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Items: 1 to 20 of 52

1.

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.

Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, Sabedot TS, Malta TM, Pagnotta SM, Castiglioni I, Ceccarelli M, Bontempi G, Noushmehr H.

Nucleic Acids Res. 2015 Dec 23. pii: gkv1507. [Epub ahead of print]

2.

Using shRNA experiments to validate gene regulatory networks.

Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Quackenbush J, Haibe-Kains B.

Genom Data. 2015 Apr 1;4:123-6. doi: 10.1016/j.gdata.2015.03.011. eCollection 2015 Jun.

3.

Integrative Analysis with Monte Carlo Cross-Validation Reveals miRNAs Regulating Pathways Cross-Talk in Aggressive Breast Cancer.

Colaprico A, Cava C, Bertoli G, Bontempi G, Castiglioni I.

Biomed Res Int. 2015;2015:831314. doi: 10.1155/2015/831314. Epub 2015 Jul 9.

4.

Ocean plankton. Determinants of community structure in the global plankton interactome.

Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans coordinators, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J.

Science. 2015 May 22;348(6237):1262073. doi: 10.1126/science.1262073.

PMID:
25999517
5.

Relevance of different prior knowledge sources for inferring gene interaction networks.

Olsen C, Bontempi G, Emmert-Streib F, Quackenbush J, Haibe-Kains B.

Front Genet. 2014 Jun 24;5:177. doi: 10.3389/fgene.2014.00177. eCollection 2014.

6.

Inference and validation of predictive gene networks from biomedical literature and gene expression data.

Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Haibe-Kains B, Quackenbush J.

Genomics. 2014 May-Jun;103(5-6):329-36. doi: 10.1016/j.ygeno.2014.03.004. Epub 2014 Mar 29.

7.

Temporal profiling of cytokine-induced genes in pancreatic β-cells by meta-analysis and network inference.

Lopes M, Kutlu B, Miani M, Bang-Berthelsen CH, Størling J, Pociot F, Goodman N, Hood L, Welsh N, Bontempi G, Eizirik DL.

Genomics. 2014 Apr;103(4):264-75. doi: 10.1016/j.ygeno.2013.12.007. Epub 2014 Jan 24.

PMID:
24462878
8.

Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data.

Lopes M, Bontempi G.

Front Genet. 2013 Dec 24;4:303. doi: 10.3389/fgene.2013.00303. eCollection 2013.

9.

Genome-wide gene expression profiling to predict resistance to anthracyclines in breast cancer patients.

Haibe-Kains B, Desmedt C, Di Leo A, Azambuja E, Larsimont D, Selleslags J, Delaloge S, Duhem C, Kains JP, Carly B, Maerevoet M, Vindevoghel A, Rouas G, Lallemand F, Durbecq V, Cardoso F, Salgado R, Rovere R, Bontempi G, Michiels S, Buyse M, Nogaret JM, Qi Y, Symmans F, Pusztai L, D'Hondt V, Piccart-Gebhart M, Sotiriou C.

Genom Data. 2013 Oct 1;1:7-10. doi: 10.1016/j.gdata.2013.09.001. eCollection 2013 Dec.

10.

Association between the PNPLA3 (rs738409 C>G) variant and hepatocellular carcinoma: Evidence from a meta-analysis of individual participant data.

Trépo E, Nahon P, Bontempi G, Valenti L, Falleti E, Nischalke HD, Hamza S, Corradini SG, Burza MA, Guyot E, Donati B, Spengler U, Hillon P, Toniutto P, Henrion J, Franchimont D, Devière J, Mathurin P, Moreno C, Romeo S, Deltenre P.

Hepatology. 2014 Jun;59(6):2170-7. doi: 10.1002/hep.26767. Epub 2014 Apr 25.

PMID:
24114809
11.

A comprehensive overview of Infinium HumanMethylation450 data processing.

Dedeurwaerder S, Defrance M, Bizet M, Calonne E, Bontempi G, Fuks F.

Brief Bioinform. 2014 Nov;15(6):929-41. doi: 10.1093/bib/bbt054. Epub 2013 Aug 29. Review.

12.

mRMRe: an R package for parallelized mRMR ensemble feature selection.

De Jay N, Papillon-Cavanagh S, Olsen C, El-Hachem N, Bontempi G, Haibe-Kains B.

Bioinformatics. 2013 Sep 15;29(18):2365-8. doi: 10.1093/bioinformatics/btt383. Epub 2013 Jul 3.

13.

[A technological platform for cerebral palsy - the ICT4Rehab project].

Van Sint Jan S, Wermenbol V, Van Bogaert P, Desloovere K, Degelaen M, Dan B, Salvia P, Ortibus E, Bonnechère B, Le Borgne YA, Bontempi G, Vansummeren S, Sholukha V, Moiseev F, Rooze M.

Med Sci (Paris). 2013 May;29(5):529-36. doi: 10.1051/medsci/2013295017. Epub 2013 May 28. French.

14.

Comparison and validation of genomic predictors for anticancer drug sensitivity.

Papillon-Cavanagh S, De Jay N, Hachem N, Olsen C, Bontempi G, Aerts HJ, Quackenbush J, Haibe-Kains B.

J Am Med Inform Assoc. 2013 Jul-Aug;20(4):597-602. doi: 10.1136/amiajnl-2012-001442. Epub 2013 Jan 26.

15.

D-peaks: a visual tool to display ChIP-seq peaks along the genome.

Brohée S, Bontempi G.

Transcription. 2012 Sep-Oct;3(5):255-9. doi: 10.4161/trns.22457. Epub 2012 Sep 1.

16.

A three-gene model to robustly identify breast cancer molecular subtypes.

Haibe-Kains B, Desmedt C, Loi S, Culhane AC, Bontempi G, Quackenbush J, Sotiriou C.

J Natl Cancer Inst. 2012 Feb 22;104(4):311-25. doi: 10.1093/jnci/djr545. Epub 2012 Jan 18.

17.

Multiple-input multiple-output causal strategies for gene selection.

Bontempi G, Haibe-Kains B, Desmedt C, Sotiriou C, Quackenbush J.

BMC Bioinformatics. 2011 Nov 25;12:458. doi: 10.1186/1471-2105-12-458.

18.

Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks.

Haibe-Kains B, Olsen C, Djebbari A, Bontempi G, Correll M, Bouton C, Quackenbush J.

Nucleic Acids Res. 2012 Jan;40(Database issue):D866-75. doi: 10.1093/nar/gkr1050. Epub 2011 Nov 16.

19.

Multifactorial approach to predicting resistance to anthracyclines.

Desmedt C, Di Leo A, de Azambuja E, Larsimont D, Haibe-Kains B, Selleslags J, Delaloge S, Duhem C, Kains JP, Carly B, Maerevoet M, Vindevoghel A, Rouas G, Lallemand F, Durbecq V, Cardoso F, Salgado R, Rovere R, Bontempi G, Michiels S, Buyse M, Nogaret JM, Qi Y, Symmans F, Pusztai L, D'Hondt V, Piccart-Gebhart M, Sotiriou C.

J Clin Oncol. 2011 Apr 20;29(12):1578-86. doi: 10.1200/JCO.2010.31.2231. Epub 2011 Mar 21.

20.

STAT1 is a master regulator of pancreatic {beta}-cell apoptosis and islet inflammation.

Moore F, Naamane N, Colli ML, Bouckenooghe T, Ortis F, Gurzov EN, Igoillo-Esteve M, Mathieu C, Bontempi G, Thykjaer T, Ørntoft TF, Eizirik DL.

J Biol Chem. 2011 Jan 14;286(2):929-41. doi: 10.1074/jbc.M110.162131. Epub 2010 Oct 27.

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