetti L, Calzone L, Bonnet E, Barillot E, Zinovyev A.

Front Genet. 2016 Feb 19;7:18. doi: 10.3389/fgene.2016.00018. eCollection 2016.


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

Ancelin K, Syx L, Borensztein M, Ranisavljevic N, Vassilev I, Briseño-Roa L, Liu T, Metzger E, Servant N, Barillot E, Chen CJ, Schüle R, Heard E.

Elife. 2016 Feb 2;5. pii: e08851. doi: 10.7554/eLife.08851.


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

Iakovishina D, Janoueix-Lerosey I, Barillot E, Regnier M, Boeva V.

Bioinformatics. 2016 Apr 1;32(7):984-92. doi: 10.1093/bioinformatics/btv751. Epub 2016 Jan 6.


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

Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, Vert JP, Heard E, Dekker J, Barillot E.

Genome Biol. 2015 Dec 1;16:259. doi: 10.1186/s13059-015-0831-x.


Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration.

Cohen DP, Martignetti L, Robine S, Barillot E, Zinovyev A, Calzone L.

PLoS Comput Biol. 2015 Nov 3;11(11):e1004571. doi: 10.1371/journal.pcbi.1004571. eCollection 2015 Nov.


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

Czerwinska U, Calzone L, Barillot E, Zinovyev A.

BMC Syst Biol. 2015 Aug 14;9:46. doi: 10.1186/s12918-015-0189-4.


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

Kuperstein I, Bonnet E, Nguyen HA, Cohen D, Viara E, Grieco L, Fourquet S, Calzone L, Russo C, Kondratova M, Dutreix M, Barillot E, Zinovyev A.

Oncogenesis. 2015 Jul 20;4:e160. doi: 10.1038/oncsis.2015.19.


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

Dorel M, Barillot E, Zinovyev A, Kuperstein I.

Biochem Biophys Res Commun. 2015 Aug 21;464(2):386-91. doi: 10.1016/j.bbrc.2015.06.094. Epub 2015 Jun 15. Review.


Detection of miRNA regulatory effect on triple negative breast cancer transcriptome.

Martignetti L, Tesson B, Almeida A, Zinovyev A, Tucker GC, Dubois T, Barillot E.

BMC Genomics. 2015;16:S4. doi: 10.1186/1471-2164-16-S6-S4. Epub 2015 Jun 1.


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

Ciaudo C, Jay F, Okamoto I, Chen CJ, Sarazin A, Servant N, Barillot E, Heard E, Voinnet O.

PLoS Genet. 2015 May 14;11(5):e1005247. doi: 10.1371/journal.pgen.1005247. eCollection 2015 May. No abstract available.


Predicting genetic interactions from Boolean models of biological networks.

Calzone L, Barillot E, Zinovyev A.

Integr Biol (Camb). 2015 Aug;7(8):921-9. doi: 10.1039/c5ib00029g. Epub 2015 May 11.


NaviCell Web Service for network-based data visualization.

Bonnet E, Viara E, Kuperstein I, Calzone L, Cohen DP, Barillot E, Zinovyev A.

Nucleic Acids Res. 2015 Jul 1;43(W1):W560-5. doi: 10.1093/nar/gkv450. Epub 2015 May 9.


Combinatorial code governing cellular responses to complex stimuli.

Cappuccio A, Zollinger R, Schenk M, Walczak A, Servant N, Barillot E, Hupé P, Modlin RL, Soumelis V.

Nat Commun. 2015 Apr 21;6:6847. doi: 10.1038/ncomms7847.


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

Kuperstein I, Grieco L, Cohen DP, Thieffry D, Zinovyev A, Barillot E.

Mutagenesis. 2015 Mar;30(2):191-204. doi: 10.1093/mutage/geu078. Review.


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

Biton A, Bernard-Pierrot I, Lou Y, Krucker C, Chapeaublanc E, Rubio-Pérez C, López-Bigas N, Kamoun A, Neuzillet Y, Gestraud P, Grieco L, Rebouissou S, de Reyniès A, Benhamou S, Lebret T, Southgate J, Barillot E, Allory Y, Zinovyev A, Radvanyi F.

Cell Rep. 2014 Nov 20;9(4):1235-45. doi: 10.1016/j.celrep.2014.10.035. Epub 2014 Nov 13.


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

Chanrion M, Kuperstein I, Barrière C, El Marjou F, Cohen D, Vignjevic D, Stimmer L, Paul-Gilloteaux P, Bièche I, Tavares Sdos R, Boccia GF, Cacheux W, Meseure D, Fre S, Martignetti L, Legoix-Né P, Girard E, Fetler L, Barillot E, Louvard D, Zinovyev A, Robine S.

Nat Commun. 2014 Oct 8;5:5005. doi: 10.1038/ncomms6005.


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

Boeva V, Popova T, Lienard M, Toffoli S, Kamal M, Le Tourneau C, Gentien D, Servant N, Gestraud P, Rio Frio T, Hupé P, Barillot E, Laes JF.

Bioinformatics. 2014 Dec 15;30(24):3443-50. doi: 10.1093/bioinformatics/btu436. Epub 2014 Jul 12.


[Biological network modelling and precision medicine in oncology].

Calzone L, Kuperstein I, Cohen D, Grieco L, Bonnet E, Servant N, Hupé P, Zinovyev A, Barillot E.

Bull Cancer. 2014 Jun;101 Suppl 1:S18-21. doi: 10.1684/bdc.2014.1973. Review. French.


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

Servant N, Roméjon J, Gestraud P, La Rosa P, Lucotte G, Lair S, Bernard V, Zeitouni B, Coffin F, Jules-Clément G, Yvon F, Lermine A, Poullet P, Liva S, Pook S, Popova T, Barette C, Prud'homme F, Dick JG, Kamal M, Le Tourneau C, Barillot E, Hupé P.

Front Genet. 2014 May 30;5:152. doi: 10.3389/fgene.2014.00152. eCollection 2014. Review.


Developmental dynamics and disease potential of random monoallelic gene expression.

Gendrel AV, Attia M, Chen CJ, Diabangouaya P, Servant N, Barillot E, Heard E.

Dev Cell. 2014 Feb 24;28(4):366-80. doi: 10.1016/j.devcel.2014.01.016.

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