@book(Alon:introduction06,
 author       = "U Alon",
 year         = "2006",
 title        = "An introduction to systems biology: design principles of biological circuits",
 publisher    = "Chapman and Hall/CRC Press",
 address      = "London",
)
@article(Barenco:ranked06,
 author       = "M. Barenco and D. Tomescu and D. Brewer and R. Callard and J. Stark and M. Hubank",
 year         = "2006",
 title        = "Ranked prediction of p53 targets using hidden variable dynamic modeling",
 journal      = "Genome Biology",
 volume       = "7",
 number       = "3",
 pages        = "R25",
 doi          = "10.1186/gb-2006-7-3-r25",
)
@book(Bishop:pattern06,
 author       = "CM Bishop",
 year         = "2006",
 title        = "Pattern recognition and machine learning",
 publisher    = "Springer",
 address      = "Berlin",
)
@article(Bortolussi:fluid12,
 author       = "L Bortolussi and J Hillston",
 year         = "2012",
 title        = "Fluid Model Checking",
 journal      = "CONCUR 2012 -- Concurrency Theory",
 pages        = "333--347",
 doi          = "10.1007/978-3-642-32940-1_24",
)
@article(Elowitz:stochastic02,
 author       = "MB Elowitz and AJ Levine and ED Siggia and PS Swain",
 year         = "2002",
 title        = "Stochastic gene expression in a single cell",
 journal      = "Science",
 volume       = "297",
 pages        = "1183--6",
 doi          = "10.1126/science.1070919",
)
@book(Kampen:stochastic81,
 author       = "NG Van Kampen",
 year         = "1981",
 title        = "Stochastic processes in physics and chemistry",
 publisher    = "North-Holland",
 address      = "Amsterdam",
)
@inproceedings(Lawrence:modelling06,
 author       = "N.D. Lawrence and G. Sanguinetti and M. Rattray",
 year         = "2007",
 title        = "Modelling transcriptional regulation using Gaussian processes",
 editor       = "B Sch\"{o}lkopf and J Platt and T Hoffman",
 booktitle    = "Advances in Neural Information Processing Systems 19",
 pages        = "785--792",
)
@article(Liao:network03,
 author       = "JC Liao and R Boscolo and YL Yang and LM Tran and C Sabatti and VP Roychowdhury",
 year         = "2003",
 title        = "Network component analysis: reconstruction of regulatory signals in biological systems",
 journal      = "Proceedings of the National Academy of Sciences",
 volume       = "100",
 number       = "26",
 pages        = "15522--15527",
 doi          = "10.1073/pnas.2136632100",
)
@article(OconeMillarSanguinetti,
 author       = "A Ocone and AJ Millar and G Sanguinetti",
 year         = "2013",
 title        = "Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics",
 journal      = "Bioinformatics",
 volume       = "29",
 number       = "7",
 pages        = "910--6",
 doi          = "10.1093/bioinformatics/btt069",
)
@article(Ocone:reconstructing11,
 author       = "A Ocone and G Sanguinetti",
 year         = "2011",
 title        = "Reconstructing transcription factor activities in hierarchical transcription network motifs.",
 journal      = "Bioinformatics",
 volume       = "27",
 number       = "20",
 pages        = "2873--9",
 doi          = "10.1093/bioinformatics/btr487",
)
@book(Opper:advanced01,
 author       = "M Opper and D Saad",
 year         = "2001",
 title        = "Advanced mean field methods: theory and practice",
 publisher    = "The MIT Press",
 address      = "Cambridge, MA",
)
@article(Opper:learning10,
 author       = "M Opper and G Sanguinetti",
 year         = "2010",
 title        = "Learning combinatorial transcriptional dynamics from gene expression data.",
 journal      = "Bioinformatics",
 volume       = "26",
 number       = "13",
 pages        = "1623--9",
 doi          = "10.1093/bioinformatics/btq244",
)
@inproceedings(Opper:approximate10,
 author       = "Manfred Opper and Andreas Ruttor and Guido Sanguinetti",
 year         = "2010",
 title        = "Approximate inference in continuous time Gaussian-jump processes",
 editor       = "John D. Lafferty and Christopher K. I. Williams and John Shawe-Taylor and Richard S. Zemel and Aron Culotta",
 booktitle    = "Advances in Neural Information Processing Systems 23",
 pages        = "1831--1839",
)
@inproceedings(Pola:stochastic03,
 author       = "G Pola and ML Bujorianu and J Lygeros and MDD Benedetto",
 year         = "2003",
 title        = "Stochastic hybrid models: An overview",
 booktitle    = "Proceedings of the IFAC Conference on Analysis and Design of Hybrid Systems",
 pages        = "45--50",
)
@book(Ptashne:genes02,
 author       = "M Ptashne and A Gann",
 year         = "2002",
 title        = "Genes and signals",
 publisher    = "Cold Harbor Spring Laboratory Press",
 address      = "New York",
)
@article(Sanguinetti:probabilistic06,
 author       = "G. Sanguinetti and M. Rattray and N.D. Lawrence",
 year         = "2006",
 title        = "A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription",
 journal      = "Bioinformatics",
 volume       = "22",
 number       = "14",
 pages        = "1753--1759",
 doi          = "10.1093/bioinformatics/btl154",
)
@article(Sanguinetti:switching09,
 author       = "Guido Sanguinetti and Andreas Ruttor and Manfred Opper and C Archambeau",
 year         = "2009",
 title        = "Switching regulatory models of cellular stress response.",
 journal      = "Bioinformatics",
 volume       = "25",
 number       = "10",
 pages        = "1280--6",
 doi          = "10.1093/bioinformatics/btp138",
)
@book(Sterratt:principles11,
 author       = "D Sterratt and B Graham and A Gillies and D Willshaw",
 year         = "2011",
 title        = "Principles of computational modelling in neuroscience",
 publisher    = "Cambridge University Press",
 address      = "Cambridge",
 doi          = "10.1017/CBO9780511975899",
)
@article(Swain:intrinsic02,
 author       = "PS Swain and MB Elowitz and ED Siggia",
 year         = "2002",
 title        = "Intrinsic and extrinsic contributions to stochasticity in gene expression",
 journal      = "Proceedings of the National Academy of Sciences",
 volume       = "99",
 number       = "20",
 pages        = "12795--800",
 doi          = "10.1073/pnas.162041399",
)