@manual(SystemVerilog,
 author       = "{Accelera Organization, Inc.}",
 year         = "2004",
 title        = "SystemVerilog 3.1a Language Reference Manual",
)
@article(Alur_MITL,
 author       = "R. Alur and T. Feder and T. A. Henzinger",
 year         = "1996",
 title        = "The benefits of relaxing punctuality",
 journal      = "J ACM",
 volume       = "43",
 number       = "1",
 pages        = "116--146",
 doi          = "10.1145/227595.227602",
)
@article(Alur_TPTL,
 author       = "R. Alur and T. A. Henzinger",
 year         = "1994",
 title        = "A really temporal logic",
 journal      = "J ACM",
 volume       = "41",
 number       = "1",
 pages        = "181--203",
 doi          = "10.1145/174644.174651",
)
@article(Paolo,
 author       = "P. Ballarini and M. L. Guerriero",
 year         = "2010",
 title        = "Query-based verification of qualitative trends and oscillations in biochemical systems",
 journal      = "Theor. Comput. Sci.",
 volume       = "411",
 number       = "20",
 pages        = "2019--2036",
 doi          = "10.1016/j.tcs.2010.02.010",
)
@article(BBS10,
 author       = "J. Barnat and L. Brim and D. \v {S}afr\'anek",
 year         = "2010",
 title        = "High-performance analysis of biological systems dynamics with the DiVin E model checker",
 journal      = "Brief. in Bioinformatics",
 volume       = "11",
 pages        = "301--312",
 doi          = "10.1093/bib/bbp074",
)
@article(Bartocci,
 author       = "E. Bartocci and F. Corradini and E. Merelli and L. Tesei",
 year         = "2010",
 title        = "Detecting synchronisation of biological oscillators by model checking",
 journal      = "Theoretical Computer Science",
 volume       = "411",
 number       = "20",
 pages        = "1999 -- 2018",
 doi          = "10.1016/j.tcs.2009.12.019",
)
@inproceedings(BRJ+05,
 author       = "G. Batt and D. Ropers and H. de Jong and J. Geiselmann and R. Mateescu and M. Page and D. Schneider",
 year         = "2005",
 title        = "Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in {\it Escherichia coli}",
 booktitle    = "ISMB (Supplement of Bioinformatics)",
 pages        = "19--28",
)
@book(GeometricAlgorithms,
 author       = "M. de Berg and O. Cheong and M. van Kreveld and M. Overmars",
 year         = "2008",
 title        = "Computational Geometry: Algorithms and Applications",
 edition      = "3",
 publisher    = "Springer",
 address      = "Berlin",
)
@article(Calzone,
 author       = "L. Calzone and N. Chabrier-rivier and F. Fages and S. Soliman",
 year         = "2006",
 title        = "Machine learning biochemical networks from temporal logic properties",
 journal      = "Trans Comput Syst Biol",
 volume       = "4220",
 pages        = "68--94",
 doi          = "10.1007/11880646\_4",
)
@mastersthesis(Dluhos,
 author       = "P. Dluho\v {s}",
 year         = "2012",
 title        = "Specification and monitoring of oscillation properties in dynamical systems",
 school       = "Masaryk University",
 url          = "http://is.muni.cz/th/269281/fi_m/thesis.pdf",
)
@inproceedings(Donze_Robustness,
 author       = "A. Donz{\'e} and O. Maler",
 year         = "2010",
 title        = "Robust satisfaction of temporal logic over real-valued signals",
 booktitle    = "FORMATS'10",
 publisher    = "Springer-Verlag",
 address      = "Berlin, Heidelberg",
 pages        = "92--106",
 doi          = "10.1007/978-3-642-15297-9\_9",
)
@manual(ATVA,
 author       = "A. Donz\'e and O. Maler and E. Bartocci and D. Nickovic and R. Grosu and S. Smolka",
 year         = "2012",
 title        = "On Temporal Logic and Signal Processing",
 note         = "Accepted to ATVA 2012.",
)
@inproceedings(EF08,
 author       = "C. Eisner and D. Fisman",
 year         = "2008",
 title        = "Augmenting a regular expression-based temporal logic with local variables",
 booktitle    = "FMCAD '08",
 publisher    = "IEEE Press",
 pages        = "23:1--23:8",
 doi          = "10.1.1.140.3930",
)
@article(Elowitz_Repressilator,
 author       = "M. B. Elowitz and S. Leibler",
 year         = "2000",
 title        = "A synthetic oscillatory network of transcriptional regulators",
 journal      = "Nature",
 volume       = "403",
 number       = "6767",
 pages        = "335--338",
 doi          = "10.1038/35002125",
)
@article(Kholodenko,
 author       = "B. N. Kholodenko",
 year         = "2000",
 title        = "Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades",
 journal      = "Eur J Biochem",
 volume       = "267",
 number       = "6",
 pages        = "1583--1588",
 doi          = "10.1046/j.1432-1327.2000.01197.x",
)
@manual(mpt,
 author       = "M. Kvasnica and P. Grieder and M. Baoti\'{c}",
 year         = "2004",
 title        = "{Multi-Parametric Toolbox (MPT)}",
)
@inproceedings(Maler_STL,
 author       = "O. Maler and D. Nickovic",
 year         = "2004",
 title        = "Monitoring temporal properties of continuous signals",
 booktitle    = "Proc. of FORMATS-FTRTFT",
 publisher    = "Springer",
 pages        = "152--166",
 doi          = "10.1.1.102.2905",
)
@incollection(MNP+08,
 author       = "O. Maler and D. Nickovic and A. Pnueli",
 year         = "2008",
 title        = "Checking Temporal Properties of Discrete, Timed and Continuous Behaviors",
 booktitle    = "Pillars of Computer Science",
 series       = "LNCS",
 volume       = "4800",
 publisher    = "Springer",
 pages        = "475--505",
 doi          = "10.1007/978-3-540-78127-1\_26",
)
@article(Pedro11,
 author       = "R. Mateescu and P. T. Monteiro and E. Dumas and H. de Jong",
 year         = "2011",
 title        = "CTRL: Extension of CTL with regular expressions and fairness operators to verify genetic regulatory networks",
 journal      = "Theor. Comput. Sci.",
 volume       = "412",
 number       = "26",
 pages        = "2854--2883",
 doi          = "10.1016/j.tcs.2010.05.009",
)
@article(Miyoshi,
 author       = "F. Miyoshi and Y. Nakayama and K. Kaizu and H. Iwasaki and M. Tomita",
 year         = "2007",
 title        = "A Mathematical Model for the Kai-Protein-Based Chemical Oscillator and Clock Gene Expression Rhythms in Cyanobacteria",
 journal      = "Journal of Biological Rhythms",
 volume       = "22",
 number       = "1",
 pages        = "69--80",
 doi          = "10.1177/0748730406295749",
)
@inproceedings(AMT,
 author       = "D. Nickovic and O. Maler",
 year         = "2007",
 title        = "AMT: a property-based monitoring tool for analog systems",
 booktitle    = "Proceedings of the 5th international conference on Formal modeling and analysis of timed systems",
 series       = "FORMATS'07",
 publisher    = "Springer-Verlag",
 address      = "Berlin, Heidelberg",
 pages        = "304--319",
)
@inproceedings(Rizk,
 author       = "A. Rizk and G. Batt and F. Fages and S. Soliman",
 year         = "2008",
 title        = "On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology",
 booktitle    = "Proc. of CMSB'08",
 publisher    = "Springer",
 pages        = "251--268",
 doi          = "10.1007/978-3-540-88562-7\_19",
)
@article(Nedbal,
 author       = "J. \v {C}erven\'y and L. Nedbal",
 year         = "2009",
 title        = "Metabolic Rhythms of the Cyanobacterium Cyanothece sp. ATCC 51142 Correlate with Modeled Dynamics of Circadian Clock",
 journal      = "J Biol Rhythms",
 volume       = "24",
 number       = "4",
 pages        = "295--303",
 doi          = "10.1177/0748730409338367",
)