@phdthesis(Andrei08,
 author       = "Oana Andrei",
 year         = "2008",
 title        = "{A Rewriting Calculus for Graphs: Applications to Biology and Autonomous Systems}",
 school       = "{Institut National Polytechnique de Lorraine}",
 url          = "http://tel.archives-ouvertes.fr/tel-00337558/fr/",
)
@inproceedings(AndreiC10a,
 author       = "Oana Andrei and Muffy Calder",
 year         = "2010",
 title        = "{A Model and Analysis of the {\sf AKAP} Scaffold}",
 booktitle    = "{Proc. of CS2Bio'10}",
 series       = "To appear in Electronic Notes in Theoretical Computer Science",
)
@inproceedings(AndreiIK06,
 author       = "Oana Andrei and Liliana Ibanescu and H{\'e}l{\`e}ne Kirchner",
 year         = "2006",
 title        = "{Non-intrusive Formal Methods and Strategic Rewriting for a Chemical Application.}",
 editor       = "Kokichi Futatsugi and Jean-Pierre Jouannaud and Jos{\'e} Meseguer",
 booktitle    = "{Algebra, Meaning, and Computation}",
 series       = "Lecture Notes in Computer Science",
 volume       = "4060",
 publisher    = "Springer",
 pages        = "194--215",
)
@inproceedings(AndreiK08c,
 author       = "Oana Andrei and H{\'e}l{\`e}ne Kirchner",
 year         = "2009",
 title        = "{A Higher-Order Graph Calculus for Autonomic Computing}",
 editor       = "M. Lipshteyn and V.E. Levit and R.M. McConnell",
 booktitle    = "{Graph Theory, Computational Intelligence and Thought}",
 series       = "Lecture Notes in Computer Science",
 volume       = "5420",
 publisher    = "Springer",
 pages        = "15--26",
)
@inproceedings(AndreiK09,
 author       = "Oana Andrei and H{\'e}l{\`e}ne Kirchner",
 year         = "2009",
 title        = "{A Port Graph Calculus for Autonomic Computing and Invariant Verification}",
 booktitle    = "{Proceedings of the Fifth International Workshop on Computing with Terms and Graphs (TERMGRAPH 2009)}",
 series       = "Electronic Notes in Theoretical Computer Science",
 volume       = "253",
 pages        = "17--38",
)
@incollection(tulip2003,
 author       = "David Auber",
 year         = "2003",
 title        = "{Tulip -- A huge graph visualization framework}",
 editor       = "P. Mutzel and M. J{\"u}nger",
 booktitle    = "{Graph Drawing Software}",
 series       = "Mathematics and Visualization Series",
 publisher    = "Springer Verlag",
 pages        = "105--126",
)
@article(BalasubramanianNBK06,
 author       = "Daniel Balasubramanian and Anantha Narayanan and Christopher P. van Buskirk and Gabor Karsai",
 year         = "2006",
 title        = "{The Graph Rewriting and Transformation Language: GReAT}",
 journal      = "{ECEASST}",
 volume       = "1",
)
@inproceedings(BournezCCKI03,
 author       = "Olivier Bournez and Guy-Marie C{\^o}me and Val{\'e}rie Conraud and H{\'e}l{\`e}ne Kirchner and Liliana Ibanescu",
 year         = "2003",
 title        = "{A Rule-Based Approach for Automated Generation of Kinetic Chemical Mechanisms.}",
 editor       = "Robert Nieuwenhuis",
 booktitle    = "{RTA}",
 series       = "Lecture Notes in Computer Science",
 volume       = "2706",
 publisher    = "Springer",
 pages        = "30--45",
)
@article(cordella:04,
 author       = "L. P. Cordella and P. Foggia and C. Sansone and M. Vento",
 year         = "2004",
 title        = "A (Sub)Graph Isomorphism Algorithm for Matching Large Graphs",
 journal      = "{IEEE} Trans. on Pattern Analysis and Machine Intelligence",
 volume       = "26",
 number       = "10",
 pages        = "1367--1372",
)
@incollection(Courcelle90,
 author       = "Bruno Courcelle",
 year         = "1990",
 title        = "{Graph Rewriting: An Algebraic and Logic Approach}",
 editor       = "J. van Leeuwen",
 booktitle    = "{Handbook of Theoretical Computer Science, Volume B: Formal Models and Semantics}",
 publisher    = "Elsevier Science Publishers and MIT Press",
 pages        = "193--242",
)
@article(DanosL04,
 author       = "Vincent Danos and Cosimo Laneve",
 year         = "2004",
 title        = "{Formal Molecular Biology.}",
 journal      = "{Theoretical Computer Science}",
 volume       = "325",
 number       = "1",
 pages        = "69--110",
)
@book(1997handbook2,
 editor       = "Hartmut Ehrig and Gregor Engels and Hans-J{\"o}rg Kreowski and Grzegorz Rozenberg",
 year         = "1997",
 title        = "{Handbook of Graph Grammars and Computing by Graph Transformations, Volume 2: Applications, Languages, and Tools}",
 publisher    = "{World Scientific}",
)
@book(1997handbook3,
 editor       = "Hartmut Ehrig and Hans-J{\"o}rg Kreowski and Ugo Montanari and Grzegorz Rozenberg",
 year         = "1997",
 title        = "{Handbook of Graph Grammars and Computing by Graph Transformations, Volume 3: Concurrency, Parallelism, and Distribution}",
 publisher    = "{World Scientific}",
)
@incollection(ErmelRT97,
 author       = "Claudia Ermel and Michael Rudolf and Gabriele Taentzer",
 year         = "1997",
 title        = "The {AGG} Approach: Language and Environment",
 booktitle    = "\cite {1997handbook2}",
 publisher    = "{World Scientific}",
 pages        = "551--603",
)
@incollection(FaederBH09,
 author       = "James R. Faeder and Michael L. Blinov and William S. Hlavacek",
 year         = "2009",
 title        = "{Rule-Based Modeling of Biochemical Systems with BioNetGen}",
 editor       = "Ivan V. Maly",
 booktitle    = "{Systems Biology}",
 series       = "{Methods in Molecular Biology}",
 publisher    = "Humana Press",
 pages        = "133--168",
)
@misc(FN10,
 author       = "Maribel Fern\'andez and H{\'e}l{\`e}ne Kirchner and Olivier Namet",
 year         = "2010",
 title        = "{A strategy language for graph rewriting}",
 note         = "Submitted, see \url {http://www.oliviernamet.co.uk/Publications.html}",
)
@inproceedings(FernandezN10a,
 author       = "Maribel Fern{\'a}ndez and Olivier Namet",
 year         = "2010",
 title        = "{Strategic Programming on Graph Rewriting Systems}",
 booktitle    = "{Proc. of the $1^{st}$ International Workshop on Strategies in Rewriting, Proving, and Programming}",
)
@article(FoxLC,
 author       = "Chris Fox and Maribel Fern{\'a}ndez and Shalom Lappin",
 year         = "2008",
 title        = "{Lambda Calculus, Type Theory, and Natural Language II}",
 journal      = "J. Log. Comput.",
 volume       = "18",
 number       = "2",
 pages        = "203",
)
@inproceedings(GeissBGHS06,
 author       = "Rubino Gei{\ss } and Gernot Veit Batz and Daniel Grund and Sebastian Hack and Adam Szalkowski",
 year         = "{2006}",
 title        = "{GrGen: A Fast SPO-Based Graph Rewriting Tool}",
 editor       = "Andrea Corradini and Hartmut Ehrig and Ugo Montanari and Leila Ribeiro and Grzegorz Rozenberg",
 booktitle    = "{ICGT}",
 series       = "Lecture Notes in Computer Science",
 volume       = "4178",
 publisher    = "Springer",
 pages        = "383--397",
)
@article(KrivineMT08,
 author       = "Jean Krivine and Robin Milner and Angelo Troina",
 year         = "2008",
 title        = "{Stochastic Bigraphs}",
 journal      = "{Electr. Notes Theor. Comput. Sci.}",
 volume       = "218",
 pages        = "73--96",
)
@inproceedings(LafontY:intn,
 author       = "Yves Lafont",
 year         = "1990",
 title        = "{Interaction Nets}",
 booktitle    = "Proc. of the $17^{th}$ {ACM} Symposium on Principles of Programming Languages ({POPL}'90)",
 publisher    = "ACM Press",
 pages        = "95--108",
)
@inproceedings(NickelNZ00,
 author       = "Ulrich Nickel and J{\"o}rg Niere and Albert Z{\"u}ndorf",
 year         = "2000",
 title        = "{The FUJABA environment}",
 booktitle    = "{ICSE}",
 pages        = "742--745",
)
@inproceedings(Plump09,
 author       = "Detlef Plump",
 year         = "2009",
 title        = "{The Graph Programming Language GP}",
 editor       = "Symeon Bozapalidis and George Rahonis",
 booktitle    = "{CAI}",
 series       = "Lecture Notes in Computer Science",
 volume       = "5725",
 publisher    = "Springer",
 pages        = "99--122",
)
@inproceedings(Rensink03,
 author       = "Arend Rensink",
 year         = "2003",
 title        = "{The GROOVE Simulator: A Tool for State Space Generation}",
 editor       = "John L. Pfaltz and Manfred Nagl and Boris B{\"o}hlen",
 booktitle    = "{AGTIVE}",
 series       = "Lecture Notes in Computer Science",
 volume       = "3062",
 publisher    = "Springer",
 pages        = "479--485",
)
@book(1997handbook1,
 editor       = "Grzegorz Rozenberg",
 year         = "1997",
 title        = "{Handbook of Graph Grammars and Computing by Graph Transformations, Volume 1: Foundations}",
 publisher    = "{World Scientific}",
)
@incollection(Schurr97b,
 author       = "Andy Sch{\"u}rr and Andreas J. Winter and Albert Z{\"u}ndorf",
 year         = "1997",
 title        = "{The PROGRES Approach: Language and Environment.}",
 booktitle    = "\cite {1997handbook2}",
 publisher    = "{World Scientific}",
 pages        = "479--546",
)
@article(ullmann:76,
 author       = "J. R. Ullmann",
 year         = "1976",
 title        = "An Algorithm for Subgraph Isomorphism",
 journal      = "JACM",
 volume       = "23",
 number       = "1",
 pages        = "31--42",
)
@inproceedings(ZhangZ97,
 author       = "Daqian Zhang and Kang Zhang",
 year         = "1997",
 title        = "{Reserved Graph Grammar: A Specification Tool for Diagrammatic VPLs}",
 booktitle    = "{Proc. of VL'97}",
 publisher    = "{IEEE Computer Society}",
 pages        = "284",
)