@article(bio-robust1,
 author       = "Maximino Aldana and Philippe Cluzel",
 year         = "2003",
 title        = "A natural class of robust networks",
 journal      = "Proceedings of the National Academy of Sciences",
 volume       = "100",
 number       = "15",
 pages        = "8710--8714",
 doi          = "10.1073/pnas.1536783100",
)
@article(timed-automata-alur-dill,
 author       = "Rajeev Alur and David L. Dill",
 year         = "1994",
 title        = "A Theory of Timed Automata",
 journal      = "Theor. Comput. Sci.",
 volume       = "126",
 number       = "2",
 pages        = "183--235",
 doi          = "10.1016/0304-3975(94)90010-8",
)
@article(inverse-ta1,
 author       = "\'{E}tienne Andr\'{e} and Thomas Chatain and Laurent Fribourg and Emmanuelle Encrenaz",
 year         = "2008",
 title        = "An Inverse Method for Parametric Timed Automata",
 journal      = "Electronic Notes in Theoretical Computer Science",
 volume       = "223",
 number       = "0",
 pages        = "29 -- 46",
 doi          = "10.1016/j.entcs.2008.12.029",
)
@inproceedings(imitator2,
 author       = "{\'E}tienne Andr{\'e}",
 year         = "2010",
 title        = "{IMITATOR II}: A Tool for Solving the Good Parameters Problem in Timed Automata",
 booktitle    = "INFINITY",
 pages        = "91--99",
 doi          = "10.4204/EPTCS.39.7",
)
@inproceedings(robust-ta1,
 author       = "Patricia Bouyer and Nicolas Markey and Pierre-Alain Reynier",
 year         = "2006",
 title        = "Robust Model-Checking of Linear-Time Properties in Timed Automata",
 booktitle    = "LATIN",
 pages        = "238--249",
 doi          = "10.1007/11682462_25",
)
@incollection(biocham,
 author       = "Nathalie Chabrier-Rivier and François Fages and Sylvain Soliman",
 year         = "2005",
 title        = "The Biochemical Abstract Machine BIOCHAM",
 editor       = "Vincent Danos and Vincent Schachter",
 booktitle    = "Computational Methods in Systems Biology",
 series       = "Lecture Notes in Computer Science",
 volume       = "3082",
 publisher    = "Springer Berlin Heidelberg",
 pages        = "172--191",
 doi          = "10.1007/978-3-540-25974-9_14",
)
@incollection(ginsim,
 author       = "Claudine Chaouiya and Elisabeth Remy and Brigitte Moss\'{e} and Denis Thieffry",
 year         = "2003",
 title        = "Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework",
 editor       = "Luca Benvenuti and Alberto De Santis and Lorenzo Farina",
 booktitle    = "Positive Systems",
 series       = "Lecture Notes in Control and Information Sciences",
 volume       = "294",
 publisher    = "Springer",
 address      = "Berlin / Heidelberg",
 pages        = "830--832",
 doi          = "10.1007/978-3-540-44928-7_17",
)
@article(biopepa-interface,
 author       = "Federica Ciocchetta and Adam Duguid and Stephen Gilmore and Maria Luisa Guerriero and Jane Hillston",
 year         = "2009",
 title        = "{The Bio-PEPA Tool Suite}",
 journal      = "International Conference on Quantitative Evaluation of Systems",
 pages        = "309--310",
 doi          = "10.1109/QEST.2009.27",
)
@inproceedings(robust-ta2,
 author       = "Conrado Daws and Piotr Kordy",
 year         = "2006",
 title        = "Symbolic Robustness Analysis of Timed Automata",
 booktitle    = "FORMATS",
 pages        = "143--155",
 doi          = "10.1007/11867340_11",
)
@article(blenx,
 author       = "Lorenzo Dematt\'{e} and Corrado Priami and Alessandro Romanel",
 year         = "2008",
 title        = "{Modelling and simulation of biological processes in BlenX}",
 journal      = "SIGMETRICS Perform. Eval. Rev.",
 volume       = "35",
 pages        = "32--39",
 doi          = "10.1145/1364644.1364653",
)
@inproceedings(breach,
 author       = "Alexandre Donz{\'e}",
 year         = "2010",
 title        = "Breach, a Toolbox for Verification and Parameter Synthesis of Hybrid Systems",
 booktitle    = "Proceedings of the 22Nd International Conference on Computer Aided Verification",
 series       = "CAV'10",
 publisher    = "Springer-Verlag",
 address      = "Berlin, Heidelberg",
 pages        = "167--170",
 doi          = "10.1007/978-3-642-14295-6_17",
)
@article(ex-bio,
 author       = "Jasmin Fisher and Thomas A. Henzinger",
 year         = "2007",
 title        = "{Executable cell biology.}",
 journal      = "Nature Biotechnology",
 volume       = "25",
 number       = "11",
 pages        = "1239--1249",
 doi          = "10.1038/nbt1356",
)
@incollection(inverse-ta2,
 author       = "Laurent Fribourg and Ulrich K\"{u}hne",
 year         = "2011",
 title        = "Parametric Verification and Test Coverage for Hybrid Automata Using the Inverse Method",
 editor       = "Giorgio Delzanno and Igor Potapov",
 booktitle    = "Reachability Problems",
 series       = "LNCS",
 volume       = "6945",
 publisher    = "Springer Berlin Heidelberg",
 pages        = "191--204",
 doi          = "10.1007/978-3-642-24288-5_17",
)
@book(thread-pool,
 author       = "Rajat P. Garg and Ilya Sharapov",
 year         = "2002",
 title        = "Techniques for Optimizing Applications: High Performance Computing",
 publisher    = "Prentice Hall Professional Technical Reference",
)
@article(param-mc,
 author       = "Thomas Hune and Judi Romijn and Mari\"{e}lle Stoelinga and Frits Vaandrager",
 year         = "2002",
 title        = "Linear parametric model checking of timed automata",
 journal      = "The Journal of Logic and Algebraic Programming",
 volume       = "52-53",
 number       = "0",
 pages        = "183 -- 220",
 doi          = "10.1016/S1567-8326(02)00037-1",
)
@article(gna,
 author       = "Hidde de Jong and Johannes Geiselmann and C\'{e}line Hernandez and Michel Page",
 year         = "2003",
 title        = "{Genetic Network Analyzer: qualitative simulation of genetic regulatory networks}",
 journal      = "Bioinformatics",
 volume       = "19",
 number       = "3",
 pages        = "336--344",
 doi          = "10.1093/bioinformatics/btf851",
)
@article(cytoscape,
 author       = "Sarah Killcoyne and Gregory W. Carter and Jennifer Smith and John Boyle",
 year         = "2009",
 title        = "{Cytoscape: a community-based framework for network modeling.}",
 journal      = "Methods in molecular biology (Clifton, N.J.)",
 volume       = "563",
 pages        = "219--239",
 doi          = "10.1007/978-1-60761-175-2_12",
)
@article(robust-ta3,
 author       = "P. T. {Kordy} and R. {Langerak} and J. W. {Polderman}",
 year         = "2010",
 title        = "Re-verification of a {L}ip Synchronization Protocol using Robust Reachability",
 journal      = "Electronic Proceedings in Theoretical Computer Science",
 volume       = "20",
 pages        = "49--62",
 doi          = "10.4204/EPTCS.20.5",
)
@article(kinfer,
 author       = "Paola Lecca and Alida Palmisano and Adaoha Ihekwaba and Corrado Priami",
 year         = "2010",
 title        = "Calibration of dynamic models of biological systems with KInfer",
 journal      = "European Biophysics Journal",
 volume       = "39",
 number       = "6",
 pages        = "1019 -- 1039",
 doi          = "10.1007/s00249-009-0520-3",
)
@article(bio-robust2,
 author       = "Petros Lenas and Malcolm Moos Jr. and Frank P. Luyten",
 year         = "2009",
 title        = "Developmental Engineering: A New Paradigm for the Design and Manufacturing of Cell-Based Products. Part II. From Genes to Networks: Tissue Engineering from the Viewpoint of Systems Biology and Network Science",
 journal      = "Tissue Engineering Part B: Reviews",
 volume       = "15",
 number       = "4",
 pages        = "395--422",
 doi          = "10.1089/ten.teb.2009.0461",
)
@article(bayes-infer,
 author       = "Wenhui Liao and Qiang Ji",
 year         = "2009",
 title        = "Learning Bayesian network parameters under incomplete data with domain knowledge",
 journal      = "Pattern Recognition",
 volume       = "42",
 number       = "11",
 pages        = "3046 -- 3056",
 doi          = "10.1016/j.patcog.2009.04.006",
)
@incollection(copasi,
 author       = "Pedro Mendes and Stefan Hoops and Sven Sahle and Ralph Gauges and Joseph Dada and Ursula Kummer",
 year         = "2009",
 title        = "{Computational modeling of biochemical networks using COPASI systems biology}",
 editor       = "Ivan V. Maly and John M. Walker and John M. Walker",
 booktitle    = "Systems Biology",
 chapter      = "2",
 series       = "Methods in Molecular Biology",
 volume       = "500",
 publisher    = "Humana Press",
 address      = "Totowa, NJ",
 pages        = "17--59",
 doi          = "10.1007/978-1-59745-525-1_2",
)
@inproceedings(decidability-ta-ha,
 author       = "Joseph S. Miller",
 year         = "2000",
 title        = "Decidability and Complexity Results for Timed Automata and Semi-linear Hybrid Automata",
 booktitle    = "Proceedings of the Third International Workshop on Hybrid Systems: Computation and Control",
 series       = "HSCC '00",
 publisher    = "Springer-Verlag",
 address      = "London, UK",
 pages        = "296--309",
 doi          = "10.1007/3-540-46430-1_26",
)
@article(cell-illustrator,
 author       = "Masao Nagasaki and Ayumu Saito and Euna Jeong and Chen Li and Kaname Kojima and Emi Ikeda and Satoru Miyano",
 year         = "2011",
 title        = "Cell illustrator 4.0: a computational platform for systems biology.",
 journal      = "Stud Health Technol Inform",
 volume       = "162",
 pages        = "160--81",
)
@article(priami-alg-sys-bio,
 author       = "Corrado Priami",
 year         = "2009",
 title        = "Algorithmic systems biology",
 journal      = "Commun. ACM",
 volume       = "52",
 pages        = "80--88",
 doi          = "10.1145/1506409.1506427",
)
@article(animo-ieee,
 author       = "Stefano Schivo and Jetse Scholma and Brend Wanders and Ricardo A. Urquidi Camacho and Paul E. van der Vet and Marcel Karperien and Rom Langerak and Jaco van de Pol and Janine N. Post",
 year         = "2013",
 title        = "Modelling biological pathway dynamics with {Timed Automata}",
 journal      = "IEEE Journal of Biomedical and Health Informatics",
 volume       = "In press",
 doi          = "10.1109/JBHI.2013.2292880",
)
@article(animo-gene,
 author       = "Jetse Scholma and Stefano Schivo and Ricardo A. Urquidi Camacho and Jaco van de Pol and Marcel Karperien and Janine N. Post",
 year         = "2014",
 title        = "Biological networks 101: Computational modeling for molecular biologists",
 journal      = "Gene",
 volume       = "533",
 number       = "1",
 pages        = "379--384",
 doi          = "10.1016/j.gene.2013.10.010",
)
@article(rulebender,
 author       = "Adam Smith and Wen Xu and Yao Sun and James Faeder and G Elisabeta Marai",
 year         = "2012",
 title        = "RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry",
 journal      = "BMC Bioinformatics",
 volume       = "13",
 number       = "Suppl 8",
 pages        = "S3",
 doi          = "10.1186/1471-2105-13-S8-S3",
)
@incollection(test-based-modelling,
 author       = "Jan Tretmans",
 year         = "2011",
 title        = "Model-Based Testing and Some Steps towards Test-Based Modelling",
 editor       = "Marco Bernardo and Val\'{e}rie Issarny",
 booktitle    = "Formal Methods for Eternal Networked Software Systems",
 series       = "Lecture Notes in Computer Science",
 volume       = "6659",
 publisher    = "Springer",
 address      = "Berlin / Heidelberg",
 pages        = "297--326",
 doi          = "10.1007/978-3-642-21455-4_9",
)
@article(robust-ta4,
 author       = "Martin Wulf and Laurent Doyen and Nicolas Markey and Jean-Fran\c {c}ois Raskin",
 year         = "2008",
 title        = "Robust safety of timed automata",
 journal      = "Form. Methods Syst. Des.",
 volume       = "33",
 number       = "1-3",
 pages        = "45--84",
 doi          = "10.1007/s10703-008-0056-7",
)