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Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C.

Ay F, Vu TH, Zeitz MJ, Varoquaux N, Carette JE, Vert JP, Hoffman AR, Noble WS.

BMC Genomics. 2015 Feb 25;16:121. doi: 10.1186/s12864-015-1236-7.


A Bayesian active learning strategy for sequential experimental design in systems biology.

Pauwels E, Lajaunie C, Vert JP.

BMC Syst Biol. 2014 Sep 26;8(1):102. [Epub ahead of print]


Epigenomic alterations in breast carcinoma from primary tumor to locoregional recurrences.

Moarii M, Pinheiro A, Sigal-Zafrani B, Fourquet A, Caly M, Servant N, Stoven V, Vert JP, Reyal F.

PLoS One. 2014 Aug 6;9(8):e103986. doi: 10.1371/journal.pone.0103986. eCollection 2014.


The Wnt receptor Ryk reduces neuronal and cell survival capacity by repressing FOXO activity during the early phases of mutant huntingtin pathogenicity.

Tourette C, Farina F, Vazquez-Manrique RP, Orfila AM, Voisin J, Hernandez S, Offner N, Parker JA, Menet S, Kim J, Lyu J, Choi SH, Cormier K, Edgerly CK, Bordiuk OL, Smith K, Louise A, Halford M, Stacker S, Vert JP, Ferrante RJ, Lu W, Neri C.

PLoS Biol. 2014 Jun 24;12(6):e1001895. doi: 10.1371/journal.pbio.1001895. eCollection 2014 Jun.


A statistical approach for inferring the 3D structure of the genome.

Varoquaux N, Ay F, Noble WS, Vert JP.

Bioinformatics. 2014 Jun 15;30(12):i26-33. doi: 10.1093/bioinformatics/btu268.


Efficient RNA isoform identification and quantification from RNA-Seq data with network flows.

Bernard E, Jacob L, Mairal J, Vert JP.

Bioinformatics. 2014 Sep 1;30(17):2447-55. doi: 10.1093/bioinformatics/btu317. Epub 2014 May 9.


Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression.

Ay F, Bunnik EM, Varoquaux N, Bol SM, Prudhomme J, Vert JP, Noble WS, Le Roch KG.

Genome Res. 2014 Jun;24(6):974-88. doi: 10.1101/gr.169417.113. Epub 2014 Mar 26.


SegAnnDB: interactive Web-based genomic segmentation.

Hocking TD, Boeva V, Rigaill G, Schleiermacher G, Janoueix-Lerosey I, Delattre O, Richer W, Bourdeaut F, Suguro M, Seto M, Bach F, Vert JP.

Bioinformatics. 2014 Jun 1;30(11):1539-46. doi: 10.1093/bioinformatics/btu072. Epub 2014 Feb 3.


Pax3 and Zic1 trigger the early neural crest gene regulatory network by the direct activation of multiple key neural crest specifiers.

Plouhinec JL, Roche DD, Pegoraro C, Figueiredo AL, Maczkowiak F, Brunet LJ, Milet C, Vert JP, Pollet N, Harland RM, Monsoro-Burq AH.

Dev Biol. 2014 Feb 15;386(2):461-72. doi: 10.1016/j.ydbio.2013.12.010. Epub 2013 Dec 17.


Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks.

Zhao Y, Tamura T, Akutsu T, Vert JP.

Bioinformatics. 2013 Sep 1;29(17):2178-85. doi: 10.1093/bioinformatics/btt364. Epub 2013 Jul 4.


Learning smoothing models of copy number profiles using breakpoint annotations.

Hocking TD, Schleiermacher G, Janoueix-Lerosey I, Boeva V, Cappo J, Delattre O, Bach F, Vert JP.

BMC Bioinformatics. 2013 May 22;14:164. doi: 10.1186/1471-2105-14-164.


Supervised inference of gene regulatory networks from positive and unlabeled examples.

Mordelet F, Vert JP.

Methods Mol Biol. 2013;939:47-58. doi: 10.1007/978-1-62703-107-3_5.


TIGRESS: Trustful Inference of Gene REgulation using Stability Selection.

Haury AC, Mordelet F, Vera-Licona P, Vert JP.

BMC Syst Biol. 2012 Nov 22;6:145. doi: 10.1186/1752-0509-6-145.


DSIR: assessing the design of highly potent siRNA by testing a set of cancer-relevant target genes.

Filhol O, Ciais D, Lajaunie C, Charbonnier P, Foveau N, Vert JP, Vandenbrouck Y.

PLoS One. 2012;7(10):e48057. doi: 10.1371/journal.pone.0048057. Epub 2012 Oct 30.


Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants.

Houdayer C, Caux-Moncoutier V, Krieger S, Barrois M, Bonnet F, Bourdon V, Bronner M, Buisson M, Coulet F, Gaildrat P, Lefol C, Léone M, Mazoyer S, Muller D, Remenieras A, Révillion F, Rouleau E, Sokolowska J, Vert JP, Lidereau R, Soubrier F, Sobol H, Sevenet N, Bressac-de Paillerets B, Hardouin A, Tosi M, Sinilnikova OM, Stoppa-Lyonnet D.

Hum Mutat. 2012 Aug;33(8):1228-38. doi: 10.1002/humu.22101. Epub 2012 May 11.


Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons.

Lejeune FX, Mesrob L, Parmentier F, Bicep C, Vazquez-Manrique RP, Parker JA, Vert JP, Tourette C, Neri C.

BMC Genomics. 2012 Mar 13;13:91. doi: 10.1186/1471-2164-13-91.


The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures.

Haury AC, Gestraud P, Vert JP.

PLoS One. 2011;6(12):e28210. doi: 10.1371/journal.pone.0028210. Epub 2011 Dec 21.


ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples.

Mordelet F, Vert JP.

BMC Bioinformatics. 2011 Oct 6;12:389. doi: 10.1186/1471-2105-12-389.


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

Boeva V, Zinovyev A, Bleakley K, Vert JP, Janoueix-Lerosey I, Delattre O, Barillot E.

Bioinformatics. 2011 Jan 15;27(2):268-9. doi: 10.1093/bioinformatics/btq635. Epub 2010 Nov 15.

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