@inproceedings(BEL17, author = {A. Bouajjani and C. Enea and S. Lahiri}, year = {2017}, title = {Abstract Semantic Diffing of Evolving Concurrent Programs}, booktitle = {International Static Analysis Symposium SAS 2017: Static Analysis}, series = {LNCS}, volume = {10422}, pages = {46--65}, doi = {10.1007/978-3-319-66706-5_3}, ) @unpublished(BFKF18, author = {P. Boutillier and J. Feret and J. Krivine and W. Fontana}, year = {2018}, title = {The Kappa Language and Kappa Tools, A User Manual and Guide,v4}, url = {https://kappalanguage.org/sites/kappalanguage.org/files/inline-files/Kappa_Manual.pdf}, ) @article(CCGKP08, author = {L. Cardelli and E. Caron and P. Gardner and Kahramano{\u g}ullar{\i}, O. and A. Phillips}, year = {2009}, title = {A Process Model of {Rho GTP}-binding Proteins}, journal = {Theoretical Computer Science}, volume = {410/33-34}, pages = {3166--3185}, doi = {10.1016/j.tcs.2009.04.029}, ) @article(CKL16, author = {L. Cardelli and M. Kwiatkowska and L. Laurenti}, year = {2016}, title = {Stochastic Analysis of Chemical Reaction Networks Using Linear Noise Approximation}, journal = {Biosystems}, volume = {149}, pages = {26--33}, doi = {10.1016/j.biosystems.2016.09.004}, ) @article(CTTV17, author = {L. Cardelli and M. Tribastone and M. Tschaikowski and A. Vandin}, year = {2017}, title = {Maximal aggregation of polynomial dynamical systems}, journal = {Proceedings of the National Academy of Sciences}, doi = {10.1073/pnas.1702697114}, ) @article(Gil77, author = {D. T. Gillespie}, year = {1977}, title = {Exact Stochastic Simulation of Coupled Chemical Reactions}, journal = {The Journal of Physical Chemistry}, volume = {81}, number = {25}, pages = {2340--2361}, doi = {10.1021/j100540a008}, ) @article(Kah09, author = {Kahramano{\u g}ullar{\i}, O.}, year = {2009}, title = {On Linear Logic Planning and Concurrency}, journal = {Information and Computation}, volume = {207}, pages = {1229--1258}, doi = {10.1016/j.ic.2009.02.008}, ) @inproceedings(Kah17, author = {Kahramano{\u g}ullar\i, O.}, year = {2017}, title = {Quantifying Information Flow in Chemical Reaction Networks}, booktitle = {Proceedings of 4th International Conference on Algorithms for Computational Biology, AlCoB 2017}, series = {LNCS}, volume = {10252}, pages = {155--166}, doi = {10.1007/978-3-319-58163-7_11}, ) @article(Kah15, author = {Kahramano{\u g}ullar{\i}, O. and L. Cardelli}, year = {2015}, title = {Gener: a minimal programming module for chemical controllers based on DNA strand displacement}, journal = {Bioinformatics}, volume = {31 (17)}, pages = {2906--2908}, doi = {10.1093/bioinformatics/btv286}, ) @article(Kah12, author = {Kahramano{\u g}ullar\i, O. and G. Fantaccini and P. Lecca and D. Morpurgo and C. Priami}, year = {2012}, title = {Algorithmic modeling quantifies the complementary contribution of metabolic inhibitions to gemcitabine efficacy}, journal = {PLoS ONE}, volume = {7}, number = {12}, pages = {e50176}, doi = {10.1371/journal.pone.0050176}, ) @article(flux, author = {Kahramano{\u g}ullar{\i}, O. and J. Lynch}, year = {2013}, title = {Stochastic Flux Analysis of Chemical Reaction Networks}, journal = {BMC Systems Biology}, volume = {7}, number = {133}, doi = {10.1186/1752-0509-7-133}, ) @article(LYPEP11, author = {M. R. Lakin and S. Youssef and F. Polo and S. Emmott and A. Phillips}, year = {2011}, title = {Visual DSD: a design and analysis tool for DNA strand displacement systems}, journal = {Bioinformatics}, volume = {27}, pages = {3211--3213}, doi = {10.1093/bioinformatics/btr543}, ) @article(NPW81, author = {M. Nielsen and G. Plotkin and G. Winskel}, year = {1981}, title = {Petri Nets, Event Structures and Domains, part 1}, journal = {Theoretical Computer Science}, volume = {13}, number = {1}, pages = {85--108}, doi = {10.1016/0304-3975(81)90112-2}, ) @article(SF12, author = {J. A. P. Sekar and J. R. Faeder}, year = {2012}, title = {Rule-Based Modeling of Signal Transduction: A Primer}, journal = {Computational Modeling of Signaling Networks. Methods in Molecular Biology (Methods and Protocols)}, volume = {880}, pages = {139--218}, doi = {10.1007/978-1-61779-833-7_9}, ) @article(Sha03, author = {P. Shannon and A. Markiel and O. Ozier and N. S. Baliga and J. T. Wang and D. Ramage and N. Amin and B. Schwikowski and T. Ideker}, year = {2003}, title = {Cytoscape: a software environment for integrated models of biomolecular interaction networks}, journal = {Genome Research}, volume = {13(11)}, pages = {2498--2504}, doi = {10.1101/gr.1239303}, ) @article(VLD11, author = {L. Venkatraman and H. Li and C. F. Jr. Dewey and J. K. White and S. S. Bhowmick and H. Yu and Tucker-Kellogg, L.}, year = {2011}, title = {Steady states and dynamics of urokinase-mediated plasmin activation in silico and in vitro}, journal = {Biophysical Journal}, volume = {101 (8)}, pages = {1825--1834}, doi = {10.1016/j.bpj.2011.08.054}, )