Jakob L Andersen, Christoph Flamm, Daniel Merkle & Peter F Stadler (2013):
Inferring chemical reaction patterns using rule composition in graph grammars.
Journal of Systems Chemistry 4(1),
pp. 4,
doi:10.1186/1759-2208-4-4.
Jakob L. Andersen, Christoph Flamm, Daniel Merkle & Peter F. Stadler (2016):
A Software Package for Chemically Inspired Graph Transformation.
In: Graph Transformation.
Springer International Publishing,
pp. 73–88,
doi:10.1007/978-3-319-40530-8_5.
Jakob L. Andersen, Christoph Flamm, Daniel Merkle & Peter F. Stadler (2019):
Chemical Transformation Motifs — Modelling Pathways as Integer Hyperflows.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 16(2),
pp. 510–523,
doi:10.1109/tcbb.2017.2781724.
Jakob Lykke Andersen, Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle & Peter F Stadler (2018):
Towards mechanistic prediction of mass spectra using graph transformation.
MATCH Commun. Math. Comput. Chem 80,
pp. 705–731.
Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle & Peter F. Stadler (2014):
50 Shades of Rule Composition.
In: Formal Methods in Macro-Biology.
Springer International Publishing,
pp. 117–135,
doi:10.1007/978-3-319-10398-3_9.
Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle & Peter F Stadler (2018):
Rule composition in graph transformation models of chemical reactions.
MATCH Commun. Math. Comput. Chem 80(661-704),
pp. 45.
Paolo Baldan (2000):
Modelling Concurrent Computations: from Contextual Petri Nets to Graph Grammars.
PhD thesis, University of Pisa.
Paolo Baldan, Andrea Corradini, Tobias Heindel, Barbara König & PawełSobociński (2006):
Processes for Adhesive Rewriting Systems.
Lecture Notes in Computer Science,
pp. 202–216,
doi:10.1007/11690634_14.
Paolo Baldan, Andrea Corradini, Tobias Heindel, Barbara König & PawełSobociński (2009):
Unfolding Grammars in Adhesive Categories.
Lecture Notes in Computer Science,
pp. 350–366,
doi:10.1007/978-3-642-03741-2_24.
Paolo Baldan, Andrea Corradini, Tobias Heindel, Barbara König & PawełSobociński (2014):
Processes and unfoldings: concurrent computations in adhesive categories.
Mathematical Structures in Computer Science 24(04),
doi:10.1017/s096012951200031x.
Paolo Baldan, Andrea Corradini & Ugo Montanari (1998):
Concatenable graph processes: Relating processes and derivation traces.
Lecture Notes in Computer Science,
pp. 283–295,
doi:10.1007/bfb0055061.
Paolo Baldan, Andrea Corradini & Ugo Montanari (2000):
Unfolding of Double-Pushout Graph Grammars is a Coreflection.
In: Theory and Application of Graph Transformations.
Springer Berlin Heidelberg,
pp. 145–163,
doi:10.1007/978-3-540-46464-8_11.
Paolo Baldan, Andrea Corradini, Ugo Montanari & Leila Ribeiro (2007):
Unfolding semantics of graph transformation.
Information and Computation 205(5),
pp. 733–782,
doi:10.1016/j.ic.2006.11.004.
Paolo Baldan, Andrea Corradini, Ugo Montanari, Francesca Rossi, Hartmut Ehrig & Michael Löwe (1999):
Concurrent Semantics of Algebraic Graph Transformations.
Handbook of Graph Grammars and Computing by Graph Transformation,
pp. 107–187,
doi:10.1142/9789812814951_0003.
Wolfgang Banzhaf, Christoph Flamm, Daniel Merkle & Peter F. Stadler (2015):
Algorithmic Cheminformatics (Dagstuhl Seminar 14452).
Dagstuhl Reports 4(11),
pp. 22–39,
doi:10.4230/DagRep.4.11.22.
Nicolas Behr (2019):
Sesqui-Pushout Rewriting: Concurrency, Associativity and Rule Algebra Framework.
In: Rachid Echahed & Detlef Plump: Proceedings of theTenth International Workshop on Graph Computation Models (GCM 2019) in Eindhoven, The Netherlands,
Electronic Proceedings in Theoretical Computer Science 309.
Open Publishing Association,
pp. 23–52,
doi:10.4204/eptcs.309.2.
Nicolas Behr, Vincent Danos & Ilias Garnier (2016):
Stochastic mechanics of graph rewriting.
In: Proceedings of the 31st Annual ACM/IEEE Symposium on Logic in Computer Science - LICS '16.
ACM Press,
doi:10.1145/2933575.2934537.
Nicolas Behr & Jean Krivine (2019):
Compositionality of Rewriting Rules with Conditions.
arXiv preprint 1904.09322.
Nicolas Behr & Pawel Sobocinski (2018):
Rule Algebras for Adhesive Categories.
In: Dan Ghica & Achim Jung: 27th EACSL Annual Conference on Computer Science Logic (CSL 2018),
Leibniz International Proceedings in Informatics (LIPIcs) 119.
Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik,
Dagstuhl, Germany,
pp. 11:1–11:21,
doi:10.4230/LIPIcs.CSL.2018.11.
Gil Benkö, Christoph Flamm & Peter F. Stadler (2003):
A Graph-Based Toy Model of Chemistry.
Journal of Chemical Information and Computer Sciences 43(4),
pp. 1085–1093,
doi:10.1021/ci0200570.
M. L. Blinov, J. R. Faeder, B. Goldstein & W. S. Hlavacek (2004):
BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains.
Bioinformatics 20(17),
pp. 3289–3291,
doi:10.1093/bioinformatics/bth378.
Paul Boehm, Harald-Reto Fonio & Annegret Habel (1987):
Amalgamation of graph transformations: A synchronization mechanism.
Journal of Computer and System Sciences 34(2-3),
pp. 377–408,
doi:10.1016/0022-0000(87)90030-4.
Pierre Boutillier, Mutaamba Maasha, Xing Li, Héctor F Medina-Abarca, Jean Krivine, Jérôme Feret, Ioana Cristescu, Angus G Forbes & Walter Fontana (2018):
The Kappa platform for rule-based modeling.
Bioinformatics 34(13),
pp. i583–i592,
doi:10.1093/bioinformatics/bty272.
Benjamin Braatz, Hartmut Ehrig, Karsten Gabriel & Ulrike Golas (2010):
Finitary M -Adhesive Categories.
Lecture Notes in Computer Science,
pp. 234–249,
doi:10.1007/978-3-642-15928-2_16.
A. Corradini, H. Ehrig, M. Löwe, U. Montanari & F. Rossi (1994):
Abstract graph derivations in the double pushout approach.
In: Graph Transformations in Computer Science.
Springer Berlin Heidelberg,
pp. 86–103,
doi:10.1007/3-540-57787-4_6.
Andrea Corradini, Tobias Heindel, Frank Hermann & Barbara König (2006):
Sesqui-Pushout Rewriting.
In: Lecture Notes in Computer Science.
Springer Berlin Heidelberg,
pp. 30–45,
doi:10.1007/11841883_4.
Vincent Danos, Jerome Feret, Walter Fontana, Russell Harmer, Jonathan Hayman, Jean Krivine, Chris Thompson-Walsh & Glynn Winskel (2012):
Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models.
In: Deepak D'Souza, Telikepalli Kavitha & Jaikumar Radhakrishnan: IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2012),
Leibniz International Proceedings in Informatics (LIPIcs) 18.
Schloss Dagstuhl–Leibniz-Zentrum fuer Informatik,
Dagstuhl, Germany,
pp. 276–288,
doi:10.4230/LIPIcs.FSTTCS.2012.276.
Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer & Jean Krivine (2007):
Rule-Based Modelling of Cellular Signalling.
Lecture Notes in Computer Science,
pp. 17–41,
doi:10.1007/978-3-540-74407-8_3.
Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer & Jean Krivine (2008):
Rule-Based Modelling, Symmetries, Refinements.
In: Jasmin Fisher: Formal Methods in Systems Biology.
Springer Berlin Heidelberg,
Berlin, Heidelberg,
pp. 103–122,
doi:10.1007/978-3-540-68413-8_8.
Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer & Jean Krivine (2010):
Abstracting the differential semantics of rule-based models: exact and automated model reduction.
In: 25th Annual IEEE Symposium on Logic in Computer Science (LICS 2010).
IEEE,
pp. 362–381,
doi:10.1109/LICS.2010.44.
Vincent Danos, Jérôme Feret, Walter Fontana & Jean Krivine (2007):
Scalable Simulation of Cellular Signaling Networks.
Lecture Notes in Computer Science,
pp. 139–157,
doi:10.1007/978-3-540-76637-7_10.
Vincent Danos, Jérôme Feret, Walter Fontana & Jean Krivine (2008):
Abstract Interpretation of Cellular Signalling Networks.
Lecture Notes in Computer Science,
pp. 83–97,
doi:10.1007/978-3-540-78163-9_11.
Vincent Danos & Cosimo Laneve (2003):
Core Formal Molecular Biology.
Lecture Notes in Computer Science,
pp. 302–318,
doi:10.1007/3-540-36575-3_21.
Vincent Danos & Cosimo Laneve (2003):
Graphs for Core Molecular Biology.
Lecture Notes in Computer Science,
pp. 34–46,
doi:10.1007/3-540-36481-1_4.
Vincent Danos & Cosimo Laneve (2004):
Formal molecular biology.
Theoretical Computer Science 325(1),
pp. 69–110,
doi:10.1016/j.tcs.2004.03.065.
H. Ehrig, K. Ehrig, U. Prange & G. Taentzer (2006):
Fundamentals of Algebraic Graph Transformation.
Monographs in Theoretical Computer Science (An EATCS Series),
doi:10.1007/3-540-31188-2.
Hartmut Ehrig, Gregor Engels, Hans-Jörg Kreowski & Grzegorz Rozenberg (1997):
Handbook of Graph Grammars and Computing by Graph Transformation 1-3.
world Scientific,
doi:10.1142/3303.
Hartmut Ehrig, Ulrike Golas, Annegret Habel, Leen Lambers & Fernando Orejas (2014):
M-adhesive transformation systems with nested application conditions. Part 1: parallelism, concurrency and amalgamation.
Mathematical Structures in Computer Science 24(04),
doi:10.1017/s0960129512000357.
Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle & Peter F. Stadler (2018):
Finding the K best synthesis plans.
Journal of Cheminformatics 10(1),
doi:10.1186/s13321-018-0273-z.
Ulrike Golas, Hartmut Ehrig & Annegret Habel (2010):
Multi-Amalgamation in Adhesive Categories.
Lecture Notes in Computer Science,
pp. 346–361,
doi:10.1007/978-3-642-15928-2_23.
Ulrike Golas, Annegret Habel & Hartmut Ehrig (2014):
Multi-amalgamation of rules with application conditions in M-adhesive categories.
Mathematical Structures in Computer Science 24(04),
doi:10.1017/s0960129512000345.
Annegret Habel & Karl-Heinz Pennemann (2009):
Correctness of high-level transformation systems relative to nested conditions.
Mathematical Structures in Computer Science 19(02),
pp. 245,
doi:10.1017/s0960129508007202.
Leonard A. Harris, Justin S. Hogg, José-Juan Tapia, John A. P. Sekar, Sanjana Gupta, Ilya Korsunsky, Arshi Arora, Dipak Barua, Robert P. Sheehan & James R. Faeder (2016):
BioNetGen 2.2: advances in rule-based modeling.
Bioinformatics 32(21),
pp. 3366–3368,
doi:10.1093/bioinformatics/btw469.
Hans-Jörg Kreowski (1987):
Is parallelism already concurrency? Part 1: Derivations in graph grammars.
In: Lecture Notes in Computer Science.
Springer Berlin Heidelberg,
pp. 343–360,
doi:10.1007/3-540-18771-5_63.
Stephen Lack & PawełSobociński (2005):
Adhesive and quasiadhesive categories.
RAIRO - Theoretical Informatics and Applications 39(3),
pp. 511–545,
doi:10.1051/ita:2005028.
Karl-Heinz Pennemann (2008):
Resolution-Like Theorem Proving for High-Level Conditions.
Lecture Notes in Computer Science,
pp. 289–304,
doi:10.1007/978-3-540-87405-8_20.
Grzegorz Rozenberg (1997):
Handbook of Graph Grammars and Computing by Graph Transformations, Volume 1: Foundations.
World Scientific,
doi:10.1142/9789812384720.