U900 – Bioinformatics, Biostatistics, Epidemiology and Computational Systems. Biology of Cancer

Teams in this computational unit study several aspects of the cancer pathology through observation of the underlying molecular and cellular mechanisms: initiation (etiology, through the modelling of gene and environment interaction), development and tumor progression (inferring and modelling the gene and protein networks involved, analysis of phenotypes through bioimaging), and improvement in therapeutic strategies (diagnosis, prognosis, design and analysis of clinical trials, identification of therapeutic targets, virtual selection of therapeutic molecules).

Research projects are conducted in close collaboration with biologists and clinicians and always involved a mix of experimental and theoretical approaches, in iterative cycles from the wet biology to the mathematical model and back, which ultimately lead to validated and thus predictive models. They take advantage of new high throughput biological technologies at both the molecular and cellular levels (spectrometry, microarrays, high-throughput cellular phenotyping, deep sequencing) and use state-of-the-art and innovative methods of data integration and systems biology, statistical analysis, high dimension statistical learning, study of complexity, network modeling, virtual screening and bioimaging.

 

Key publications

Year of publication 2017

Maud Borensztein, Laurène Syx, Katia Ancelin, Patricia Diabangouaya, Christel Picard, Tao Liu, Jun-Bin Liang, Ivaylo Vassilev, Rafael Galupa, Nicolas Servant, Emmanuel Barillot, Azim Surani, Chong-Jian Chen, Edith Heard (2017 Jan 31)

Xist-dependent imprinted X inactivation and the early developmental consequences of its failure.

Nature structural & molecular biology : DOI : 10.1038/nsmb.3365

Year of publication 2016

Wael Jdey, Sylvain Thierry, Christophe Russo, Flavien Devun, Muthana Al Abo, Patricia Noguiez-Hellin, Jian-Sheng Sun, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein, Yves Pommier, Marie Dutreix (2016 Aug 26)

Drug Driven Synthetic Lethality: bypassing tumor cell genetics with a combination of Dbait and PARP inhibitors.

Clinical cancer research : an official journal of the American Association for Cancer Research : DOI : clincanres.1193.2016

Year of publication 2014

Elsa Bernard, Laurent Jacob, Julien Mairal, Jean-Philippe Vert (2014 May 9)

Efficient RNA isoform identification and quantification from RNA-Seq data with network flows.

Bioinformatics (Oxford, England) : 2447-55 : DOI : 10.1093/bioinformatics/btu317
Daniel J Park, Kayoko Tao, Florence Le Calvez-Kelm, Tu Nguyen-Dumont, Nivonirina Robinot, Fleur Hammet, Fabrice Odefrey, Helen Tsimiklis, Zhi L Teo, Louise B Thingholm, Erin L Young, Catherine Voegele, Andrew Lonie, Bernard J Pope, Terrell C Roane, Russell Bell, Hao Hu, Shankaracharya, Chad D Huff, Jonathan Ellis, Jun Li, Igor V Makunin, Esther M John, Irene L Andrulis, Mary B Terry, Mary Daly, Saundra S Buys, Carrie Snyder, Henry T Lynch, Peter Devilee, Graham G Giles, John L Hopper, Bing-Jian Feng, Fabienne Lesueur, Sean V Tavtigian, Melissa C Southey, David E Goldgar (2014 May 2)

Rare mutations in RINT1 predispose carriers to breast and Lynch syndrome-spectrum cancers.

Cancer discovery : 804-15 : DOI : 10.1158/2159-8290.CD-14-0212
Maia Chanrion, Inna Kuperstein, Cédric Barrière, Fatima El Marjou, David Cohen, Danijela Vignjevic, Lev Stimmer, Perrine Paul-Gilloteaux, Ivan Bièche, Silvina Dos Reis Tavares, Giuseppe-Fulvio Boccia, Wulfran Cacheux, Didier Meseure, Silvia Fre, Loredana Martignetti, Patricia Legoix-Né, Elodie Girard, Luc Fetler, Emmanuel Barillot, Daniel Louvard, Andreï Zinovyev, Sylvie Robine (2014 Apr 9)

Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut.

Nature communications : 5005 : DOI : 10.1038/ncomms6005
Ferhat Ay, Evelien M Bunnik, Nelle Varoquaux, Sebastiaan M Bol, Jacques Prudhomme, Jean-Philippe Vert, William Stafford Noble, Karine G Le Roch (2014 Mar 26)

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression.

Genome research : 974-88 : DOI : 10.1101/gr.169417.113