@article{10.1093/nar/gkac1041,
author = {Teixeira, Miguel Cacho and Viana, Romeu and Palma, Margarida and Oliveira, Jorge and Galocha, Mónica and Mota, Marta Neves and Couceiro, Diogo and Pereira, Maria Galhardas and Antunes, Miguel and Costa, Inês V and Pais, Pedro and Parada, Carolina and Chaouiya, Claudine and Sá-Correia, Isabel and Monteiro, Pedro Tiago},
title = {{YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis}},
journal = {Nucleic Acids Research},
year = {2022},
month = {11},
doi = {10.1093/nar/gkac1041},
url = {https://doi.org/10.1093/nar/gkac1041},
note = {gkac1041},
eprint = {https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkac1041/46901921/gkac1041.pdf}
}
@article{10.1093/bib/bbac212,
author = {Niarakis, Anna and Waltemath, Dagmar and Glazier, James and Schreiber, Falk and Keating, Sarah M and Nickerson, David and Chaouiya, Claudine and Siegel, Anne and Noël, Vincent and Hermjakob, Henning and Helikar, Tomáš and Soliman, Sylvain and Calzone, Laurence},
title = {{Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology}},
journal = {Briefings in Bioinformatics},
year = {2022},
doi = {10.1093/bib/bbac212},
url = {https://doi.org/10.1093/bib/bbac212}
}
@article{10.1093/bioinformatics/btab229,
author = {Dräger, Andreas and Helikar, Tomáš and Barberis, Matteo and Birtwistle, Marc and Calzone, Laurence and Chaouiya, Claudine and Hasenauer, Jan and Karr, Jonathan R and Niarakis, Anna and Rodríguez Martínez, María and Saez-Rodriguez, Julio and Thakar, Juilee},
title = {{SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems}},
journal = {Bioinformatics},
year = {2021},
abstract = {{Computational models of biological systems can exploit a broad range of rapidly developing approaches, including novel experimental approaches, bioinformatics data analysis, emerging modelling paradigms, data standards and algorithms. A discussion about the most recent advances among experts from various domains is crucial to foster data-driven computational modelling and its growing use in assessing and predicting the behaviour of biological systems. Intending to encourage the development of tools, approaches and predictive models, and to deepen our understanding of biological systems, the Community of Special Interest (COSI) was launched in Computational Modelling of Biological Systems (SysMod) in 2016. SysMod’s main activity is an annual meeting at the Intelligent Systems for Molecular Biology (ISMB) conference, which brings together computer scientists, biologists, mathematicians, engineers, computational and systems biologists. In the five years since its inception, SysMod has evolved into a dynamic and expanding community, as the increasing number of contributions and participants illustrate. SysMod maintains several online resources to facilitate interaction among the community members, including an online forum, a calendar of relevant meetings and a YouTube channel with talks and lectures of interest for the modelling community. For more than half a decade, the growing interest in computational systems modelling and multi-scale data integration has inspired and supported the SysMod community. Its members get progressively more involved and actively contribute to the annual COSI meeting and several related community workshops and meetings, focusing on specific topics, including particular techniques for computational modelling or standardisation efforts.}},
issn = {1367-4803},
doi = {10.1093/bioinformatics/btab229},
url = {https://doi.org/10.1093/bioinformatics/btab229},
note = {btab229},
eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btab229/38831473/btab229.pdf}
}
@article{ijms22094897,
author = {Selvaggio, Gianluca and Chaouiya, Claudine and Janody, Florence},
title = {In Silico Logical Modelling to Uncover Cooperative Interactions in Cancer},
journal = {International Journal of Molecular Sciences},
volume = {22},
year = {2021},
number = {9},
article-number = {4897},
url = {https://www.mdpi.com/1422-0067/22/9/4897},
issn = {1422-0067},
doi = {10.3390/ijms22094897}
}
@article{Niarakis:2021,
author = {Niarakis, Anna and Kuiper, Martin and Ostaszewski, Marek and Malik Sheriff, Rahuman S and Casals-Casas, Cristina and Thieffry, Denis and Freeman, Tom C and Thomas, Paul and Tour{\'e}, Vasundra and Noël, Vincent and Stoll, Gautier and Saez-Rodriguez, Julio and Naldi, Aur{\'e}lien and Oshurko, Eugenia and Xenarios, Ioannis and Soliman, Sylvain and Chaouiya, Claudine and Helikar, Tom\'a\v{s} and Calzone, Laurence},
journal = {Briefings in Bioinformatics},
title = {{Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop}},
year = {2021},
issn = {1477-4054},
note = {bbaa046},
doi = {10.1093/bib/bbaa046},
url = {https://doi.org/10.1093/bib/bbaa046}
}
@article{10.1093/bioinformatics/btaa622,
author = {Tour{\'e}, Vasundra and Vercruysse, Steven and Acencio, Marcio Luis and Lovering, Ruth C and Orchard, Sandra and Bradley, Glyn and Casals-Casas, Cristina and Chaouiya, Claudine and del-Toro, Noemi and Flobak, \r{A}smund and Gaudet, Pascale and Hermjakob, Henning and Hoyt, Charles Tapley and Licata, Luana and L{\ae}greid, Astrid and Mungall, Christopher J and Niknejad, Anne and Panni, Simona and Perfetto, Livia and Porras, Pablo and Pratt, Dexter and Saez-Rodriguez, Julio and Thieffry, Denis and Thomas, Paul D and T\"{u}rei, D{\'e}nes and Kuiper, Martin},
journal = {Bioinformatics},
title = {{The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)}},
year = {2020},
issn = {1367-4803},
note = {btaa622},
doi = {10.1093/bioinformatics/btaa622},
url = {https://doi.org/10.1093/bioinformatics/btaa622}
}
@article{Selvaggio:2020,
author = {Selvaggio, Gianluca and Canato, Sara and Pawar, Archana and Monteiro, Pedro T and Guerreiro, Patr{\'\i}cia S. and Br{\'a}s, M. Manuela and Janody, Florence and Chaouiya, Claudine},
title = {{Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors}},
elocation-id = {canres.3147.2019},
year = {2020},
doi = {10.1158/0008-5472.CAN-19-3147},
publisher = {American Association for Cancer Research},
issn = {0008-5472},
url = {https://cancerres.aacrjournals.org/content/early/2020/03/26/0008-5472.CAN-19-3147},
journal = {Cancer Research}
}
@article{Hucka:2019aa,
author = {Hucka, Michael and Bergmann, Frank T and Chaouiya, Claudine and Dr{\"a}ger, Andreas and Hoops, Stefan and Keating, Sarah M and K{\"o}nig, Matthias and Nov{\`e}re, Nicolas Le and Myers, Chris J and Olivier, Brett G and Sahle, Sven and Schaff, James C and Sheriff, Rahuman and Smith, Lucian P and Waltemath, Dagmar and Wilkinson, Darren J and Zhang, Fengkai},
journal = {J Integr Bioinform},
title = {{The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2}},
year = {2019},
month = {Jun},
number = {2},
volume = {16},
bdsk-url-1 = {http://dx.doi.org/10.1515/jib-2019-0021},
date-added = {2020-03-24 10:05:30 +0000},
date-modified = {2020-03-24 10:09:53 +0000},
doi = {10.1515/jib-2019-0021},
journal-full = {Journal of integrative bioinformatics},
keywords = {Representation; Standards; Systems Biology Markup Language; Visualization},
mesh = {Computer Simulation; Models, Biological; Programming Languages; Systems Biology},
pmc = {PMC6798823},
pmid = {31219795},
pst = {epublish}
}
@article{Tonello2019,
author = {Tonello, Elisa and Farcot, Etienne and Chaouiya, Claudine},
journal = {SIAM Journal on Applied Dynamical Systems},
title = {{Local Negative Circuits and Cyclic Attractors in {B}oolean Networks with at most Five Components}},
year = {2019},
issn = {1536-0040},
month = {jan},
number = {1},
pages = {68--79},
volume = {18},
bdsk-url-1 = {https://epubs.siam.org/doi/10.1137/18M1173988},
bdsk-url-2 = {http://dx.doi.org/10.1137/18M1173988},
date-added = {2019-01-15 22:54:08 +0000},
date-modified = {2019-01-15 22:54:08 +0000},
doi = {10.1137/18M1173988},
url = {https://epubs.siam.org/doi/10.1137/18M1173988}
}
@article{NALDI20112207,
abstract = {To cope with the increasing complexity of regulatory networks, we define a reduction method for multi-valued logical models. Starting with a detailed model, we use decision diagrams to compute reduced models by iteratively ``removing'' regulatory components. To keep a consistent dynamical behaviour, the logical rules associated with the targets of each removed node are actualised to account for the (indirect) effects of its regulators. This construction of reduced models preserves crucial dynamical properties of the original model, including stable states and more complex attractors. In this respect, the relationship between the attractor configuration of the original model and those of reduced models is formally established. We further analyse the issue of attractor reachability. Finally, we illustrate the flexibility and efficiency of the proposed reduction method by its application to a multi-valued model of the fly segment polarity network, which is involved in the control of segmentation during early embryogenesis.},
author = {Aur{\'e}lien Naldi and Elisabeth Remy and Denis Thieffry and Claudine Chaouiya},
date-added = {2018-12-24 10:00:08 +0000},
date-modified = {2018-12-24 10:00:08 +0000},
doi = {https://doi.org/10.1016/j.tcs.2010.10.021},
issn = {0304-3975},
journal = {Theoretical Computer Science},
keywords = {Regulatory networks, Logical modelling, Model reduction, Decision diagrams, Attractors, Drosophila segmentation},
note = {Selected Papers from the 7th International Conference on Computational Methods in Systems Biology},
number = {21},
pages = {2207 - 2218},
title = {Dynamically consistent reduction of logical regulatory graphs},
url = {http://www.sciencedirect.com/science/article/pii/S0304397510005839},
volume = {412},
year = {2011},
bdsk-url-1 = {http://www.sciencedirect.com/science/article/pii/S0304397510005839},
bdsk-url-2 = {https://doi.org/10.1016/j.tcs.2010.10.021}
}
@article{CHAOUIYA2008165,
author = {Claudine Chaouiya and Elisabeth Remy and Denis Thieffry},
date-added = {2018-12-23 17:46:37 +0000},
date-modified = {2018-12-23 17:46:37 +0000},
doi = {https://doi.org/10.1016/j.jda.2007.06.003},
issn = {1570-8667},
journal = {Journal of Discrete Algorithms},
keywords = {Gene networks, Regulatory circuits, Logical modelling, Petri nets, Lambda bacteriophage},
note = {Selected papers from CompBioNets 2004},
number = {2},
pages = {165 - 177},
title = {Petri net modelling of biological regulatory networks},
url = {http://www.sciencedirect.com/science/article/pii/S1570866707000524},
volume = {6},
year = {2008},
bdsk-url-1 = {http://www.sciencedirect.com/science/article/pii/S1570866707000524},
bdsk-url-2 = {https://doi.org/10.1016/j.jda.2007.06.003}
}
@article{Chaouiya2011,
author = {Chaouiya, C. and Naldi, A. and Remy, E. and Thieffry, D.},
date-added = {2018-12-23 17:43:43 +0000},
date-modified = {2018-12-23 17:43:50 +0000},
day = {01},
doi = {10.1007/s11047-010-9178-0},
issn = {1572-9796},
journal = {Natural Computing},
month = {Jun},
number = {2},
pages = {727--750},
title = {Petri net representation of multi-valued logical regulatory graphs},
url = {https://doi.org/10.1007/s11047-010-9178-0},
volume = {10},
year = {2011},
bdsk-url-1 = {https://doi.org/10.1007/s11047-010-9178-0},
bdsk-url-2 = {http://dx.doi.org/10.1007/s11047-010-9178-0}
}
@article{Chaouiya2000,
author = {Chaouiya, Claudine and Liberopoulos, George and Dallery, Yves},
date-added = {2018-12-23 17:37:44 +0000},
date-modified = {2018-12-23 17:37:44 +0000},
day = {01},
doi = {10.1023/A:1007624917603},
issn = {1573-9724},
journal = {IIE Transactions},
month = {Oct},
number = {10},
pages = {999--1012},
title = {The extended kanban control system for production coordination of assembly manufacturing systems},
url = {https://doi.org/10.1023/A:1007624917603},
volume = {32},
year = {2000},
bdsk-url-1 = {https://doi.org/10.1023/A:1007624917603},
bdsk-url-2 = {http://dx.doi.org/10.1023/A:1007624917603}
}
@article{Abou-Jaoude:2014aa,
author = {Abou-Jaoud{\'e}, Wassim and Monteiro, Pedro T and Naldi, Aur{\'e}lien and Grandclaudon, Maximilien and Soumelis, Vassili and Chaouiya, Claudine and Thieffry, Denis},
journal = {Front Bioeng Biotechnol},
title = {Model checking to assess {T}-helper cell plasticity},
year = {2014},
pages = {86},
volume = {2},
bdsk-url-1 = {http://dx.doi.org/10.3389/fbioe.2014.00086},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 10:54:03 +0000},
doi = {10.3389/fbioe.2014.00086},
journal-full = {Frontiers in bioengineering and biotechnology},
keywords = {T-helper lymphocyte; cell differentiation; cell plasticity; logical modeling; model checking; signaling networks},
pmc = {PMC4309205},
pmid = {25674559},
pst = {epublish}
}
@article{Abou-Jaoude:2016aa,
author = {Abou-Jaoud{\'e}, Wassim and Traynard, Pauline and Monteiro, Pedro T and Saez-Rodriguez, Julio and Helikar, Tom{\'a}{\v s} and Thieffry, Denis and Chaouiya, Claudine},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:31:46 +0000},
doi = {10.3389/fgene.2016.00094},
journal = {Front Genet},
journal-full = {Frontiers in genetics},
keywords = {T cells activation and differentiation; attractors; cell cycle control; discrete dynamics; logical modeling; reachability analysis; regulatory and signaling networks; simulation},
pages = {94},
pmc = {PMC4885885},
pmid = {27303434},
pst = {epublish},
title = {Logical Modeling and Dynamical Analysis of Cellular Networks},
volume = {7},
year = {2016},
bdsk-url-1 = {http://dx.doi.org/10.3389/fgene.2016.00094}
}
@article{Berenguier:2013aa,
author = {B{\'e}renguier, D and Chaouiya, C and Monteiro, P T and Naldi, A and Remy, E and Thieffry, D and Tichit, L},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 10:54:11 +0000},
doi = {10.1063/1.4809783},
journal = {Chaos},
journal-full = {Chaos (Woodbury, N.Y.)},
mesh = {Animals; Bacteriophage lambda; Cell Differentiation; Cell Polarity; Computer Simulation; Humans; Models, Biological; Signal Transduction; T-Lymphocytes, Helper-Inducer},
month = {Jun},
number = {2},
pages = {025114},
pmid = {23822512},
pst = {ppublish},
title = {Dynamical modeling and analysis of large cellular regulatory networks},
volume = {23},
year = {2013},
bdsk-url-1 = {http://dx.doi.org/10.1063/1.4809783}
}
@article{Buchel:2013aa,
author = {B{\"u}chel, Finja and Rodriguez, Nicolas and Swainston, Neil and Wrzodek, Clemens and Czauderna, Tobias and Keller, Roland and Mittag, Florian and Schubert, Michael and Glont, Mihai and Golebiewski, Martin and van Iersel, Martijn and Keating, Sarah and Rall, Matthias and Wybrow, Michael and Hermjakob, Henning and Hucka, Michael and Kell, Douglas B and M{\"u}ller, Wolfgang and Mendes, Pedro and Zell, Andreas and Chaouiya, Claudine and Saez-Rodriguez, Julio and Schreiber, Falk and Laibe, Camille and Dr{\"a}ger, Andreas and Le Nov{\`e}re, Nicolas},
journal = {BMC Syst Biol},
title = {{Path2Models:} large-scale generation of computational models from biochemical pathway maps},
year = {2013},
month = {Nov},
pages = {116},
volume = {7},
bdsk-url-1 = {http://dx.doi.org/10.1186/1752-0509-7-116},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 10:54:20 +0000},
doi = {10.1186/1752-0509-7-116},
journal-full = {BMC systems biology},
mesh = {Computer Simulation; Genomics; Humans; Kinetics; Metabolic Networks and Pathways; Software; Systems Biology},
pmc = {PMC4228421},
pmid = {24180668},
pst = {epublish}
}
@article{Castanhinha:2013aa,
author = {Castanhinha, Rui and Ara{\'u}jo, Ricardo and J{\'u}nior, Lu{\'\i}s C and Angielczyk, Kenneth D and Martins, Gabriel G and Martins, Rui M S and Chaouiya, Claudine and Beckmann, Felix and Wilde, Fabian},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 10:54:28 +0000},
doi = {10.1371/journal.pone.0080974},
journal = {PLoS One},
journal-full = {PloS one},
mesh = {Animals; Biological Evolution; Ecosystem; Extinction, Biological; Fossils; Herbivory; Mozambique; Paleontology; Phylogeny; Reptiles; Skull; Tomography, Emission-Computed},
number = {12},
pages = {e80974},
pmc = {PMC3852158},
pmid = {24324653},
pst = {epublish},
title = {Bringing dicynodonts back to life: paleobiology and anatomy of a new emydopoid genus from the Upper Permian of Mozambique},
volume = {8},
year = {2013},
bdsk-url-1 = {http://dx.doi.org/10.1371/journal.pone.0080974}
}
@article{Chaouiya:2006aa,
author = {Chaouiya, Claudine and de Jong, Hidde and Thieffry, Denis},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 10:50:12 +0000},
doi = {10.1016/j.biosystems.2005.10.002},
journal = {Biosystems},
journal-full = {Bio Systems},
mesh = {Models, Biological; Models, Genetic; Systems Theory},
month = {May},
number = {2},
pages = {77-80},
pmid = {16386357},
pst = {ppublish},
title = {Dynamical modeling of biological regulatory networks},
volume = {84},
year = {2006},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.biosystems.2005.10.002}
}
@article{Chaouiya:2007aa,
author = {Chaouiya, Claudine},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 10:54:40 +0000},
doi = {10.1093/bib/bbm029},
journal = {Brief Bioinform},
journal-full = {Briefings in bioinformatics},
mesh = {Animals; Drosophila Proteins; Models, Genetic; Signal Transduction; Systems Biology},
month = {Jul},
number = {4},
pages = {210-9},
pmid = {17626066},
pst = {ppublish},
title = {Petri net modelling of biological networks},
volume = {8},
year = {2007},
bdsk-url-1 = {http://dx.doi.org/10.1093/bib/bbm029}
}
@article{Chaouiya:2012aa,
author = {Chaouiya, Claudine and Naldi, Aur{\'e}lien and Thieffry, Denis},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 10:54:48 +0000},
doi = {10.1007/978-1-61779-361-5_23},
journal = {Methods Mol Biol},
journal-full = {Methods in molecular biology (Clifton, N.J.)},
mesh = {Bacteriolysis; Bacteriophage lambda; Gene Regulatory Networks; Lysogeny; Mathematical Concepts; Models, Genetic; Software; Systems Biology},
pages = {463-79},
pmid = {22144167},
pst = {ppublish},
title = {Logical modelling of gene regulatory networks with GINsim},
volume = {804},
year = {2012},
bdsk-url-1 = {http://dx.doi.org/10.1007/978-1-61779-361-5_23}
}
@article{Chaouiya:2013aa,
author = {Chaouiya, Claudine and B{\'e}renguier, Duncan and Keating, Sarah M and Naldi, Aur{\'e}lien and van Iersel, Martijn P and Rodriguez, Nicolas and Dr{\"a}ger, Andreas and B{\"u}chel, Finja and Cokelaer, Thomas and Kowal, Bryan and Wicks, Benjamin and Gon{\c c}alves, Emanuel and Dorier, Julien and Page, Michel and Monteiro, Pedro T and von Kamp, Axel and Xenarios, Ioannis and de Jong, Hidde and Hucka, Michael and Klamt, Steffen and Thieffry, Denis and Le Nov{\`e}re, Nicolas and Saez-Rodriguez, Julio and Helikar, Tom{\'a}{\v s}},
journal = {BMC Syst Biol},
title = {{SBML} qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools},
year = {2013},
month = {Dec},
pages = {135},
volume = {7},
bdsk-url-1 = {http://dx.doi.org/10.1186/1752-0509-7-135},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 10:54:56 +0000},
doi = {10.1186/1752-0509-7-135},
journal-full = {BMC systems biology},
mesh = {Animals; Cells; Epidermal Growth Factor; Internet; Models, Biological; Programming Languages; Signal Transduction; Tumor Necrosis Factor-alpha},
pmc = {PMC3892043},
pmid = {24321545},
pst = {epublish}
}
@article{Chaouiya:2013ab,
author = {Chaouiya, Claudine and Ourrad, Ouerdia and Lima, Ricardo},
journal = {PLoS One},
title = {Majority rules with random tie-breaking in {B}oolean gene regulatory networks},
year = {2013},
number = {7},
pages = {e69626},
volume = {8},
bdsk-url-1 = {http://dx.doi.org/10.1371/journal.pone.0069626},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 10:55:03 +0000},
doi = {10.1371/journal.pone.0069626},
journal-full = {PloS one},
mesh = {Cell Cycle; Gene Regulatory Networks; Models, Genetic; Saccharomyces cerevisiae},
pmc = {PMC3724945},
pmid = {23922761},
pst = {epublish}
}
@article{Chaouiya:2013ac,
author = {Chaouiya, Claudine and Remy, Elisabeth},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 10:50:12 +0000},
doi = {10.1007/s11538-013-9863-0},
journal = {Bull Math Biol},
journal-full = {Bulletin of mathematical biology},
mesh = {Animals; Gene Regulatory Networks; Humans; Logic; Mathematical Concepts; Models, Genetic},
month = {Jun},
number = {6},
pages = {891-5},
pmid = {23722297},
pst = {ppublish},
title = {Logical modelling of regulatory networks, methods and applications},
volume = {75},
year = {2013},
bdsk-url-1 = {http://dx.doi.org/10.1007/s11538-013-9863-0}
}
@article{Chaouiya:2015aa,
author = {Chaouiya, Claudine and Keating, Sarah M and Berenguier, Duncan and Naldi, Aur{\'e}lien and Thieffry, Denis and van Iersel, Martijn P and Le Nov{\`e}re, Nicolas and Helikar, Tom{\'a}{\v s}},
journal = {J Integr Bioinform},
title = {{The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1}},
year = {2015},
month = {Sep},
number = {2},
pages = {270},
volume = {12},
bdsk-url-1 = {http://dx.doi.org/10.2390/biecoll-jib-2015-270},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:31:58 +0000},
doi = {10.2390/biecoll-jib-2015-270},
journal-full = {Journal of integrative bioinformatics},
mesh = {Animals; Biological Ontologies; Computer Graphics; Datasets as Topic; Documentation; Guidelines as Topic; Humans; Information Storage and Retrieval; Internationality; Models, Biological; Programming Languages; Proteome; Signal Transduction; Systems Biology},
pmid = {26528568},
pst = {epublish}
}
@article{Didier:2011aa,
author = {Didier, Gilles and Remy, Elisabeth and Chaouiya, Claudine},
journal = {J Theor Biol},
title = {Mapping multivalued onto{ B}oolean dynamics},
year = {2011},
month = {Feb},
number = {1},
pages = {177-84},
volume = {270},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.jtbi.2010.09.017},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:33:17 +0000},
doi = {10.1016/j.jtbi.2010.09.017},
journal-full = {Journal of theoretical biology},
mesh = {Algorithms; Cell Nucleus; Cytoplasm; Gene Regulatory Networks; Models, Biological; Proto-Oncogene Proteins c-mdm2; Tumor Suppressor Protein p53},
pmid = {20868697},
pst = {ppublish}
}
@article{Faure:2006aa,
author = {Faur{\'e}, Adrien and Naldi, Aur{\'e}lien and Chaouiya, Claudine and Thieffry, Denis},
journal = {Bioinformatics},
title = {Dynamical analysis of a generic {B}oolean model for the control of the mammalian cell cycle},
year = {2006},
month = {Jul},
number = {14},
pages = {e124-31},
volume = {22},
bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btl210},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:34:18 +0000},
doi = {10.1093/bioinformatics/btl210},
journal-full = {Bioinformatics (Oxford, England)},
mesh = {Animals; Cell Cycle; Cell Cycle Proteins; Computer Simulation; Gene Expression Regulation; Humans; Kinetics; Logistic Models; Models, Biological; Regulatory Elements, Transcriptional; Signal Transduction; Transcription Factors},
pmid = {16873462},
pst = {ppublish}
}
@article{Faure:2009aa,
author = {Faur{\'e}, Adrien and Naldi, Aur{\'e}lien and Lopez, Fabrice and Chaouiya, Claudine and Ciliberto, Andrea and Thieffry, Denis},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:33:29 +0000},
doi = {10.1039/B910101m},
journal = {Mol Biosyst},
journal-full = {Molecular bioSystems},
mesh = {Cell Cycle; Computer Simulation; Fungal Proteins; Models, Biological; Mutation; Saccharomycetales; Signal Transduction; Systems Biology},
month = {Dec},
number = {12},
pages = {1787-96},
pmid = {19763337},
pst = {ppublish},
title = {Modular logical modelling of the budding yeast cell cycle},
volume = {5},
year = {2009},
bdsk-url-1 = {http://dx.doi.org/10.1039/B910101m}
}
@article{Faure:2014aa,
author = {Faur{\'e}, Adrien and Vreede, Barbara M I and Sucena, Elio and Chaouiya, Claudine},
journal = {PLoS Comput Biol},
title = {A discrete model of {D}rosophila eggshell patterning reveals cell-autonomous and juxtacrine effects},
year = {2014},
month = {Mar},
number = {3},
pages = {e1003527},
volume = {10},
bdsk-url-1 = {http://dx.doi.org/10.1371/journal.pcbi.1003527},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:32:12 +0000},
doi = {10.1371/journal.pcbi.1003527},
journal-full = {PLoS computational biology},
mesh = {Animals; Bone Morphogenetic Proteins; Computational Biology; Computer Simulation; Drosophila melanogaster; Egg Proteins; Epidermal Growth Factor; Epithelium; Gene Expression Regulation, Developmental; Gene Regulatory Networks; Morphogenesis; Mutation; Oocytes; Oogenesis; Signal Transduction; Software; Vitelline Membrane},
pmc = {PMC3967936},
pmid = {24675973},
pst = {epublish}
}
@article{Gonzalez:2006aa,
author = {Gonz{\'a}lez, Aitor and Chaouiya, Claudine and Thieffry, Denis},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:34:13 +0000},
doi = {10.1534/genetics.106.061218},
journal = {Genetics},
journal-full = {Genetics},
mesh = {Animals; Body Patterning; Computer Simulation; Drosophila; Drosophila Proteins; Embryo, Nonmammalian; Gene Expression Regulation, Developmental; Genes, Insect; Homeodomain Proteins; Models, Genetic; Mutation; Nuclear Proteins; Proto-Oncogene Proteins; Receptors, Notch; Signal Transduction; Transcription Factors; Wings, Animal; Wnt1 Protein},
month = {Nov},
number = {3},
pages = {1625-34},
pmc = {PMC1667057},
pmid = {16951066},
pst = {ppublish},
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 = {http://dx.doi.org/10.1534/genetics.106.061218}
}
@article{Gonzalez:2006ab,
author = {Gonzalez, A Gonzalez and Naldi, A and S{\'a}nchez, L and Thieffry, D and Chaouiya, C},
journal = {Biosystems},
title = {{GINsim:} a software suite for the qualitative modelling, simulation and analysis of regulatory networks},
year = {2006},
month = {May},
number = {2},
pages = {91-100},
volume = {84},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.biosystems.2005.10.003},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:34:32 +0000},
doi = {10.1016/j.biosystems.2005.10.003},
journal-full = {Bio Systems},
mesh = {Animals; Computer Simulation; Drosophila; Software; Wings, Animal},
pmid = {16434137},
pst = {ppublish}
}
@article{Gonzalez:2008aa,
author = {Gonz{\'a}lez, Aitor and Chaouiya, Claudine and Thieffry, Denis},
journal = {Bioinformatics},
title = {Logical modelling of the role of the {Hh} pathway in the patterning of the Drosophila wing disc},
year = {2008},
month = {Aug},
number = {16},
pages = {i234-40},
volume = {24},
bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btn266},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:33:54 +0000},
doi = {10.1093/bioinformatics/btn266},
journal-full = {Bioinformatics (Oxford, England)},
mesh = {Animals; Body Patterning; Computer Simulation; Drosophila; Drosophila Proteins; Hedgehog Proteins; Logistic Models; Models, Biological; Signal Transduction; Wings, Animal},
pmid = {18689831},
pst = {ppublish}
}
@article{Mendes:2013aa,
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},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:32:55 +0000},
doi = {10.1093/bioinformatics/btt033},
journal = {Bioinformatics},
journal-full = {Bioinformatics (Oxford, England)},
mesh = {Algorithms; Body Patterning; Cell Communication; Computational Biology; Intracellular Signaling Peptides and Proteins; Membrane Proteins; Models, Biological; Receptors, Notch; Signal Transduction},
month = {Mar},
number = {6},
pages = {749-57},
pmid = {23341501},
pst = {ppublish},
title = {Composition and abstraction of logical regulatory modules: application to multicellular systems},
volume = {29},
year = {2013},
bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btt033}
}
@article{Mendes:2018aa,
author = {Mendes, Nuno D and Henriques, Rui and Remy, Elisabeth and Carneiro, Jorge and Monteiro, Pedro T and Chaouiya, Claudine},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:31:00 +0000},
doi = {10.3389/fphys.2018.01161},
journal = {Front Physiol},
journal-full = {Frontiers in physiology},
keywords = {attractors; discrete asynchronous dynamics; logical modeling; reachability; regulatory network},
pages = {1161},
pmc = {PMC6137237},
pmid = {30245634},
pst = {epublish},
title = {Estimating Attractor Reachability in Asynchronous Logical Models},
volume = {9},
year = {2018},
bdsk-url-1 = {http://dx.doi.org/10.3389/fphys.2018.01161}
}
@article{Mombach:2014aa,
author = {Mombach, Jos{\'e} C M and Bugs, Cristhian A and Chaouiya, Claudine},
journal = {BMC Genomics},
title = {Modelling the onset of senescence at the {G1/S} cell cycle checkpoint},
year = {2014},
pages = {S7},
volume = {15 Suppl 7},
bdsk-url-1 = {http://dx.doi.org/10.1186/1471-2164-15-S7-S7},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:32:25 +0000},
doi = {10.1186/1471-2164-15-S7-S7},
journal-full = {BMC genomics},
mesh = {Apoptosis; Ataxia Telangiectasia Mutated Proteins; Cellular Senescence; DNA Damage; DNA Repair; G1 Phase Cell Cycle Checkpoints; Humans; Mitogen-Activated Protein Kinase 14; Models, Biological; Mutation; S Phase Cell Cycle Checkpoints; Signal Transduction},
pmc = {PMC4243082},
pmid = {25573782},
pst = {ppublish}
}
@article{Naldi:2009aa,
author = {Naldi, A and Berenguier, D and Faur{\'e}, A and Lopez, F and Thieffry, D and Chaouiya, C},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:33:36 +0000},
doi = {10.1016/j.biosystems.2009.04.008},
journal = {Biosystems},
journal-full = {Bio Systems},
mesh = {Algorithms; Cell Cycle; Computational Biology; Computer Graphics; Computer Simulation; Gene Expression Profiling; Gene Regulatory Networks; Internet; Models, Theoretical; Schizosaccharomyces; Software; Systems Biology; Systems Theory; User-Computer Interface},
month = {Aug},
number = {2},
pages = {134-9},
pmid = {19426782},
pst = {ppublish},
title = {Logical modelling of regulatory networks with GINsim 2.3},
volume = {97},
year = {2009},
bdsk-url-1 = {http://dx.doi.org/10.1016/j.biosystems.2009.04.008}
}
@article{Naldi:2010aa,
author = {Naldi, Aur{\'e}lien and Carneiro, Jorge and Chaouiya, Claudine and Thieffry, Denis},
journal = {PLoS Comput Biol},
title = {Diversity and plasticity of {Th} cell types predicted from regulatory network modelling},
year = {2010},
month = {Sep},
number = {9},
pages = {e1000912},
volume = {6},
bdsk-url-1 = {http://dx.doi.org/10.1371/journal.pcbi.1000912},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:33:23 +0000},
doi = {10.1371/journal.pcbi.1000912},
journal-full = {PLoS computational biology},
mesh = {Animals; Cell Differentiation; Humans; Interleukins; Lymphocyte Activation; Mice; Models, Immunological; Signal Transduction; Systems Biology; T-Lymphocytes, Helper-Inducer; Transcription Factors},
pmc = {PMC2932677},
pmid = {20824124},
pst = {epublish}
}
@article{Naldi:2015aa,
author = {Naldi, Aur{\'e}lien and Monteiro, Pedro T and M{\"u}ssel, Christoph and {Consortium for Logical Models and Tools} and Kestler, Hans A and Thieffry, Denis and Xenarios, Ioannis and Saez-Rodriguez, Julio and Helikar, Tomas and Chaouiya, Claudine},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:32:05 +0000},
doi = {10.1093/bioinformatics/btv013},
journal = {Bioinformatics},
journal-full = {Bioinformatics (Oxford, England)},
mesh = {Animals; Cells; Computer Simulation; Humans; Metabolic Networks and Pathways; Models, Theoretical; Societies, Scientific; Software; Systems Biology},
month = {Apr},
number = {7},
pages = {1154-9},
pmid = {25619997},
pst = {ppublish},
title = {Cooperative development of logical modelling standards and tools with CoLoMoTo},
volume = {31},
year = {2015},
bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btv013}
}
@article{Naldi:2018aa,
author = {Naldi, Aur{\'e}lien and Hernandez, C{\'e}line and Levy, Nicolas and Stoll, Gautier and Monteiro, Pedro T and Chaouiya, Claudine and Helikar, Tom{\'a}{\v s} and Zinovyev, Andrei and Calzone, Laurence and Cohen-Boulakia, Sarah and Thieffry, Denis and Paulev{\'e}, Lo{\"\i}c},
journal = {Front Physiol},
title = {The {CoLoMoTo} Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks},
year = {2018},
pages = {680},
volume = {9},
bdsk-url-1 = {http://dx.doi.org/10.3389/fphys.2018.00680},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:31:07 +0000},
doi = {10.3389/fphys.2018.00680},
journal-full = {Frontiers in physiology},
keywords = {Boolean networks; Python programming language; computational systems biology; model analysis; reproducibility},
pmc = {PMC6018415},
pmid = {29971009},
pst = {epublish}
}
@article{Naldi:2018ab,
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},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:31:14 +0000},
doi = {10.3389/fphys.2018.00646},
journal = {Front Physiol},
journal-full = {Frontiers in physiology},
keywords = {discrete dynamics; logical model; p53-Mdm2 network; regulatory circuit; regulatory network},
pages = {646},
pmc = {PMC6018412},
pmid = {29971008},
pst = {epublish},
title = {Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0},
volume = {9},
year = {2018},
bdsk-url-1 = {http://dx.doi.org/10.3389/fphys.2018.00646}
}
@article{Remy:2003aa,
author = {Remy, E and Moss{\'e}, B and Chaouiya, C and Thieffry, D},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:34:48 +0000},
journal = {Bioinformatics},
journal-full = {Bioinformatics (Oxford, England)},
mesh = {Algorithms; Computer Simulation; Gene Expression Profiling; Gene Expression Regulation; Models, Biological; Proteome; Signal Transduction},
month = {Oct},
pages = {ii172-8},
pmid = {14534187},
pst = {ppublish},
title = {A description of dynamical graphs associated to elementary regulatory circuits},
volume = {19 Suppl 2},
year = {2003}
}
@article{Remy:2015aa,
author = {Remy, Elisabeth and Rebouissou, Sandra and Chaouiya, Claudine and Zinovyev, Andrei and Radvanyi, Fran{\c c}ois and Calzone, Laurence},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:31:52 +0000},
doi = {10.1158/0008-5472.CAN-15-0602},
journal = {Cancer Res},
journal-full = {Cancer research},
mesh = {Animals; Carcinoma, Transitional Cell; Cell Transformation, Neoplastic; Comparative Genomic Hybridization; Datasets as Topic; Epistasis, Genetic; Gene Deletion; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Gene Regulatory Networks; Genes, Neoplasm; Humans; Mice; Models, Genetic; Mutation; Neoplasm Invasiveness; Neoplasm Proteins; Phenotype; Probability; Urinary Bladder Neoplasms},
month = {Oct},
number = {19},
pages = {4042-52},
pmid = {26238783},
pst = {ppublish},
title = {A Modeling Approach to Explain Mutually Exclusive and Co-Occurring Genetic Alterations in Bladder Tumorigenesis},
volume = {75},
year = {2015},
bdsk-url-1 = {http://dx.doi.org/10.1158/0008-5472.CAN-15-0602}
}
@article{Sahin:2009aa,
author = {Sahin, Ozg{\"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},
journal = {BMC Syst Biol},
title = {Modeling {ERBB } receptor-regulated {G1/S} transition to find novel targets for de novo trastuzumab resistance},
year = {2009},
month = {Jan},
pages = {1},
volume = {3},
bdsk-url-1 = {http://dx.doi.org/10.1186/1752-0509-3-1},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:33:45 +0000},
doi = {10.1186/1752-0509-3-1},
journal-full = {BMC systems biology},
mesh = {Antibodies, Monoclonal; Antibodies, Monoclonal, Humanized; Blotting, Western; Breast Neoplasms; Cell Line, Tumor; Computer Simulation; DNA-Binding Proteins; Drug Delivery Systems; ErbB Receptors; Female; G1 Phase; Humans; Models, Biological; Protein Engineering; Reverse Transcriptase Polymerase Chain Reaction; Signal Transduction; Transcription Factors; Trastuzumab},
pmc = {PMC2652436},
pmid = {19118495},
pst = {epublish}
}
@article{Sanchez:2008aa,
author = {S{\'a}nchez, Lucas and Chaouiya, Claudine and Thieffry, Denis},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:34:02 +0000},
doi = {10.1387/ijdb.072439ls},
journal = {Int J Dev Biol},
journal-full = {The International journal of developmental biology},
mesh = {Animals; Body Patterning; Drosophila; Drosophila Proteins; Feedback, Physiological; Gene Expression Regulation, Developmental; Gene Regulatory Networks; Genes, Insect; Homeodomain Proteins; Models, Biological; Models, Genetic; Mutation; Signal Transduction; Systems Biology; Transcription Factors; Wnt1 Protein},
number = {8},
pages = {1059-75},
pmid = {18956339},
pst = {ppublish},
title = {Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module},
volume = {52},
year = {2008},
bdsk-url-1 = {http://dx.doi.org/10.1387/ijdb.072439ls}
}
@article{Sanchez:2016aa,
abstract = {BACKGROUND: Primary sex determination in placental mammals is a very well studied developmental process. Here, we aim to investigate the currently established scenario and to assess its adequacy to fully recover the observed phenotypes, in the wild type and perturbed situations. Computational modelling allows clarifying network dynamics, elucidating crucial temporal constrains as well as interplay between core regulatory modules.
RESULTS: Relying on a comprehensive revision of the literature, we define a logical model that integrates the current knowledge of the regulatory network controlling this developmental process. Our analysis indicates the necessity for some genes to operate at distinct functional thresholds and for specific developmental conditions to ensure the reproducibility of the sexual pathways followed by bi-potential gonads developing into either testes or ovaries. Our model thus allows studying the dynamics of wild type and mutant XX and XY gonads. Furthermore, the model analysis reveals that the gonad sexual fate results from the operation of two sub-networks associated respectively with an initiation and a maintenance phases. At the core of the process is the resolution of two connected feedback loops: the mutual inhibition of Sox9 and {\ss}-catenin at the initiation phase, which in turn affects the mutual inhibition between Dmrt1 and Foxl2, at the maintenance phase. Three developmental signals related to the temporal activity of those sub-networks are required: a signal that determines Sry activation, marking the beginning of the initiation phase, and two further signals that define the transition from the initiation to the maintenance phases, by inhibiting the Wnt4 signalling pathway on the one hand, and by activating Foxl2 on the other hand.
CONCLUSIONS: Our model reproduces a wide range of experimental data reported for the development of wild type and mutant gonads. It also provides a formal support to crucial aspects of the gonad sexual development and predicts gonadal phenotypes for mutations not tested yet.},
author = {S{\'a}nchez, Lucas and Chaouiya, Claudine},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 10:50:12 +0000},
doi = {10.1186/s12918-016-0282-3},
journal = {BMC Syst Biol},
journal-full = {BMC systems biology},
keywords = {Gene regulatory network; Logical modelling; Placental mammals; Primary sex determination},
mesh = {Animals; Cell Differentiation; Female; Granulosa Cells; Male; Mammals; Models, Biological; Mutation; Placenta; Pregnancy; Sertoli Cells; Sex Determination Processes},
month = {05},
number = {1},
pages = {37},
pmc = {PMC4880855},
pmid = {27229461},
pst = {epublish},
title = {Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells},
volume = {10},
year = {2016},
bdsk-url-1 = {http://dx.doi.org/10.1186/s12918-016-0282-3}
}
@article{Sanchez:2018aa,
author = {S{\'a}nchez, Lucas and Chaouiya, Claudine},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:30:52 +0000},
doi = {10.1098/rsif.2018.0165},
journal = {J R Soc Interface},
journal-full = {Journal of the Royal Society, Interface},
keywords = {chicken; gene regulatory network; logical modelling; primary sex determination},
month = {May},
number = {142},
pmc = {PMC6000168},
pmid = {29792308},
pst = {ppublish},
title = {Logical modelling uncovers developmental constraints for primary sex determination of chicken gonads},
volume = {15},
year = {2018},
bdsk-url-1 = {http://dx.doi.org/10.1098/rsif.2018.0165}
}
@article{Simao:2005aa,
author = {Sim{\~a}o, E and Remy, E and Thieffry, D and Chaouiya, C},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:34:40 +0000},
doi = {10.1093/bioinformatics/bti1130},
journal = {Bioinformatics},
journal-full = {Bioinformatics (Oxford, England)},
mesh = {Computer Simulation; Escherichia coli; Escherichia coli Proteins; Gene Expression Regulation; Models, Biological; Neural Networks (Computer); Signal Transduction; Tryptophan},
month = {Sep},
pages = {ii190-6},
pmid = {16204102},
pst = {ppublish},
title = {Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.coli},
volume = {21 Suppl 2},
year = {2005},
bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/bti1130}
}
@article{Varela:2018aa,
author = {Varela, Pedro L and Ramos, Camila V and Monteiro, Pedro T and Chaouiya, Claudine},
journal = {F1000Res},
title = {{EpiLog: }A software for the logical modelling of epithelial dynamics},
year = {2018},
pages = {1145},
volume = {7},
bdsk-url-1 = {http://dx.doi.org/10.12688/f1000research.15613.1},
date-added = {2018-12-23 10:50:12 +0000},
date-modified = {2018-12-23 17:31:21 +0000},
doi = {10.12688/f1000research.15613.1},
journal-full = {F1000Research},
keywords = {Cellular automaton; Hexagonal grid; Logical modelling; Multicellular regulatory networks},
pmc = {PMC6173114},
pmid = {30363398},
pst = {epublish}
}
@article{Keating2020,
author = {Keating, Sarah M and Waltemath, Dagmar and K\"{o}nig, Matthias and Zhang, Fengkai and Dr\"{a}ger, Andreas and Chaouiya, Claudine and Bergmann, Frank T and Finney, Andrew and Gillespie, Colin S and Helikar, Tom\'a\v{s} and Hoops, Stefan and Malik-Sheriff, Rahuman S and Moodie, Stuart L and Moraru, Ion I and Myers, Chris J and Naldi, Aur{\'e}lien and Olivier, Brett G and Sahle, Sven and Schaff, James C and Smith, Lucian P and Swat, Maciej J and Thieffry, Denis and Watanabe, Leandro and Wilkinson, Darren J and Blinov, Michael L and Begley, Kimberly and Faeder, James R and G\'omez, Harold F and Hamm, Thomas M and Inagaki, Yuichiro and Liebermeister, Wolfram and Lister, Allyson L and Lucio, Daniel and Mjolsness, Eric and Proctor, Carole J and Raman, Karthik and Rodriguez, Nicolas and Shaffer, Clifford A and Shapiro, Bruce E and Stelling, Joerg and Swainston, Neil and Tanimura, Naoki and Wagner, John and Meier-Schellersheim, Martin and Sauro, Herbert M and Palsson, Bernhard and Bolouri, Hamid and Kitano, Hiroaki and Funahashi, Akira and Hermjakob, Henning and Doyle, John C and Hucka, Michael and SBML Level 3 Community members},
journal = {Molecular Systems Biology},
title = {{SBML Level 3}: an extensible format for the exchange and reuse of biological models},
year = {2020},
number = {8},
pages = {e9110},
volume = {16},
abstract = {Abstract Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.},
doi = {10.15252/msb.20199110},
eprint = {https://www.embopress.org/doi/pdf/10.15252/msb.20199110},
keywords = {computational modeling, file format, interoperability, reproducibility, systems biology},
url = {https://www.embopress.org/doi/abs/10.15252/msb.20199110}
}
@article{Monteiro2020,
author = {Pedro T. Monteiro and Tiago Pedreira and Monica Galocha and Miguel C. Teixeira and Claudine Chaouiya},
journal = {Scientific Reports},
title = {Assessing regulatory features of the current transcriptional network of Saccharomyces cerevisiae},
year = {2020},
month = {oct},
number = {1},
volume = {10},
doi = {10.1038/s41598-020-74043-7},
publisher = {Springer Science and Business Media {LLC}}
}
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