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Items: 1 to 50 of 73

1.

LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes.

Collier O, Stoven V, Vert JP.

PLoS Comput Biol. 2019 Sep 30;15(9):e1007381. doi: 10.1371/journal.pcbi.1007381. eCollection 2019 Sep.

2.

Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics.

Menegaux R, Vert JP.

J Comput Biol. 2019 Jun;26(6):509-518. doi: 10.1089/cmb.2018.0174. Epub 2019 Feb 19.

PMID:
30785347
3.

Publisher Correction: A general and flexible method for signal extraction from single-cell RNA-seq data.

Risso D, Perraudeau F, Gribkova S, Dudoit S, Vert JP.

Nat Commun. 2019 Feb 4;10(1):646. doi: 10.1038/s41467-019-08614-2.

4.

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.

5.

MetaVW: Large-Scale Machine Learning for Metagenomics Sequence Classification.

Vervier K, Mahé P, Vert JP.

Methods Mol Biol. 2018;1807:9-20. doi: 10.1007/978-1-4939-8561-6_2.

PMID:
30030800
6.

Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages.

Bunnik EM, Cook KB, Varoquaux N, Batugedara G, Prudhomme J, Cort A, Shi L, Andolina C, Ross LS, Brady D, Fidock DA, Nosten F, Tewari R, Sinnis P, Ay F, Vert JP, Noble WS, Le Roch KG.

Nat Commun. 2018 May 15;9(1):1910. doi: 10.1038/s41467-018-04295-5.

7.

Improving prediction of heterodimeric protein complexes using combination with pairwise kernel.

Ruan P, Hayashida M, Akutsu T, Vert JP.

BMC Bioinformatics. 2018 Feb 19;19(Suppl 1):39. doi: 10.1186/s12859-018-2017-5.

8.

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications.

Van den Berge K, Perraudeau F, Soneson C, Love MI, Risso D, Vert JP, Robinson MD, Dudoit S, Clement L.

Genome Biol. 2018 Feb 26;19(1):24. doi: 10.1186/s13059-018-1406-4.

9.

A general and flexible method for signal extraction from single-cell RNA-seq data.

Risso D, Perraudeau F, Gribkova S, Dudoit S, Vert JP.

Nat Commun. 2018 Jan 18;9(1):284. doi: 10.1038/s41467-017-02554-5. Erratum in: Nat Commun. 2019 Feb 4;10(1):646.

10.

A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates.

Plouhinec JL, Medina-Ruiz S, Borday C, Bernard E, Vert JP, Eisen MB, Harland RM, Monsoro-Burq AH.

PLoS Biol. 2017 Oct 19;15(10):e2004045. doi: 10.1371/journal.pbio.2004045. eCollection 2017 Oct.

11.

The Kendall and Mallows Kernels for Permutations.

Jiao Y, Vert JP, Yunlong Jiao, Vert JP, Jiao Y, Vert JP.

IEEE Trans Pattern Anal Mach Intell. 2018 Jul;40(7):1755-1769. doi: 10.1109/TPAMI.2017.2719680. Epub 2017 Oct 5.

PMID:
28981406
12.

Kernel Multitask Regression for Toxicogenetics.

Bernard E, Jiao Y, Scornet E, Stoven V, Walter T, Vert JP.

Mol Inform. 2017 Oct;36(10). doi: 10.1002/minf.201700053. Epub 2017 Sep 26.

PMID:
28949440
13.

NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis.

Le Morvan M, Zinovyev A, Vert JP.

PLoS Comput Biol. 2017 Jun 26;13(6):e1005573. doi: 10.1371/journal.pcbi.1005573. eCollection 2017 Jun.

14.

Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium, Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Bridges SL Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM.

Nat Commun. 2016 Oct 10;7:13205. doi: 10.1038/ncomms13205. No abstract available.

15.

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.

Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VSK, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium, Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TWJ, Kurreeman F, Allaart CF, Louis Bridges S Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM.

Nat Commun. 2016 Aug 23;7:12460. doi: 10.1038/ncomms12460. Erratum in: Nat Commun. 2016 Oct 10;7:13205.

16.

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.

17.

Large-scale machine learning for metagenomics sequence classification.

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

Bioinformatics. 2016 Apr 1;32(7):1023-32. doi: 10.1093/bioinformatics/btv683. Epub 2015 Nov 20.

18.

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

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

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

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.
26.

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]

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

PMID:
23192540
37.

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.

38.

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.

39.

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.

PMID:
22505045
40.

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.

41.

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.

42.

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.

43.

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.

44.

Large-scale prediction of protein-protein interactions from structures.

Hue M, Riffle M, Vert JP, Noble WS.

BMC Bioinformatics. 2010 Mar 18;11:144. doi: 10.1186/1471-2105-11-144.

45.

A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction.

Hoffmann B, Zaslavskiy M, Vert JP, Stoven V.

BMC Bioinformatics. 2010 Feb 22;11:99. doi: 10.1186/1471-2105-11-99.

46.

A path following algorithm for the graph matching problem.

Zaslavskiy M, Bach F, Vert JP.

IEEE Trans Pattern Anal Mach Intell. 2009 Dec;31(12):2227-42. doi: 10.1109/TPAMI.2008.245.

PMID:
19834143
47.

Global alignment of protein-protein interaction networks by graph matching methods.

Zaslavskiy M, Bach F, Vert JP.

Bioinformatics. 2009 Jun 15;25(12):i259-67. doi: 10.1093/bioinformatics/btp196.

48.

Virtual screening with support vector machines and structure kernels.

Mahé P, Vert JP.

Comb Chem High Throughput Screen. 2009 May;12(4):409-23. Review.

49.

Machine learning for in silico virtual screening and chemical genomics: new strategies.

Vert JP, Jacob L.

Comb Chem High Throughput Screen. 2008 Sep;11(8):677-85. Review.

50.

Virtual screening of GPCRs: an in silico chemogenomics approach.

Jacob L, Hoffmann B, Stoven V, Vert JP.

BMC Bioinformatics. 2008 Sep 6;9:363. doi: 10.1186/1471-2105-9-363.

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