Cancer bioinformatics and systems biology

 Jacques COLINGE

 IRCM - U 1194

 208 avenue des Apothicaires, 34298 Montpellier

Phone: +33 4 67 61 23 92

Email: jacques.colinge@inserm.fr

Website

Functional analysis of complex omics datasets through systems or network biology approaches with applications in cancer research: personalized medicine and biomarkers, translational cancer research, drug mechanism of action, drug side effect inference and repurposing, combined therapies, and cancer pathways modeling at multiple scales. We also have projects in innate immunology.

We mainly contribute to the fields above through the development of computational methods involving network science, basic mathematical modeling, and data integration. The team also has long standing experience in computational proteomics, i.e. algorithms to analyze mass spectrometry data.

Keywords: systems biology, network biology, bioinformatics, computational proteomics

Main publications

• Blomen VA, Májek P, Jae LT, Bigenzahn JW, Nieuwenhuis J, Staring J, Sacco R, van Diemen FR, Olk N, Stukalov A, Marceau C, Janssen H, Carette JE, Bennett KL, Colinge J*, Superti-Furga G*, Brummelkamp TR*. Gene essentiality and synthetic lethality in haploid human cells. Science, 2015, 350:1092-1096. *corresponding
• Muellner MK, Mair B, Ibrahim Y, Kerzendorfer C, Lechtermann H, Trefzer C, Klepsch F, Müller AC, Leitner E, Macho-Maschler S, Superti-Furga G, Bennett KL, Baselga J, Rix U, Kubicek S, Colinge J, Serra V, Nijman SM. Targeting a cell state common to triple-negative breast cancers. Mol Syst Biol, 2015, 11(2):789.
• Rix1 U#, Colinge J#, Blatt K, Gridling M, Remsing Rix LL, Parapatics K, Cerny-Reiterer S, Burkard TR, Jäger U, Melo JV, Bennett KL, Valent P, Superti-Furga G: A target-disease network model of second-generation BCR-ABL inhibitor action in Ph+ ALL, PLoS ONE, 2013, 8:e77155. #Equal contribution.
• Duernberger G, Burckstummer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Muller AC, Schonegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, Colinge J: Experimental characterization of the human non-sequence-specific nucleic acid interactome, Genome Biol, 2013, 14:R81.
• Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, Al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin ZY, Badillo BG, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga G, Colinge J, Heck AJ, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras AC, Nesvizhskii AI: The CRAPome: a contaminant repository for affinity purification-mass spectrometry data, Nat Methods, 2013, 10:730-736.
• Pichlmair A, Kandasamy K, Alvisi G, Mulhern O, Sacco R, Habjan M, Binder M, Stefanovic A, Eberle CA, Goncalves A, Bürckstümmer T, Müller A, Fauster A, Holze C, Lindsten K, Goodbourn S, Kochs G, Weber F, Bartenschlager R, Bowie AG, Bennett KL,  Colinge J, Superti-Furga G: Viral immune modulators perturb the human molecular network by common and unique strategies, Nature, 2012, 487:486-90.
• Stukalov A, Superti-Furga G, Colinge J: Deconvolution of targeted protein-protein interaction maps. J Proteome Res, 2012, 11:4102-9.
• Breitwieser FP, Muller A, Dayon L, Kocher T, Hainard A, Pichler P, Schmidt-Erfurth U, Superti-Furga G, Sanchez JC, Mechtler K, Bennett KL, Colinge J: General Statistical Modeling of Data from Protein Relative Expression Isobaric Tags. J Proteome Res 2011, 10(6):2758-2766.
• Colinge J*, Chiappe D, Lagache S, Moniatte M, Bougueleret L: Differential proteomics via probabilistic peptide identification scores. Anal Chem 2005, 77(2):596-606. *corresponding
• Colinge J*, Masselot A, Giron M, Dessingy T, Magnin J: OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics 2003, 3(8):1454-1463. *corresponding