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E. and Setty, Y. and Shavit, S. and Zaslaver, A. and Alon, U. }, citeulike-article-id = {582434}, doi = {10.1371/journal.pbio.0040045}, issn = {1545-7885}, journal = {PLoS Biol}, keywords = {evolution genecircuits}, month = {April}, number = {4}, priority = {2}, title = {Plasticity of the cis-Regulatory Input Function of a Gene.}, url = {http://dx.doi.org/10.1371/journal.pbio.0040045}, volume = {4}, year = {2006} } @article{citeulike:333353, address = {Departments of Molecular Cell Biology and Physics of Complex Systems, The Weizmann Institute of Science, Rehovot 76100, Israel.}, author = {Kashtan, Nadav and Alon, Uri }, citeulike-article-id = {333353}, doi = {10.1073/pnas.0503610102}, issn = {0027-8424}, journal = {Proc Natl Acad Sci U S A}, keywords = {evolution modularity network simulation}, month = {September}, priority = {4}, title = {Spontaneous evolution of modularity and network motifs.}, url = {http://www.pnas.org/cgi/content/abstract/102/39/13773}, year = {2005} } @Book{bshoganftgtti2003, editor = {Stefan Bornholdt and Heinz Georg Schuster}, title = {Handbook of Graphs and Networks - From the Genome to the Internet}, year = {2003}, publisher = {Wiley-VCH}, } @article{SchilstraGRN, author = {Davidson, Eric H. and Rast, Jonathan P. and Oliveri, Paola and Ransick, Andrew and Calestani, Cristina and Yuh, Chiou-Hwa and Minokawa, Takuya and Amore, Gabriele and Hinman, Veronica and Arenas-Mena, Cesar and Otim, Ochan and Brown, C. Titus and Livi, Carolina B. and Lee, Pei Yun and Revilla, Roger and Rust, Alistair G. and Pan, Zheng jun and Schilstra, Maria J. and Clarke, Peter J. C. and Arnone, Maria I. and Rowen, Lee and Cameron, R. Andrew and McClay, David R. and Hood, Leroy and Bolouri, Hamid}, title = {{A Genomic Regulatory Network for Development}}, journal = {Science}, volume = {295}, number = {5560}, pages = {1669-1678}, doi = {10.1126/science.1069883}, year = {2002}, URL = {http://www.sciencemag.org/cgi/content/abstract/295/5560/1669}, ee = {http://www.sciencemag.org/cgi/reprint/295/5560/1669.pdf} } @article{citeulike307461, author = {Shen-Orr, Shai S. and Milo, Ron and Mangan, Shmoolik and Alon, Uri }, citeulike-article-id = {307461}, doi = {10.1038/ng881}, journal = {Nat Genet}, keywords = {ecoli networks regulation}, month = {May}, number = {1}, pages = {64--68}, priority = {2}, title = {Network motifs in the transcriptional regulation network of Escherichia coli}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11967538}, volume = {31}, year = {2002} } @article{GAWray09012003, author = {Wray, Gregory A. and Hahn, Matthew W. and Abouheif, Ehab and Balhoff, James P. and Pizer, Margaret and Rockman, Matthew V. and Romano, Laura A.}, title = {{The Evolution of Transcriptional Regulation in Eukaryotes}}, journal = {Mol Biol Evol}, volume = {20}, number = {9}, pages = {1377-1419}, doi = {10.1093/molbev/msg140}, year = {2003}, URL = {http://mbe.oxfordjournals.org/cgi/content/abstract/20/9/1377}, ee = {http://mbe.oxfordjournals.org/cgi/reprint/20/9/1377.pdf} } @article{Hinton07282006, author = {Hinton, G. E. and Salakhutdinov, R. R.}, title = {{Reducing the Dimensionality of Data with Neural Networks}}, journal = {Science}, volume = {313}, number = {5786}, pages = {504-507}, doi = {10.1126/science.1127647}, year = {2006}, abstract = {High-dimensional data can be converted to low-dimensional codes by training a multilayer neural network with a small central layer to reconstruct high-dimensional input vectors. Gradient descent can be used for fine-tuning the weights in such "autoencoder" networks, but this works well only if the initial weights are close to a good solution. We describe an effective way of initializing the weights that allows deep autoencoder networks to learn low-dimensional codes that work much better than principal components analysis as a tool to reduce the dimensionality of data. }, URL = {http://www.sciencemag.org/cgi/content/abstract/313/5786/504}, ee = {http://www.sciencemag.org/cgi/reprint/313/5786/504.pdf} } @article{citeulike:566295, author = {Sanjay Jain and Sandeep Krishna}, citeulike-article-id = {566295}, eprint = {nlin.AO/0210070}, keywords = {artificialchemistry emergence graphteory networks topology}, month = {Oct}, priority = {3}, title = {Graph Theory and the Evolution of Autocatalytic Networks}, url = {http://arxiv.org/abs/nlin.AO/0210070}, year = {2002} } @book{citeulike:700987, author = {Eric D. Schneider and Dorion Sagan}, citeulike-article-id = {700987}, howpublished = {Hardcover}, isbn = {0226739368}, keywords = {book ecosystemthermodynamics keypaper originsoflife}, month = {June}, priority = {3}, publisher = {{University Of Chicago Press}}, title = {Into the Cool : Energy Flow, Thermodynamics, and Life}, year = {2005} } @PhdThesis{KeySelfOrg, author = {J. J. Kay}, title = {Self-Organization In Living Systems}, school = {Department of Systems Design Engineering, University of Waterloo}, year = {1984}, address = {Waterloo, Ontario, Canada}, url = {http://www.nesh.ca/jameskay/www.fes.uwaterloo.ca/u/jjkay/pubs/thesis/toc.html} } @Article{deepseeorigin, author = {G. 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Kim and J. Ziegler}, volume = {2801}, series = {Lecture Notes in Artificial Intelligence}, publisher = {Springer Verlag Berlin, Heidelberg} } @article{KimTmaze04, author = {DaeEun Kim}, title = {{Evolving internal memory for T-maze tasks in noisy environments}}, journal = {Connection Science}, volume = {16}, number = {3}, pages = {183-210}, year = {2004}, ee = {http://dx.doi.org/10.1080/09540090412331314812} } @Article{SchneiderThermodynamics, author = {E.D. Schneider and J.J. 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Szathmary}, title={The Major Transitions in Evolution}, year={1997}, url={http://www.isrl.uiuc.edu/~amag/langev/paper/maynardsmith1997majorTransitions.html}, publisher={New York: Oxford University Press} } @Book{evoStruktUnsoeld, author = {Albrecht Unsoeld}, title = {Evolution kosmischer, biologischer und geistiger Strukturen}, publisher = {Wissenschaftliche Verlagsgesellschaft mbH Stuttgart}, year = {1983}, series = {Buecher der Zeitschrift Naturwissenschaftliche Rundschau}, address = {Stuttgart}, edition = {2. Auflage} } @Book{OrganismalFormBook, editor = {Gerd B. Mueller and Stuart A. Newman}, title = {Origination of Organismal Form}, publisher = {MIT Press}, year = {2003} } @book{286918, author = {Gary William Flake}, title = {The computational beauty of nature}, year = {1998}, isbn = {0-262-06200-3}, publisher = {MIT Press}, address = {Cambridge, MA, USA}, } @article{DBLP:journals/ki/Kim00, author = {Jan T. 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Schuster}, title={Evolutionary Dynamics: Exploring the Interplay of Selection, Accident, Neutrality and Function.}, year={2003}, publisher={Oxford University Press} } @Book{Zuse, publisher = {Vieweg & Sohn}, title = {Rechnender Raum}, series = {Schriften zur Datenverarbeitung}, author = {Konrad Zuse}, year = {1967}, ee = {ftp://ftp.idsia.ch/pub/juergen/zuserechnenderraum.pdf}, address = {Braunschweig}} @misc{ schuster02networks, author = {P. Schuster and P. Stadler}, title = {Networks in molecular evolution}, journal ={Complexity}, volume={8}, pages={34--42}, year = {2002}, url = {http://citeseer.ist.psu.edu/schuster02networks.html}, ee={http://citeseer.ist.psu.edu/rd/0%2C598572%2C1%2C0.25%2CDownload/http://citeseer.ist.psu.edu/cache/papers/cs/29378/http:zSzzSzwww.tbi.univie.ac.atzSzpaperszSzAbstractszSz02-pks-003.pdf/schuster02networks.pdf} } @Book{LodishMolCellBio, author = {Harvey F. Lodish and D. Baltimore and A. Berk and S. L. Zipursky and P. Matsudaira and James E. Darnell}, title = {Molecular Cell Biology}, publisher = {W. H. Freeman}, address = {New York, NY, USA}, edition = {Fifth}, year = {2004} } @misc{lerena96biomachines, author = {P. Lerena and M. Courant}, title = {Bio-machines}, text = {P. Lerena and M. Courant. Bio--machines. In Proceedings of Artificial Life, volume V, Nara, Japan, 1996.}, year = {1996}, ee = {http://citeseer.csail.mit.edu/cache/papers/cs/2526/ftp:zSzzSzftp-iiuf.unifr.chzSzpubzSzi3smzSzpublicationszSz96zSz65-PL-MC-ALV.pdf/bio-machines.pdf}, url = "citeseer.ist.psu.edu/51823.html" } @book{BioClocks, author={Arthur T. Winfree}, title={The Timing of Biological Clocks}, publisher={Scientific American Books, Inc.}, year=1986 } @article{Lieberman05a, author = {Erez Lieberman and Christoph Hauert and Martin A. 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Conery}, citeulike-article-id = {307330}, doi = {10.1126/science.290.5494.1151}, journal = {Science}, keywords = {evolution gene-duplication}, month = {November}, number = {5494}, pages = {1151--1155}, priority = {0}, title = {The Evolutionary Fate and Consequences of Duplicate Genes}, ee = {http://bioportal.weizmann.ac.il/course/evogen/GeneDup/Lynch_Conery.pdf}, volume = {290}, year = {2000} } @book{601161, author = {Scott Camazine and Nigel R. Franks and James Sneyd and Eric Bonabeau and Jean-Louis Deneubourg and Guy Theraula}, title = {Self-Organization in Biological Systems}, year = {2001}, isbn = {0691012113}, publisher = {Princeton University Press}, address = {Princeton, NJ, USA}, } @article{CoevolutionaryFreeLunches, author = {D. H. Wolpert and W. G. Macready}, doi = {10.1109/TEVC.2005.856205}, journal = {IEEE Transactions on Evolutionary Computation}, month = {December}, number = {6}, pages = {721--735}, title = {Coevolutionary free lunches}, volume = {9}, year = {2005} } @Article{12914657, AUTHOR = {Hooper, Sean and Berg, Otto}, TITLE = {Duplication is more common among laterally transferred genes than among indigenous genes}, JOURNAL = {Genome Biology}, VOLUME = {4}, YEAR = {2003}, NUMBER = {8}, PAGES = {R48}, URL = {http://genomebiology.com/2003/4/8/R48}, DOI = {http://dx.doi.org/10.1186/gb-2003-4-8-r48}, ISSN = {1465-6906}, } @article{francino-adaptive-radiation-model-2005, author = {Pilar P. Francino}, citeulike-article-id = {212295}, doi = {10.1038/ng1579}, issn = {1061-4036}, journal = {Nature Genetics}, keywords = {no-tag}, month = {May}, number = {6}, pages = {573--578}, priority = {4}, publisher = {Nature Publishing Group}, title = {An adaptive radiation model for the origin of new gene functions}, ee = {http://repositories.cdlib.org/cgi/viewcontent.cgi?article=3776&context=lbnl}, volume = {37}, year = {2005} } @book{buss, author={L. W. Buss}, title={The Evolution of Individuality}, year={1987}, address={New York}, publisher={Columbia University Press} } @book{DNAtoDiversity, author = {Sean B. Carroll and Jennifer K. Grenier and Scott D. Weatherbee}, isbn = {0632045116}, publisher = {{Blackwell Science}}, title = {From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design}, year = {2001} } @inproceedings{ wuensche98genomic, booktitle={Procceedings of Pacic Symposium on Biocomputing'98}, author = {A. 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Montoya and Sergi Valverde}, title = {Selection, Tinkering, and Emergence in Complex Networks - Crossing the Land of Tinkering}, url = {citeseer.ist.psu.edu/sole03selection.html} } @article{citeulike:101, address = {Departments of Physics of Complex Systems and Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 76100.}, author = {Milo, R. and Shen-Orr, S. and Itzkovitz, S. and Kashtan, N. and Chklovskii, D. and Alon, U.}, citeulike-article-id = {101}, comment = {Studies the frequency of small units of links (rings, stars, etc.) in different network types.}, doi = {10.1126/science.298.5594.824}, issn = {1095-9203}, journal = {Science}, keywords = {web-graph}, month = {October}, number = {5594}, pages = {824--827}, priority = {0}, title = {Network motifs: simple building blocks of complex networks.}, url = {http://www.sciencemag.org/cgi/content/abstract/298/5594/824}, volume = {298}, year = {2002} } @misc{ frank99population, author = {S. Frank}, title = {Population and quantitative genetics of regulatory networks}, text = {S. A. Frank. Population and quantitative genetics of regulatory networks. Journal of Theoretical Biology, 197:281--294, 1999. [Link].}, year = {1999}, url = {citeseer.csail.mit.edu/frank99population.html} } @article {Albert-2002-SMC, author= {Reka Albert and Albert-Laszlo Barabasi}, journal= {Reviews of Modern Physics}, number= {1}, pages= {48--97}, title= {Statistical Mechanics of Complex Networks}, volume= {72}, year= {2002}, url= {http://prola.aps.org/abstract/RMP/v74/i1/p47_1} } @article{sordino95hox, AUTHOR = {P. Sordino and F. Van Der Hoeven and D. Duboule}, TITLE = {Hox Gene Expression in Teleost Fins and the Origin of Vertebrate Digits}, JOURNAL = {Nature}, YEAR = {1995}, volume = {375}, number = {6533}, pages = {678-681}, month = jun } @book{judson96theeighth, author={Horace Freeland Judson}, title={The eighth day of creation: makers of the revolution in biology}, year={1996}, address={Plainview, N.Y.}, keywords={distk}, publisher={CSHL Press} } @article{NadavKashtan09272005, author = {Kashtan, Nadav and Alon, Uri}, title = {{From the Cover: Spontaneous evolution of modularity and network motifs}}, journal = {PNAS}, volume = {102}, number = {39}, pages = {13773-13778}, doi = {10.1073/pnas.0503610102}, year = {2005}, abstract = {Biological networks have an inherent simplicity: they are modular with a design that can be separated into units that perform almost independently. Furthermore, they show reuse of recurring patterns termed network motifs. Little is known about the evolutionary origin of these properties. Current models of biological evolution typically produce networks that are highly nonmodular and lack understandable motifs. Here, we suggest a possible explanation for the origin of modularity and network motifs in biology. We use standard evolutionary algorithms to evolve networks. A key feature in this study is evolution under an environment (evolutionary goal) that changes in a modular fashion. That is, we repeatedly switch between several goals, each made of a different combination of subgoals. We find that such "modularly varying goals" lead to the spontaneous evolution of modular network structure and network motifs. The resulting networks rapidly evolve to satisfy each of the different goals. Such switching between related goals may represent biological evolution in a changing environment that requires different combinations of a set of basic biological functions. The present study may shed light on the evolutionary forces that promote structural simplicity in biological networks and offers ways to improve the evolutionary design of engineered systems. }, URL = {http://www.pnas.org/cgi/content/abstract/102/39/13773}, ee = {http://www.pnas.org/cgi/reprint/102/39/13773.pdf} } @article{citeulike:449993, address = {ICREA-Complex Systems Lab, Universitat Pompeu Fabra (GRIB), Barcelona, Spain. ricard.sole@upf.edu}, author = {R. V. Sole and P. Fernandez and S. A. Kauffman}, issn = {0214-6282}, journal = {Int J Dev Biol}, keywords = {gene networks paleontology}, number = {7-8}, pages = {685--693}, priority = {0}, title = {Adaptive walks in a gene network model of morphogenesis: insights into the Cambrian explosion.}, ee = {http://www.santafe.edu/research/publications/workingpapers/03-07-043.pdf} volume = {47}, year = {2003} } @inproceedings{DBLP:conf/ices/KumarB03, author = {Sanjeev Kumar and Peter J. Bentley}, title = {Biologically Inspired Evolutionary Development.}, booktitle = {ICES}, year = {2003}, pages = {57-68}, ee = {http://www.cs.ucl.ac.uk/staff/P.Bentley/KUBEC3.pdf}, bibsource = {DBLP, http://dblp.uni-trier.de} } @book{citeulike:238626, author = {Sean B. Carroll}, howpublished = {Hardcover}, isbn = {0393060160}, month = {April}, publisher = {{W. W. Norton and Company}}, title = {Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom}, year = {2005} } @book{citeulike:369764, author = {M. W. Kirschner and J. C. Gerhart}, citeulike-article-id = {369764}, howpublished = {Hardcover}, isbn = {0300108656}, keywords = {evolution}, month = {October}, priority = {2}, publisher = {{Yale University Press}}, title = {The Plausibility of Life: Resolving Darwin's Dilemma}, year = {2005} } @book{, abstract = {{<b>The Evolution of the Genome</b> provides a much needed overview of genomic study through clear, detailed, expert-authored discussions of the key areas in genome biology. This includes the evolution of genome size, genomic parasites, gene and ancient genome duplications, polypoidy, comparative genomics, and the implications of these genome-level phenomena for evolutionary theory. In addition to reviewing the current state of knowledge of these fields in an accessible way, the various chapters also provide historical and conceptual background information, highlight the ways in which the critical questions are actually being studied, indicate some important areas for future research, and build bridges across traditional professional and taxonomic boundaries.<br><br><b>The Evolution of the Genome</b> will serve as a critical resource for graduate students, postdoctoral fellows, and established scientists alike who are interested in the issue of genome evolution in the broadest sense.<br><br>&#183; Provides detailed, clearly written chapters authored by leading researchers in their respective fields<br>&#183; Presents a much-needed overview of the historical and theoretical context of the various areas of genomic study<br>&#183; Creates important links between topics in order to promote integration across subdisciplines, including descriptions of how each subject is actually studied<br>&#183; Provides information specifically designed to be accessible to established researchers, postdoctoral fellows, and graduate students alike}}, author = {Ryan T. Gregory}, isbn = {0123014638}, keywords = {book genome genome_evolution genome_size}, month = {December}, priority = {2}, publisher = {{Academic Press}}, title = {The Evolution of the Genome}, year = {2004} } @inproceedings{796570, author = {R. Kumar and P. Raghavan and S. Rajagopalan and D. Sivakumar and A. Tomkins and E. Upfal}, title = {Stochastic models for the Web graph}, booktitle = {FOCS '00: Proceedings of the 41st Annual Symposium on Foundations of Computer Science}, year = {2000}, isbn = {0-7695-0850-2}, pages = {57}, publisher = {IEEE Computer Society}, address = {Washington, DC, USA}, ee = {http://www.cs.brown.edu/research/webagent/focs-2000.pdf} } @Article{, author = {Austin L. 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