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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. 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.


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

Jubin C, Serero A, Loeillet S, Barillot E, Nicolas A.

G3 (Bethesda). 2014 Apr 16;4(4):707-15. doi: 10.1534/g3.113.009464.


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

Brito I, Hupé P, Neuvial P, Barillot E.

PLoS One. 2013 Dec 5;8(12):e81458. doi: 10.1371/journal.pone.0081458. eCollection 2013.


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. 2013 Nov;9(11):e1003791. doi: 10.1371/journal.pgen.1003791. Epub 2013 Nov 7.


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

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

BMC Syst Biol. 2013 Oct 7;7:100. doi: 10.1186/1752-0509-7-100.


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

Ashoor H, Hérault A, Kamoun A, Radvanyi F, Bajic VB, Barillot E, Boeva V.

Bioinformatics. 2013 Dec 1;29(23):2979-86. doi: 10.1093/bioinformatics/btt524. Epub 2013 Sep 9.


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

Boeva V, Jouannet S, Daveau R, Combaret V, Pierre-Eugène C, Cazes A, Louis-Brennetot C, Schleiermacher G, Ferrand S, Pierron G, Lermine A, Rio Frio T, Raynal V, Vassal G, Barillot E, Delattre O, Janoueix-Lerosey I.

PLoS One. 2013 Aug 26;8(8):e72182. doi: 10.1371/journal.pone.0072182. eCollection 2013.


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

Tarabeux J, Zeitouni B, Moncoutier V, Tenreiro H, Abidallah K, Lair S, Legoix-Né P, Leroy Q, Rouleau E, Golmard L, Barillot E, Stern MH, Rio-Frio T, Stoppa-Lyonnet D, Houdayer C.

Eur J Hum Genet. 2014 Apr;22(4):535-41. doi: 10.1038/ejhg.2013.181. Epub 2013 Aug 14.


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

Stoll G, Surdez D, Tirode F, Laud K, Barillot E, Zinovyev A, Delattre O.

Nucleic Acids Res. 2013 Oct;41(19):8853-71. doi: 10.1093/nar/gkt678. Epub 2013 Aug 8.


Practical use of BiNoM: a biological network manager software.

Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A.

Methods Mol Biol. 2013;1021:127-46. doi: 10.1007/978-1-62703-450-0_7.


From a biological hypothesis to the construction of a mathematical model.

Cohen D, Kuperstein I, Barillot E, Zinovyev A, Calzone L.

Methods Mol Biol. 2013;1021:107-25. doi: 10.1007/978-1-62703-450-0_6.


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

Maire V, Baldeyron C, Richardson M, Tesson B, Vincent-Salomon A, Gravier E, Marty-Prouvost B, De Koning L, Rigaill G, Dumont A, Gentien D, Barillot E, Roman-Roman S, Depil S, Cruzalegui F, Pierré A, Tucker GC, Dubois T.

PLoS One. 2013 May 20;8(5):e63712. doi: 10.1371/journal.pone.0063712. Print 2013.


Germline BAP1 mutations predispose to renal cell carcinomas.

Popova T, Hebert L, Jacquemin V, Gad S, Caux-Moncoutier V, Dubois-d'Enghien C, Richaudeau B, Renaudin X, Sellers J, Nicolas A, Sastre-Garau X, Desjardins L, Gyapay G, Raynal V, Sinilnikova OM, Andrieu N, Manié E, de Pauw A, Gesta P, Bonadona V, Maugard CM, Penet C, Avril MF, Barillot E, Cabaret O, Delattre O, Richard S, Caron O, Benfodda M, Hu HH, Soufir N, Bressac-de Paillerets B, Stoppa-Lyonnet D, Stern MH.

Am J Hum Genet. 2013 Jun 6;92(6):974-80. doi: 10.1016/j.ajhg.2013.04.012. Epub 2013 May 16.


OCSANA: optimal combinations of interventions from network analysis.

Vera-Licona P, Bonnet E, Barillot E, Zinovyev A.

Bioinformatics. 2013 Jun 15;29(12):1571-3. doi: 10.1093/bioinformatics/btt195. Epub 2013 Apr 26.

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