@incollection(bal-con,
 author       = {P.~Baldan and A.~Corradini},
 year         = {2005},
 title        = {{On the Concurrent Semantics of Algebraic Graph Grammars}},
 booktitle    = {{Formal Methods in Software and Systems Modeling}},
 series       = {Lecture Notes in Computer Science},
 volume       = {3393},
 publisher    = {Springer},
 pages        = {3--23},
 doi          = {10.1007/978-3-540-31847-7\_1},
)
@inproceedings(ben-gr,
 author       = {M.~Benk and G.~Benko and G.~J. Eble and C.~Famm and S.~Muller, P.~Stadler},
 year         = {2004},
 title        = {{Graph Grammars as Models for the Evolution of Developmental Pathways}},
 booktitle    = {The Logic of Artificial Life: Abstracting and Synthesizing the Principles of Living Systems; Proceedings of the 6th German Workshop on Artificial Life, April 14-16, 2004, Bamberg, Germany},
 organization = {IOS Press},
 pages        = {8--15},
)
@incollection(cor-al,
 author       = {A.~Corradini and U.~Montanari and F.~Rossi and H.~Ehrig and R.~Heckel and M.~L{\"o}we},
 year         = {1997},
 title        = {{Algebraic Approaches to Graph Transformation-Part I: Basic Concepts and Double Pushout Approach}},
 booktitle    = {{Handbook of Graph Grammars and Computing by Graph Transformation}},
 publisher    = {World Scientific Publishing},
 pages        = {163--245},
 doi          = {10.1142/9789812384720\_0003},
)
@incollection(cor2,
 author       = {H.~Ehrig and R.~Heckel and M.~Korff and M.~L{\"o}we and L.~Ribeiro and A.~Wagner and A.~Corradini},
 year         = {1997},
 title        = {{Algebraic approaches to graph transformation-Part II: Single pushout approach and comparison with double pushout approach}},
 booktitle    = {{Handbook of Graph Grammars and Computing by Graph Transformation}},
 publisher    = {World Scientific Publishing},
 pages        = {247--312},
 doi          = {10.1142/9789812384720\_0004},
)
@article(fl_bey,
 author       = {C.~Flamm and I.~L. Hofacker},
 year         = {2008},
 title        = {{Beyond Energy Minimization: Approaches to the Kinetic Folding of RNA}},
 journal      = {Monatshefte f{\"u}r Chemie-Chemical Monthly},
 volume       = {139},
 number       = {4},
 pages        = {447--457},
 doi          = {10.1007/s00706-008-0895-3},
)
@article(vina-rna,
 author       = {A.~R. Gruber and R.~Lorenz and S.~H. Bernhart and R.~Neub{\"o}ck and I.~L. Hofacker},
 year         = {2008},
 title        = {{The Vienna RNA Websuite}},
 journal      = {Nucleic acids research},
 volume       = {36},
 number       = {2},
 pages        = {W70--W74},
 doi          = {10.1093/nar/gkn188},
)
@incollection(hof-stad,
 author       = {I.~L. Hofacker and P.~F. Stadler},
 year         = {2007},
 title        = {{RNA Secondary Structures}},
 editor       = {T.~Lengauer},
 booktitle    = {{Bioinformatics: From Genomes to Therapies}},
 publisher    = {Wiley-VCH},
 address      = {Weinheim, Germany},
 pages        = {439--489},
 doi          = {10.1002/9783527619368.ch14},
)
@article(mere_adp,
 author       = {E.~Merelli and N.~Paoletti and L.~Tesei},
 year         = {2016},
 title        = {{Adaptability Checking in Complex Systems}},
 journal      = {Science of Computer Programming},
 volume       = {115-116},
 pages        = {23--46},
 doi          = {10.1016/j.scico.2015.03.004},
)
@article(em-tp,
 author       = {E.~Merelli and M.~Pettini and M.~Rasetti},
 year         = {2015},
 title        = {{Topology Driven Modeling: The IS Metaphor}},
 journal      = {Nat. Comput.},
 volume       = {14},
 number       = {3},
 pages        = {421--430},
 doi          = {10.1007/s11047-014-9436-7},
)
@article(mr-tp,
 author       = {E.~Merelli and M.~Rucco and P.~Sloot and L.~Tesei},
 year         = {2015},
 title        = {{Topological Characterization of Complex Systems: Using Persistent Entropy}},
 journal      = {Entropy},
 volume       = {17},
 number       = {10},
 pages        = {6872--6892},
 doi          = {10.3390/e17106872},
)
@article(mor-r,
 author       = {K.~V. Morris and J.~S. Mattick},
 year         = {2014},
 title        = {{The Rise of Regulatory RNA}},
 journal      = {Nature Reviews Genetics},
 volume       = {15},
 number       = {6},
 pages        = {423--437},
 doi          = {10.1038/nrg3722},
)
@article(reidys,
 author       = {C.~M. Reidys and F.~W.~D. Huang and J.~E. Andersen and R.~C. Penner and P.~F. Stdler and M.~E. Nebel},
 year         = {2011},
 title        = {{Topology and prediction of RNA pseudoknots}},
 journal      = {Bioinformatics},
 volume       = {27},
 number       = {8},
 pages        = {1076--1085},
 doi          = {10.1093/bioinformatics/btr090},
)
@incollection(groove,
 author       = {A.~Rensink},
 year         = {2003},
 title        = {{The GROOVE Simulator: A Tool for State Space Generation}},
 booktitle    = {Applications of Graph Transformations with Industrial Relevance},
 publisher    = {Springer},
 pages        = {479--485},
 doi          = {10.1007/978-3-540-25959-6\_4},
)
@article(gr-gn,
 author       = {J.~Schimmel and T.~Gelhausen and C.~Schaefer},
 year         = {2009},
 title        = {{Gene Expression with General Purpose Graph Rewriting Systems}},
 journal      = {Electronic Communications of the EASST},
 volume       = {18},
 doi          = {10.14279/tuj.eceasst.18.276.259},
)
@article(st-gr,
 author       = {K.~St-Onge and P.~Thibault and S.~Hamel and F.~Major},
 year         = {2007},
 title        = {{Modeling RNA Tertiary Structure Motifs by Graph-Grammars}},
 journal      = {Nucleic acids research},
 volume       = {35},
 number       = {5},
 pages        = {1726--1736},
 doi          = {10.1093/nar/gkm069},
)
@article(zuker_rna,
 author       = {M.~Zuker and D.~Sankoff},
 year         = {1984},
 title        = {{RNA Secondary Structures and their Prediction}},
 journal      = {Bulletin of Mathematical Biology},
 volume       = {46},
 number       = {4},
 pages        = {591--621},
 doi          = {10.1007/bf02459506},
)
@article(zuk_opt,
 author       = {M.~Zuker and P.~Stiegler},
 year         = {1981},
 title        = {{Optimal Computer Folding of Large RNA Sequences Using Thermodynamics and Auxiliary Information}},
 journal      = {Nucleic Acids Research},
 volume       = {9},
 number       = {1},
 pages        = {133--148},
 doi          = {10.1093/nar/9.1.133},
)