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@article{Berenguier2013,
	author = {B{\'e}renguier, D. and Chaouiya, C. and Monteiro, P. T. and Naldi, A. and Remy, E. and Thieffry, D. and Tichit, L.},
	doi = {10.1063/1.4809783},
	issn = {1089-7682},
	journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science},
	month = jun,
	number = {2},
	publisher = {AIP Publishing},
	title = {Dynamical modeling and analysis of large cellular regulatory networks},
	volume = {23},
	year = {2013},
	bdsk-url-1 = {https://doi.org/10.1063/1.4809783}}

@inbook{Chaouiya2006,
	author = {Chaouiya, Claudine and Remy, Elisabeth and Thieffry, Denis},
	booktitle = {Transactions on Computational Systems Biology VI},
	doi = {10.1007/11880646_5},
	isbn = {9783540462361},
	issn = {1611-3349},
	pages = {95--112},
	publisher = {Springer Berlin Heidelberg},
	title = {Qualitative Petri Net Modelling of Genetic Networks},
	year = {2006},
	bdsk-url-1 = {https://doi.org/10.1007/11880646_5}}

@article{Chaouiya2008,
	author = {Chaouiya, Claudine and Remy, Elisabeth and Thieffry, Denis},
	doi = {10.1016/j.jda.2007.06.003},
	issn = {1570-8667},
	journal = {Journal of Discrete Algorithms},
	month = jun,
	number = {2},
	pages = {165--177},
	publisher = {Elsevier BV},
	title = {Petri net modelling of biological regulatory networks},
	volume = {6},
	year = {2008},
	bdsk-url-1 = {https://doi.org/10.1016/j.jda.2007.06.003}}

@inbook{Chaouiya2012,
	author = {Chaouiya, Claudine and Naldi, Aur{\'e}lien and Thieffry, Denis},
	booktitle = {Bacterial Molecular Networks},
	doi = {10.1007/978-1-61779-361-5_23},
	isbn = {9781617793615},
	issn = {1940-6029},
	month = oct,
	pages = {463-479},
	publisher = {Springer New York},
	title = {Logical Modelling of Gene Regulatory Networks with GINsim},
	year = {2012},
}

@article{Mendes2013,
	author = {Mendes, Nuno D. and Lang, Fr{\'e}d{\'e}ric and Le Cornec, Yves-Stan and Mateescu, Radu and Batt, Gregory and Chaouiya, Claudine},
	doi = {10.1093/bioinformatics/btt033},
	issn = {1367-4803},
	journal = {Bioinformatics},
	month = jan,
	number = {6},
	pages = {749--757},
	publisher = {Oxford University Press (OUP)},
	title = {Composition and abstraction of logical regulatory modules: application to multicellular systems},
	volume = {29},
	year = {2013},
	bdsk-url-1 = {https://doi.org/10.1093/bioinformatics/btt033}}

@inbook{Monteiro2012,
	author = {Monteiro, Pedro T. and Chaouiya, Claudine},
	booktitle = {6th International Conference on Practical Applications of Computational Biology & Bioinformatics},
	doi = {10.1007/978-3-642-28839-5_30},
	isbn = {9783642288395},
	issn = {1867-5670},
	pages = {259--267},
	publisher = {Springer Berlin Heidelberg},
	title = {Efficient Verification for Logical Models of Regulatory Networks},
	year = {2012},
	bdsk-url-1 = {https://doi.org/10.1007/978-3-642-28839-5_30}}

@inbook{Naldi2007,
	author = {Naldi, Aur{\'e}lien and Thieffry, Denis and Chaouiya, Claudine},
	booktitle = {Computational Methods in Systems Biology},
	doi = {10.1007/978-3-540-75140-3_16},
	isbn = {9783540751403},
	issn = {1611-3349},
	pages = {233--247},
	publisher = {Springer Berlin Heidelberg},
	title = {Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks},
	year = {2007},
	bdsk-url-1 = {https://doi.org/10.1007/978-3-540-75140-3_16}}

@article{Naldi2009,
	author = {Naldi, A. and Berenguier, D. and Faur{\'e}, A. and Lopez, F. and Thieffry, D. and Chaouiya, C.},
	doi = {10.1016/j.biosystems.2009.04.008},
	issn = {0303-2647},
	journal = {Biosystems},
	month = aug,
	number = {2},
	pages = {134--139},
	publisher = {Elsevier BV},
	title = {Logical modelling of regulatory networks with GINsim 2.3},
	volume = {97},
	year = {2009},
	bdsk-url-1 = {https://doi.org/10.1016/j.biosystems.2009.04.008}}

@article{Naldi2010,
	author = {Naldi, Aur{\'e}lien and Carneiro, Jorge and Chaouiya, Claudine and Thieffry, Denis},
	doi = {10.1371/journal.pcbi.1000912},
	editor = {Bonneau, Richard},
	issn = {1553-7358},
	journal = {PLoS Computational Biology},
	month = sep,
	number = {9},
	pages = {e1000912},
	publisher = {Public Library of Science (PLoS)},
	title = {Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling},
	volume = {6},
	year = {2010},
	bdsk-url-1 = {https://doi.org/10.1371/journal.pcbi.1000912}}

@article{Naldi2011,
	author = {Naldi, Aur{\'e}lien and Remy, Elisabeth and Thieffry, Denis and Chaouiya, Claudine},
	doi = {10.1016/j.tcs.2010.10.021},
	issn = {0304-3975},
	journal = {Theoretical Computer Science},
	month = may,
	number = {21},
	pages = {2207--2218},
	publisher = {Elsevier BV},
	title = {Dynamically consistent reduction of logical regulatory graphs},
	volume = {412},
	year = {2011},
	bdsk-url-1 = {https://doi.org/10.1016/j.tcs.2010.10.021}}

@inbook{Naldi2012,
	author = {Naldi, Aur{\'e}lien and Monteiro, Pedro T. and Chaouiya, Claudine},
	booktitle = {Computational Methods in Systems Biology},
	doi = {10.1007/978-3-642-33636-2_17},
	isbn = {9783642336362},
	issn = {1611-3349},
	pages = {288--306},
	publisher = {Springer Berlin Heidelberg},
	title = {Efficient Handling of Large Signalling-Regulatory Networks by Focusing on Their Core Control},
	year = {2012},
	bdsk-url-1 = {https://doi.org/10.1007/978-3-642-33636-2_17}}

@article{Thieffry1995,
	author = {Thieffry, Denis and Thomas, Ren{\'e}},
	doi = {10.1007/bf02460619},
	issn = {1522-9602},
	journal = {Bulletin of Mathematical Biology},
	month = mar,
	number = {2},
	pages = {277--297},
	publisher = {Springer Science and Business Media LLC},
	title = {Dynamical behaviour of biological regulatory networks---II. Immunity control in bacteriophage lambda},
	volume = {57},
	year = {1995},
	bdsk-url-1 = {https://doi.org/10.1007/bf02460619}}

@article{Thieffry2007,
	author = {Thieffry, D.},
	doi = {10.1093/bib/bbm028},
	issn = {1477-4054},
	journal = {Briefings in Bioinformatics},
	month = mar,
	number = {4},
	pages = {220--225},
	publisher = {Oxford University Press (OUP)},
	title = {Dynamical roles of biological regulatory circuits},
	volume = {8},
	year = {2007},
	bdsk-url-1 = {https://doi.org/10.1093/bib/bbm028}}

@article{ginsim3,
	author = {Naldi, Aur{\'e}lien and Hernandez, C{\'e}line and Abou-Jaoud{\'e}, Wassim and Monteiro, Pedro T. and Chaouiya, Claudine and Thieffry, Denis},
	doi = {10.3389/fphys.2018.00646},
	issn = {1664-042X},
	journal = {Frontiers in Physiology},
	month = jun,
	publisher = {Frontiers Media SA},
	title = {Logical Modeling and Analysis of Cellular Regulatory Networks With {GINsim} 3.0},
	volume = {9},
	year = {2018},
	bdsk-url-1 = {https://doi.org/10.3389/fphys.2018.00646}}

@article{deJong2002,
	author = {de Jong, Hidde},
	doi = {10.1089/10665270252833208},
	issn = {1557-8666},
	journal = {Journal of Computational Biology},
	month = jan,
	number = {1},
	pages = {67--103},
	publisher = {Mary Ann Liebert Inc},
	title = {Modeling and Simulation of Genetic Regulatory Systems: A Literature Review},
	volume = {9},
	year = {2002},
	bdsk-url-1 = {https://doi.org/10.1089/10665270252833208}}

@article{Gonzalez2006,
	author = {Gonzalez, A. Gonzalez and Naldi, A. and S{\'a}nchez, L. and Thieffry, D. and Chaouiya, C.},
	doi = {10.1016/j.biosystems.2005.10.003},
	issn = {0303-2647},
	journal = {Biosystems},
	month = may,
	number = {2},
	pages = {91--100},
	publisher = {Elsevier BV},
	title = {{GINsim}: A software suite for the qualitative modelling, simulation and analysis of regulatory networks},
	volume = {84},
	year = {2006},
	bdsk-url-1 = {https://doi.org/10.1016/j.biosystems.2005.10.003}}

@article{Gonzalez2006b,
	author = {Gonz{\'a}lez, Aitor and Chaouiya, Claudine and Thieffry, Denis},
	doi = {10.1534/genetics.106.061218},
	issn = {1943-2631},
	journal = {Genetics},
	month = nov,
	number = {3},
	pages = {1625--1634},
	publisher = {Oxford University Press (OUP)},
	title = {Dynamical Analysis of the Regulatory Network Defining the Dorsal--Ventral Boundary of the Drosophila Wing Imaginal Disc},
	volume = {174},
	year = {2006},
	bdsk-url-1 = {https://doi.org/10.1534/genetics.106.061218}}

@article{Simao2005,
	author = {Sim{\~a}o, E. and Remy, E. and Thieffry, D. and Chaouiya, C.},
	doi = {10.1093/bioinformatics/bti1130},
	issn = {1367-4803},
	journal = {Bioinformatics},
	month = sep,
	number = {suppl_2},
	pages = {ii190--ii196},
	publisher = {Oxford University Press (OUP)},
	title = {Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli},
	volume = {21},
	year = {2005},
	bdsk-url-1 = {https://doi.org/10.1093/bioinformatics/bti1130}}

@book{Ptashne1992,
	address = {Cambridge (Mass.)},
	author = {Ptashne, Mark},
	edition = {2nd},
	isbn = {0865422095},
	publisher = {Cell Press : Blackwell Scientific Publications},
	title = {A Genetic Switch: Phage lambda and Higher Organisms},
	url = {http://lib.ugent.be/catalog/rug01:000263939},
	year = {1992},
	bdsk-url-1 = {http://lib.ugent.be/catalog/rug01:000263939}}

@article{Faure2006,
	author = {Faur{\'e}, Adrien and Naldi, Aur{\'e}lien and Chaouiya, Claudine and Thieffry, Denis},
	doi = {10.1093/bioinformatics/btl210},
	issn = {1367-4803},
	journal = {Bioinformatics},
	month = jul,
	number = {14},
	pages = {e124--e131},
	publisher = {Oxford University Press (OUP)},
	title = {Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle},
	volume = {22},
	year = {2006},
	bdsk-url-1 = {https://doi.org/10.1093/bioinformatics/btl210}}

@article{Hou1997,
	author = {Hou, X},
	doi = {10.1016/s0168-9525(97)01006-8},
	issn = {0168-9525},
	journal = {Trends in Genetics},
	month = mar,
	number = {3},
	pages = {105--110},
	publisher = {Elsevier BV},
	title = {The JAK-STAT pathway in Drosophila},
	volume = {13},
	year = {1997},
	bdsk-url-1 = {https://doi.org/10.1016/s0168-9525(97)01006-8}}

@article{Luo2001,
	author = {Luo, Hong and Dearolf, Charles R.},
	doi = {10.1002/bies.10016},
	issn = {1521-1878},
	journal = {BioEssays},
	month = nov,
	number = {12},
	pages = {1138--1147},
	publisher = {Wiley},
	title = {The JAK/STAT pathway and Drosophila development},
	volume = {23},
	year = {2001},
	bdsk-url-1 = {https://doi.org/10.1002/bies.10016}}

@article{Johnson2011,
	author = {Johnson, Aaron N. and Mokalled, Mayssa H. and Haden, Tom N. and Olson, Eric N.},
	doi = {10.1242/dev.071464},
	issn = {0950-1991},
	journal = {Development},
	month = nov,
	number = {21},
	pages = {4627--4638},
	publisher = {The Company of Biologists},
	title = {JAK/Stat signaling regulates heart precursor diversification inDrosophila},
	volume = {138},
	year = {2011},
	bdsk-url-1 = {https://doi.org/10.1242/dev.071464}}

@article{Kiger2001,
	author = {Kiger, Amy A. and Jones, D. Leanne and Schulz, Cordula and Rogers, Madolyn B. and Fuller, Margaret T.},
	doi = {10.1126/science.1066707},
	issn = {1095-9203},
	journal = {Science},
	month = dec,
	number = {5551},
	pages = {2542--2545},
	publisher = {American Association for the Advancement of Science (AAAS)},
	title = {Stem Cell Self-Renewal Specified by JAK-STAT Activation in Response to a Support Cell Cue},
	volume = {294},
	year = {2001},
	bdsk-url-1 = {https://doi.org/10.1126/science.1066707}}

@article{Denef2003,
	author = {Denef, Natalie and Sch\"{u}pbach, Trudi},
	doi = {10.1016/s0960-9822(03)00317-8},
	issn = {0960-9822},
	journal = {Current Biology},
	month = may,
	number = {10},
	pages = {R388--R390},
	publisher = {Elsevier BV},
	title = {Patterning: JAK-STAT Signalling in the Drosophila Follicular Epithelium},
	volume = {13},
	year = {2003},
	bdsk-url-1 = {https://doi.org/10.1016/s0960-9822(03)00317-8}}

@article{Xi2003,
	author = {Xi, Rongwen and McGregor, Jennifer R. and Harrison, Douglas A.},
	doi = {10.1016/s1534-5807(02)00412-4},
	issn = {1534-5807},
	journal = {Developmental Cell},
	month = feb,
	number = {2},
	pages = {167--177},
	publisher = {Elsevier BV},
	title = {A Gradient of JAK Pathway Activity Patterns the Anterior-Posterior Axis of the Follicular Epithelium},
	volume = {4},
	year = {2003},
	bdsk-url-1 = {https://doi.org/10.1016/s1534-5807(02)00412-4}}

@article{Harrison2001,
	author = {Harrison, Jacob C. and Bardes, Elaine S.G. and Ohya, Yoshikazu and Lew, Daniel J.},
	doi = {10.1038/35070104},
	issn = {1476-4679},
	journal = {Nature Cell Biology},
	month = mar,
	number = {4},
	pages = {417--420},
	publisher = {Springer Science and Business Media LLC},
	title = {A role for the Pkc1p/Mpk1p kinase cascade in the morphogenesis checkpoint},
	volume = {3},
	year = {2001},
	bdsk-url-1 = {https://doi.org/10.1038/35070104}}

@article{Klingensmith1994,
	author = {Klingensmith, John and Nusse, Roel},
	doi = {10.1006/dbio.1994.1325},
	issn = {0012-1606},
	journal = {Developmental Biology},
	month = dec,
	number = {2},
	pages = {396--414},
	publisher = {Elsevier BV},
	title = {Signaling by wingless in Drosophila},
	volume = {166},
	year = {1994},
	bdsk-url-1 = {https://doi.org/10.1006/dbio.1994.1325}}

@article{Michelson2003,
	author = {Michelson, Alan M.},
	doi = {10.1126/stke.2003.192.pe30},
	issn = {1525-8882},
	journal = {Science's STKE},
	month = jul,
	number = {192},
	publisher = {American Association for the Advancement of Science (AAAS)},
	title = {Running Interference for Hedgehog Signaling},
	volume = {2003},
	year = {2003},
	bdsk-url-1 = {https://doi.org/10.1126/stke.2003.192.pe30}}

@article{Perrimon2012,
	author = {Perrimon, N. and Pitsouli, C. and Shilo, B.-Z.},
	doi = {10.1101/cshperspect.a005975},
	issn = {1943-0264},
	journal = {Cold Spring Harbor Perspectives in Biology},
	month = aug,
	number = {8},
	pages = {a005975--a005975},
	publisher = {Cold Spring Harbor Laboratory},
	title = {Signaling Mechanisms Controlling Cell Fate and Embryonic Patterning},
	volume = {4},
	year = {2012},
	bdsk-url-1 = {https://doi.org/10.1101/cshperspect.a005975}}

@article{Swarup2012,
	author = {Swarup, S. and Verheyen, E. M.},
	doi = {10.1101/cshperspect.a007930},
	issn = {1943-0264},
	journal = {Cold Spring Harbor Perspectives in Biology},
	month = apr,
	number = {6},
	pages = {a007930--a007930},
	publisher = {Cold Spring Harbor Laboratory},
	title = {Wnt/Wingless Signaling in Drosophila},
	volume = {4},
	year = {2012},
	bdsk-url-1 = {https://doi.org/10.1101/cshperspect.a007930}}

@article{Tauc2012,
	author = {Tauc, Helen M. and Mann, Tabea and Werner, Kathrin and Pandur, Petra},
	doi = {10.1002/dvg.22021},
	issn = {1526-968X},
	journal = {genesis},
	month = apr,
	number = {6},
	pages = {466--481},
	publisher = {Wiley},
	title = {A role for Drosophila Wnt-4 in heart development},
	volume = {50},
	year = {2012},
	bdsk-url-1 = {https://doi.org/10.1002/dvg.22021}}

@article{Duchek2001,
	author = {Duchek, Peter and Somogyi, K{\'a}lm{\'a}n and J{\'e}kely, G{\'a}sp{\'a}r and Beccari, Simone and R{\o}rth, Pernille},
	doi = {10.1016/s0092-8674(01)00502-5},
	issn = {0092-8674},
	journal = {Cell},
	month = oct,
	number = {1},
	pages = {17--26},
	publisher = {Elsevier BV},
	title = {Guidance of Cell Migration by the Drosophila PDGF/VEGF Receptor},
	volume = {107},
	year = {2001},
	bdsk-url-1 = {https://doi.org/10.1016/s0092-8674(01)00502-5}}

@article{Bruckner2004,
	author = {Br\"{u}ckner, Katja and Kockel, Lutz and Duchek, Peter and Luque, Carlos M and R{\o}rth, Pernille and Perrimon, Norbert},
	doi = {10.1016/j.devcel.2004.06.007},
	issn = {1534-5807},
	journal = {Developmental Cell},
	month = jul,
	number = {1},
	pages = {73--84},
	publisher = {Elsevier BV},
	title = {The PDGF/VEGF Receptor Controls Blood Cell Survival in Drosophila},
	volume = {7},
	year = {2004},
	bdsk-url-1 = {https://doi.org/10.1016/j.devcel.2004.06.007}}

@article{Wood2006,
	author = {Wood, Will and Faria, Celia and Jacinto, Antonio},
	doi = {10.1083/jcb.200508161},
	issn = {0021-9525},
	journal = {The Journal of Cell Biology},
	month = may,
	number = {3},
	pages = {405--416},
	publisher = {Rockefeller University Press},
	title = {Distinct mechanisms regulate hemocyte chemotaxis during development and wound healing in Drosophila melanogaster},
	volume = {173},
	year = {2006},
	bdsk-url-1 = {https://doi.org/10.1083/jcb.200508161}}

@article{Harris2007,
	author = {Harris, Katherine E. and Schnittke, Nikolai and Beckendorf, Steven K.},
	doi = {10.1016/j.mod.2007.03.003},
	issn = {0925-4773},
	journal = {Mechanisms of Development},
	month = jul,
	number = {6},
	pages = {441--448},
	publisher = {Elsevier BV},
	title = {Two ligands signal through the Drosophila PDGF/VEGF receptor to ensure proper salivary gland positioning},
	volume = {124},
	year = {2007},
	bdsk-url-1 = {https://doi.org/10.1016/j.mod.2007.03.003}}

@article{Sims2009,
	author = {Sims, David and Duchek, Peter and Baum, Buzz},
	doi = {10.1186/gb-2009-10-2-r20},
	issn = {1474-760X},
	journal = {Genome Biology},
	month = feb,
	number = {2},
	publisher = {Springer Science and Business Media LLC},
	title = {PDGF/VEGF signaling controls cell size in Drosophila},
	volume = {10},
	year = {2009},
	bdsk-url-1 = {https://doi.org/10.1186/gb-2009-10-2-r20}}

@article{Vincent1998,
	author = {Vincent, St{\'e}phane and Wilson, Robert and Coelho, Carmen and Affolter, Markus and Leptin, Maria},
	doi = {10.1016/s1097-2765(00)80151-3},
	issn = {1097-2765},
	journal = {Molecular Cell},
	month = oct,
	number = {4},
	pages = {515--525},
	publisher = {Elsevier BV},
	title = {The Drosophila Protein Dof Is Specifically Required for FGF Signaling},
	volume = {2},
	year = {1998},
	bdsk-url-1 = {https://doi.org/10.1016/s1097-2765(00)80151-3}}

@article{Brunner1994,
	author = {Brunner, Damian and D\"{u}cker, Klaus and Oellers, Nadja and Hafen, Ernst and Scholzi, Henrike and Klambt, Christian},
	doi = {10.1038/370386a0},
	issn = {1476-4687},
	journal = {Nature},
	month = aug,
	number = {6488},
	pages = {386--389},
	publisher = {Springer Science and Business Media LLC},
	title = {The ETS domain protein Pointed-P2 is a target of MAP kinase in the Sevenless signal transduction pathway},
	volume = {370},
	year = {1994},
	bdsk-url-1 = {https://doi.org/10.1038/370386a0}}

@article{ONeill1994,
	author = {O'Neill, Elizabeth M. and Rebay, Ilaria and Tjian, Robert and Rubin, Gerald M.},
	doi = {10.1016/0092-8674(94)90580-0},
	issn = {0092-8674},
	journal = {Cell},
	month = jul,
	number = {1},
	pages = {137--147},
	publisher = {Elsevier BV},
	title = {The activities of two Ets-related transcription factors required for drosophila eye development are modulated by the Ras/MAPK pathway},
	volume = {78},
	year = {1994},
	bdsk-url-1 = {https://doi.org/10.1016/0092-8674(94)90580-0}}

@article{Novak2004,
	author = {Nov{\'a}k, B{\'e}la and Tyson, John J.},
	doi = {10.1016/j.jtbi.2004.04.039},
	issn = {0022-5193},
	journal = {Journal of Theoretical Biology},
	month = oct,
	number = {4},
	pages = {563--579},
	publisher = {Elsevier BV},
	title = {A model for restriction point control of the mammalian cell cycle},
	volume = {230},
	year = {2004},
	bdsk-url-1 = {https://doi.org/10.1016/j.jtbi.2004.04.039}}

@article{Klamt2006,
	author = {Klamt, Steffen and Saez-Rodriguez, Julio and Lindquist, Jonathan A and Simeoni, Luca and Gilles, Ernst D},
	doi = {10.1186/1471-2105-7-56},
	issn = {1471-2105},
	journal = {BMC Bioinformatics},
	month = feb,
	number = {1},
	publisher = {Springer Science and Business Media LLC},
	title = {A methodology for the structural and functional analysis of signaling and regulatory networks},
	volume = {7},
	year = {2006},
	bdsk-url-1 = {https://doi.org/10.1186/1471-2105-7-56}}

@article{Orlando2008,
	author = {Orlando, David A. and Lin, Charles Y. and Bernard, Allister and Wang, Jean Y. and Socolar, Joshua E. S. and Iversen, Edwin S. and Hartemink, Alexander J. and Haase, Steven B.},
	doi = {10.1038/nature06955},
	issn = {1476-4687},
	journal = {Nature},
	month = may,
	number = {7197},
	pages = {944--947},
	publisher = {Springer Science and Business Media LLC},
	title = {Global control of cell-cycle transcription by coupled CDK and network oscillators},
	volume = {453},
	year = {2008},
	bdsk-url-1 = {https://doi.org/10.1038/nature06955}}

@article{Davidich2008,
	author = {Davidich, Maria I. and Bornholdt, Stefan},
	doi = {10.1371/journal.pone.0001672},
	editor = {Stolovitzky, Gustavo},
	issn = {1932-6203},
	journal = {PLoS ONE},
	month = feb,
	number = {2},
	pages = {e1672},
	publisher = {Public Library of Science (PLoS)},
	title = {Boolean Network Model Predicts Cell Cycle Sequence of Fission Yeast},
	volume = {3},
	year = {2008},
	bdsk-url-1 = {https://doi.org/10.1371/journal.pone.0001672}}

@article{Faure2009,
	author = {Faur{\'e}, Adrien and Thieffry, Denis},
	doi = {10.1039/b907562n},
	issn = {1742-2051},
	journal = {Molecular BioSystems},
	number = {12},
	pages = {1569},
	publisher = {Royal Society of Chemistry (RSC)},
	title = {Logical modelling of cell cycle control in eukaryotes: a comparative study},
	volume = {5},
	year = {2009},
	bdsk-url-1 = {https://doi.org/10.1039/b907562n}}

@article{Irons2009,
	author = {Irons, D.J.},
	doi = {10.1016/j.jtbi.2008.12.028},
	issn = {0022-5193},
	journal = {Journal of Theoretical Biology},
	month = apr,
	number = {4},
	pages = {543--559},
	publisher = {Elsevier BV},
	title = {Logical analysis of the budding yeast cell cycle},
	volume = {257},
	year = {2009},
	bdsk-url-1 = {https://doi.org/10.1016/j.jtbi.2008.12.028}}

@article{Chen2004,
	author = {Chen, Katherine C. and Calzone, Laurence and Csikasz-Nagy, Attila and Cross, Frederick R. and Novak, Bela and Tyson, John J.},
	doi = {10.1091/mbc.e03-11-0794},
	issn = {1939-4586},
	journal = {Molecular Biology of the Cell},
	month = aug,
	number = {8},
	pages = {3841--3862},
	publisher = {American Society for Cell Biology (ASCB)},
	title = {Integrative Analysis of Cell Cycle Control in Budding Yeast},
	volume = {15},
	year = {2004},
	bdsk-url-1 = {https://doi.org/10.1091/mbc.e03-11-0794}}

@article{Faure2009b,
	author = {Faur{\'e}, Adrien and Naldi, Aur{\'e}lien and Lopez, Fabrice and Chaouiya, Claudine and Ciliberto, Andrea and Thieffry, Denis},
	doi = {10.1039/b910101m},
	issn = {1742-2051},
	journal = {Molecular BioSystems},
	number = {12},
	pages = {1787},
	publisher = {Royal Society of Chemistry (RSC)},
	title = {Modular logical modelling of the budding yeast cell cycle},
	volume = {5},
	year = {2009},
	bdsk-url-1 = {https://doi.org/10.1039/b910101m}}

@article{Ciliberto2003,
	author = {Ciliberto, Andrea and Novak, Bela and Tyson, John J.},
	doi = {10.1083/jcb.200306139},
	issn = {0021-9525},
	journal = {The Journal of Cell Biology},
	month = dec,
	number = {6},
	pages = {1243--1254},
	publisher = {Rockefeller University Press},
	title = {Mathematical model of the morphogenesis checkpoint in budding yeast},
	volume = {163},
	year = {2003},
	bdsk-url-1 = {https://doi.org/10.1083/jcb.200306139}}

@article{Queralt2006,
	author = {Queralt, Ethel and Lehane, Chris and Novak, Bela and Uhlmann, Frank},
	doi = {10.1016/j.cell.2006.03.038},
	issn = {0092-8674},
	journal = {Cell},
	month = may,
	number = {4},
	pages = {719--732},
	publisher = {Elsevier BV},
	title = {Downregulation of PP2ACdc55 Phosphatase by Separase Initiates Mitotic Exit in Budding Yeast},
	volume = {125},
	year = {2006},
	bdsk-url-1 = {https://doi.org/10.1016/j.cell.2006.03.038}}

@article{Letort2018,
	author = {Letort, Gaelle and Montagud, Arnau and Stoll, Gautier and Heiland, Randy and Barillot, Emmanuel and Macklin, Paul and Zinovyev, Andrei and Calzone, Laurence},
	doi = {10.1093/bioinformatics/bty766},
	editor = {Wren, Jonathan},
	issn = {1367-4811},
	journal = {Bioinformatics},
	month = aug,
	number = {7},
	pages = {1188--1196},
	publisher = {Oxford University Press (OUP)},
	title = {PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling},
	volume = {35},
	year = {2018},
	bdsk-url-1 = {https://doi.org/10.1093/bioinformatics/bty766}}

@article{Anderson2000,
	author = {Anderson, Kathryn V},
	doi = {10.1016/s0952-7915(99)00045-x},
	issn = {0952-7915},
	journal = {Current Opinion in Immunology},
	month = feb,
	number = {1},
	pages = {13--19},
	publisher = {Elsevier BV},
	title = {Toll signaling pathways in the innate immune response},
	volume = {12},
	year = {2000},
	bdsk-url-1 = {https://doi.org/10.1016/s0952-7915(99)00045-x}}

@article{Sun2003,
	author = {Sun, Huaiyu and Towb, Par and Chiem, Daniel N and Foster, Byron A and Wasserman, Steven A},
	doi = {10.1038/sj.emboj.7600033},
	issn = {1460-2075},
	journal = {The EMBO Journal},
	month = dec,
	number = {1},
	pages = {100--110},
	publisher = {Springer Science and Business Media LLC},
	title = {Regulated assembly of the Toll signaling complex drives Drosophila dorsoventral patterning},
	volume = {23},
	year = {2003},
	bdsk-url-1 = {https://doi.org/10.1038/sj.emboj.7600033}}

@article{Tanji2005,
	author = {Tanji, Takahiro and Ip, Y. Tony},
	doi = {10.1016/j.it.2005.02.006},
	issn = {1471-4906},
	journal = {Trends in Immunology},
	month = apr,
	number = {4},
	pages = {193--198},
	publisher = {Elsevier BV},
	title = {Regulators of the Toll and Imd pathways in the Drosophila innate immune response},
	volume = {26},
	year = {2005},
	bdsk-url-1 = {https://doi.org/10.1016/j.it.2005.02.006}}

@article{Valanne2011,
	author = {Valanne, Susanna and Wang, Jing-Huan and R\"{a}met, Mika},
	doi = {10.4049/jimmunol.1002302},
	issn = {1550-6606},
	journal = {The Journal of Immunology},
	month = jan,
	number = {2},
	pages = {649--656},
	publisher = {Oxford University Press (OUP)},
	title = {The Drosophila Toll Signaling Pathway},
	volume = {186},
	year = {2011},
	bdsk-url-1 = {https://doi.org/10.4049/jimmunol.1002302}}

@article{Morisato1994,
	author = {Morisato, Donald and Anderson, Kathryn V.},
	doi = {10.1016/0092-8674(94)90507-x},
	issn = {0092-8674},
	journal = {Cell},
	month = feb,
	number = {4},
	pages = {677--688},
	publisher = {Elsevier BV},
	title = {The sp\"{a}tzle gene encodes a component of the extracellular signaling pathway establishing the dorsal-ventral pattern of the Drosophila embryo},
	volume = {76},
	year = {1994},
	bdsk-url-1 = {https://doi.org/10.1016/0092-8674(94)90507-x}}

@article{Weber2003,
	author = {Weber, Alexander N R and Tauszig-Delamasure, Servane and Hoffmann, Jules A and Leli{\`e}vre, Eric and Gascan, Hugues and Ray, Keith P and Morse, Mary A and Imler, Jean-Luc and Gay, Nicholas J},
	doi = {10.1038/ni955},
	issn = {1529-2916},
	journal = {Nature Immunology},
	month = jul,
	number = {8},
	pages = {794--800},
	publisher = {Springer Science and Business Media LLC},
	title = {Binding of the Drosophila cytokine Sp\"{a}tzle to Toll is direct and establishes signaling},
	volume = {4},
	year = {2003},
	bdsk-url-1 = {https://doi.org/10.1038/ni955}}

@article{Royet2004,
	author = {Royet, J.},
	doi = {10.1007/s00018-003-3243-0},
	issn = {1420-9071},
	journal = {Cellular and Molecular Life Sciences (CMLS)},
	month = mar,
	number = {5},
	pages = {537--546},
	publisher = {Springer Science and Business Media LLC},
	title = {Drosophila melanogaster innate immunity: an emerging role for peptidoglycan recognition proteins in bacteria detection},
	volume = {61},
	year = {2004},
	bdsk-url-1 = {https://doi.org/10.1007/s00018-003-3243-0}}

@article{Gobert2003,
	author = {Gobert, Vanessa and Gottar, Marie and Matskevich, Alexey A. and Rutschmann, Sophie and Royet, Julien and Belvin, Marcia and Hoffmann, Jules A. and Ferrandon, Dominique},
	doi = {10.1126/science.1085432},
	issn = {1095-9203},
	journal = {Science},
	month = dec,
	number = {5653},
	pages = {2126--2130},
	publisher = {American Association for the Advancement of Science (AAAS)},
	title = {Dual Activation of the Drosophila Toll Pathway by Two Pattern Recognition Receptors},
	volume = {302},
	year = {2003},
	bdsk-url-1 = {https://doi.org/10.1126/science.1085432}}

@article{Ligoxygakis2002,
	author = {Ligoxygakis, P.},
	doi = {10.1093/emboj/cdf661},
	issn = {1460-2075},
	journal = {The EMBO Journal},
	month = dec,
	number = {23},
	pages = {6330--6337},
	publisher = {Springer Science and Business Media LLC},
	title = {A serpin mutant links Toll activation to melanization in the host defence of Drosophila},
	volume = {21},
	year = {2002},
	bdsk-url-1 = {https://doi.org/10.1093/emboj/cdf661}}

@article{Ligoxygakis2002b,
	author = {Ligoxygakis, Petros and Pelte, Nad{\`e}ge and Hoffmann, Jules A. and Reichhart, Jean-Marc},
	doi = {10.1126/science.1072391},
	issn = {1095-9203},
	journal = {Science},
	month = jul,
	number = {5578},
	pages = {114--116},
	publisher = {American Association for the Advancement of Science (AAAS)},
	title = {Activation of Drosophila Toll During Fungal Infection by a Blood Serine Protease},
	volume = {297},
	year = {2002}
}

@article{Pelte2006,
	author = {Pelte, Nad{\`e}ge and Robertson, Andrew S. and Zou, Zhen and Belorgey, Didier and Dafforn, Timothy R. and Jiang, Haobo and Lomas, David and Reichhart, Jean-Marc and Gubb, David},
	doi = {10.1016/j.ibmb.2005.10.004},
	issn = {0965-1748},
	journal = {Insect Biochemistry and Molecular Biology},
	month = jan,
	number = {1},
	pages = {37--46},
	publisher = {Elsevier BV},
	title = {Immune challenge induces N-terminal cleavage of the Drosophila serpin Necrotic},
	volume = {36},
	year = {2006}
}

@article{Bischoff2004,
	author = {Bischoff, Vincent and Vignal, C{\'e}cile and Boneca, Ivo G and Michel, Tatiana and Hoffmann, Jules A and Royet, Julien},
	doi = {10.1038/ni1123},
	issn = {1529-2916},
	journal = {Nature Immunology},
	month = sep,
	number = {11},
	pages = {1175--1180},
	publisher = {Springer Science and Business Media LLC},
	title = {Function of the drosophila pattern-recognition receptor PGRP-SD in the detection of Gram-positive bacteria},
	volume = {5},
	year = {2004},
	bdsk-url-1 = {https://doi.org/10.1038/ni1123}}

@article{Eldar2002,
	author = {Eldar, Avigdor and Dorfman, Ruslan and Weiss, Daniel and Ashe, Hilary and Shilo, Ben-Zion and Barkai, Naama},
	doi = {10.1038/nature01061},
	issn = {1476-4687},
	journal = {Nature},
	month = sep,
	number = {6904},
	pages = {304--308},
	publisher = {Springer Science and Business Media LLC},
	title = {Robustness of the BMP morphogen gradient in Drosophila embryonic patterning},
	volume = {419},
	year = {2002},
	bdsk-url-1 = {https://doi.org/10.1038/nature01061}}

@article{Kamiya2008,
	author = {Kamiya, Yuto and Miyazono, Kohei and Miyazawa, Keiji},
	doi = {10.1016/j.febslet.2008.05.052},
	issn = {1873-3468},
	journal = {FEBS Letters},
	month = jun,
	number = {17},
	pages = {2496--2500},
	publisher = {Wiley},
	title = {Specificity of the inhibitory effects of Dad on TGF-β family type I receptors, Thickveins, Saxophone, and Baboon in Drosophila},
	volume = {582},
	year = {2008},
	bdsk-url-1 = {https://doi.org/10.1016/j.febslet.2008.05.052}}

@article{Wartlick2011,
	author = {Wartlick, O. and Mumcu, P. and Kicheva, A. and Bittig, T. and Seum, C. and J\"{u}licher, F. and Gonz{\'a}lez-Gait{\'a}n, M.},
	doi = {10.1126/science.1200037},
	issn = {1095-9203},
	journal = {Science},
	month = mar,
	number = {6021},
	pages = {1154--1159},
	publisher = {American Association for the Advancement of Science (AAAS)},
	title = {Dynamics of Dpp Signaling and Proliferation Control},
	volume = {331},
	year = {2011},
	bdsk-url-1 = {https://doi.org/10.1126/science.1200037}}

@article{BaenaLopez2012,
	author = {Baena-Lopez, Luis Alberto and Nojima, Hisashi and Vincent, Jean-Paul},
	doi = {10.1016/j.ceb.2011.12.010},
	issn = {0955-0674},
	journal = {Current Opinion in Cell Biology},
	month = apr,
	number = {2},
	pages = {166--172},
	publisher = {Elsevier BV},
	title = {Integration of morphogen signalling within the growth regulatory network},
	volume = {24},
	year = {2012},
	bdsk-url-1 = {https://doi.org/10.1016/j.ceb.2011.12.010}}

@article{Brooks2012,
	author = {Brooks, Alexander and Dou, Wei and Yang, Xiaoying and Brosnan, Tara and Pargett, Michael and Raftery, Laurel A. and Umulis, David M.},
	doi = {10.1016/j.febslet.2012.03.050},
	issn = {1873-3468},
	journal = {FEBS Letters},
	month = mar,
	number = {14},
	pages = {1942--1952},
	publisher = {Wiley},
	title = {BMP signaling in wing development: A critical perspective on quantitative image analysis},
	volume = {586},
	year = {2012},
	bdsk-url-1 = {https://doi.org/10.1016/j.febslet.2012.03.050}}

@article{Yokouchi1999,
	author = {Yokouchi, Masahiro and Kondo, Takeshi and Houghton, Adam and Bartkiewicz, Marcjanna and Horne, William C. and Zhang, Hui and Yoshimura, Akihiko and Baron, Roland},
	doi = {10.1074/jbc.274.44.31707},
	issn = {0021-9258},
	journal = {Journal of Biological Chemistry},
	month = oct,
	number = {44},
	pages = {31707--31712},
	publisher = {Elsevier BV},
	title = {Ligand-induced Ubiquitination of the Epidermal Growth Factor Receptor Involves the Interaction of the c-Cbl RING Finger and UbcH7},
	volume = {274},
	year = {1999},
	bdsk-url-1 = {https://doi.org/10.1074/jbc.274.44.31707}}

@article{Levkowitz1999,
	author = {Levkowitz, Gil and Waterman, Hadassa and Ettenberg, Seth A and Katz, Menachem and Tsygankov, Alexander Y and Alroy, Iris and Lavi, Sara and Iwai, Kazuhiro and Reiss, Yuval and Ciechanover, Aaron and Lipkowitz, Stanley and Yarden, Yosef},
	doi = {10.1016/s1097-2765(00)80231-2},
	issn = {1097-2765},
	journal = {Molecular Cell},
	month = dec,
	number = {6},
	pages = {1029--1040},
	publisher = {Elsevier BV},
	title = {Ubiquitin Ligase Activity and Tyrosine Phosphorylation Underlie Suppression of Growth Factor Signaling by c-Cbl/Sli-1},
	volume = {4},
	year = {1999},
	bdsk-url-1 = {https://doi.org/10.1016/s1097-2765(00)80231-2}}

@article{Waterman1999,
	author = {Waterman, Hadassa and Levkowitz, Gil and Alroy, Iris and Yarden, Yosef},
	doi = {10.1074/jbc.274.32.22151},
	issn = {0021-9258},
	journal = {Journal of Biological Chemistry},
	month = aug,
	number = {32},
	pages = {22151--22154},
	publisher = {Elsevier BV},
	title = {The RING Finger of c-Cbl Mediates Desensitization of the Epidermal Growth Factor Receptor},
	volume = {274},
	year = {1999},
	bdsk-url-1 = {https://doi.org/10.1074/jbc.274.32.22151}}

@article{Pai2000,
	author = {Pai, Li-Mei and Barcelo, Gail and Sch\"{u}pbach, Trudi},
	doi = {10.1016/s0092-8674(00)00104-5},
	issn = {0092-8674},
	journal = {Cell},
	month = sep,
	number = {1},
	pages = {51--61},
	publisher = {Elsevier BV},
	title = {D-cbl, a Negative Regulator of the Egfr Pathway, Is Required for Dorsoventral Patterning in Drosophila Oogenesis},
	volume = {103},
	year = {2000},
	bdsk-url-1 = {https://doi.org/10.1016/s0092-8674(00)00104-5}}

@article{Sutherland1996,
	author = {Sutherland, David and Samakovlis, Christos and Krasnow, Mark A},
	doi = {10.1016/s0092-8674(00)81803-6},
	issn = {0092-8674},
	journal = {Cell},
	month = dec,
	number = {6},
	pages = {1091--1101},
	publisher = {Elsevier BV},
	title = {branchless Encodes a Drosophila FGF Homolog That Controls Tracheal Cell Migration and the Pattern of Branching},
	volume = {87},
	year = {1996},
	bdsk-url-1 = {https://doi.org/10.1016/s0092-8674(00)81803-6}}

@article{Klint1995,
	author = {Klint, Peter and Kanda, Shigeru and Claesson-Welsh, Lena},
	doi = {10.1074/jbc.270.40.23337},
	issn = {0021-9258},
	journal = {Journal of Biological Chemistry},
	month = oct,
	number = {40},
	pages = {23337--23344},
	publisher = {Elsevier BV},
	title = {Shc and a Novel 89-kDa Component Couple to the Grb2-Sos Complex in Fibroblast Growth Factor-2-stimulated Cells},
	volume = {270},
	year = {1995},
	bdsk-url-1 = {https://doi.org/10.1074/jbc.270.40.23337}}

@article{Kouhara1997,
	author = {Kouhara, H and Hadari, Y.R and Spivak-Kroizman, T and Schilling, J and Bar-Sagi, D and Lax, I and Schlessinger, J},
	doi = {10.1016/s0092-8674(00)80252-4},
	issn = {0092-8674},
	journal = {Cell},
	month = may,
	number = {5},
	pages = {693--702},
	publisher = {Elsevier BV},
	title = {A Lipid-Anchored Grb2-Binding Protein That Links FGF-Receptor Activation to the Ras/MAPK Signaling Pathway},
	volume = {89},
	year = {1997},
	bdsk-url-1 = {https://doi.org/10.1016/s0092-8674(00)80252-4}}

@article{Lee1994,
	author = {Lee, J. and Ekker, S. and von Kessler, D. and Porter, J. and Sun, B. and Beachy, P.},
	doi = {10.1126/science.7985023},
	issn = {1095-9203},
	journal = {Science},
	month = dec,
	number = {5190},
	pages = {1528--1537},
	publisher = {American Association for the Advancement of Science (AAAS)},
	title = {Autoproteolysis in hedgehog protein biogenesis},
	volume = {266},
	year = {1994},
	bdsk-url-1 = {https://doi.org/10.1126/science.7985023}}

@article{Porter1996,
	author = {Porter, Jeffery A. and Young, Keith E. and Beachy, Philip A.},
	doi = {10.1126/science.274.5285.255},
	issn = {1095-9203},
	journal = {Science},
	month = oct,
	number = {5285},
	pages = {255--259},
	publisher = {American Association for the Advancement of Science (AAAS)},
	title = {Cholesterol Modification of Hedgehog Signaling Proteins in Animal Development},
	volume = {274},
	year = {1996},
	bdsk-url-1 = {https://doi.org/10.1126/science.274.5285.255}}

@article{Ingham2001,
	author = {Ingham, Philip W. and McMahon, Andrew P.},
	doi = {10.1101/gad.938601},
	issn = {1549-5477},
	journal = {Genes & Development},
	month = dec,
	number = {23},
	pages = {3059--3087},
	publisher = {Cold Spring Harbor Laboratory},
	title = {Hedgehog signaling in animal development: paradigms and principles},
	volume = {15},
	year = {2001},
	bdsk-url-1 = {https://doi.org/10.1101/gad.938601}}

@article{Pepinsky1998,
	author = {Pepinsky, R. Blake and Zeng, Chenhui and Wen, Dingyi and Rayhorn, Paul and Baker, Darren P. and Williams, Kevin P. and Bixler, Sarah A. and Ambrose, Christine M. and Garber, Ellen A. and Miatkowski, Konrad and Taylor, Frederick R. and Wang, Elizabeth A. and Galdes, Alphonse},
	doi = {10.1074/jbc.273.22.14037},
	issn = {0021-9258},
	journal = {Journal of Biological Chemistry},
	month = may,
	number = {22},
	pages = {14037--14045},
	publisher = {Elsevier BV},
	title = {Identification of a Palmitic Acid-modified Form of Human Sonic hedgehog},
	volume = {273},
	year = {1998},
	bdsk-url-1 = {https://doi.org/10.1074/jbc.273.22.14037}}

@article{Wang2000,
	author = {Wang, Gelin and Amanai, Kazuhito and Wang, Bing and Jiang, Jin},
	doi = {10.1101/gad.843900},
	issn = {1549-5477},
	journal = {Genes & Development},
	month = nov,
	number = {22},
	pages = {2893--2905},
	publisher = {Cold Spring Harbor Laboratory},
	title = {Interactions with Costal2 and Suppressor of fused regulate nuclear translocation and activity of Cubitus interruptus},
	volume = {14},
	year = {2000},
	bdsk-url-1 = {https://doi.org/10.1101/gad.843900}}

@article{Amanai2001,
	author = {Amanai, Kazuhito and Jiang, Jin},
	doi = {10.1242/dev.128.24.5119},
	issn = {0950-1991},
	journal = {Development},
	month = dec,
	number = {24},
	pages = {5119--5127},
	publisher = {The Company of Biologists},
	title = {Distinct roles of Central missing and Dispatched in sending the Hedgehog signal},
	volume = {128},
	year = {2001},
	bdsk-url-1 = {https://doi.org/10.1242/dev.128.24.5119}}

@article{Chamoun2001,
	author = {Chamoun, Zeina and Mann, Randall K. and Nellen, Denise and von Kessler, Doris P. and Bellotto, Manolo and Beachy, Philip A. and Basler, Konrad},
	doi = {10.1126/science.1064437},
	issn = {1095-9203},
	journal = {Science},
	month = sep,
	number = {5537},
	pages = {2080--2084},
	publisher = {American Association for the Advancement of Science (AAAS)},
	title = {Skinny Hedgehog, an Acyltransferase Required for Palmitoylation and Activity of the Hedgehog Signal},
	volume = {293},
	year = {2001},
	bdsk-url-1 = {https://doi.org/10.1126/science.1064437}}

@article{Lee2001,
	author = {Lee, Jeffrey D. and Treisman, Jessica E.},
	doi = {10.1242/dev.128.9.1519},
	issn = {1477-9129},
	journal = {Development},
	month = may,
	number = {9},
	pages = {1519--1529},
	publisher = {The Company of Biologists},
	title = {The role of Wingless signaling in establishing the anteroposterior and dorsoventral axes of the eye disc},
	volume = {128},
	year = {2001},
	bdsk-url-1 = {https://doi.org/10.1242/dev.128.9.1519}}

@article{Micchelli2002,
	author = {Micchelli, Craig A. and The, Inge and Selva, Erica and Mogila, Vladic and Perrimon, Norbert},
	doi = {10.1242/dev.129.4.843},
	issn = {0950-1991},
	journal = {Development},
	month = feb,
	number = {4},
	pages = {843--851},
	publisher = {The Company of Biologists},
	title = {rasp, a putative transmembrane acyltransferase, is required for Hedgehog signaling},
	volume = {129},
	year = {2002},
	bdsk-url-1 = {https://doi.org/10.1242/dev.129.4.843}}

@article{Alcedo1996,
	author = {Alcedo, Joy and Ayzenzon, Marina and Von Ohlen, Tonia and Noll, Markus and Hooper, Joan E},
	doi = {10.1016/s0092-8674(00)80094-x},
	issn = {0092-8674},
	journal = {Cell},
	month = jul,
	number = {2},
	pages = {221--232},
	publisher = {Elsevier BV},
	title = {The Drosophila smoothened Gene Encodes a Seven-Pass Membrane Protein, a Putative Receptor for the Hedgehog Signal},
	volume = {86},
	year = {1996},
	bdsk-url-1 = {https://doi.org/10.1016/s0092-8674(00)80094-x}}

@article{Chen1996,
	author = {Chen, Yu and Struhl, Gary},
	doi = {10.1016/s0092-8674(00)81374-4},
	issn = {0092-8674},
	journal = {Cell},
	month = nov,
	number = {3},
	pages = {553--563},
	publisher = {Elsevier BV},
	title = {Dual Roles for Patched in Sequestering and Transducing Hedgehog},
	volume = {87},
	year = {1996},
	bdsk-url-1 = {https://doi.org/10.1016/s0092-8674(00)81374-4}}

@article{Lum2003,
	author = {Lum, Lawrence and Yao, Shenqin and Mozer, Brian and Rovescalli, Alessandra and Von Kessler, Doris and Nirenberg, Marshall and Beachy, Philip A.},
	doi = {10.1126/science.1081403},
	issn = {1095-9203},
	journal = {Science},
	month = mar,
	number = {5615},
	pages = {2039--2045},
	publisher = {American Association for the Advancement of Science (AAAS)},
	title = {Identification of Hedgehog Pathway Components by RNAi in Drosophila Cultured Cells},
	volume = {299},
	year = {2003},
	bdsk-url-1 = {https://doi.org/10.1126/science.1081403}}

@article{Ayers2009,
	author = {Ayers, Katie L. and Rodriguez, Ralph and Gallet, Armel and Ruel, Laurent and Th{\'e}rond, Pascal},
	doi = {10.1016/j.ydbio.2009.02.037},
	issn = {0012-1606},
	journal = {Developmental Biology},
	month = may,
	number = {2},
	pages = {280--293},
	publisher = {Elsevier BV},
	title = {Tow (Target of Wingless), a novel repressor of the Hedgehog pathway in Drosophila},
	volume = {329},
	year = {2009},
	bdsk-url-1 = {https://doi.org/10.1016/j.ydbio.2009.02.037}}

@article{Ayers2010,
	author = {Ayers, Katie L. and Th{\'e}rond, Pascal P.},
	doi = {10.1016/j.tcb.2010.02.002},
	issn = {0962-8924},
	journal = {Trends in Cell Biology},
	month = may,
	number = {5},
	pages = {287--298},
	publisher = {Elsevier BV},
	title = {Evaluating Smoothened as a G-protein-coupled receptor for Hedgehog signalling},
	volume = {20},
	year = {2010},
	bdsk-url-1 = {https://doi.org/10.1016/j.tcb.2010.02.002}}

@article{Aikin2008,
	author = {Aikin, Reid A and Ayers, Katie L and Th{\'e}rond, Pascal P},
	doi = {10.1038/embor.2008.38},
	issn = {1469-3178},
	journal = {EMBO reports},
	month = apr,
	number = {4},
	pages = {330--336},
	publisher = {Springer Science and Business Media LLC},
	title = {The role of kinases in the Hedgehog signalling pathway},
	volume = {9},
	year = {2008},
	bdsk-url-1 = {https://doi.org/10.1038/embor.2008.38}}

@article{Wilson2006,
	author = {Wilson, Christopher W. and Chuang, Pao-Tien},
	doi = {10.1016/j.cell.2006.04.016},
	issn = {0092-8674},
	journal = {Cell},
	month = may,
	number = {3},
	pages = {435--438},
	publisher = {Elsevier BV},
	title = {New ``Hogs'' in Hedgehog Transport and Signal Reception},
	volume = {125},
	year = {2006},
	bdsk-url-1 = {https://doi.org/10.1016/j.cell.2006.04.016}}

@article{Fuerstenberg1998,
	author = {Fuerstenberg, Sal and Giniger, Edward},
	doi = {10.1006/dbio.1998.8944},
	issn = {0012-1606},
	journal = {Developmental Biology},
	month = sep,
	number = {1},
	pages = {66--77},
	publisher = {Elsevier BV},
	title = {Multiple Roles forNotchinDrosophilaMyogenesis},
	volume = {201},
	year = {1998},
	bdsk-url-1 = {https://doi.org/10.1006/dbio.1998.8944}}

@article{TapanesCastillo2004,
	author = {Tapanes-Castillo, Alexis and Baylies, Mary K.},
	doi = {10.1242/dev.01113},
	issn = {0950-1991},
	journal = {Development},
	month = may,
	number = {10},
	pages = {2359--2372},
	publisher = {The Company of Biologists},
	title = {Notch signaling patternsDrosophilamesodermal segments by regulating the bHLH transcription factortwist},
	volume = {131},
	year = {2004},
	bdsk-url-1 = {https://doi.org/10.1242/dev.01113}}

@article{Ciglar2009,
	author = {Ciglar, Lucia and Furlong, Eileen EM},
	doi = {10.1016/j.ceb.2009.10.001},
	issn = {0955-0674},
	journal = {Current Opinion in Cell Biology},
	month = dec,
	number = {6},
	pages = {754--760},
	publisher = {Elsevier BV},
	title = {Conservation and divergence in developmental networks: a view from Drosophila myogenesis},
	volume = {21},
	year = {2009},
	bdsk-url-1 = {https://doi.org/10.1016/j.ceb.2009.10.001}}

@article{Baylies1996,
	author = {Baylies, Mary K. and Bate, Michael},
	doi = {10.1126/science.272.5267.1481},
	issn = {1095-9203},
	journal = {Science},
	month = jun,
	number = {5267},
	pages = {1481--1484},
	publisher = {American Association for the Advancement of Science (AAAS)},
	title = {twist: A Myogenic Switch Drosophila},
	volume = {272},
	year = {1996},
}

@article{Bate1993,
	author = {Bate, M and Rushton, E},
	journal = {Comptes rendus de l'Acad\'emie des sciences. S\'erie III, Sciences de la vie},
	month = Sep,
	pages = {1047-61},
	title = {Myogenesis and muscle patterning in Drosophila.},
	volume = {316},
	year = {1993}}

@article{Gupta2020,
	author = {Shantanu Gupta and Daner A. Silveira and Jose Carlos M. Mombach},
	journal = {FEBS Letter},
	month = Oct,
	pages = {227-39},
  doi = {10.1002/1873-3468.13615},
	title = {ATM/miR-34a-5p axis regulates a p21-dependent senescence-apoptosis switch in non-small cell lung cancer: a Boolean model of G1/S checkpoint regulation},
	volume = {594},
	year = {2020}
}

@article{Sanchez2001,
  author = {S\'anchez, Lucas and Thieffry, Denis},
  doi = {10.1006/jtbi.2001.2335},
  journal = {Journal of Theoretical Biology},
  volume = {211},
  number = {2},
  pages = {115--141},
  title = {A Logical Analysis of the Drosophila Gap-gene System},
  year = {2001}
}

@article{Sanchez2003,
  title = {Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module},
  volume = {224},
  DOI = {10.1016/s0022-5193(03)00201-7},
  number = {4},
  journal = {Journal of Theoretical Biology},
  publisher = {Elsevier BV},
  author = {S\'anchez, Lucas and Thieffry, Denis},
  year = {2003},
  month = oct,
  pages = {517-537}
}

@article{Mendoza2006,
  title = {A network model for the control of the differentiation process in Th cells},
  volume = {84},
  ISSN = {0303-2647},
  DOI = {10.1016/j.biosystems.2005.10.004},
  number = {2},
  journal = {Biosystems},
  publisher = {Elsevier BV},
  author = {Mendoza,  Luis},
  year = {2006},
  month = may,
  pages = {101-114}
}

@article{Gonzalez2008,
  title = {Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc},
  volume = {24},
  ISSN = {1367-4803},
  DOI = {10.1093/bioinformatics/btn266},
  number = {16},
  journal = {Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  author = {Gonz\'alez,  Aitor and Chaouiya,  Claudine and Thieffry,  Denis},
  year = {2008},
  month = aug,
  pages = {i234-i240}
}

@article{Sanchez2008,
  title = {Segmenting the fly embryo: logical analysis of the role of the Segment Polarity cross-regulatory module},
  volume = {52},
  ISSN = {0214-6282},
  DOI = {10.1387/ijdb.072439ls},
  number = {8},
  journal = {The International Journal of Developmental Biology},
  publisher = {UPV/EHU Press},
  author = {Sanchez,  Lucas and Chaouiya,  Claudine and Thieffry,  Denis},
  year = {2008},
  pages = {1059-1075}
}

@article{Zhang2008,
  title = {Network model of survival signaling in large granular lymphocyte leukemia},
  volume = {105},
  ISSN = {1091-6490},
  DOI = {10.1073/pnas.0806447105},
  number = {42},
  journal = {Proceedings of the National Academy of Sciences},
  author = {Zhang,  Ranran and Shah,  Mithun Vinod and Yang,  Jun and Nyland,  Susan B. and Liu,  Xin and Yun,  Jong K. and Albert,  R\'eka and Loughran,  Thomas P.},
  year = {2008},
  month = oct,
  pages = {16308-16313}
}

@article{Sahin2009,
  title = {Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance},
  volume = {3},
  ISSN = {1752-0509},
  DOI = {10.1186/1752-0509-3-1},
  number = {1},
  journal = {BMC Systems Biology},
  publisher = {Springer Science and Business Media LLC},
  author = {Sahin,  \"{O}zg\"{u}r and Fr\"{o}hlich,  Holger and L\"{o}bke,  Christian and Korf,  Ulrike and Burmester,  Sara and Majety,  Meher and Mattern,  Jens and Schupp,  Ingo and Chaouiya,  Claudine and Thieffry,  Denis and Poustka,  Annemarie and Wiemann,  Stefan and Beissbarth,  Tim and Arlt,  Dorit},
  year = {2009},
  month = jan 
}

@article{AbouJaoude2009,
  title = {From structure to dynamics: Frequency tuning in the p53-Mdm2 network},
  volume = {258},
  ISSN = {0022-5193},
  DOI = {10.1016/j.jtbi.2009.02.005},
  number = {4},
  journal = {Journal of Theoretical Biology},
  publisher = {Elsevier BV},
  author = {Abou-Jaoud\'e,  Wassim and Ouattara,  Djomangan A. and Kaufman,  Marcelle},
  year = {2009},
  month = jun,
  pages = {561-577}
}

@article{Calzone2010,
  title = {Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement},
  volume = {6},
  ISSN = {1553-7358},
  DOI = {10.1371/journal.pcbi.1000702},
  number = {3},
  journal = {PLoS Computational Biology},
  publisher = {Public Library of Science (PLoS)},
  author = {Calzone,  Laurence and Tournier,  Laurent and Fourquet,  Simon and Thieffry,  Denis and Zhivotovsky,  Boris and Barillot,  Emmanuel and Zinovyev,  Andrei},
  editor = {Ranganathan,  Rama},
  year = {2010},
  month = mar,
  pages = {e1000702}
}

@article{Coolen2012,
  title = {miR-9 Controls the Timing of Neurogenesis through the Direct Inhibition of Antagonistic Factors},
  volume = {22},
  ISSN = {1534-5807},
  DOI = {10.1016/j.devcel.2012.03.003},
  number = {5},
  journal = {Developmental Cell},
  publisher = {Elsevier BV},
  author = {Coolen,  Marion and Thieffry,  Denis and Drivenes,  \Oyvind and Becker,  Thomas S. and Bally-Cuif,  Laure},
  year = {2012},
  month = may,
  pages = {1052-1064}
}

@article{Weinstein2013,
  title = {A network model for the specification of vulval precursor cells and cell fusion control in Caenorhabditis elegans},
  volume = {4},
  ISSN = {1664-8021},
  DOI = {10.3389/fgene.2013.00112},
  journal = {Frontiers in Genetics},
  publisher = {Frontiers Media SA},
  author = {Weinstein,  Nathan and Mendoza,  Luis},
  year = {2013}
}

@article{Mbodj2013,
  title = {Logical modelling of Drosophila signalling pathways},
  volume = {9},
  ISSN = {1742-2051},
  DOI = {10.1039/c3mb70187e},
  number = {9},
  journal = {Molecular BioSystems},
  publisher = {Royal Society of Chemistry (RSC)},
  author = {Mbodj,  Abibatou and Junion,  Guillaume and Brun,  Christine and Furlong,  Eileen E. M. and Thieffry,  Denis},
  year = {2013},
  pages = {2248}
}

@article{Grieco2013,
  title = {Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision},
  volume = {9},
  ISSN = {1553-7358},
  DOI = {10.1371/journal.pcbi.1003286},
  number = {10},
  journal = {PLoS Computational Biology},
  publisher = {Public Library of Science (PLoS)},
  author = {Grieco,  Luca and Calzone,  Laurence and Bernard-Pierrot,  Isabelle and Radvanyi,  Fran\c{c}ois and Kahn-Perl\`es,  Brigitte and Thieffry,  Denis},
  editor = {Miyano,  Satoru},
  year = {2013},
  month = oct,
  pages = {e1003286}
}

@article{Faure2014,
  title = {A Discrete Model of Drosophila Eggshell Patterning Reveals Cell-Autonomous and Juxtacrine Effects},
  volume = {10},
  ISSN = {1553-7358},
  DOI = {10.1371/journal.pcbi.1003527},
  number = {3},
  journal = {PLoS Computational Biology},
  publisher = {Public Library of Science (PLoS)},
  author = {Faur\'e,  Adrien and Vreede,  Barbara M. I. and Sucena,  \'Elio and Chaouiya,  Claudine},
  editor = {Shvartsman,  Stanislav},
  year = {2014},
  month = mar,
  pages = {e1003527}
}

@inbook{Niarakis2014,
  title = {Computational Modeling of the Main Signaling Pathways Involved in Mast Cell Activation},
  ISBN = {9783319079110},
  ISSN = {2196-9965},
  DOI = {10.1007/978-3-319-07911-0_4},
  booktitle = {Fc Receptors},
  publisher = {Springer International Publishing},
  author = {Niarakis,  Anna and Bounab,  Yacine and Grieco,  Luca and Roncagalli,  Romain and Hesse,  Anne-Marie and Garin,  J\'er\^ome and Malissen,  Bernard and Da\"eron,  Marc and Thieffry,  Denis},
  year = {2014},
  pages = {69-93}
}

@article{Mombach2014,
  title = {Modelling the onset of senescence at the G1/S cell cycle checkpoint},
  volume = {15},
  ISSN = {1471-2164},
  DOI = {10.1186/1471-2164-15-s7-s7},
  number = {S7},
  journal = {BMC Genomics},
  publisher = {Springer Science and Business Media LLC},
  author = {Mombach,  Jos\'e CM and Bugs,  Cristhian A and Chaouiya,  Claudine},
  year = {2014},
  month = oct 
}

@article{AbouJaoude2015,
  title = {Model Checking to Assess T-Helper Cell Plasticity},
  volume = {2},
  ISSN = {2296-4185},
  DOI = {10.3389/fbioe.2014.00086},
  journal = {Frontiers in Bioengineering and Biotechnology},
  publisher = {Frontiers Media SA},
  author = {Abou-Jaoud\'e,  Wassim and Monteiro,  Pedro T. and Naldi,  Aur\'elien and Grandclaudon,  Maximilien and Soumelis,  Vassili and Chaouiya,  Claudine and Thieffry,  Denis},
  year = {2015},
  month = jan 
}

@article{Remy2015,
  title = {A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis},
  volume = {75},
  ISSN = {1538-7445},
  DOI = {10.1158/0008-5472.can-15-0602},
  number = {19},
  journal = {Cancer Research},
  publisher = {American Association for Cancer Research (AACR)},
  author = {Remy,  Elisabeth and Rebouissou,  Sandra and Chaouiya,  Claudine and Zinovyev,  Andrei and Radvanyi,  Fran\c{c}ois and Calzone,  Laurence},
  year = {2015},
  month = sep,
  pages = {4042-4052}
}

@article{Flobak2015,
  title = {Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling},
  volume = {11},
  ISSN = {1553-7358},
  DOI = {10.1371/journal.pcbi.1004426},
  number = {8},
  journal = {PLOS Computational Biology},
  publisher = {Public Library of Science (PLoS)},
  author = {Flobak, {\AA}smund and Baudot,  Ana\"is and Remy,  Elisabeth and Thommesen,  Liv and Thieffry,  Denis and Kuiper,  Martin and L{\ae}greid,  Astrid},
  editor = {Xenarios,  Ioannis},
  year = {2015},
  month = aug,
  pages = {e1004426}
}

@article{Cohen2015,
  title = {Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration},
  volume = {11},
  ISSN = {1553-7358},
  DOI = {10.1371/journal.pcbi.1004571},
  number = {11},
  journal = {PLOS Computational Biology},
  publisher = {Public Library of Science (PLoS)},
  author = {Cohen,  David P. A. and Martignetti,  Loredana and Robine,  Sylvie and Barillot,  Emmanuel and Zinovyev,  Andrei and Calzone,  Laurence},
  editor = {Wang,  Edwin},
  year = {2015},
  month = nov,
  pages = {e1004571}
}

@article{Desterke2015,
  title = {Inflammation as a Keystone of Bone Marrow Stroma Alterations in Primary Myelofibrosis},
  volume = {2015},
  ISSN = {1466-1861},
  DOI = {10.1155/2015/415024},
  number = {1},
  journal = {Mediators of Inflammation},
  publisher = {Wiley},
  author = {Desterke,  Christophe and Martinaud,  Christophe and Ruzehaji,  Nadira and Le Bousse-Kerdil\`es,  Marie-Caroline},
  editor = {Hasselbalch,  Hans Carl},
  year = {2015},
  month = jan 
}

@article{Mbodj2016,
  title = {Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes},
  volume = {12},
  ISSN = {1553-7358},
  DOI = {10.1371/journal.pcbi.1005073},
  number = {9},
  journal = {PLOS Computational Biology},
  publisher = {Public Library of Science (PLoS)},
  author = {Mbodj,  Abibatou and Gustafson,  E. Hilary and Ciglar,  Lucia and Junion,  Guillaume and Gonzalez,  Aitor and Girardot,  Charles and Perrin,  Laurent and Furlong,  Eileen E. M. and Thieffry,  Denis},
  editor = {Peirce,  Shayn M},
  year = {2016},
  month = sep,
  pages = {e1005073}
}

@article{Traynard2016,
  title = {Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation},
  volume = {32},
  ISSN = {1367-4811},
  DOI = {10.1093/bioinformatics/btw457},
  number = {17},
  journal = {Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  author = {Traynard,  Pauline and Faur\'e,  Adrien and Fages,  Fran\c{c}ois and Thieffry,  Denis},
  year = {2016},
  month = aug,
  pages = {i772-i780}
}

@article{Verlingue2016,
  title = {A comprehensive approach to the molecular determinants of lifespan using a Boolean model of geroconversion},
  volume = {15},
  ISSN = {1474-9726},
  DOI = {10.1111/acel.12504},
  number = {6},
  journal = {Aging Cell},
  publisher = {Wiley},
  author = {Verlingue,  Loic and Dugourd,  Aur\'elien and Stoll,  Gautier and Barillot,  Emmanuel and Calzone,  Laurence and Londo\~no-Vallejo,  Arturo},
  year = {2016},
  month = sep,
  pages = {1018-1026}
}

@article{Enciso2016,
  title = {Modeling the Pro-inflammatory Tumor Microenvironment in Acute Lymphoblastic Leukemia Predicts a Breakdown of Hematopoietic-Mesenchymal Communication Networks},
  volume = {7},
  ISSN = {1664-042X},
  DOI = {10.3389/fphys.2016.00349},
  journal = {Frontiers in Physiology},
  publisher = {Frontiers Media SA},
  author = {Enciso,  Jennifer and Mayani,  Hector and Mendoza,  Luis and Pelayo,  Rosana},
  year = {2016},
  month = aug 
}

@article{Sanchez2016,
  title = {Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells},
  volume = {10},
  ISSN = {1752-0509},
  DOI = {10.1186/s12918-016-0282-3},
  number = {1},
  journal = {BMC Systems Biology},
  publisher = {Springer Science and Business Media LLC},
  author = {S\'anchez,  Lucas and Chaouiya,  Claudine},
  year = {2016},
  month = may 
}

@inproceedings{SanchezOsorio2017,
  title = {Modeling Asymmetric Cell Division in Caulobacter crescentus Using a Boolean Logic Approach},
  ISBN = {9783319531502},
  ISSN = {1861-0412},
  DOI = {10.1007/978-3-319-53150-2_1},
  booktitle = {Asymmetric Cell Division in Development,  Differentiation and Cancer},
  publisher = {Springer International Publishing},
  author = {S\'anchez-Osorio,  Ismael and Hern\'andez-Mart\'inez,  Carlos A. and Mart\'inez-Antonio,  Agustino},
  year = {2017},
  pages = {1-21}
}

@article{Collombet2017,
  title = {Logical modeling of lymphoid and myeloid cell specification and transdifferentiation},
  volume = {114},
  ISSN = {1091-6490},
  DOI = {10.1073/pnas.1610622114},
  number = {23},
  journal = {Proceedings of the National Academy of Sciences},
  publisher = {Proceedings of the National Academy of Sciences},
  author = {Collombet,  Samuel and van Oevelen,  Chris and Sardina Ortega,  Jose Luis and Abou-Jaoud\'e,  Wassim and Di Stefano,  Bruno and Thomas-Chollier,  Morgane and Graf,  Thomas and Thieffry,  Denis},
  year = {2017},
  month = jun,
  pages = {5792-5799}
}

@article{Sanchez2018,
  title = {Logical modelling uncovers developmental constraints for primary sex determination of chicken gonads},
  volume = {15},
  ISSN = {1742-5662},
  DOI = {10.1098/rsif.2018.0165},
  number = {142},
  journal = {Journal of The Royal Society Interface},
  publisher = {The Royal Society},
  author = {S\'anchez,  Lucas and Chaouiya,  Claudine},
  year = {2018},
  month = may,
  pages = {20180165}
}

@article{RodriguezJorge2019,
  title = {Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4+ T cell activation},
  volume = {12},
  ISSN = {1937-9145},
  DOI = {10.1126/scisignal.aar3641},
  number = {577},
  journal = {Science Signaling},
  publisher = {American Association for the Advancement of Science (AAAS)},
  author = {Rodr\'iguez-Jorge,  Otoniel and Kempis-Calanis,  Linda A. and Abou-Jaoud\'e,  Wassim and Guti\'errez-Reyna,  Darely Y. and Hernandez,  C\'eline and Ramirez-Pliego,  Oscar and Thomas-Chollier,  Morgane and Spicuglia,  Salvatore and Santana,  Maria A. and Thieffry,  Denis},
  year = {2019},
  month = apr 
}

@article{Villanueva2024,
  doi = {10.5281/ZENODO.10901795},
  author = {S\'anchez-Villanueva J and N'Guyen L and Poplineau M and Duprez E and Remy \'E and Thieffry D},
  language = {en},
  title = {Dynamical modelling of the regulatory network underlying Retinoic Acid resistance in Acute Promyelocytic Leukaemia},
  publisher = {Zenodo},
  year = {2024},
  copyright = {Creative Commons Attribution 4.0 International}
}

@article{Villanueva2019,
  title = {Contribution of ROS and metabolic status to neonatal and adult CD8+ T cell activation},
  volume = {14},
  ISSN = {1932-6203},
  DOI = {10.1371/journal.pone.0226388},
  number = {12},
  journal = {PLOS ONE},
  publisher = {Public Library of Science (PLoS)},
  author = {S\'anchez-Villanueva,  Jos\'e Antonio and Rodr\'iguez-Jorge,  Otoniel and Ram\'irez-Pliego,  Oscar and Rosas Salgado,  Gabriela and Abou-Jaoud\'e,  Wassim and Hernandez,  C\'eline and Naldi,  Aur\'elien and Thieffry,  Denis and Santana,  Mar\'ia Ang\'elica},
  editor = {Chatenoud,  Lucienne},
  year = {2019},
  month = dec,
  pages = {e0226388}
}

@inbook{Cacace2020,
  title = {Logical modeling of cell fate specification-Application to T cell commitment},
  ISBN = {9780128131800},
  ISSN = {0070-2153},
  DOI = {10.1016/bs.ctdb.2020.02.008},
  booktitle = {Gene Regulatory Networks},
  publisher = {Elsevier},
  author = {Cacace,  Elisabetta and Collombet,  Samuel and Thieffry,  Denis},
  year = {2020},
  pages = {205-238}
}

@article{CorralJara2021,
  title = {Interplay between SMAD2 and STAT5A is a critical determinant of IL-17A/IL-17F differential expression},
  volume = {2},
  ISSN = {2662-8651},
  DOI = {10.1186/s43556-021-00034-3},
  number = {1},
  journal = {Molecular Biomedicine},
  publisher = {Springer Science and Business Media LLC},
  author = {Corral-Jara,  Karla Fabiola and Chauvin,  Camille and Abou-Jaoud\'e,  Wassim and Grandclaudon,  Maximilien and Naldi,  Aur\'elien and Soumelis,  Vassili and Thieffry,  Denis},
  year = {2021},
  month = apr 
}

@article{Selvaggio2020,
  title = {Hybrid Epithelial-Mesenchymal Phenotypes Are Controlled by Microenvironmental Factors},
  volume = {80},
  ISSN = {1538-7445},
  DOI = {10.1158/0008-5472.can-19-3147},
  number = {11},
  journal = {Cancer Research},
  publisher = {American Association for Cancer Research (AACR)},
  author = {Selvaggio,  Gianluca and Canato,  Sara and Pawar,  Archana and Monteiro,  Pedro T. and Guerreiro,  Patr\'icia S. and Br\'as,  M. Manuela and Janody,  Florence and Chaouiya,  Claudine},
  year = {2020},
  month = jun,
  pages = {2407-2420}
}

@article{Kondratova2020,
  title = {Modelling of Immune Checkpoint Network Explains Synergistic Effects of Combined Immune Checkpoint Inhibitor Therapy and the Impact of Cytokines in Patient Response},
  volume = {12},
  ISSN = {2072-6694},
  DOI = {10.3390/cancers12123600},
  number = {12},
  journal = {Cancers},
  publisher = {MDPI AG},
  author = {Kondratova,  Maria and Barillot,  Emmanuel and Zinovyev,  Andrei and Calzone,  Laurence},
  year = {2020},
  month = dec,
  pages = {3600}
}

@article{Zanudo2018,
  title = {Discrete dynamic network modeling of oncogenic signaling: Mechanistic insights for personalized treatment of cancer},
  volume = {9},
  ISSN = {2452-3100},
  DOI = {10.1016/j.coisb.2018.02.002},
  journal = {Current Opinion in Systems Biology},
  publisher = {Elsevier BV},
  author = {G.T. Za\~nudo,  Jorge and Steinway,  Steven N. and Albert,  R\'eka},
  year = {2018},
  month = jun,
  pages = {1-10}
}

@article{Hernandez2020,
  title = {Computational Verification of Large Logical Models-Application to the Prediction of T Cell Response to Checkpoint Inhibitors},
  volume = {11},
  ISSN = {1664-042X},
  DOI = {10.3389/fphys.2020.558606},
  journal = {Frontiers in Physiology},
  publisher = {Frontiers Media SA},
  author = {Hernandez,  C\'eline and Thomas-Chollier,  Morgane and Naldi,  Aur\'elien and Thieffry,  Denis},
  year = {2020},
  month = sep 
}

@article{Flochlay2020,
  title = {Deciphering and modelling the TGF-$\beta$ signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo},
  ISSN = {0950-1991},
  DOI = {10.1242/dev.189944},
  journal = {Development},
  publisher = {The Company of Biologists},
  author = {Floc'hlay,  Swann and Molina,  Maria Dolores and Hernandez,  C\'eline and Haillot,  Emmanuel and Thomas-Chollier,  Morgane and Lepage,  Thierry and Thieffry,  Denis},
  year = {2020},
  month = jan 
}

@article{Beal2021,
  title = {Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers},
  volume = {17},
  ISSN = {1553-7358},
  DOI = {10.1371/journal.pcbi.1007900},
  number = {1},
  journal = {PLOS Computational Biology},
  publisher = {Public Library of Science (PLoS)},
  author = {B\'eal,  Jonas and Pantolini,  Lorenzo and No\"el,  Vincent and Barillot,  Emmanuel and Calzone,  Laurence},
  editor = {Stelling,  Joerg},
  year = {2021},
  month = jan,
  pages = {e1007900}
}

@article{NunezReza2021,
  title = {Logical modelling of
            in vitro
            differentiation of human monocytes into dendritic cells unravels novel transcriptional regulatory interactions},
  volume = {11},
  ISSN = {2042-8901},
  DOI = {10.1098/rsfs.2020.0061},
  number = {4},
  journal = {Interface Focus},
  publisher = {The Royal Society},
  author = {Nu\~nez-Reza,  Karen J. and Naldi,  Aur\'elien and S\'anchez-Jim\'enez,  Arantza and Leon-Apodaca,  Ana V. and Santana,  M. Ang\'elica and Thomas-Chollier,  Morgane and Thieffry,  Denis and Medina-Rivera,  Alejandra},
  year = {2021},
  month = jun,
  pages = {20200061}
}

@article{Montagud2022,
  title = {Patient-specific Boolean models of signalling networks guide personalised treatments},
  volume = {11},
  ISSN = {2050-084X},
  DOI = {10.7554/elife.72626},
  journal = {eLife},
  publisher = {eLife Sciences Publications,  Ltd},
  author = {Montagud,  Arnau and B\'eal,  Jonas and Tobalina,  Luis and Traynard,  Pauline and Subramanian,  Vigneshwari and Szalai,  Bence and Alf\"{o}ldi,  R\'obert and Pusk\'as,  L\'aszl\'o and Valencia,  Alfonso and Barillot,  Emmanuel and Saez-Rodriguez,  Julio and Calzone,  Laurence},
  year = {2022},
  month = feb 
}

@article{Noel2025,
  title = {Reproducible Boolean model analyses and simulations with the {CoLoMoTo} software suite: a tutorial},
  volume = {15},
  ISSN = {2042-8901},
  DOI = {10.1098/rsfs.2025.0002},
  number = {3},
  journal = {Interface Focus},
  publisher = {The Royal Society},
  author = {No\"el, Vincent and Naldi, Aur\'elien and Calzone, Laurence and Paulev\'e, Loic and Thieffry, Denis},
  year = {2025},
  month = aug 
}

@article{Herault2023,
  title = {A novel Boolean network inference strategy to model early hematopoiesis aging},
  volume = {21},
  ISSN = {2001-0370},
  url = {http://dx.doi.org/10.1016/j.csbj.2022.10.040},
  DOI = {10.1016/j.csbj.2022.10.040},
  journal = {Computational and Structural Biotechnology Journal},
  publisher = {American Association for the Advancement of Science (AAAS)},
  author = {H\'erault, L\'eonard and Poplineau, Mathilde and Duprez, Estelle and Remy, \'Elisabeth},
  year = {2023},
  pages = {21-33}
}

@article{Checcoli2020,
  title = {Dynamical Boolean Modeling of Immunogenic Cell Death},
  volume = {11},
  ISSN = {1664-042X},
  url = {http://dx.doi.org/10.3389/fphys.2020.590479},
  DOI = {10.3389/fphys.2020.590479},
  journal = {Frontiers in Physiology},
  publisher = {Frontiers Media SA},
  author = {Checcoli,  Andrea and Pol,  Jonathan G. and Naldi,  Aurelien and Noel,  Vincent and Barillot,  Emmanuel and Kroemer,  Guido and Thieffry,  Denis and Calzone,  Laurence and Stoll,  Gautier},
  year = {2020},
  month = Nov
}