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Paper.bib
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@article{sbml,
author = {Hucka, M. and Finney, A. and Sauro, H. M. and Bolouri, H. and Doyle, J. C. and Kitano, H. and the rest of
the SBML Forum},
title = {The systems biology markup language ({SBML}): a medium for representation and exchange of biochemical network
models},
volume = {19},
number = {4},
pages = {524--531},
year = {2003},
journal = {Bioinformatics}
}
@article{cytoscape,
title = {{Cytoscape: a community-based framework for network modeling.}},
author = {Killcoyne, Sarah and Carter, Gregory W. and Smith, Jennifer and Boyle, John},
issn = {1064-3745},
journal = {Methods in molecular biology (Clifton, N.J.)},
pages = {219--239},
priority = {2},
volume = {563},
UNUSEDdoi={10.1007/978-1-60761-175-2_12},
year = {2009}
}
@article {uppaal,
author = {Larsen, Kim G. and Pettersson, Paul and Yi, Wang},
affiliation = {Department of Computer Science and Mathematics, Aalborg University, Denmark; E-mail: [email protected] DK},
title = {{UPPAAL} in a nutshell},
journal = {International Journal on Software Tools for Technology Transfer (STTT)},
publisher = {Springer Berlin / Heidelberg},
issn = {1433-2779},
pages = {134--152},
volume = {1},
issue = {1},
year = {1997}
}
@incollection {uppaal-smc,
author = {David, Alexandre and Larsen, Kim and Legay, Axel and Miku\v{c}ionis, Marius and Wang, Zheng},
affiliation = {Computer Science, Aalborg University, Denmark},
title = {Time for Statistical Model Checking of Real-Time Systems},
booktitle = {Computer Aided Verification},
series = {Lecture Notes in Computer Science},
editor = {Gopalakrishnan, Ganesh and Qadeer, Shaz},
publisher = {Springer},
address = {Berlin / Heidelberg},
isbn = {978-3-642-22109-5},
keyword = {Computer Science},
pages = {349-355},
volume = {6806},
year = {2011}
}
@incollection {uppaal-tutorial,
author = {Behrmann, Gerd and David, Alexandre and Larsen, Kim},
affiliation = {Department of Computer Science, Aalborg University, Denmark},
title = {A Tutorial on {UPPAAL}},
booktitle = {Formal Methods for the Design of Real-Time Systems},
series = {Lecture Notes in Computer Science},
editor = {Bernardo, Marco and Corradini, Flavio},
publisher = {Springer Berlin / Heidelberg},
isbn = {},
pages = {33--35},
volume = {3185},
year = {2004}
}
@article{timed-automata-alur-dill,
author = {Rajeev Alur and
David L. Dill},
title = {A Theory of Timed Automata},
journal = {Theor. Comput. Sci.},
volume = {126},
number = {2},
year = {1994},
UNUSEDdoi = {10.1016/0304-3975(94)90010-8},
pages = {183-235}
}
@article{timed-automata,
author = {Bengtsson, Johan and Yi, Wang},
journal = {Lectures on Concurrency and Petri Nets},
keywords = {rts, ta, uppaal},
pages = {87--124},
posted-at = {2009-08-21 18:53:46},
priority = {2},
title = {{Timed Automata}: semantics, algorithms and tools},
year = {2004}
}
@article{ta-audio-protocol,
title = "Automated verification of an audio-control protocol using {UPPAAL}",
journal = "The Journal of Logic and Algebraic Programming",
volume = "52-53",
number = "0",
pages = "163 - 181",
year = "2002",
issn = "1567-8326",
author = "J. Bengtsson and W.O. David Griffioen and K. J. Kristoffersen and K. G. Larsen and F. Larsson and P. Pettersson and W. Yi"
}
@inproceedings{ta-wap-gateway,
author = {Hessel, Anders and Pettersson, Paul},
title = {Model-based testing of a WAP gateway: an industrial case-study},
booktitle = {Proceedings of the 11th international workshop, FMICS 2006 and 5th international workshop, PDMC conference on Formal methods: Applications and technology},
series = {FMICS'06/PDMC'06},
year = {2007},
isbn = {978-3-540-70951-0},
location = {Bonn, Germany},
pages = {116--131},
numpages = {16},
publisher = {Springer-Verlag},
address = {Berlin, Heidelberg}
}
@article{ta-ws-bap,
year={2013},
issn={1433-2779},
journal={International Journal on Software Tools for Technology Transfer},
volume={15},
number={2},
title={Model-checking web services business activity protocols},
publisher={Springer-Verlag},
author={A. P. {Marques Jr.} and A. P. Ravn and J. Srba and S. Vighio},
pages={125-147}
}
@incollection {model-checking,
author = {Clarke, Edmund},
affiliation = {Carnegie Mellon Department of Computer Science Pittsburgh},
title = {Model checking},
booktitle = {Foundations of Software Technology and Theoretical Computer Science},
series = {Lecture Notes in Computer Science},
editor = {Ramesh, S. and Sivakumar, G},
publisher = {Springer},
address = {Berlin / Heidelberg},
isbn = {},
pages = {54--56},
volume = {1346},
year = {1997}
}
@article{ctl,
title = "Using branching time temporal logic to synthesize synchronization skeletons ",
journal = "Science of Computer Programming ",
volume = "2",
number = "3",
pages = "241 - 266",
year = "1982",
issn = "0167-6423",
author = "E. Allen Emerson and Edmund M. Clarke"
}
@article {model-checking-biology,
author = {Antoniotti, Marco and Policriti, Alberto and Ugel, Nadia and Mishra, Bud},
affiliation = {New York University Courant Institute of Mathematical Sciences NY},
title = {Model building and model checking for biochemical processes},
journal = {Cell Biochemistry and Biophysics},
publisher = {Humana Press Inc.},
issn = {1085-9195},
keyword = {Biomedical and Life Sciences},
pages = {271--286},
volume = {38},
issue = {3},
year = {2003}
}
@article{ex-bio,
author = {Fisher, Jasmin and Henzinger, Thomas A.},
day = {07},
issn = {1087-0156},
journal = {Nature Biotechnology},
keywords = {executable},
month = nov,
number = {11},
pages = {1239--1249},
publisher = {Nature Publishing Group},
title = {{Executable cell biology.}},
volume = {25},
UNUSEDdoi = {10.1038/nbt1356},
year = {2007}
}
@article{priami-alg-sys-bio,
author = {Priami, Corrado},
title = {Algorithmic systems biology},
journal = {Commun. ACM},
issue_date = {May 2009},
volume = {52},
issue = {5},
month = {May},
year = {2009},
issn = {0001-0782},
pages = {80--88},
numpages = {9},
acmid = {1506427},
publisher = {ACM},
address = {New York, NY, USA},
UNUSEDdoi = {10.1145/1506409.1506427}
}
@article{user-centered-design,
author = {Pavelin, Katrina and Cham, Jennifer A. and de Matos, Paula and Brooksbank, Cath and Cameron, Graham and Steinbeck, Christoph},
journal = {PLoS Comput Biol},
publisher = {Public Library of Science},
title = {Bioinformatics Meets User-Centred Design: a Perspective},
year = {2012},
month = {07},
volume = {8},
pages = {e1002554},
number = {7}
}
@article{kwiatowska-heath-pathways,
author = {Kwiatkowska, Marta Z. and Heath, John K.},
title = {Biological pathways as communicating computer systems},
booktitle = {J Cell Sci},
day = {15},
issn = {0021-9533},
journal = {Journal of Cell Science},
keywords = {pathways, review},
month = aug,
number = {16},
pages = {2793--2800},
volume = {122},
year = {2009}
}
@ARTICLE{hidde-review,
author = {Hidde {de Jong}},
title = {Modeling and simulation of genetic regulatory systems: A literature review},
journal = {Journal of Computational Biology},
year = {2002},
volume = {9},
pages = {67--103}
}
@article{gna,
author = {de Jong, Hidde and Geiselmann, Johannes and Hernandez, C\'{e}line and Page, Michel},
day = {12},
journal = {Bioinformatics},
month = feb,
number = {3},
pages = {336--344},
priority = {2},
title = {{Genetic Network Analyzer: qualitative simulation of genetic regulatory networks}},
volume = {19},
UNUSEDdoi = {10.1093/bioinformatics/btf851},
year = {2003}
}
@article{hidde-templates,
author = {Monteiro, Pedro T. and Ropers, Delphine and Mateescu, Radu and Freitas, Ana T. and de Jong, Hidde},
title = {Temporal logic patterns for querying dynamic models of cellular interaction networks},
volume = {24},
number = {16},
pages = {i227-i233},
year = {2008},
journal = {Bioinformatics}
}
@article{logic-based-models,
author = {Morris, Melody K. and Saez-Rodriguez, Julio and Sorger, Peter K. and Lauffenburger, Douglas A.},
day = {20},
issn = {1520-4995},
journal = {Biochemistry},
keywords = {networks},
month = apr,
number = {15},
pages = {3216--3224},
title = {{Logic-based models for the analysis of cell signaling networks.}},
volume = {49},
year = {2010}
}
@article{cellnopt,
AUTHOR = {Terfve, Camille and Cokelaer, Thomas and Henriques, David and MacNamara, Aidan and Goncalves, Emanuel and Morris, Melody and Iersel, Martijn van and Lauffenburger, Douglas and Saez-Rodriguez, Julio},
TITLE = {CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms},
JOURNAL = {BMC Systems Biology},
VOLUME = {6},
YEAR = {2012},
NUMBER = {1},
PAGES = {133},
URL = {http://www.biomedcentral.com/1752-0509/6/133},
ISSN = {1752-0509}
}
@article{cellnoptr,
AUTHOR = {Terfve, Camille and Cokelaer, Thomas and Henriques, David and MacNamara, Aidan and Goncalves, Emanuel and Morris, Melody and Iersel, Martijn van and Lauffenburger, Douglas and Saez-Rodriguez, Julio},
TITLE = {CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms},
JOURNAL = {BMC Systems Biology},
VOLUME = {6},
YEAR = {2012},
NUMBER = {1},
PAGES = {133},
URL = {http://www.biomedcentral.com/1752-0509/6/133},
ISSN = {1752-0509}
}
@article{boolean-networks,
author = {Kauffman, Stuart A.},
journal = {Journal of Theoretical Biology},
keywords = {epigenesis, genetic-net, metabolic, theory},
month = mar,
number = {3},
pages = {437--467},
title = {{Metabolic stability and epigenesis in randomly constructed genetic nets}},
volume = {22},
year = {1969}
}
@article{boolean-networks2,
author = {Shmulevich, Ilya and Zhang, Wei},
day = {1},
journal = {Bioinformatics},
keywords = {binarization, comps, discretization, quantization},
month = apr,
number = {4},
pages = {555--565},
title = {{Binary analysis and optimization-based normalization of gene expression data}},
volume = {18},
year = {2002}
}
@article{boolean-networks-flower,
author = {Mendoza, Luis and Thieffry, Denis and Alvarez-Buylla, Elena R.},
title = {Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis.},
volume = {15},
number = {7},
pages = {593--606},
year = {1999},
journal = {Bioinformatics}
}
@article{qualitative-networks,
author = {Schaub, Marc and Henzinger, Thomas and Fisher, Jasmin},
issn = {1752-0509},
journal = {BMC Systems Biology},
keywords = {boolean\_networks, computational},
number = {1},
pages = {4+},
title = {{Qualitative networks: a symbolic approach to analyze biological signaling networks}},
volume = {1},
year = {2007}
}
@inproceedings{petri-nets0,
author = {Reddy, Venkatramana N. and Mavrovouniotis, Michael L. and Liebman, Michael N.},
title = {Petri Net Representations in Metabolic Pathways},
booktitle = {Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology},
year = {1993},
isbn = {0-929280-47-4},
pages = {328--336},
numpages = {9},
publisher = {AAAI Press},
}
@incollection {petri-nets,
author = {Reisig, Wolfgang},
affiliation = {Department of Computer Science, Humboldt-Universit\"{a}t zu Berlin, Unter den Linden 6, 10099 Berlin, Germany},
title = {Petri Nets},
booktitle = {Modeling in Systems Biology},
series = {Computational Biology},
editor = {Koch, Ina and Reisig, Wolfgang and Schreiber, Falk and Dress, Andreas and Vingron, Martin and Myers, Gene and Giegerich, Robert and Fitch, Walter and Pevzner, Pavel A.},
publisher = {Springer},
address = {London},
isbn = {978-1-84996-474-6},
keyword = {Computer Science},
pages = {37--56},
volume = {16},
year = {2011}
}
@article{petri-nets2,
author = {Nicola Bonzanni and Elzbieta Krepska and K. Anton Feenstra and Wan Fokkink and Thilo Kielmann and Henri E. Bal and Jaap Heringa},
title = {Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development},
journal = {Bioinformatics/computer Applications in The Biosciences},
volume = {25},
year = {2009},
pages = {2049--2056},
}
@incollection {ode-ma-anche-altro,
author = {Daigle, Bernie J. and Srinivasan, Balaji S. and Flannick, Jason A. and Novak, Antal F. and Batzoglou, Serafim},
affiliation = {Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA},
title = {Current Progress in Static and Dynamic Modeling of Biological Networks},
booktitle = {Systems Biology for Signaling Networks},
series = {Systems Biology},
editor = {Choi, Sangdun},
publisher = {Springer},
address = {New York},
isbn = {978-1-4419-5797-9},
keyword = {Biomedical and Life Sciences},
pages = {13-73},
volume = {1},
year = {2010}
}
@incollection{copasi,
address = {Totowa, NJ},
author = {Mendes, Pedro and Hoops, Stefan and Sahle, Sven and Gauges, Ralph and Dada, Joseph and Kummer, Ursula},
chapter = {2},
editor = {Maly, Ivan V. and Walker, John M. and Walker, John M.},
isbn = {978-1-934115-64-0},
issn = {1064-3745},
journal = {Methods in molecular biology (Clifton, N.J.)},
keywords = {copasi, gepasi, pedro-mendes, systems-biology, ursula-kummer},
pages = {17--59},
publisher = {Humana Press},
series = {Methods in Molecular Biology},
title = {{Computational modeling of biochemical networks using COPASI systems biology}},
volume = {500},
UNUSEDdoi={10.1007/978-1-59745-525-1_2},
year = {2009}
}
@article{e-cell,
address = {Laboratory for Bioinformatics, Keio University, 5322 Endo, Fujisawa, 252, [email protected]},
author = {Tomita, M. and Hashimoto, K. and Takahashi, K. and Shimizu, T. S. and Matsuzaki, Y. and Miyoshi, F. and Saito, K. and Tanida, S. and Yugi, K. and Venter, J. C. and Hutchison, C. A.},
day = {1},
issn = {1367-4803},
journal = {Bioinformatics},
month = jan,
number = {1},
pages = {72--84},
title = {{E-CELL: software environment for whole-cell simulation.}},
volume = {15},
year = {1999}
}
@misc{cellucidate,
title={Rulebase web site},
author={ },
howpublished={\url{http://rulebase.org}},
year={2012}
}
@article{cell-illustrator,
author = {Nagasaki, Masao and Saito, Ayumu and Jeong, Euna and Li, Chen and Kojima, Kaname and Ikeda, Emi and Miyano, Satoru},
title = {Cell illustrator 4.0: a computational platform for systems biology.},
journal = {Stud Health Technol Inform},
volume = {162},
year = {2011},
number = {},
pages = {160--81},
issn = {0926-9630}
}
@inproceedings{pathway-logic-assistant,
author = {A. Abate and Y. Bai and N. Sznajder and C. Talcott and A. Tiwari},
title = {Quantitative and Probabilistic Modeling in Pathway Logic},
booktitle = {Proc. 7th {IEEE} Intl. Conf. on BioInformatics and BioEngineering, BIBE07},
pages = {922--929},
month = {Oct},
year = {2007},
address = {Boston, MA}
}
@article{statecharts,
author = {Harel, David and Setty, Yaki and Efroni, Sol and Swerdlin, Naamah and Cohen, Irun R.},
title = {Concurrency in Biological Modeling: Behavior, Execution and Visualization},
journal = {Electron. Notes Theor. Comput. Sci.},
volume = {194},
issue = {3},
month = {January},
year = {2008},
issn = {1571-0661},
pages = {119--131},
numpages = {13},
publisher = {Elsevier Science Publishers B. V.},
address = {Amsterdam, The Netherlands, The Netherlands}
}
@article{biocharts,
author = {Kugler, Hillel and Larjo, Antti and Harel, David},
day = {6},
issn = {1742-5662},
journal = {Journal of The Royal Society Interface},
keywords = {diagrammatic, multiscale, pathways, statecharts, systems\_engineering},
month = jul,
number = {48},
pages = {1015--1024},
pmid = {20022895},
title = {{Biocharts: a visual formalism for complex biological systems}},
volume = {7},
year = {2010}
}
@book{pi-calculus,
author = {Milner, Robin},
day = {15},
edition = {1st},
howpublished = {Paperback},
isbn = {0521658691},
month = jun,
publisher = {Cambridge University Press},
title = {{Communicating and Mobile Systems: the Pi-Calculus}},
year = {1999}
}
@article{regev-shapiro,
author={A. Regev and E. Shapiro},
title={Cellular abstractions: Cells as computation},
journal={Nature},
year={2002},
volume={419},
number={6905},
pages={343}
}
@article{biochem-pi,
author = {Priami, Corrado and Regev, Aviv and Shapiro, Ehud and Silverman, William},
title = {Application of a stochastic name-passing calculus to representation and simulation of molecular processes},
journal = {Inf. Process. Lett.},
volume = {80},
issue = {1},
month = {October},
year = {2001},
issn = {0020-0190},
pages = {25--31},
numpages = {7},
publisher = {Elsevier North-Holland, Inc.},
address = {Amsterdam, The Netherlands, The Netherlands}
}
@incollection {beta-binders,
author = {Priami, Corrado and Quaglia, Paola},
affiliation = {Dipartimento di Informatica e Telecomunicazioni, Università di Trento, Italy},
title = {{Beta Binders for biological interactions}},
booktitle = {Computational Methods in Systems Biology},
series = {Lecture Notes in Computer Science},
editor = {Danos, Vincent and Schachter, Vincent},
publisher = {Springer Berlin / Heidelberg},
pages = {20--33},
volume = {3082},
year = {2005}
}
@article{beta-binders-stoch,
author = {Degano, Pierpaolo and Prandi, Davide and Priami, Corrado and Quaglia, Paola},
booktitle = {Proceedings of the 4th International Workshop on Quantitative Aspects of Programming Languages (QAPL 2006), Quantitative Aspects of Programming Languages 2006},
day = {26},
journal = {Electronic Notes in Theoretical Computer Science},
keywords = {beta-binders, modeling, quantitative},
month = oct,
number = {3},
pages = {101--117},
title = {{Beta-Binders for biological quantitative experiments}},
volume = {164},
year = {2006}
}
@book{pepa,
author = {Hillston, Jane},
title = {A compositional approach to performance modelling},
year = {1996},
isbn = {0-521-57189-8},
publisher = {Cambridge University Press},
address = {New York, NY, USA}
}
@article{bio-pepa,
author = {Ciocchetta, Federica and Hillston, Jane},
title = {{Bio-PEPA: A framework for the modelling and analysis of biological systems}},
journal = {Theor. Comput. Sci.},
volume = {410},
issue = {33-34},
month = {August},
year = {2009},
issn = {0304-3975},
pages = {3065--3084},
numpages = {20},
publisher = {Elsevier Science Publishers Ltd.},
address = {Essex, UK}
}
@incollection{blenx4bio,
author = {Priami, Corrado and Ballarini, Paolo and Quaglia, Paola},
affiliation = {CoSBi Italy},
title = {{BlenX4Bio - BlenX for biologists}},
booktitle = {Computational Methods in Systems Biology},
series = {Lecture Notes in Computer Science},
editor = {Degano, Pierpaolo and Gorrieri, Roberto},
publisher = {Springer Berlin / Heidelberg},
pages = {26--51},
volume = {5688},
note = {10.1007/978-3-642-03845-7\_{}3},
year = {2009}
}
@misc{cosbilab,
note={{COSBILab} web page \url{http://www.cosbi.eu/index.php/research/cosbi-lab}},
author={ },
year={2012}
}
@article{biopepa-interface,
author = {Federica Ciocchetta and Adam Duguid and Stephen Gilmore and Maria Luisa Guerriero and Jane Hillston},
title = {{The Bio-PEPA Tool Suite}},
journal ={International Conference on Quantitative Evaluation of Systems},
isbn = {978-0-7695-3808-2},
year = {2009},
pages = {309--310},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
UNUSEDdoi = {10.1109/QEST.2009.27}
}
@article{biopepa-ctmc-ode,
author = {Ciocchetta, Federica and Degasperi, Andrea and Hillston, Jane and Calder, Muffy},
title = {{Some investigations concerning the CTMC and the ODE model derived from Bio-PEPA}},
journal = {Electron. Notes Theor. Comput. Sci.},
volume = {229},
issue = {1},
month = {February},
year = {2009},
issn = {1571-0661},
pages = {145--163},
numpages = {19},
publisher = {Elsevier Science Publishers B. V.},
address = {Amsterdam, The Netherlands, The Netherlands}
}
@article{blenx,
author = {Dematt\'{e}, Lorenzo and Priami, Corrado and Romanel, Alessandro},
title = {{Modelling and simulation of biological processes in BlenX}},
journal = {SIGMETRICS Perform. Eval. Rev.},
volume = {35},
issue = {4},
month = {March},
year = {2008},
issn = {0163-5999},
pages = {32--39},
numpages = {8},
publisher = {ACM},
UNUSEDdoi = {10.1145/1364644.1364653},
address = {New York, NY, USA}
}
@INPROCEEDINGS{blenx-ode,
author = {Alida Palmisano and I. Mura and Corrado Priami},
TITLE = {{From ODES to language-based, executable models of biological systems}},
booktitle = {Pacific Symposium on Biocomputing'09},
PAGES = {239--250},
year = {2009}
}
@incollection {ginsim,
author = {Chaouiya, Claudine and Remy, Elisabeth and Moss\'{e}, Brigitte and Thieffry, Denis},
affiliation = {LGPD-IBDM, Campus de Luminy, Case 907, 13288 Marseille Cedex 9, France},
title = {Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework},
booktitle = {Positive Systems},
series = {Lecture Notes in Control and Information Sciences},
editor = {Benvenuti, Luca and De Santis, Alberto and Farina, Lorenzo},
publisher = {Springer},
address = {Berlin / Heidelberg},
isbn = {978-3-540-40342-5},
keyword = {Engineering},
pages = {830--832},
volume = {294},
UNUSEDdoi = {10.1007/978-3-540-44928-7_17},
year = {2003}
}
@misc{rhapsody,
note= {{IBM Rational Rhapsody} web page \url{http://www-01.ibm.com/software/rational/products/rhapsody/designer}},
author={ },
year={2012}
}
@BOOK{ctmc,
author = {John G. Kemeny and J. Laurie Snell},
TITLE = {{Finite Markov Chains}},
PUBLISHER = {Springer},
year = {1976}
}
@inproceedings{prism,
author = {Marta Z. Kwiatkowska and
Gethin Norman and
David Parker},
title = {PRISM 4.0: Verification of Probabilistic Real-Time Systems},
booktitle = {CAV},
year = {2011},
pages = {585--591},
publisher={Springer},
series={LNCS},
volume={6806}
}
@inbook{prism-biology,
author={Marta Kwiatkowska and Gethin Norman and David Parker},
title={Symbolic Systems Biology},
chapter={Probabilistic Model Checking for Systems Biology},
pages={31--59},
publisher={Jones and Bartlett},
year={2010}
}
@article{pathway-compendium,
address = {Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.},
author = {Gaudet, Suzanne and Janes, Kevin A. and Albeck, John G. and Pace, Emily A. and Lauffenburger, Douglas A.
and Sorger, Peter K.},
issn = {1535-9476},
journal = {Mol Cell Proteomics},
keywords = {systems\_biology},
month = oct,
number = {10},
pages = {1569--1590},
title = {{A compendium of signals and responses triggered by prodeath and prosurvival cytokines.}},
volume = {4},
year = {2005}
}
@article{pathway-autocrine,
title = "The Response of Human Epithelial Cells to {TNF} Involves an Inducible Autocrine Cascade",
journal = "Cell",
volume = "124",
number = "6",
pages = "1225--1239",
year = "2006",
note = "",
issn = "0092-8674",
author = "Kevin A. Janes and Suzanne Gaudet and John G. Albeck and Ulrik B. Nielsen and Douglas A. Lauffenburger and
Peter K. Sorger"
}
@article{pathway-fuzzy,
author = {Aldridge, Bree B. and Saez-Rodriguez, Julio and Muhlich, Jeremy L. and Sorger, Peter K. and Lauffenburger, Douglas A.},
day = {3},
issn = {1553-7358},
journal = {PLoS Comput Biol},
keywords = {logic, systemsbiology},
month = apr,
number = {4},
pages = {e1000340+},
publisher = {Public Library of Science},
title = {{Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/Insulin-induced signaling}},
volume = {5},
year = {2009}
}
@article{pathway-fuzzy2,
author = {Morris, Melody K. AND Saez-Rodriguez, Julio AND Clarke, David C. AND Sorger, Peter K. AND Lauffenburger, Douglas A.},
journal = {PLoS Comput Biol},
publisher = {Public Library of Science},
title = {Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli},
year = {2011},
month = {03},
volume = {7},
pages = {e1001099},
number = {3}
}
@article{pathway-leastsquare,
author = {Janes, Kevin A. and Albeck, John G. and Gaudet, Suzanne and Sorger, Peter K. and Lauffenburger, Douglas A. and Yaffe, Michael B.},
title = {A Systems Model of Signaling Identifies a Molecular Basis Set for Cytokine-Induced Apoptosis},
volume = {310},
number = {5754},
pages = {1646--1653},
year = {2005},
journal = {Science}
}
@article{jnk-signaling,
title = "Signal Transduction by the {JNK} Group of {MAP} Kinases",
journal = "Cell",
volume = "103",
number = "2",
pages = "239--252",
year = "2000",
issn = "0092-8674",
author = "Roger J Davis"
}
@article{cfos-cjun,
address = {Wellcome/CRC Institute, Cambridge, UK.},
author = {Bannister, A. J. and Brown, H. J. and Sutherland, J. A. and Kouzarides, T.},
journal = {Nucleic Acids Res},
month = dec,
number = {24},
pages = {5173-6+},
title = {{Phosphorylation of the c-Fos and c-Jun HOB1 motif stimulates its activation capacity.}},
volume = {22},
year = {1994}
}
@article{ras-mekk1,
author = {Russell, Marijane and Lange-Carter, Carol A. and Johnson, Gary L.},
title = {Direct Interaction between {Ras} and the Kinase Domain of Mitogen-activated Protein Kinase Kinase Kinase ({MEKK1})},
volume = {270},
number = {20},
pages = {11757--11760},
year = {1995},
journal = {Journal of Biological Chemistry}
}
@article{ras-jnk1,
title = "{JNK1}: A protein kinase stimulated by UV light and Ha-Ras that binds and phosphorylates the c-{Jun} activation domain",
journal = "Cell",
volume = "76",
number = "6",
pages = "1025--1037",
year = "1994",
issn = "0092-8674",
author = "Benoit D{\'{e}}rijard and Masahiko Hibi and I-Huan Wu and Tamera Barrett and Bing Su and Tiliang Deng and Michael Karin and Roger J. Davis"
}
@article{ap1-il1a,
title = "The transcription factor {AP-1} binds to the human interleukin 1 alpha promoter",
journal= "European Cytokine Network",
volume = "7",
number = "2",
pages = "125--128",
year = "1996",
author = "S. Bailly and M. Fay and N. Isra{\"{e}}l and M. A. Gougerot-Pocidalo"
}
@article{tnfr-internalization,
title = "Subcellular compartmentalization of {TNF} receptor-1 and {CD95} signaling pathways",
journal = "European Journal of Cell Biology",
volume = "90",
number = "6 - 7",
pages = "467--475",
year = "2011",
issn = "0171-9335",
author = {Vladimir Tchikov and Uwe Bertsch and J{\"{u}}rgen Fritsch and B{\"{a}}rbel Edelmann and Stefan Sch{\"{u}}tze}
}
@article {casp3-casp8,
author = {Ferreira, Karine and Kreutz, Clemens and MacNelly, Sabine and Neubert, Karin and Haber, Angelika and Bogyo,
Matthew and Timmer, Jens and Borner, Christoph},
affiliation = {Institute of Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier-Str. 17, 79104
Freiburg, Germany},
title = {Caspase-3 feeds back on caspase-8, {Bid} and {XIAP} in type {I} {Fas} signaling in primary mouse
hepatocytes},
journal = {Apoptosis},
publisher = {Springer Netherlands},
issn = {1360-8185},
keyword = {Medicine},
pages = {1--13},
year={2012}
}
@article{kegg,
address = {Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan. [email protected]},
author = {Kanehisa, Minoru and Goto, Susumu},
day = {1},
issn = {0305-1048},
journal = {Nucleic Acids Research},
keywords = {kegg, pathway},
month = jan,
number = {1},
pages = {27--30},
title = {{KEGG: Kyoto Encyclopedia of Genes and Genomes}},
volume = {28},
year = {2000}
}
@article {phosphosite,
author = {Hornbeck, Peter V. and Chabra, Indy and Kornhauser, Jon M. and Skrzypek, Elzbieta and Zhang, Bin},
title = {{PhosphoSite}: A bioinformatics resource dedicated to physiological protein phosphorylation},
journal = {Proteomics},
volume = {4},
number = {6},
publisher = {WILEY-VCH Verlag},
issn = {1615-9861},
pages = {1551--1561},
keywords = {Database, Kinase, Phosphorylation, Phosphorylation site, Signal transduction},
year = {2004}
}
@article{interacting-sm1,
author = {Fisher, Jasmin and Piterman, Nir and Hubbard, E. Jane Albert and Stern, Michael J. and Harel, David},
title = {Computational insights into Caenorhabditis elegans vulval development},
volume = {102},
number = {6},
pages = {1951--1956},
year = {2005},
journal = {Proceedings of the National Academy of Sciences of the United States of America}
}
@article{interacting-sm2,
author = {Efroni, Sol and Harel, David and Cohen, Irun R.},
title = {Toward Rigorous Comprehension of Biological Complexity: Modeling, Execution, and Visualization of Thymic T-Cell Maturation},
volume = {13},
number = {11},
pages = {2485--2497},
year = {2003},
journal = {Genome Research}
}
@article{visualizing,
author = {O'Donoghue, Se\'{a}n I. and Gavin, Anne-Claude C. and Gehlenborg, Nils and Goodsell, David S. and H\'{e}rich\'{e}, Jean-Karim K. and Nielsen, Cydney B. and North, Chris and Olson, Arthur J. and Procter, James B. and Shattuck, David W. and Walter, Thomas and Wong, Bang},
issn = {1548-7105},
journal = {Nature methods},
keywords = {visualisation},
month = mar,
number = {3 Suppl},
pages = {S2--S4},
title = {Visualizing biological data-now and in the future.},
volume = {7},
year = {2010}
}
@article{ta-siebert,
author = {Siebert, Heike and Bockmayr, Alexander},
title = {Temporal constraints in the logical analysis of regulatory networks},
journal = {Theor. Comput. Sci.},
issue_date = {February, 2008},
volume = {391},
number = {3},
month = feb,
year = {2008},
issn = {0304-3975},
pages = {258--275},
numpages = {18},
publisher = {Elsevier Science Publishers Ltd.},
address = {Essex, UK}
}
@article{thomas-formalism,
author = {R. Thomas},
title = {Boolean formalization of genetic control circuits},
journal = {J. Theor. Biol.},
year = {1973},
month = {December},
volume = {42},
number = {3},
pages = {563--585}
}
@article{bartocci-oscillators,
title = "Model Checking Biological Oscillators",
journal = "Electronic Notes in Theoretical Computer Science",
volume = "229",
number = "1",
pages = "41--58",
year = "2009",
note = "Proceedings of the Second Workshop From Biology to Concurrency and Back (FBTC 2008)",
issn = "1571-0661",
url = "http://www.sciencedirect.com/science/article/pii/S1571066109000097",
author = "Ezio Bartocci and Flavio Corradini and Emanuela Merelli and Luca Tesei"
}
@inproceedings{oded-ode-ta-discretization,
author = {Batt, Gr{\'e}gory and Salah, Ramzi Ben and Maler, Oded},
title = {On timed models of gene networks},
booktitle = {Proceedings of the 5th international conference on Formal modeling and analysis of timed systems},
series = {FORMATS'07},
year = {2007},
location = {Salzburg, Austria},
pages = {38--52},
numpages = {15},
publisher = {Springer-Verlag},
address = {Berlin, Heidelberg}
}
@inproceedings{ta-giapponesi,
author = {Shota Nakano and Shingo Yamaguchi},
title = {Two modeling methods for signaling pathways with multiple signals using {UPPAAL}},
booktitle = {Proceedings of the 2nd International Workshop on Biological Processes \& Petri Nets {(BioPPN2011)}},
year = 2011,
pages={87--101},
publisher={CEUR-WS.org},
issn={1613-0073},
address={Aachen}
}