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Items: 1 to 20 of 58


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.


Large-scale machine learning for metagenomics sequence classification.

Vervier K, Mahé P, Tournoud M, Veyrieras JB, Vert JP.

Bioinformatics. 2015 Nov 20. pii: btv683. [Epub ahead of print]


Changes in correlation between promoter methylation and gene expression in cancer.

Moarii M, Boeva V, Vert JP, Reyal F.

BMC Genomics. 2015 Oct 28;16(1):873. doi: 10.1186/s12864-015-1994-2.


Integrative DNA methylation and gene expression analysis to assess the universality of the CpG island methylator phenotype.

Moarii M, Reyal F, Vert JP.

Hum Genomics. 2015 Oct 13;9:26. doi: 10.1186/s40246-015-0048-9.


Φ-score: A cell-to-cell phenotypic scoring method for sensitive and selective hit discovery in cell-based assays.

Guyon L, Lajaunie C, Fer F, Bhajun R, Sulpice E, Pinna G, Campalans A, Radicella JP, Rouillier P, Mary M, Combe S, Obeid P, Vert JP, Gidrol X.

Sci Rep. 2015 Sep 18;5:14221. doi: 10.1038/srep14221.


A convex formulation for joint RNA isoform detection and quantification from multiple RNA-seq samples.

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

BMC Bioinformatics. 2015 Aug 19;16:262. doi: 10.1186/s12859-015-0695-9.


A generic methodological framework for studying single cell motility in high-throughput time-lapse data.

Schoenauer Sebag A, Plancade S, Raulet-Tomkiewicz C, Barouki R, Vert JP, Walter T.

Bioinformatics. 2015 Jun 15;31(12):i320-8. doi: 10.1093/bioinformatics/btv225.


Accurate identification of centromere locations in yeast genomes using Hi-C.

Varoquaux N, Liachko I, Ay F, Burton JN, Shendure J, Dunham MJ, Vert JP, Noble WS.

Nucleic Acids Res. 2015 Jun 23;43(11):5331-9. doi: 10.1093/nar/gkv424. Epub 2015 May 4.


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.

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