The big challenges of big data, Nature, vol.8, issue.7453, pp.255-260, 2013. ,
DOI : 10.1371/journal.pcbi.1002816
Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis, The Journal of Cell Biology, vol.15, issue.6, pp.839-851, 2004. ,
DOI : 10.1038/sj.bjc.6601330
URL : http://jcb.rupress.org/content/jcb/166/6/839.full.pdf
Topologically inferring risk-active pathways toward precise cancer classification by directed random walk, Bioinformatics, vol.102, issue.17, pp.2169-77, 2013. ,
DOI : 10.1111/j.1349-7006.2011.01930.x
URL : https://academic.oup.com/bioinformatics/article-pdf/29/17/2169/16919006/btt373.pdf
The Rb/E2F pathway and cancer,. Human molecular genetics, pp.699-703, 2001. ,
DOI : 10.1093/hmg/10.7.699
URL : https://academic.oup.com/hmg/article-pdf/10/7/699/9813636/100699.pdf
Integrative approaches for finding modular structure in biological networks, Nature Reviews Genetics, vol.333, issue.10, pp.719-751, 2013. ,
DOI : 10.1186/1471-2105-11-95
URL : http://europepmc.org/articles/pmc3940161?pdf=render
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments, Statistica Sinica, vol.12, issue.1, pp.111-139, 2002. ,
KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol.28, issue.1, pp.27-30, 2000. ,
DOI : 10.1093/nar/28.1.27
Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems, Database, vol.19, issue.2, p.30, 2015. ,
DOI : 10.1016/j.drudis.2013.09.012
Reactome pathway analysis: a high-performance in-memory approach, BMC Bioinformatics, vol.39, issue.1, pp.142-12859, 2017. ,
DOI : 10.1093/nar/gkq1156
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1559-2?site=bmcbioinformatics.biomedcentral.com
Disruption of endothelial adherens junction by invasive breast cancer cells is mediated by reactive oxygen species and is attenuated by AHCC, Life Sciences, vol.93, issue.25-26, pp.25-26994, 2013. ,
DOI : 10.1016/j.lfs.2013.10.027
Detecting overlapping protein complexes in protein-protein interaction networks, Nature Methods, vol.57, issue.5, pp.471-472, 2012. ,
DOI : 10.1093/bioinformatics/btn376
URL : http://europepmc.org/articles/pmc3543700?pdf=render
Network-Based Enriched Gene Subnetwork Identification: A Game-Theoretic Approach, Biomed Eng Comput Biol, vol.7, issue.2, pp.1-14, 2016. ,
Dynamic networks reveal key players in aging, Bioinformatics, vol.223, issue.12, pp.1721-1730, 2014. ,
DOI : 10.1016/S0022-5193(03)00071-7
An integer linear programming approach for finding deregulated subgraphs in regulatory networks, Nucleic Acids Research, vol.2010, issue.6, p.43, 2012. ,
DOI : 10.1186/1752-0509-4-S2-S7
URL : https://academic.oup.com/nar/article-pdf/40/6/e43/16955814/gkr1227.pdf
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE), Bioinformatics, vol.22, issue.21, pp.2757-2764, 2013. ,
DOI : 10.1101/gr.120477.111
URL : https://academic.oup.com/bioinformatics/article-pdf/29/21/2757/18533331/btt471.pdf
CoRegNet: reconstruction and integrated analysis of co-regulatory networks: Fig. 1., Bioinformatics, vol.16, issue.4, pp.3066-3068, 2015. ,
DOI : 10.1038/cdd.2008.116
Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies, BMC Bioinformatics, vol.7, issue.4, pp.345-12859, 2015. ,
DOI : 10.1039/c1mb05261f
URL : https://hal.archives-ouvertes.fr/hal-01225228
Multiple myeloma: 2016 update on diagnosis, risk-stratification, and management, American Journal of Hematology, vol.73, issue.1, pp.719-753, 2016. ,
DOI : 10.1038/bjc.1996.212
URL : http://onlinelibrary.wiley.com/doi/10.1002/ajh.24402/pdf
What is answer set programming?, Proceedings of the 23rd National Conference on Artificial Intelligence, pp.1594-1601, 2008. ,
Answer Set Solving in Practice, Synthesis Lectures on Artificial Intelligence and Machine Learning, vol.6702, issue.2, pp.1-238, 2012. ,
DOI : 10.1109/ICCAD.2001.968634
PID: the Pathway Interaction Database, Nucleic Acids Research, vol.15, issue.suppl_1, pp.674-683, 2009. ,
DOI : 10.1197/jamia.M2522
URL : https://academic.oup.com/nar/article-pdf/37/suppl_1/D674/16757229/gkn653.pdf
Exploring network structure, dynamics, and function using NetworkX, Proc 7th Python Sci Conf (SciPy2008). Pasadena, pp.11-15, 2008. ,
R: A Language and Environment for Statistical Computing Vienna: R Foundation for Statistical Computing ,
Logic programming reveals alteration of key transcription factors in multiple myeloma, Scientific Reports, vol.16, issue.Suppl 1, pp.9257-41598, 2017. ,
DOI : 10.1158/1078-0432.CCR-09-0787
URL : https://hal.archives-ouvertes.fr/inserm-01611119
Positioning NK-??B in multiple myeloma, Blood, vol.115, issue.17, pp.3422-3426, 2010. ,
DOI : 10.1182/blood-2010-01-264796
URL : http://www.bloodjournal.org/content/bloodjournal/115/17/3422.full.pdf
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees, Nucleic Acids Research, vol.40, issue.D1, pp.377-86, 1118. ,
DOI : 10.1093/nar/gkr1014
Apoptosis, cancer and cancer therapy, Surgical Oncology, vol.6, issue.3, pp.133-142, 1997. ,
DOI : 10.1016/S0960-7404(97)00015-7
clusterMaker: a multi-algorithm clustering plugin for Cytoscape, BMC Bioinformatics, vol.12, issue.1, pp.436-1471, 2011. ,
DOI : 10.1093/bioinformatics/btp330
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-12-436?site=bmcbioinformatics.biomedcentral.com