@article(MITL,
 author       = "Rajeev Alur and Tom\'{a}s Feder and Thomas A. Henzinger",
 year         = "1996",
 title        = "{The Benefits of Relaxing Punctuality}",
 journal      = "Journal of the ACM",
 volume       = "43",
 number       = "1",
 pages        = "116--146",
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)
@incollection(FP-taliro,
 author       = "Yashwanth Singh Rahul Annapureddy and Che Liu and Georgios E. Fainekos and Sriram Sankaranarayanan",
 year         = "2011",
 title        = "{S-TaLiRo: A~Tool for Temporal Logic Falsification for Hybrid Systems}",
 booktitle    = "{Tools and Algorithms for the Construction and Analysis of Systems}",
 series       = "Lecture Notes in Computer Science",
 volume       = "6605",
 publisher    = "Springer",
 pages        = "254--257",
 doi          = "10.1007/978-3-642-19835-9\_21",
)
@incollection(SFM,
 author       = "Lubo\v {s} Brim and Milan \v {C}e\v {s}ka and David \v {S}afr\'anek",
 year         = "2013",
 title        = "Model Checking of Biological Systems",
 editor       = "Marco Bernardo and Erik Vink and Alessandra Pierro and Herbert Wiklicky",
 booktitle    = "Formal Methods for Dynamical Systems",
 series       = "Lecture Notes in Computer Science",
 volume       = "7938",
 publisher    = "Springer Berlin Heidelberg",
 pages        = "63--112",
 doi          = "10.1007/978-3-642-38874-3\_3",
)
@article(biocham,
 author       = "Laurence Calzone and Fran\c {c}ois Fages and Sylvain Soliman",
 year         = "2006",
 title        = "{BIOCHAM: An Environment for Modeling Biological Systems and Formalizing Experimental Knowledge}",
 journal      = "Bioinformatics",
 volume       = "22",
 number       = "14",
 pages        = "1805--1807",
 doi          = "10.1093/bioinformatics/btl172",
)
@book(modelchecking,
 author       = "Edmund M. Clarke and Orna Grumberg and Doron A. Peled",
 year         = "2000",
 title        = "{Model Checking}",
 publisher    = "MIT Press",
)
@book(nonsmooth_analysis,
 author       = "Frank H. Clarke",
 year         = "1983",
 title        = "{Optimization and Nonsmooth Analysis}",
 publisher    = "S.I.A.M.",
)
@inproceedings(Dluhos-stlstar,
 author       = "Petr Dluho\v {s} and Lubo\v {s} Brim and David \v {S}afr\'anek",
 year         = "2012",
 title        = "{On Expressing and Monitoring Oscillatory Dynamics}",
 booktitle    = "{Proceedings First International Workshop on Hybrid Systems and Biology}",
 publisher    = "Open Publ. Assoc.",
 pages        = "73--87",
 doi          = "10.4204/EPTCS.92.6",
)
@incollection(STL-breach,
 author       = "Alexandre Donz\'e",
 year         = "2010",
 title        = "Breach, A Toolbox for Verification and Parameter Synthesis of Hybrid Systems",
 editor       = "Tayssir Touili and Byron Cook and Paul Jackson",
 booktitle    = "Computer Aided Verification",
 series       = "Lecture Notes in Computer Science",
 volume       = "6174",
 publisher    = "Springer Berlin Heidelberg",
 pages        = "167--170",
 doi          = "10.1007/978-3-642-14295-6\_17",
)
@incollection(STL-parameters,
 author       = "Alexandre Donz\'{e} and Gilles Clermont and Axel Legay and Christopher J. Langmead",
 year         = "2009",
 title        = "{Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology}",
 booktitle    = "{Research in Computational Molecular Biology}",
 series       = "Lecture Notes in Computer Science",
 volume       = "5541",
 publisher    = "Springer",
 pages        = "155--169",
 doi          = "10.1007/978-3-642-02008-7\_11",
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@incollection(DFM13,
 author       = "Alexandre Donz\'e and Thomas Ferrère and Oded Maler",
 year         = "2013",
 title        = "Efficient Robust Monitoring for STL",
 editor       = "Natasha Sharygina and Helmut Veith",
 booktitle    = "Computer Aided Verification",
 series       = "Lecture Notes in Computer Science",
 volume       = "8044",
 publisher    = "Springer Berlin Heidelberg",
 pages        = "264--279",
 doi          = "10.1007/978-3-642-39799-8\_19",
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@inproceedings(STL-robustness,
 author       = "Alexandre Donz{\'e} and Oded Maler",
 year         = "2010",
 title        = "{Robust Satisfaction of Temporal Logic over Real-Valued Signals}",
 booktitle    = "{FORMATS 2010}",
 publisher    = "Springer",
 pages        = "92--106",
 doi          = "10.1007/978-3-642-15297-9\_9",
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@manual(parasim,
 organization = "Faculty of Informatics, Masaryk University",
 year         = "2013",
 title        = "{Parasim: Tool for Parallel Simulations and Verification}",
 url          = "https://github.com/sybila/parasim/wiki",
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@incollection(FP-robustness0,
 author       = "Georgios Fainekos and George Pappas",
 year         = "2006",
 title        = "Robustness of Temporal Logic Specifications",
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 booktitle    = "Formal Approaches to Software Testing and Runtime Verification",
 series       = "Lecture Notes in Computer Science",
 volume       = "4262",
 publisher    = "Springer Berlin Heidelberg",
 pages        = "178--192",
 doi          = "10.1007/11940197\_12",
)
@article(FP-robustness,
 author       = "Georgios E. Fainekos and George J. Pappas",
 year         = "2009",
 title        = "{Robustness of Temporal Logic Specifications For Continuous-Time Signals}",
 journal      = "Theoretical Computer Science",
 volume       = "410",
 number       = "42",
 pages        = "4262--4291",
 doi          = "10.1016/j.tcs.2009.06.021",
)
@article(limitcycles,
 author       = "Leon Glass and JoelS. Pasternack",
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 title        = "Prediction of limit cycles in mathematical models of biological oscillations",
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 number       = "1",
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@incollection(eziocav11,
 author       = "Radu Grosu and Gregory Batt and FlavioH. Fenton and James Glimm and Colas Guernic and ScottA. Smolka and Ezio Bartocci",
 year         = "2011",
 title        = "From Cardiac Cells to Genetic Regulatory Networks",
 editor       = "Ganesh Gopalakrishnan and Shaz Qadeer",
 booktitle    = "Computer Aided Verification",
 series       = "Lecture Notes in Computer Science",
 volume       = "6806",
 publisher    = "Springer Berlin Heidelberg",
 pages        = "396--411",
 doi          = "10.1007/978-3-642-22110-1\_31",
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@article(sybi-periodic,
 author       = "Benno Hess",
 year         = "2000",
 title        = "{Periodic Patterns in Biology}",
 journal      = "Naturwissenschaften",
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@article(kaplanthe2008,
 author       = "Shai Kaplan and Anat Bren and Erez Dekel and Uri Alon",
 year         = "2008",
 title        = "The incoherent feed-forward loop can generate non-monotonic input functions for genes",
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@article(SIR,
 author       = "William O. Kermack and Anderson G. McKendrick",
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@article(Kitano-robustness,
 author       = "Hiroaki Kitano",
 year         = "2004",
 title        = "{Biological Robustness}",
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@article(MTL,
 author       = "Ron Koymans",
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@article(Krejci2004152,
 author       = "Pavel Krejci and Vitezslav Bryja and Jiri Pachernik and Ales Hampl and Robert Pogue and Pertchoui Mekikian and William R Wilcox",
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 title        = "{FGF2} inhibits proliferation and alters the cartilage-like phenotype of {RCS} cells",
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@book(lotka,
 author       = "Alfred J. Lotka",
 year         = "1925",
 title        = "Elements of Physical Biology",
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@incollection(Maler_STL,
 author       = "Oded Maler and Dejan Nickovic",
 year         = "2004",
 title        = "Monitoring Temporal Properties of Continuous Signals",
 editor       = "Yassine Lakhnech and Sergio Yovine",
 booktitle    = "Formal Techniques, Modelling and Analysis of Timed and Fault-Tolerant Systems",
 series       = "Lecture Notes in Computer Science",
 volume       = "3253",
 publisher    = "Springer Berlin Heidelberg",
 pages        = "152--166",
 doi          = "10.1007/978-3-540-30206-3\_12",
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@article(biocham-practice,
 author       = "Elisabetta De Maria and Fran\c {c}ois Fages and Aur\'{e}lien Rizk and Sylvain Soliman",
 year         = "2011",
 title        = "{Design, Optimization and Predictions of a~Coupled Model of the Cell Cycle, Circadian Clock, DNA Repair System, Irinotecan Metabolism and Exposure Control under Temporal Logic Constraints}",
 journal      = "Theoretical Computer Science",
 volume       = "412",
 number       = "21",
 pages        = "2108--2127",
 doi          = "10.1016/j.tcs.2010.10.036",
)
@article(robustness-property,
 author       = "Aur{\'e}lien Rizk and Gr{\'e}gory Batt and Fran\c {c}ois Fages and Sylvain Soliman",
 year         = "2011",
 title        = "Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures",
 journal      = "Theor. Comput. Sci.",
 volume       = "412",
 number       = "26",
 pages        = "2827--2839",
 doi          = "10.1016/j.tcs.2010.05.008",
)
@article(FagesRobustness,
 author       = "Aurélien Rizk and Gregory Batt and François Fages and Sylvain Soliman",
 year         = "2009",
 title        = "A general computational method for robustness analysis with applications to synthetic gene networks",
 journal      = "Bioinformatics",
 volume       = "25",
 number       = "12",
 pages        = "i169--i178",
 doi          = "10.1093/bioinformatics/btp200",
)
@article(STL-use,
 author       = "{Szymon Stoma et al.}",
 year         = "2013",
 title        = "STL-based Analysis of TRAIL-induced Apoptosis Challenges the Notion of Type I/Type II Cell Line Classification",
 journal      = "PLoS Comput Biol",
 volume       = "9",
 number       = "5",
 pages        = "e1003056",
 doi          = "10.1371/journal.pcbi.1003056",
)
@mastersthesis(src,
 author       = "Tom\'{a}\v {s} Vejpustek",
 year         = "2013",
 title        = "{Robustness Analysis of Extended Signal Temporal Logic STL*}",
 school       = "Masaryk University, Faculty of Informatics",
 url          = "http://is.muni.cz/th/324713/fi_m/",
)
@article(volterra,
 author       = "Vito Volterra",
 year         = "1928",
 title        = "Variations and Fluctuations of the Number of Individuals in Animal Species living together",
 journal      = "Journal du Conseil",
 volume       = "3",
 number       = "1",
 pages        = "3--51",
 doi          = "10.1093/icesjms/3.1.3",
)