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Items: 1 to 50 of 67

1.

Comprehensive identification of long noncoding RNAs in colorectal cancer.

James de Bony E, Bizet M, Van Grembergen O, Hassabi B, Calonne E, Putmans P, Bontempi G, Fuks F.

Oncotarget. 2018 Jun 12;9(45):27605-27629. doi: 10.18632/oncotarget.25218. eCollection 2018 Jun 12.

2.

In-Silico Integration Approach to Identify a Key miRNA Regulating a Gene Network in Aggressive Prostate Cancer.

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

Int J Mol Sci. 2018 Mar 19;19(3). pii: E910. doi: 10.3390/ijms19030910.

3.

Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis.

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

BMC Genomics. 2018 Jan 6;19(1):25. doi: 10.1186/s12864-017-4423-x.

4.

Combination of Gene Expression Signature and Model for End-Stage Liver Disease Score Predicts Survival of Patients With Severe Alcoholic Hepatitis.

Trépo E, Goossens N, Fujiwara N, Song WM, Colaprico A, Marot A, Spahr L, Demetter P, Sempoux C, Im GY, Saldarriaga J, Gustot T, Devière J, Thung SN, Minsart C, Sersté T, Bontempi G, Abdelrahman K, Henrion J, Degré D, Lucidi V, Rubbia-Brandt L, Nair VD, Moreno C, Deltenre P, Hoshida Y, Franchimont D.

Gastroenterology. 2018 Mar;154(4):965-975. doi: 10.1053/j.gastro.2017.10.048. Epub 2017 Nov 20.

PMID:
29158192
5.

Credit Card Fraud Detection: A Realistic Modeling and a Novel Learning Strategy.

Dal Pozzolo A, Boracchi G, Caelen O, Alippi C, Bontempi G.

IEEE Trans Neural Netw Learn Syst. 2018 Aug;29(8):3784-3797. doi: 10.1109/TNNLS.2017.2736643. Epub 2017 Sep 14.

PMID:
28920909
6.

Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability.

Reggiani C, Coppens S, Sekhara T, Dimov I, Pichon B, Lufin N, Addor MC, Belligni EF, Digilio MC, Faletra F, Ferrero GB, Gerard M, Isidor B, Joss S, Niel-Bütschi F, Perrone MD, Petit F, Renieri A, Romana S, Topa A, Vermeesch JR, Lenaerts T, Casimir G, Abramowicz M, Bontempi G, Vilain C, Deconinck N, Smits G.

Genome Med. 2017 Jul 19;9(1):67. doi: 10.1186/s13073-017-0452-y.

7.

DNA methylation-based immune response signature improves patient diagnosis in multiple cancers.

Jeschke J, Bizet M, Desmedt C, Calonne E, Dedeurwaerder S, Garaud S, Koch A, Larsimont D, Salgado R, Van den Eynden G, Willard Gallo K, Bontempi G, Defrance M, Sotiriou C, Fuks F.

J Clin Invest. 2017 Aug 1;127(8):3090-3102. doi: 10.1172/JCI91095. Epub 2017 Jul 17.

8.

Role of muscarinic receptors in the contraction of jejunal smooth muscle in the horse: An in vitro study.

Menozzi A, Pozzoli C, Poli E, Bontempi G, Serventi P, Meucci V, Intorre L, Bertini S.

Res Vet Sci. 2017 Dec;115:387-392. doi: 10.1016/j.rvsc.2017.07.012. Epub 2017 Jul 11.

PMID:
28711697
9.

CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization.

Xu T, Le TD, Liu L, Su N, Wang R, Sun B, Colaprico A, Bontempi G, Li J.

Bioinformatics. 2017 Oct 1;33(19):3131-3133. doi: 10.1093/bioinformatics/btx378.

PMID:
28605519
10.

Study of Meta-analysis strategies for network inference using information-theoretic approaches.

Pham NC, Haibe-Kains B, Bellot P, Bontempi G, Meyer PE.

BioData Min. 2017 May 6;10:15. doi: 10.1186/s13040-017-0136-6. eCollection 2017.

11.

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages.

Silva TC, Colaprico A, Olsen C, D'Angelo F, Bontempi G, Ceccarelli M, Noushmehr H.

Version 2. F1000Res. 2016 Jun 29 [revised 2016 Jan 1];5:1542. doi: 10.12688/f1000research.8923.2. eCollection 2016.

12.

How interacting pathways are regulated by miRNAs in breast cancer subtypes.

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

BMC Bioinformatics. 2016 Nov 8;17(Suppl 12):348. doi: 10.1186/s12859-016-1196-1.

13.

SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data.

Cava C, Colaprico A, Bertoli G, Graudenzi A, Silva TC, Olsen C, Noushmehr H, Bontempi G, Mauri G, Castiglioni I.

Int J Mol Sci. 2017 Jan 27;18(2). pii: E274. doi: 10.3390/ijms18020274.

14.

Portraying breast cancers with long noncoding RNAs.

Van Grembergen O, Bizet M, de Bony EJ, Calonne E, Putmans P, Brohée S, Olsen C, Guo M, Bontempi G, Sotiriou C, Defrance M, Fuks F.

Sci Adv. 2016 Sep 2;2(9):e1600220. doi: 10.1126/sciadv.1600220. eCollection 2016 Sep.

15.

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. 2016 May 5;44(8):e71. doi: 10.1093/nar/gkv1507. Epub 2015 Dec 23.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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
25.

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.

26.

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.

PMID:
23825369
27.

[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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

PMID:
21422418
34.

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.

35.

Long-term in vitro treatment of human glioblastoma cells with temozolomide increases resistance in vivo through up-regulation of GLUT transporter and aldo-keto reductase enzyme AKR1C expression.

Le Calvé B, Rynkowski M, Le Mercier M, Bruyère C, Lonez C, Gras T, Haibe-Kains B, Bontempi G, Decaestecker C, Ruysschaert JM, Kiss R, Lefranc F.

Neoplasia. 2010 Sep;12(9):727-39. Erratum in: Neoplasia. 2011 Sep;13(9):5 p following 886.

36.

A fuzzy gene expression-based computational approach improves breast cancer prognostication.

Haibe-Kains B, Desmedt C, Rothé F, Piccart M, Sotiriou C, Bontempi G.

Genome Biol. 2010;11(2):R18. doi: 10.1186/gb-2010-11-2-r18. Epub 2010 Feb 15.

37.

Long-term temozolomide treatment induces marked amino metabolism modifications and an increase in TMZ sensitivity in Hs683 oligodendroglioma cells.

Lamoral-Theys D, Le Mercier M, Le Calvé B, Rynkowski MA, Bruyère C, Decaestecker C, Haibe-Kains B, Bontempi G, Dubois J, Lefranc F, Kiss R.

Neoplasia. 2010 Jan;12(1):69-79.

38.

Galectin 1 proangiogenic and promigratory effects in the Hs683 oligodendroglioma model are partly mediated through the control of BEX2 expression.

Le Mercier M, Fortin S, Mathieu V, Roland I, Spiegl-Kreinecker S, Haibe-Kains B, Bontempi G, Decaestecker C, Berger W, Lefranc F, Kiss R.

Neoplasia. 2009 May;11(5):485-96.

39.

On the impact of entropy estimation on transcriptional regulatory network inference based on mutual information.

Olsen C, Meyer PE, Bontempi G.

EURASIP J Bioinform Syst Biol. 2009:308959. doi: 10.1155/2009/308959. Epub 2009 Jan 12.

40.
41.

minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information.

Meyer PE, Lafitte F, Bontempi G.

BMC Bioinformatics. 2008 Oct 29;9:461. doi: 10.1186/1471-2105-9-461.

42.

Comparison of prognostic gene expression signatures for breast cancer.

Haibe-Kains B, Desmedt C, Piette F, Buyse M, Cardoso F, Van't Veer L, Piccart M, Bontempi G, Sotiriou C.

BMC Genomics. 2008 Aug 21;9:394. doi: 10.1186/1471-2164-9-394.

43.

Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes.

Desmedt C, Haibe-Kains B, Wirapati P, Buyse M, Larsimont D, Bontempi G, Delorenzi M, Piccart M, Sotiriou C.

Clin Cancer Res. 2008 Aug 15;14(16):5158-65. doi: 10.1158/1078-0432.CCR-07-4756.

44.

Distributed Principal Component Analysis for Wireless Sensor Networks.

Le Borgne YA, Raybaud S, Bontempi G.

Sensors (Basel). 2008 Aug 11;8(8):4821-4850.

45.

A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?

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

Bioinformatics. 2008 Oct 1;24(19):2200-8. doi: 10.1093/bioinformatics/btn374. Epub 2008 Jul 17.

46.

UNBS5162, a novel naphthalimide that decreases CXCL chemokine expression in experimental prostate cancers.

Mijatovic T, Mahieu T, Bruyère C, De Nève N, Dewelle J, Simon G, Dehoux MJ, van der Aar E, Haibe-Kains B, Bontempi G, Decaestecker C, Van Quaquebeke E, Darro F, Kiss R.

Neoplasia. 2008 Jun;10(6):573-86.

47.

Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen.

Loi S, Haibe-Kains B, Desmedt C, Wirapati P, Lallemand F, Tutt AM, Gillet C, Ellis P, Ryder K, Reid JF, Daidone MG, Pierotti MA, Berns EM, Jansen MP, Foekens JA, Delorenzi M, Bontempi G, Piccart MJ, Sotiriou C.

BMC Genomics. 2008 May 22;9:239. doi: 10.1186/1471-2164-9-239.

48.

Nucleolus and c-Myc: potential targets of cardenolide-mediated antitumor activity.

Mijatovic T, De Nève N, Gailly P, Mathieu V, Haibe-Kains B, Bontempi G, Lapeira J, Decaestecker C, Facchini V, Kiss R.

Mol Cancer Ther. 2008 May;7(5):1285-96. doi: 10.1158/1535-7163.MCT-07-2241.

49.

Knocking down galectin 1 in human hs683 glioblastoma cells impairs both angiogenesis and endoplasmic reticulum stress responses.

Le Mercier M, Mathieu V, Haibe-Kains B, Bontempi G, Mijatovic T, Decaestecker C, Kiss R, Lefranc F.

J Neuropathol Exp Neurol. 2008 May;67(5):456-69. doi: 10.1097/NEN.0b013e318170f892.

PMID:
18431251
50.

Information-theoretic inference of large transcriptional regulatory networks.

Meyer PE, Kontos K, Lafitte F, Bontempi G.

EURASIP J Bioinform Syst Biol. 2007:79879. doi: 10.1155/2007/79879.

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