Bentley P, Kumar S: Three Ways to Grow Designs: A Comparison of Evolved Embryogenies for a Design Problem. In Genetic and Evolutionary Computation Conference. Massachusetts: Morgan Kaufmann; 1999:35–43.
Google Scholar
Banzhaf W: On the Dynamics of an Artificial Regulatory Network. In Advances in Artificial Life, of LNCS. Volume 2801. Edited by: Banzhaf W, Christaller T, Dittrich P, Kim JT, Ziegler J. Heidelberg, Germany: Springer-Verlag; 2003:217–227. full_text
Chapter
Google Scholar
Eggenberg P: Evolving morphologies of simulated 3 D organisms based on differential gene expression. In Proc. ECAL97. Edited by: Husbands P, Harvey I. The MIT Press/Bradford Books; 1997:205–213.
Google Scholar
Geard N, Wiles J: Structure and dynamics of a gene network model. In Proc. CEC2003. Edited by: Sarker R, Reynolds R, Abbass H, Tan KC, McKay B, Essam D, Gedeon T. IEEE Press; 2003:199–206.
Google Scholar
Reil T: Dynamics of gene expression in an artificial genome - inplications for biological and artificial ontogeny. In Proc. ECAL99, of Lecture Notes in Computer Science. Volume 1674. Edited by: Floreano D, Nicoud JD, Mondada F. Berlin: Springer-Verlag; 1999:457–466. full_text
Google Scholar
Fontana W: Algorithmic Chemistry. In Artificial Life II. Edited by: Langton CG, Taylor C, Farmer JD, Rasmussen S. Redwood City, CA: Addison-Wesley; 1992:159–210.
Google Scholar
Fontana W, Buss LW: What would be conserved if `the tape were played twice'? Proc Natl Acad Sci USA 1994, 91: 757–761. 10.1073/pnas.91.2.757
Article
CAS
Google Scholar
Bagley RJ, Farmer JD: Spontaneous emergence of a metabolism. In Artificial Life II, Santa Fe Institute Studies in the Sciences of Complexity. Edited by: Langton CG, Taylor C, Farmer JD, Rasmussen S. Redwood City, CA: Addison-Wesley; 1992:93–141.
Google Scholar
Banzhaf W, Dittrich P, Eller B: Self-organization in a system of binary strings with spatial interactions. Physica D 1999, 125: 85–104. 10.1016/S0167-2789(98)00238-3
Article
Google Scholar
Speroni di Fenizio P: A less abstract artificial chemistry. In Artificial Life VII. Edited by: Bedau M, McCaskill J, Packard N, Rasmussen S. Cambridge, MA: MIT Press; 2000:49–53.
Google Scholar
Ugi I, Stein N, Knauer M, Gruber B, Bley K, Weidinger R: New Elements in the Representation of the Logical Structure of Chemistry by Qualitative Mathematical Models and Corresponding Data Structures. Top Curr Chem 1993, 166: 199–233. full_text
Article
CAS
Google Scholar
Thürk M: Ein Modell zur Selbstorganisation von Automatenalgorithmen zum Studium molekularer Evolution. PhD thesis. Universität Jena, Germany; 1993.
Google Scholar
McCaskill JS, Niemann U: Graph Replacement Chemistry for DNA Processing. In DNA Computing, of Lecture Notes in Computer Science. Volume 2054. Edited by: Condon A, Rozenberg G. Berlin, D: Springer; 2000:103–116. full_text
Google Scholar
Rossellá F, Valiente G: Chemical graphs, chemical reaction graphs, and chemical graph transformation. Electron Notes Theor Comput Sci 2005, 127: 157–166. 10.1016/j.entcs.2004.12.033
Article
Google Scholar
Dittrich P, Ziegler J, Banzhaf W: Artificial chemistries-a review. Artif Life 2001, 7: 225–75. 10.1162/106454601753238636
Article
CAS
Google Scholar
Suzuki H, Dittrich P: Artificial chemistry. Artif Life 2009, 15: 1–3. 10.1162/artl.2009.15.1.15100
Article
Google Scholar
Centler F, Kaleta C, di Fenizio PS, Dittrich P: Computing chemical organizations in biological networks. Bioinformatics 2008, 24: 1611–1618. 10.1093/bioinformatics/btn228
Article
CAS
Google Scholar
Grzybowski BA, Bishop KJM, Kowalczyk B, Wilmer CE: The wired universe of organic chemistry. Nature Chemistry 2009, 1: 31–36. 10.1038/nchem.136
Article
CAS
Google Scholar
Cayley A: On the Mathematical Theory of Isomers. Philos Mag 1874, 47: 444–446.
Google Scholar
Sylvester JJ: On an application of the new atomic theory to the graphical representation of the invariants and covariants of binary quantics, with three appendices. Amer J Math 1878, 1: 64–128. 10.2307/2369436
Article
Google Scholar
Heidrich D, Kliesch W, Quapp W: Properties of Chemically Interesting Potential Energy Surfaces, of Lecture Notes in Chemistry. Volume 56. Berlin: Springer-Verlag; 1991.
Book
Google Scholar
Benkö G, Flamm C, Stadler PF: A graph-based toy model of chemistry. J Chem Inf Comp Sci 2003, 43: 1085–93.
Article
Google Scholar
Gillespie RJ, Nyholm RS: Inorganic Stereochemistry. Quart Rev Chem Soc 1957, 11: 339–380. 10.1039/qr9571100339
Article
CAS
Google Scholar
Hoffmann R: An Extended Hückel Theory. I. Hydrocarbons. J Chem Phys 1963, 39: 1397–1412. 10.1063/1.1734456
Article
CAS
Google Scholar
Benkö G, Flamm C, Stadler PF: Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting. In Advances in Artificial Life, of Lecture Notes in Computer Science. Volume 2801. Edited by: Banzhaf W, Christaller T, Dittrich P, Kim JT, Ziegler J. Heidelberg, Germany: Springer-Verlag; 2003:10–20. full_text
Google Scholar
Benkö G, Flamm C, Stadler PF: Multi-Phase Artificial Chemistry. In The Logic of Artificial Life: Abstracting and Synthesizing the Principles of Living Systems. Edited by: Schaub H, Detje F, Brüggemann U. Berlin: IOS Press, Akademische Verlagsgesellschaft; 2004:16–22.
Google Scholar
Klopman G: Chemical reactivity and the concept of charge- and frontier-controlled reactions. J Am Chem Soc 1968, 90: 223–243. 10.1021/ja01004a002
Article
CAS
Google Scholar
Salem L: Intermolecular Orbital Theory of the Interaction between Conjugated Systems. I. General Theory. J Am Chem Soc 1968, 90: 543–552. 10.1021/ja01005a001
Article
CAS
Google Scholar
Salem L: Intermolecular Orbital Theory of the Interaction between Conjugated Systems. II. Thermal and Photochemical Calculations. J Am Chem Soc 1968, 90: 553–566. 10.1021/ja01005a002
Article
CAS
Google Scholar
Wodrich MD, Corminboeuf C, Schreiner PR, Fokin AA, von Ragué Schleyer P: How accurate are DFT treatments of organic energies? Org Lett 2007, 9: 1851–1854. 10.1021/ol070354w
Article
CAS
Google Scholar
Brittain DRB, Lin CY, Gilbert ATB, Izgorodina EI, Gill PMW, Coote ML: The role of exchange in systematic DFT errors for some organic reactions. Physical chemistry chemical physics: PCCP 2009, 11: 1138–1142.
Article
CAS
Google Scholar
Gasteiger J, Rudolph C, Sadowski J: Automatic Generation of 3 D Atomic Coordinates for Organic Molecules. Tetrahedron Comp Method 1990, 3: 537–547. 10.1016/0898-5529(90)90156-3
Article
CAS
Google Scholar
Fujita S: Description of Organic Reactions Based on Imaginary Transition Structures. 1. Introduction of new concepts. J Chem Inf Comput Sci 1986, 26: 205–212.
Article
CAS
Google Scholar
Hendrickson JB: Comprehensive System for Classification and Nomenclature of Organic Reactions. J Chem Inf Comput Sci 1997, 37: 852–860.
Article
CAS
Google Scholar
Faulon JL, Sault AG: Stochastic generator of chemical structure. 3. Reaction network generation. J Chem Inf Comput Sci 2001,41(4):894–908.
Article
CAS
Google Scholar
Félix L, Rosselló F, Valiente G: Efficient Reconstruction of Metabolic Pathways by Bidirectional Chemical Search. Bull Math Biol 2009, 71: 750–769. 10.1007/s11538-008-9380-8
Article
Google Scholar
Crabtree JD, Mehta DP: Automated Reaction Mapping. J Exp Algor 2009, 13: 1–29.
Google Scholar
Ullmann JR: An Algorithm for Subgragraph Isomorphism. J ACM 1976, 23: 31–42. 10.1145/321921.321925
Article
Google Scholar
Kotera M, Hattori M, Oh MA, Yamamoto R, Komeno T, Yabuzaki J, Tonomura K, Goto S, Kanehisa M: RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions. Genome Inform 2004, 15: P062.
Google Scholar
Nagl M: Graph-Grammatiken, Theorie, Implementierung, Anwendung. Braunschweig: Vieweg; 1979.
Book
Google Scholar
Cordella LP, Foggia P, Sansone C, Vento M: Performance Evaluation of the VF Graph Matching Algorithm. ICIAP 1999, 1172–1177.
Google Scholar
Cordella LP, Foggia P, Sansone C, Vento M: An Improved Algorithm for Matching Large Graphs. 3rd IAPR-TC15 Workshop on Graph-based Representations in Pattern Recognition 2001, 149–159.
Google Scholar
Weininger D: SMILES, a chemical language and information system. 1. introduction to methodology and encoding rules. J Chem Inf Comp Sci 1988, 28: 31–36.
Article
CAS
Google Scholar
Mann M, Flamm C: Graph Grammar Library (GGL).2010. [http://www.tbi.univie.ac.at/TBI/software.html]
Google Scholar
Read RC: Every one a winner. Ann Discr Math 1978, 2: 107–120. full_text
Article
Google Scholar
Kun A, Papp B, Szathmary E: Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks. Genome Biol 2008, 9: R51. 10.1186/gb-2008-9-3-r51
Article
Google Scholar
Weininger D, Weininger A, Weininger JL: SMILES. 2. Algorithm for generation of unique SMILES notation. J Chem Inf Comput Sci 1989, 29: 97–101.
Article
CAS
Google Scholar
Gesteland RF, Cech TR, Atkins JF: The RNA World. 3rd edition. Woodbury, NY: Cold Spring Harbor Laboratories Press; 2006.
Google Scholar
Müller UF: Re-creating an RNA world. Cell Mol Life Sci 2006, 63: 1278–1293. 10.1007/s00018-006-6047-1
Article
Google Scholar
Chen X, Li N, Ellington AD: Ribozyme Catalysis of Metabolism in the RNA World. Chemistry & Biodiv 2007, 4: 633–655.
Article
CAS
Google Scholar
Talini G, Gallori E, Maurel MC: Natural and unnatural ribozymes: Back to the primordial RNA world. Res Microbiol 2009, 160: 457–465. 10.1016/j.resmic.2009.05.005
Article
CAS
Google Scholar
Stephan-Otto Attolini C, Stadler PF, Flamm C: CelloS: a Multi-level Approach to Evolutionary Dynamics. In Advances in Artificial Life: 8th European Conference, ECAL 2005, of Lect. Notes Comp. Sci. Volume 3630. Edited by: Capcarrere MS, Freitas AA, Bentley PJ, Johnson CG, Timmis J. Berlin: Springer Verlag; 2005:500–509.
Chapter
Google Scholar
Flamm C, Endler L, Müller S, Widder S, Schuster P: A minimal and self-consistent in silico cell model based on macromolecular interactions. Philos Trans R Soc Lond B Biol Sci 2007, 362: 1831–1839. 10.1098/rstb.2007.2075
Article
CAS
Google Scholar
Fontana W, Konings DA, Stadler PF, Schuster P: Statistics of RNA secondary structures. Biopolymers 1993,33(9):1389–404. 10.1002/bip.360330909
Article
CAS
Google Scholar
Mathews DH, Sabina J, Zuker M, Turner H: Expanded Sequence Dependence of Thermodynamic Parameters Provides Robust Prediction of RNA Secondary Structure. J Mol Biol 1999, 288: 911–940. 10.1006/jmbi.1999.2700
Article
CAS
Google Scholar
Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster P: Fast Folding and Comparison of RNA Secondary Structures (The Vienna RNA Package). Monatsh Chem 1994, 125: 167–188. 10.1007/BF00818163
Article
CAS
Google Scholar
Hofacker IL: The Vienna RNA Secondary Structure Server. Nucl Acids Res 2003, 31: 3429–3431. 10.1093/nar/gkg599
Article
CAS
Google Scholar
Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL: The Vienna RNA Websuite. Nucl Acids Res 2008, 36: W70-W74. 10.1093/nar/gkn188
Article
CAS
Google Scholar
Fontana W, Schuster P: Continuity in evolution: on the nature of transitions. Science 1998, 280: 1451–5. 10.1126/science.280.5368.1451
Article
CAS
Google Scholar
Herges R: Organizing Principle of Complex Reactions and Theory of Coarctate Transition States. Angew Chem Int Ed 1994, 33: 255–276. 10.1002/anie.199402551
Article
Google Scholar
Hendrickson JB, Miller TM: Reaction indexing for reaction databases. J Chem Inf Comput Sci 1990, 30: 403–408.
Article
CAS
Google Scholar
Herges R: Coarctate Transition States: The Discovery of a Reaction Principle. J Chem Inf Comput Sci 1994, 34: 91–102.
Article
CAS
Google Scholar
Ullrich A, Flamm C: Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe. In Proceedings of the 6th International Conference on Computational Methodes in Systems Biology (CSMB), of Lect. Notes Bioinf. Volume 5307. Edited by: Istrail S. Berlin: Springer; 2008:28–43.
Google Scholar
Fontana W, Stadler PF, Tarazona P, Weinberger ED, Schuster P: RNA folding and combinatory landscapes. Physical Review E 1993, 47: 2083–2099. 10.1103/PhysRevE.47.2083
Article
CAS
Google Scholar
Ullrich A: Evolution of Metabolism in a graph-based Toy-Universe. PhD thesis. Universität Leipzig, Germany; 2008.
Google Scholar
Stadler PF: Fitness Landscapes Arising from the Sequence-Structure Maps of Biopolymers. J Mol Struct 1999,463(1–2):7–19.
Article
CAS
Google Scholar
Ullrich A, Flamm C: A Sequence-to-Function Map for Ribozyme-catalyzed Metabolisms. ECAL, Lect Notes Comp Sci 2009, in press.
Google Scholar
Palsson BO: Systems Biology: Properties of Reconstructed Networks. New York, NY, USA: Cambridge University Press; 2006.
Book
Google Scholar
Gagneur J, Klamt S: Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics 2004, 5: 175. 10.1186/1471-2105-5-175
Article
Google Scholar
Balaban AT: Highly discriminating distance-based topological index. Chem Phys Lett 1982, 89: 399–404. 10.1016/0009-2614(82)80009-2
Article
CAS
Google Scholar
Wiener H: Structural Determination of Para n Boiling Points. J Am Chem Soc 1947, 69: 17–20. 10.1021/ja01193a005
Article
CAS
Google Scholar
Axelrod R: The Complexity of Cooperation: Agent-Based Models of Competition and Collaboration. Princeton, NJ: Prince-ton University Press; 1997.
Google Scholar
Orr HA: The evolutionary genetics of adaptation: a simulation study. Genet Res Camb 1999, 74: 207–214. 10.1017/S0016672399004164
Article
CAS
Google Scholar
Pfeiffer T, Soyer OS, Bonhoeffer S: The Evolution of Connectivity in Metabolic Networks. PLoS Biol 2005, 3: e228. 10.1371/journal.pbio.0030228
Article
Google Scholar
Rohrschneider M, Heine C, Reichenbach A, Kerren A, Scheuermann G: A Novel Grid-based Visualization Approach for Metabolic Networks with Advanced Focus and Context View. In 17th International Symposium on Graph Drawing (GD09), Lect. Notes Comp. Sci. Edited by: Emden Gansner DE. Springer; 2009.
Google Scholar
Díaz-Mej a JJ, Pérez-Rueda E, Segovia L: A network perspective on the evolution of metabolism by gene duplication. Genome Biol 2007, 8: R26. 10.1186/gb-2007-8-2-r26
Article
Google Scholar
Papp B, Teusink B, Notebaart RA: A critical view of metabolic network adaptations. HFSP J 2009, 3: 24–35. 10.2976/1.3020599
Article
Google Scholar
Fani R, Fondi M: Origin and evolution of metabolic pathways. Phys Life Rev 2009, 6: 23–52. 10.1016/j.plrev.2008.12.003
Article
Google Scholar
Horowitz NH: On the evolution of biochemical syntheses. Proc Natl Acad Sci USA 1945, 31: 153–157. 10.1073/pnas.31.6.153
Article
CAS
Google Scholar
Granick S: Speculations on the origins and evolution of photosynthesis. Ann NY Acad Sci 1957, 69: 292–308. 10.1111/j.1749-6632.1957.tb49665.x
Article
CAS
Google Scholar
Ycas M: On earlier states of the biochemical system. J Theor Biol 1974, 44: 145–160. 10.1016/S0022-5193(74)80035-4
Article
CAS
Google Scholar
Jensen RA: Enzyme recruitment in evolution of new function. Annu Rev Microbiol 1976, 30: 409–425. 10.1146/annurev.mi.30.100176.002205
Article
CAS
Google Scholar
Lazcano A, Miller SL: The origin and early evolution of life: Prebiotic chemistry, the Pre-RNA world, and time. Cell 1996, 85: 793–798. 10.1016/S0092-8674(00)81263-5
Article
CAS
Google Scholar
Doolittle RF: Evolutionary aspects of whole-genome biology. Curr Opin Struct Biol 2005, 15: 248–253. 10.1016/j.sbi.2005.04.001
Article
CAS
Google Scholar
Newman MEJ: Power laws, Pareto distributions and Zipf's law. Contemporary Physics 2005, 46: 323–351. 10.1080/00107510500052444
Article
Google Scholar
Behre J, Wilhelm T, von Kamp A, Ruppin E, Schuster S: Structural robustness of metabolic networks with respect to multiple knockouts. J Theor Biol 2008, 252: 433–41. 10.1016/j.jtbi.2007.09.043
Article
CAS
Google Scholar
Haus UU, Klamt S, Stephen T: Computing knock out strategies in metabolic networks. J Comp Biol 2008, 15: 259–68. 10.1089/cmb.2007.0229
Article
CAS
Google Scholar