[1]   E. Becker, B. Robisson, C.E. Chapple, A. Guénoche, and C. Brun. Multifunctional Proteins Revealed by Overlapping Clustering in Protein Interaction Network. Bioinformatics (Oxford, England), 28(1) :84–90, nov 2012.

[2]   D. Bérenguier, C. Chaouiya, P.T. Monteiro, A. Naldi, E. Remy, D. Thieffry, and L. Tichit. Dynamical modeling and analysis of large cellular regulatory networks. Chaos (Woodbury, N.Y.), 23(2) :025114, jun 2013.

[3]   C. Chaouiya and E. Remy. Logical modelling of regulatory networks, methods and applications. Bulletin of mathematical biology, 75(6) :891–5, jun 2013.

[4]   J-P Comet, M. Noual, A. Richard, J. Aracena, L. Calzone, J. Demongeot, M. Kaufman, A. Naldi, E.H. Snoussi, and D. Thieffry. On circuit functionality in boolean networks. Bulletin of Mathematical Biology, 75(6) :906–19, jun 2013.

[5]   G. Didier, C. Brun, and A. Baudot. Identifying Communities from Multiplex Biological Networks. PeerJ, 3(e1525) :1–9, 2015.

[6]   G. Didier and E. Remy. Relations between gene regulatory networks and cell dynamics in boolean models. Discrete Applied Math., 160 :2147–57, 2012.

[7]   G. Didier, E. Remy, and C. Chaouiya. Mapping multivalued onto boolean dynamics. J. Theor. Biol., 270 :177–184, 2011.

[8]   A. Flobak, A. Baudot, E. Remy, L. Thommesen, D. Thieffry, M. Kuiper, and A. Lægreid. Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLOS Computational Biology, 11(8) :e1004426, 2015.

[9]   P. Gambette and A. Guénoche. Bootstrap clustering for graph partitioning. RAIRO - Operations Research, 45(4) :339–352, 2011.

[10]   E. Glaab, A. Baudot, N. Krasnogor, R. Schneider, and A. Valencia. EnrichNet : network-based gene set enrichment analysis. Bioinformatics, 28(18) :i451–i457, sep 2012.

[11]   A. Guénoche. Consensus of partitions : a constructive approach. Advances in Data Analysis and Classification, 2011.

[12]   A. Guénoche. Multi-clustering gives robustness to modules in network. British Journal of Mathematics and Computer Science, 4(16) :2344–2351, 2014.

[13]   K. Ibáñez, C. Boullosa, R. Tabarés-Seisdedos, A. Baudot, and A. Valencia. Molecular Evidence for the Inverse Comorbidity between Central Nervous System Disorders and Cancers Detected by Transcriptomic Meta-analyses. PLoS Genetics, 10(2) :e1004173, feb 2014.

[14]   M. Katsogiannou, C. Andrieu, V. Baylot, A. Baudot, N.J. Dusetti, O. Gayet, P. Finetti, C. Garrido, D. Birnbaum, F. Bertucci, C. Brun, and P. Rocchi. The functional landscape of Hsp27 reveals new cellular processes such as DNA repair and alternative splicing and proposes novel anticancer targets. Molecular & cellular proteomics : MCP, pages 3585–3601, oct 2014.

[15]   F. Montañana, R.A. Julien, P. Vaglio, L.R. Matthews, L. Tichit, and J.J. Ewbank. Icee an interface for c. elegans experiments. Worm, 3(3) :e959420, 2014. PMID : 26430546.

[16]   A. Naldi, J. Carneiro, C. Chaouiya, and D. Thieffry. Diversity and plasticity of th cell types predicted from regulatory network modelling. PLoS Comput. Biol., 6, 2010. e1000912.

[17]   A. Naldi, E. Remy, D. Thieffry, and C. Chaouiya. A Reduction of Logical Regulatory Graphs Preserving Essential Dynamical Properties. LNBI, 5688 :266–280, 2009.

[18]   E. Remy, B. Mossé, C. Chaouiya, and D. Thieffry. A description of dynamical graphs associated to elementary regulatory circuits. Bioinformatics, 19(Suppl. 2) :172–178, 2003.

[19]    E. Remy, S. Rebouissou, C. Chaouiya, A. Zinovyev, F. Radvanyi, and L. Calzone. A modelling approach to explain mutually exclusive and co-occurring genetic alterations in bladder tumorigenesis. Cancer research, 75(19) :4042–52, aug 2015.

[20]   L. Spinelli, P. Gambette, C.E. Chapple, B. Robisson, A. Baudot, H. Garreta, L. Tichit, A. Guénoche, and C. Brun. Clust&See : A Cytoscape plugin for the identification, visualization and manipulation of network clusters. BioSystems, 113(2) :91–95, 2013.

[21]   R. Tabarés-Seisdedos, N. Dumont, A. Baudot, J.M. Valderas, J. Climent, A. Valencia, B. Crespo-Facorro, E. Vieta, M. Gómez-Beneyto, S. Martínez, and J.L. Rubenstein. No paradox, no progress : inverse cancer comorbidity in people with other complex diseases. The lancet oncology, 12(6) :604–8, jun 2011.

[22]   S. Tripathi, A. Flobak, K. Chawla, A. Baudot, T. Bruland, L. Thommesen, M. Kuiper, and A. Lægreid. The gastrin and cholecystokinin receptors mediated signaling network : a scaffold for data analysis and new hypotheses on regulatory mechanisms. BMC Systems Biology, 9(1) :40, 2015.