Cancer bioinformatics and systems biology (IRCM teams)

Team Leader  : Jacques Colinge
Institut de Recherche en
Cancérologie de Montpellier
Campus Val d’Aurelle
34298 Montpellier cedex 5

Tél. : 33 (0)4 67 61 23 92
Fax : 33 (0)4 67 61 37 87
Research topics

Our current research falls in three axes.


Axis 1: We infer biological networks by integrating several omics with reference intra- (signaling, transcription) and inter-cell (tumor microenvironment) interactions to find active functional modules. We apply such methods to different rare, aggressive tumor cohorts or metastases, which display resistance to frontline therapy. We try to unravel resistance mechanisms and find targets able to break resistance.


Axis 2: Network inference from perturbation experiments. We set up different projects where the detailed, quantitative and predictive analysis of a chosen biological network is required. Extending modular response analysis methods (Kholodenko), we infer weighted, directed networks.


Axis 3: Computational proteomics. Main focus at the moment is the development (with clinical partners) of a an innovative experiment/computational framework to determine protein turnover parameters in biological fluids in patients and in vivo. We have obtained very promising results in the CSF and plasma introducing a new mathematical model integrated with MS data processing and bioinformatics pipelines. We want to explore a new class of biomarkers related to abnormal clearance rates or passage across biological barriers such as blood-brain in disease, e.g. Alzheimer disease


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Recent Publications


Gene essentiality and synthetic lethality in haploid human cells.

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.

Science. 2015 Nov 27;350(6264):1092-6. doi: 10.1126/science.aac7557. Epub 2015 Oct 15.


Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling.

Huber KV, Olek KM, Müller AC, Tan CS, Bennett KL, Colinge* J, Superti-Furga* G.

Nat Methods. 2015 Nov;12(11):1055-7. doi: 10.1038/nmeth.3590. Epub 2015 Sep 21.


Experimental characterization of the human non-sequence-specific nucleic acid interactome.

Dürnberger G, Bürckstümmer T, Huber K, Giambruno R, Doerks T, Karayel E, Burkard TR, Kaupe I, Müller AC, Schönegger A, Ecker GF, Lohninger H, Bork P, Bennett KL, Superti-Furga G, Colinge J.

Genome Biol. 2013 Jul 31;14(7):R81. doi: 10.1186/gb-2013-14-7-r81.


Deconvolution of targeted protein-protein interaction maps.

Stukalov A, Superti-Furga G, Colinge J.

J Proteome Res. 2012 Aug 3;11(8):4102-9. doi: 10.1021/pr300137n. Epub 2012 Jul 10.


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