@inproceedings{conf/cmsb/UllrichF08,
	title = {Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe.},
	author = {Alexander Ullrich and Christoph Flamm},
	booktitle = {CMSB},
	crossref = {conf/cmsb/2008},
	editor = {Monika Heiner and Adelinde M. Uhrmacher},
	pages = {28-43},
	publisher = {Springer},
	series = {Lecture Notes in Computer Science},
	url = {http://dblp.uni-trier.de/db/conf/cmsb/cmsb2008.html#UllrichF08},
	volume = {5307},
	year = {2008},
	biburl = {http://www.bibsonomy.org/bibtex/276924231518b1ad5d93dce3cebbbd7b4/dblp},
	description = {dblp},
	date = {2008-10-21}, ee = {http://dx.doi.org/10.1007/978-3-540-88562-7_7}, isbn = {978-3-540-88561-0},
	keywords = {dblp }
}

@article{stadler:2003:GPEM,
	title = {Barrier Trees on Poset-Valued Landscapes},
	author = {Peter F. Stadler and Christoph Flamm},
	journal = {Genetic Programming and Evolvable Machines},
	month = {March},
	number = {1},
	pages = {7--20},
	url = {http://www.tbi.univie.ac.at/papers/Abstracts/02-pfs-001.pdf},
	volume = {4},
	year = {2003},
	biburl = {http://www.bibsonomy.org/bibtex/2dea8e336f18c57b36011d96dc99d5c3a/brazovayeye},
	abstract = {Fitness landscapes have proved to be a valuable
                 concept in evolutionary biology, combinatorial
                 optimisation, and the physics of disordered systems.
                 Usually, a fitness landscape is considered as a mapping
                 from a configuration space equipped with some notion of
                 adjacency, nearness, distance, or accessibility, into
                 the real numbers. In the context of multi-objective
                 optimization problems this concept can be extended to
                 poset-valued landscapes. In a geometric analysis of
                 such a structure, local Pareto points take on the role
                 of local minima. We show that the notion of saddle
                 points, barriers, and basins can be extended to the
                 poset-valued case in a meaningful way and describe an
                 algorithm that efficiently extracts these features from
                 an exhaustive enumeration of a given generalised
                 landscape.},
	issn = {1389-2576}, notes = {Article ID:
                 5113070

                 http://www.tbi.univie.ac.at/papers/Abstracts/02-pfs-001.pdf
                 not identical to published version?}, doi = {doi:10.1023/A:1021821009420},
	keywords = {Pareto algorithms, barrier genetic landscape, ordered partially points, programming, saddle set, trees }
}

@book{flamm1995,
	title = {Entwicklung eines Systemkonzeptes zur wissensbasierten, systemtechnisch unterstützten Versuchsmethodik},
	address = {Beuth},
	annote = {II, 138 S},
	author = {{Rolf Jakob} Flamm},
	edition = {1. Aufl},
	howpublished = {Berlin [u.a.]},
	url = {http://gso.gbv.de/DB=2.1/CMD?ACT=SRCHA&SRT=YOP&IKT=1016&TRM=ppn+186124694&sourceid=fbw_bibsonomy},
	year = {1995},
	biburl = {http://www.bibsonomy.org/bibtex/29437e77a6e36ebfef2ed5541b84693ee/fbw},
	description = {imported},
	isbn = {3-410-32868-8},
	keywords = {imported }
}

@inproceedings{conf/foga/FlammHSS07,
	title = {Saddles and Barrier in Landscapes of Generalized Search Operators.},
	author = {Christoph Flamm and Ivo L. Hofacker and Bärbel M. R. Stadler and Peter F. Stadler},
	booktitle = {FOGA},
	pages = {194-212},
	url = {http://dblp.uni-trier.de/db/conf/foga/foga2007.html#FlammHSS07},
	year = {2007},
	biburl = {http://www.bibsonomy.org/bibtex/2b55d23ade027563c40a5f4af85606eb5/dblp},
	description = {dblp},
	ee = {http://dx.doi.org/10.1007/978-3-540-73482-6_11}, date = {2007-09-10},
	keywords = {dblp }
}

@article{toymodel,
	title = {A graph-based toy model of chemistry.},
	address = {Institut fur Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, 1090 Vienna, Austria.},
	author = {Gil Benko and Christopher Flamm and Peter Stadler},
	journal = {Journal of chemical information and computer sciences},
	month = {Jul-Aug},
	number = {4},
	pages = {1085-93},
	school = {Institut fur Theoretische Chemie und Molekulare Strukturbiologie},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12870897&dopt=Citation},
	volume = {43},
	year = {2003},
	biburl = {http://www.bibsonomy.org/bibtex/2e0159c8baa3c2d306c884e626e4337a0/pietrosperoni},
	description = {not so toy},
	abstract = {Large scale chemical reaction networks are a ubiquitous phenomenon, from the metabolism of living cells to processes in planetary atmospheres and chemical technology. At least some of these networks exhibit distinctive global features such as the"small world"behavior. The systematic study of such properties, however, suffers from substantial sampling biases in the few networks that are known in detail. A computational model for generating them is therefore required. Here we present a Toy Model that provides a consistent framework in which generic properties of extensive chemical reaction networks can be explored in detail and that at the same time preserves the"look-and-feel"of chemistry: Molecules are represented as labeled graphs,by their structural formulas; their basic properties are derived by a caricature version of the Extended Huckel MO theory that operates directly on the graphs; chemical reaction mechanisms are implemented as graph rewriting rules acting on the structural formulas; reactivities and selectivities are modeled by a variant of the Frontier Molecular Orbital Theory based on the Extended Huckel scheme. The approach is illustrated for two types of reaction networks: Diels-Alder reactions and the formose reaction implicated in prebiotic sugar synthesis},
	keywords = {artificialchemistry organizationtheory phd }
}

@inproceedings{conf/iv/PotzschSSWF06,
	title = {Visualization of Lattice-Based Protein Folding Simulations.},
	author = {Sebastian Potzsch and Gerik Scheuermann and Peter F. Stadler and Michael T. Wolfinger and Christoph Flamm},
	booktitle = {IV},
	crossref = {conf/iv/2006},
	pages = {89-94},
	publisher = {IEEE Computer Society},
	url = {http://dblp.uni-trier.de/db/conf/iv/iv2006.html#PotzschSSWF06},
	year = {2006},
	biburl = {http://www.bibsonomy.org/bibtex/2d08aae5257c876273ffe6a477ff30c7d/dblp},
	description = {dblp},
	ee = {http://doi.ieeecomputersociety.org/10.1109/IV.2006.127}, date = {2007-01-08},
	keywords = {dblp }
}

@article{journals/tvcg/HeineSFHS06,
	title = {Visualization of Barrier Tree Sequences.},
	author = {Christian Heine and Gerik Scheuermann and Christoph Flamm and Ivo L. Hofacker and Peter F. Stadler},
	journal = {IEEE Trans. Vis. Comput. Graph.},
	number = {5},
	pages = {781-788},
	url = {http://dblp.uni-trier.de/db/journals/tvcg/tvcg12.html#HeineSFHS06},
	volume = {12},
	year = {2006},
	biburl = {http://www.bibsonomy.org/bibtex/28a5e45adc50715854e939af81dd4a0fc/dblp},
	description = {dblp},
	ee = {http://doi.ieeecomputersociety.org/10.1109/TVCG.2006.196}, date = {2007-01-04},
	keywords = {dblp }
}

@article{journals/jcisd/BergerFGLS04,
	title = {Counterexamples in Chemical Ring Perception.},
	author = {Franziska Berger and Christoph Flamm and Petra M. Gleiss and Josef Leydold and Peter F. Stadler},
	journal = {Journal of Chemical Information and Modeling},
	number = {2},
	pages = {323-331},
	url = {http://dblp.uni-trier.de/db/journals/jcisd/jcisd44.html#BergerFGLS04},
	volume = {44},
	year = {2004},
	biburl = {http://www.bibsonomy.org/bibtex/26eb2eed2823e758a1f6a7377ca09be89/dblp},
	description = {dblp},
	ee = {http://dx.doi.org/10.1021/ci030405d}, date = {2006-10-25},
	keywords = {dblp }
}

@article{journals/bioinformatics/MachneFMLWF06,
	title = {The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks.},
	author = {Rainer Machné and Andrew Finney and Stefan Müller and James Lu and Stefanie Widder and Christoph Flamm},
	journal = {Bioinformatics},
	number = {11},
	pages = {1406-1407},
	url = {http://dblp.uni-trier.de/db/journals/bioinformatics/bioinformatics22.html#MachneFMLWF06},
	volume = {22},
	year = {2006},
	biburl = {http://www.bibsonomy.org/bibtex/211422f84895ac7a481bf47374249ee9d/dblp},
	description = {dblp},
	ee = {http://dx.doi.org/10.1093/bioinformatics/btl086}, date = {2006-08-24},
	keywords = {dblp }
}

@article{journals/bmcbi/ForstFHS06,
	title = {Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation.},
	author = {Christian V. Forst and Christoph Flamm and Ivo L. Hofacker and Peter F. Stadler},
	journal = {BMC Bioinformatics},
	pages = {67},
	url = {http://dblp.uni-trier.de/db/journals/bmcbi/bmcbi7.html#ForstFHS06},
	volume = {7},
	year = {2006},
	biburl = {http://www.bibsonomy.org/bibtex/2959344971961013a79506c2e624eedca/dblp},
	description = {dblp},
	ee = {http://dx.doi.org/10.1186/1471-2105-7-67}, date = {2006-05-18},
	keywords = {dblp }
}

@inproceedings{conf/ecal/AttoliniSF05,
	title = {CelloS: A Multi-level Approach to Evolutionary Dynamics.},
	author = {Camille Stephan-Otto Attolini and Peter F. Stadler and Christoph Flamm},
	booktitle = {ECAL},
	crossref = {conf/ecal/2005},
	editor = {Mathieu S. Capcarrère and Alex Alves Freitas and Peter J. Bentley and Colin G. Johnson and Jon Timmis},
	pages = {500-509},
	publisher = {Springer},
	series = {Lecture Notes in Computer Science},
	url = {http://dblp.uni-trier.de/db/conf/ecal/ecal2005.html#AttoliniSF05},
	volume = {3630},
	year = {2005},
	biburl = {http://www.bibsonomy.org/bibtex/27accfa98ebb5a0818ecdbb585aeeb814/dblp},
	description = {dblp},
	ee = {http://dx.doi.org/10.1007/11553090_51}, isbn = {3-540-28848-1}, date = {2005-10-26},
	keywords = {dblp }
}

@inproceedings{conf/ecal/BenkoFS05,
	title = {Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry.},
	author = {Gil Benkö and Christoph Flamm and Peter F. Stadler},
	booktitle = {ECAL},
	crossref = {conf/ecal/2005},
	editor = {Mathieu S. Capcarrère and Alex Alves Freitas and Peter J. Bentley and Colin G. Johnson and Jon Timmis},
	pages = {725-733},
	publisher = {Springer},
	series = {Lecture Notes in Computer Science},
	url = {http://dblp.uni-trier.de/db/conf/ecal/ecal2005.html#BenkoFS05},
	volume = {3630},
	year = {2005},
	biburl = {http://www.bibsonomy.org/bibtex/28925fb64f017cb013b6e385e122eee5f/dblp},
	description = {dblp},
	ee = {http://dx.doi.org/10.1007/11553090_73}, isbn = {3-540-28848-1}, date = {2005-10-26},
	keywords = {dblp }
}

@inproceedings{conf/gcb/AbfalterFS03,
	title = {Design of multi-stable nucleid acid sequences.},
	author = {Ingrid G. Abfalter and Christoph Flamm and Peter F. Stadler},
	booktitle = {German Conference on Bioinformatics},
	crossref = {conf/gcb/2003},
	pages = {1-7},
	url = {http://dblp.uni-trier.de/db/conf/gcb/gcb2003.html#AbfalterFS03},
	year = {2003},
	biburl = {http://www.bibsonomy.org/bibtex/27db7f32b08fa91442df5ab4372d9f464/dblp},
	description = {dblp},
	date = {2005-03-15},
	keywords = {dblp }
}

@inproceedings{conf/cars/BreeuwerPNMFPR03,
	title = {The detection of normal, ischemic and infarcted myocardial tissue using MRI.},
	author = {Marcel Breeuwer and Ingo Paetsch and Eike Nagel and Raja Muthupillai and Scott Flamm and Sven Plein and John P. Ridgway},
	booktitle = {CARS},
	crossref = {conf/cars/2003},
	editor = {Heinz U. Lemke and Michael W. Vannier and Kiyonari Inamura and Allan G. Farman and Kunio Doi and Johan H. C. Reiber},
	pages = {1153-1158},
	publisher = {Elsevier},
	series = {International Congress Series},
	url = {http://dblp.uni-trier.de/db/conf/cars/cars2003.html#BreeuwerPNMFPR03},
	volume = {1256},
	year = {2003},
	biburl = {http://www.bibsonomy.org/bibtex/2ed3971346d0e1691417848e026fce085/dblp},
	description = {dblp},
	isbn = {0-444-51387-6}, date = {2004-12-22},
	keywords = {dblp }
}

@inproceedings{conf/miccai/PednekarKMFK04,
	title = {Left Ventricular Segmentation in MR Using Hierarchical Multi-class Multi-feature Fuzzy Connectedness.},
	author = {Amol Pednekar and Uday Kurkure and Raja Muthupillai and Scott Flamm and Ioannis A. Kakadiaris},
	booktitle = {MICCAI (1)},
	crossref = {conf/miccai/2004-1},
	editor = {Christian Barillot and David R. Haynor and Pierre Hellier},
	pages = {402-410},
	publisher = {Springer},
	series = {Lecture Notes in Computer Science},
	url = {http://dblp.uni-trier.de/db/conf/miccai/miccai2004-1.html#PednekarKMFK04},
	volume = {3216},
	year = {2004},
	biburl = {http://www.bibsonomy.org/bibtex/2c123e68ddeb892a64f10e6c0edd2800f/dblp},
	description = {dblp},
	ee = {http://springerlink.metapress.com/openurl.asp?genre=article&issn=0302-9743&volume=3216&spage=402}, isbn = {3-540-22976-0}, date = {2004-09-06},
	keywords = {dblp }
}

@inproceedings{conf/miccai/PednekarKKMF03,
	title = {Validation of the Automatic Computation of the Ejection Fraction from Cine-MRI.},
	author = {Amol Pednekar and Ioannis A. Kakadiaris and Uday Kurkure and Raja Muthupillai and Scott Flamm},
	booktitle = {MICCAI (2)},
	crossref = {conf/miccai/2003-2},
	editor = {Randy E. Ellis and Terry M. Peters},
	pages = {987-989},
	publisher = {Springer},
	series = {Lecture Notes in Computer Science},
	url = {http://dblp.uni-trier.de/db/conf/miccai/miccai2003-2.html#PednekarKKMF03},
	volume = {2879},
	year = {2003},
	biburl = {http://www.bibsonomy.org/bibtex/218774b1a4f0d16715df282f15365a82b/dblp},
	description = {dblp},
	ee = {http://springerlink.metapress.com/openurl.asp?genre=article&issn=0302-9743&volume=2879&spage=987}, isbn = {3-540-20464-4}, date = {2004-09-06},
	keywords = {dblp }
}

@inproceedings{conf/miccai/PednekarKZMF02,
	title = {Automatic Hybrid Segmentation of Dual Contrast Cardiac MR Data.},
	author = {Amol Pednekar and Ioannis A. Kakadiaris and V. Zavaletta and Raja Muthupillai and Scott Flamm},
	booktitle = {MICCAI (1)},
	crossref = {conf/miccai/2002-1},
	editor = {Takeyoshi Dohi and Ron Kikinis},
	pages = {690-697},
	publisher = {Springer},
	series = {Lecture Notes in Computer Science},
	url = {http://dblp.uni-trier.de/db/conf/miccai/miccai2002-1.html#PednekarKZMF02},
	volume = {2488},
	year = {2002},
	biburl = {http://www.bibsonomy.org/bibtex/2579585072ef338f20edc9371d92f9773/dblp},
	description = {dblp},
	ee = {http://link.springer.de/link/service/series/0558/bibs/2488/24880690.htm}, isbn = {3-540-44224-3}, date = {2004-09-06},
	keywords = {dblp }
}

@inproceedings{conf/ecal/BenkoFS03,
	title = {Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting.},
	author = {Gil Benkö and Christoph Flamm and Peter F. Stadler},
	booktitle = {ECAL},
	crossref = {conf/ecal/2003},
	editor = {Wolfgang Banzhaf and Thomas Christaller and Peter Dittrich and Jan T. Kim and Jens Ziegler},
	pages = {10-19},
	publisher = {Springer},
	series = {Lecture Notes in Computer Science},
	url = {http://dblp.uni-trier.de/db/conf/ecal/ecal2003.html#BenkoFS03},
	volume = {2801},
	year = {2003},
	biburl = {http://www.bibsonomy.org/bibtex/23cd49e3562636fde013c63b60e1b91b3/dblp},
	description = {dblp},
	ee = {http://springerlink.metapress.com/openurl.asp?genre=article&issn=0302-9743&volume=2801&spage=10}, isbn = {3-540-20057-6}, date = {2003-11-14},
	keywords = {dblp }
}

@article{journals/jcisd/BenkoFS03,
	title = {A Graph-Based Toy Model of Chemistry.},
	author = {Gil Benkö and Christoph Flamm and Peter F. Stadler},
	journal = {Journal of Chemical Information and Computer Sciences},
	number = {4},
	pages = {1085-1093},
	url = {http://dblp.uni-trier.de/db/journals/jcisd/jcisd43.html#BenkoFS03},
	volume = {43},
	year = {2003},
	biburl = {http://www.bibsonomy.org/bibtex/2de94133760e74f76f630a1b8ea629011/dblp},
	description = {dblp},
	ee = {http://dx.doi.org/10.1021/ci0200570}, date = {2003-08-26},
	keywords = {dblp }
}

@article{journals/gpem/StadlerF03,
	title = {Barrier Trees on Poset-Valued Landscapes.},
	author = {Peter F. Stadler and Christoph Flamm},
	journal = {Genetic Programming and Evolvable Machines},
	number = {1},
	pages = {7-20},
	url = {http://dblp.uni-trier.de/db/journals/gpem/gpem4.html#StadlerF03},
	volume = {4},
	year = {2003},
	biburl = {http://www.bibsonomy.org/bibtex/287b9c047309bfc5e734760cb937ab38a/dblp},
	description = {dblp},
	date = {2003-03-25},
	keywords = {dblp }
}