Logic models of pathway biology. Drug discovery today, vol.13, pp.447-456, 2008. ,
, PLOS, vol.20, issue.23
Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks, Cell communication and signaling, vol.11, issue.1, p.43, 2013. ,
State-time spectrum of signal transduction logic models, Physical biology, vol.9, issue.4, p.45003, 2012. ,
The origins of order: Self-organization and selection in evolution, 1993. ,
Laws for the dynamics of regulatory networks, International Journal of Developmental Biology, vol.42, issue.3, pp.479-485, 2002. ,
The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster, Journal of theoretical biology, vol.223, issue.1, pp.1-18, 2003. ,
Digital clocks: simple Boolean models can quantitatively describe circadian systems, Journal of The Royal Society Interface, p.20120080, 2012. ,
Logic-based models in systems biology: a predictive and parameter-free network analysis method, Integrative biology, vol.4, issue.11, pp.1323-1337, 2012. ,
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Molecular systems biology, vol.5, 2009. ,
Exhaustively characterizing feasible logic models of a signaling network using answer set programming, Bioinformatics, vol.29, issue.18, pp.2320-2326, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00853704
Revisiting the training of logic models of protein signaling networks with ASP, Computational Methods in Systems Biology, pp.342-361, 2012. ,
Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data, PLoS computational biology, vol.5, issue.12, p.1000591, 2009. ,
Reconstructing Boolean models of signaling, Journal of Computational Biology, vol.20, issue.3, pp.249-257, 2013. ,
Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming, Biosystems, vol.149, pp.139-153, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01354075
Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method, BMC bioinformatics, vol.17, issue.1, p.410, 2016. ,
Fitting Boolean networks from steady state perturbation data. Statistical applications in genetics and molecular biology, vol.10, p.47, 2011. ,
Identification of Potential Drug Targets in Cancer Signaling Pathways using Stochastic Logical Models, Scientific reports, vol.6, 2016. ,
ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis, vol.3, 2014. ,
ReactomeFIViz: a Cytoscape app for pathway and network-based data analysis, vol.3, 2014. ,
Context specificity in causal signaling networks revealed by phosphoprotein profiling, Cell systems, vol.4, issue.1, pp.73-83, 2017. ,
Inferring causal molecular networks: empirical assessment through a community-based effort, Nature methods, vol.13, issue.4, pp.310-318, 2016. ,
Statistics Toolbox Release, 2012. ,
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data with CellNOptR, 2013. ,
Mechanism of constitutive phosphoinositide 3-kinase activation by oncogenic mutants of the p85 regulatory subunit, Journal of Biological Chemistry, vol.280, issue.30, pp.27850-27855, 2005. ,
The phosphoinositide 3-kinase regulatory subunit p85? can exert tumor suppressor properties through negative regulation of growth factor signaling, Cancer research, vol.70, issue.13, pp.5305-5315, 2010. ,
Comprehensive molecular portraits of human breast tumours, Nature, vol.490, pp.61-70, 2012. ,
miR-221 Promotes Tumorigenesis in Human Triple Negative, Breast Cancer Cells, vol.8, p.62170, 2013. ,
Computational evaluation and derivation of biological networks in cancer and stem cells, 2014. ,
A tutorial on hybrid answer set solving with clingo, Reasoning Web International Summer School, pp.167-203, 2017. ,
HPN-DREAM breast cancer network inference challenge, 2016. ,
The roles of post-translational modifications in the context of protein interaction networks, PLoS Comput Biol, vol.11, issue.2, p.1004049, 2015. ,
KEGG: kyoto encyclopedia of genes and genomes, Nucleic acids research, vol.28, issue.1, pp.27-30, 2000. ,
The Gene Ontology (GO) database and informatics resource, Nucleic acids research, vol.32, issue.1, pp.258-261, 2004. ,
WikiPathways: building research communities on biological pathways, Nucleic Acids Research, vol.40, issue.D1, p.1301, 2012. ,
, Biotech Software & Internet Report: The Computer Software Journal for Scient, vol.2, issue.3, pp.117-120, 2001.
BioGRID: a general repository for interaction datasets, Nucleic acids research, vol.34, issue.1, pp.535-539, 2006. ,
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible, Nucleic acids research, vol.45, issue.D1, pp.362-368, 2017. ,
DIP: the database of interacting proteins, Nucleic acids research, vol.28, issue.1, pp.289-291, 2000. ,
Human protein reference database as a discovery resource for proteomics, Nucleic acids research, vol.32, issue.1, pp.497-501, 2004. ,
IntAct: an open source molecular interaction database, Nucleic acids research, vol.32, issue.1, pp.452-455, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00306577
MINT: a Molecular INTeraction database, FEBS letters, vol.513, issue.1, pp.135-140, 2002. ,
iRefIndex: a consolidated protein interaction database with provenance, BMC bioinformatics, vol.9, issue.1, p.405, 2008. ,
Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome research, vol.13, issue.11, pp.2498-2504, 2003. ,
Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET, PloS one, vol.10, issue.6, p.127216, 2015. ,
Boolean Network Identification from Multiplex Time Series Data, Computational Methods in Systems Biology, vol.9308, pp.170-181, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01164751
Metabolic stability and epigenesis in randomly constructed genetic nets, Journal of theoretical biology, vol.22, issue.3, pp.437-467, 1969. ,
Logic programming for Boolean networks, IJCAI ProceedingsInternational Joint Conference on Artificial Intelligence, vol.22, p.924, 2011. ,
Nusmv 2: An opensource tool for symbolic model checking, International Conference on Computer Aided Verification, pp.359-364, 2002. ,