{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T02:42:26Z","timestamp":1776048146863,"version":"3.50.1"},"publisher-location":"New York, NY","reference-count":218,"publisher":"Springer New York","isbn-type":[{"value":"9780387758886","type":"print"},{"value":"9780387304403","type":"electronic"}],"license":[{"start":{"date-parts":[[2009,1,1]],"date-time":"2009-01-01T00:00:00Z","timestamp":1230768000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2009,1,1]],"date-time":"2009-01-01T00:00:00Z","timestamp":1230768000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009]]},"DOI":"10.1007\/978-0-387-30440-3_79","type":"book-chapter","created":{"date-parts":[[2009,6,17]],"date-time":"2009-06-17T16:41:24Z","timestamp":1245256884000},"page":"1180-1213","source":"Crossref","is-referenced-by-count":29,"title":["Complex Gene Regulatory Networks\u00a0\u2013 from Structure to Biological Observables: Cell Fate Determination"],"prefix":"10.1007","author":[{"given":"Sui","family":"Huang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stuart A.","family":"Kauffman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"79_CR1_79","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/j.cell.2005.02.013","volume":"121","author":"J Adolfsson","year":"2005","unstructured":"Adolfsson J, Mansson R, Buza-Vidas N, Hultquist A, Liuba K, Jensen CT, Bryder D, Yang L, Borge OJ, Thoren LA, Anderson K, Sitnicka E, Sasaki Y, Sigvardsson M, Jacobsen SE (2005) Identification of Flt3+ lympho\u2010myeloid stem cells lacking erythro\u2010megakaryocytic potential a\u00a0revised road map for adult blood lineage commitment. Cell 121:295\u2013306","journal-title":"Cell"},{"key":"79_CR2_79","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1093\/bib\/bbl022","volume":"7","author":"T Aittokallio","year":"2006","unstructured":"Aittokallio T, Schwikowski B (2006) Graph-based methods for analysing networks in cell biology. Brief Bioinform 7:243\u201355","journal-title":"Brief Bioinform"},{"key":"79_CR3_79","doi-asserted-by":"crossref","first-page":"4947","DOI":"10.1242\/jcs.02714","volume":"118","author":"R Albert","year":"2005","unstructured":"Albert R (2005) Scale-free networks in cell biology. J\u00a0Cell Sci 118:4947\u201357","journal-title":"J Cell Sci"},{"key":"79_CR4_79","doi-asserted-by":"crossref","unstructured":"Albert R, Othmer HG (2003) The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J\u00a0Theor Biol 223:1\u201318","DOI":"10.1016\/S0022-5193(03)00035-3"},{"key":"79_CR5_79","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1038\/35019019","volume":"406","author":"R Albert","year":"2000","unstructured":"Albert R, Jeong H, Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406:378\u201382","journal-title":"Nature"},{"key":"79_CR6_79","doi-asserted-by":"crossref","first-page":"8710","DOI":"10.1073\/pnas.1536783100","volume":"100","author":"M Aldana","year":"2003","unstructured":"Aldana M, Cluzel P (2003) A\u00a0natural class of robust networks. Proc Natl Acad Sci USA\u00a0100:8710\u20134","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR7_79","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1016\/j.jtbi.2006.10.027","volume":"245","author":"M Aldana","year":"2007","unstructured":"Aldana M, Balleza E, Kauffman S, Resendiz O (2007) Robustness and evolvability in genetic regulatory networks. J\u00a0Theor Biol 245:433\u201348","journal-title":"J Theor Biol"},{"key":"79_CR8_79","volume-title":"Perspectives and problems in nonlinear science. A celebratory volume in honor of Lawrence Sirovich","author":"M Aldana","year":"2003","unstructured":"Aldana M, Coppersmith S, Kadanoff LP (2003) Boolean dynamics with random couplings. In: Kaplan E, Marsden JE, Sreenivasan KR (eds) Perspectives and problems in nonlinear science. A\u00a0celebratory volume in honor of Lawrence Sirovich. Springer, New York"},{"key":"79_CR9_79","doi-asserted-by":"crossref","first-page":"1866","DOI":"10.1126\/science.1089072","volume":"301","author":"U Alon","year":"2003","unstructured":"Alon U (2003) Biological networks: the tinkerer as an engineer. Science 301:1866\u20137","journal-title":"Science"},{"key":"79_CR10_79","doi-asserted-by":"crossref","first-page":"11149","DOI":"10.1073\/pnas.200327197","volume":"97","author":"LA Amaral","year":"2000","unstructured":"Amaral LA, Scala A, Barthelemy M, Stanley HE (2000) Classes of small-world networks. Proc Natl Acad Sci USA 97:11149\u201352","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR11_79","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1126\/science.177.4047.393","volume":"177","author":"PW Anderson","year":"1972","unstructured":"Anderson PW (1972) More is different. Science 177:393\u2013396","journal-title":"Science"},{"key":"79_CR12_79","doi-asserted-by":"crossref","first-page":"1822","DOI":"10.1073\/pnas.0308265100","volume":"101","author":"DJE Angeli Ferrell Jr.","year":"2004","unstructured":"Angeli D, Ferrell JE Jr., Sontag ED (2004) Detection of multistability, bifurcations, and hysteresis in a\u00a0large class of biological positive\u2010feedback systems. Proc Natl Acad Sci USA 101:1822\u20131827","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR13_79","doi-asserted-by":"crossref","first-page":"4355","DOI":"10.1242\/jcs.01390","volume":"117","author":"KL Arney","year":"2004","unstructured":"Arney KL, Fisher AG (2004) Epigenetic aspects of differentiation. J\u00a0Cell Sci 117:4355\u201363","journal-title":"J Cell Sci"},{"key":"79_CR14_79","doi-asserted-by":"crossref","first-page":"1107; author re","DOI":"10.1126\/science.1099334","volume":"305","author":"Y Artzy-Randrup","year":"2004","unstructured":"Artzy-Randrup Y, Fleishman SJ, Ben-Tal N, Stone L (2004) Comment on Network motifs: simple building blocks of complex networks and Superfamilies of evolved and designed networks. Science 305:1107; author reply 1107","journal-title":"Science"},{"key":"79_CR15_79","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1086\/344413","volume":"77","author":"K Autumn","year":"2002","unstructured":"Autumn K, Ryan MJ, Wake DB (2002) Integrating historical and mechanistic biology enhances the study of adaptation. Q Rev Biol 77:383\u2013408","journal-title":"Q Rev Biol"},{"key":"79_CR16_79","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.sbi.2004.05.004","volume":"14","author":"MM Babu","year":"2004","unstructured":"Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA (2004) Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 14:283\u201391","journal-title":"Curr Opin Struct Biol"},{"key":"79_CR17_79","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1006\/jtbi.1996.0220","volume":"183","author":"RJ Bagley","year":"1996","unstructured":"Bagley RJ, Glass L (1996) Counting and classifying attractors in high dimensional dynamical systems. J\u00a0Theor Biol 183:269\u201384","journal-title":"J Theor Biol"},{"key":"79_CR18_79","doi-asserted-by":"crossref","first-page":"e501","DOI":"10.1371\/journal.pone.0000501","volume":"2","author":"D Balcan","year":"2007","unstructured":"Balcan D, Kabakcioglu A, Mungan M, Erzan A (2007) The information coded in the yeast response elements accounts for most of the topological properties of its transcriptional regulation network. PLoS ONE 2:e501","journal-title":"PLoS ONE"},{"key":"79_CR19_79","doi-asserted-by":"crossref","first-page":"e2456","DOI":"10.1371\/journal.pone.0002456","volume":"3","author":"E Balleza","year":"2008","unstructured":"Balleza E, Alvarez-Buylla ER, Chaos A, Kauffman A, Shmulevich I, Aldana M (2008) Critical dynamics in genetic regulatory networks: examples from four kingdoms. PLoS One 3:e2456","journal-title":"PLoS One"},{"key":"79_CR20_79","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1126\/science.286.5439.509","volume":"286","author":"AL Barabasi","year":"1999","unstructured":"Barabasi AL, Albert R (1999) Emergence of scaling in random networks. Science 286:509\u201312","journal-title":"Science"},{"key":"79_CR21_79","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nrg1272","volume":"5","author":"AL Barabasi","year":"2004","unstructured":"Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell\u2019s functional organization. Nat Rev Genet 5:101\u2013113","journal-title":"Nat Rev Genet"},{"key":"79_CR22_79","doi-asserted-by":"crossref","first-page":"2528","DOI":"10.1093\/emboj\/20.10.2528","volume":"20","author":"A Becskei","year":"2001","unstructured":"Becskei A, Seraphin B, Serrano L (2001) Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J 20:2528\u20132535","journal-title":"EMBO J"},{"key":"79_CR23_79","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/1471-2148-4-51","volume":"4","author":"J Berg","year":"2004","unstructured":"Berg J, Lassig M, Wagner A (2004) Structure and evolution of protein interaction networks: a\u00a0statistical model for link dynamics and gene duplications. BMC Evol Biol 4:51","journal-title":"BMC Evol Biol"},{"key":"79_CR24_79","doi-asserted-by":"crossref","first-page":"E9","DOI":"10.1371\/journal.pbio.0020009","volume":"2","author":"S Bergmann","year":"2004","unstructured":"Bergmann S, Ihmels J, Barkai N (2004) Similarities and differences in genome\u2010wide expression data of six organisms. PLoS Biol 2:E9","journal-title":"PLoS Biol"},{"key":"79_CR25_79","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.cell.2006.02.041","volume":"125","author":"BE Bernstein","year":"2006","unstructured":"Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES (2006) A\u00a0bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125:315\u201326","journal-title":"Cell"},{"key":"79_CR26_79","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1038\/nature05913","volume":"447","author":"A Bird","year":"2007","unstructured":"Bird A (2007) Perceptions of epigenetics. Nature 447:396\u20138","journal-title":"Nature"},{"key":"79_CR27_79","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/1471-2148-3-21","volume":"3","author":"JD Bloom","year":"2003","unstructured":"Bloom JD, Adami C (2003) Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein\u2013protein interactions data sets. BMC Evol Biol 3:21","journal-title":"BMC Evol Biol"},{"key":"79_CR28_79","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1471-2148-4-14","volume":"4","author":"JD Bloom","year":"2004","unstructured":"Bloom JD, Adami C (2004) Evolutionary rate depends on number of protein\u2013protein interactions independently of gene expression level: response. BMC Evol Biol 4:14","journal-title":"BMC Evol Biol"},{"key":"79_CR29_79","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.sbi.2004.05.003","volume":"14","author":"P Bork","year":"2004","unstructured":"Bork P, Jensen LJ, von Mering C, Ramani AK, Lee I, Marcotte EM (2004) Protein interaction networks from yeast to human. Curr Opin Struct Biol 14:292\u20139","journal-title":"Curr Opin Struct Biol"},{"key":"79_CR30_79","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1126\/science.1119959","volume":"310","author":"S Bornholdt","year":"2005","unstructured":"Bornholdt S (2005) Systems biology. Less is more in modeling large genetic networks. Science 310:449\u201351","journal-title":"Science"},{"key":"79_CR31_79","doi-asserted-by":"crossref","first-page":"6114","DOI":"10.1103\/PhysRevLett.84.6114","volume":"84","author":"S Bornholdt","year":"2000","unstructured":"Bornholdt S, Rohlf T (2000) Topological evolution of dynamical networks: global criticality from local dynamics. Phys Rev Lett 84:6114\u20137","journal-title":"Phys Rev Lett"},{"key":"79_CR32_79","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1016\/j.cell.2005.08.020","volume":"122","author":"LA Boyer","year":"2005","unstructured":"Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, Zucker JP, Guenther MG, Kumar RM, Murray HL, Jenner RG, Gifford DK, Melton DA, Jaenisch R, Young RA (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122:947\u201356","journal-title":"Cell"},{"key":"79_CR33_79","unstructured":"Brock A, Chang H, Huang SH Non\u2010genetic cell heterogeneity and mutation\u2010less tumor progression. Manuscript submitted"},{"key":"79_CR34_79","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1088\/1478-3967\/1\/3\/006","volume":"1","author":"KS Brown","year":"2004","unstructured":"Brown KS, Hill CC, Calero GA, Myers CR, Lee KH, Sethna JP, Cerione RA (2004) The statistical mechanics of complex signaling networks: nerve growth factor signaling. Phys Biol 1:184\u2013195","journal-title":"Phys Biol"},{"key":"79_CR35_79","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1016\/j.copbio.2006.06.015","volume":"17","author":"ML Bulyk","year":"2006","unstructured":"Bulyk ML (2006) DNA microarray technologies for measuring protein\u2010DNA interactions. Curr Opin Biotechnol 17:422\u201330","journal-title":"Curr Opin Biotechnol"},{"key":"79_CR36_79","doi-asserted-by":"crossref","first-page":"041902","DOI":"10.1103\/PhysRevE.64.041902","volume":"64","author":"DS Callaway","year":"2001","unstructured":"Callaway DS, Hopcroft JE, Kleinberg JM, Newman ME, Strogatz SH (2001) Are randomly grown graphs really random? Phys Rev E Stat Nonlin Soft Matter Phys 64:041902","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"key":"79_CR37_79","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1038\/nature06965","volume":"453","author":"HH Chang","year":"2008","unstructured":"Chang HH, Hemberg M, Barahona M, Ingber DE, Huang S (2008) Transcriptome\u2010wide noise controls lineage choice in mammalian progenitor cells. Nature 453:544\u2013547","journal-title":"Nature"},{"key":"79_CR38_79","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1471-2121-7-11","volume":"7","author":"HH Chang","year":"2006","unstructured":"Chang HH, Oh PY, Ingber DE, Huang S (2006) Multistable and multistep dynamics in neutrophil differentiation. BMC Cell Biol 7:11","journal-title":"BMC Cell Biol"},{"key":"79_CR39_79","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/1471-2105-6-44","volume":"6","author":"WC Chang","year":"2005","unstructured":"Chang WC, Li CW, Chen BS (2005) Quantitative inference of dynamic regulatory pathways via microarray data. BMC Bioinformatics 6:44","journal-title":"BMC Bioinformatics"},{"key":"79_CR40_79","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1049\/ip-syb:20050079","volume":"153","author":"M Chaves","year":"2006","unstructured":"Chaves M, Sontag ED, Albert R (2006) Methods of robustness analysis for Boolean models of gene control networks. Syst Biol (Stevenage) 153:154\u201367","journal-title":"Syst Biol (Stevenage)"},{"key":"79_CR41_79","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1038\/nrg1990","volume":"8","author":"K Chen","year":"2007","unstructured":"Chen K, Rajewsky N (2007) The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet 8:93\u2013103","journal-title":"Nat Rev Genet"},{"key":"79_CR42_79","doi-asserted-by":"crossref","first-page":"2883","DOI":"10.1093\/bioinformatics\/bti415","volume":"21","author":"KC Chen","year":"2005","unstructured":"Chen KC, Wang TY, Tseng HH, Huang CY, Kao CY (2005) A\u00a0stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae. Bioinformatics 21:2883\u201390","journal-title":"Bioinformatics"},{"key":"79_CR43_79","doi-asserted-by":"crossref","first-page":"e123","DOI":"10.1371\/journal.pcbi.0020123","volume":"2","author":"V Chickarmane","year":"2006","unstructured":"Chickarmane V, Troein C, Nuber UA, Sauro HM, Peterson C (2006) Transcriptional dynamics of the embryonic stem cell switch. PLoS Comput Biol 2:e123","journal-title":"PLoS Comput Biol"},{"key":"79_CR44_79","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1126\/science.1058969","volume":"291","author":"JM Claverie","year":"2001","unstructured":"Claverie JM (2001) Gene number. What if there are only 30,000 human genes? Science 291:1255\u20137","journal-title":"Science"},{"key":"79_CR45_79","doi-asserted-by":"crossref","first-page":"1233","DOI":"10.1182\/blood.V70.5.1233.1233","volume":"70","author":"SJ Collins","year":"1987","unstructured":"Collins SJ (1987) The HL-60 promyelocytic leukemia cell line: proliferation, differentiation, and cellular oncogene expression. Blood 70:1233\u20131244","journal-title":"Blood"},{"key":"79_CR46_79","doi-asserted-by":"crossref","first-page":"1931","DOI":"10.1093\/molbev\/msl060","volume":"23","author":"OX Cordero","year":"2006","unstructured":"Cordero OX, Hogeweg P (2006) Feed\u2010forward loop circuits as a\u00a0side effect of genome evolution. Mol Biol Evol 23:1931\u20136","journal-title":"Mol Biol Evol"},{"key":"79_CR47_79","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1016\/S0959-437X(97)80007-X","volume":"7","author":"MA Cross","year":"1997","unstructured":"Cross MA, Enver T (1997) The lineage commitment of haemopoietic progenitor cells. Curr Opin Genet Dev 7:609\u2013613","journal-title":"Curr Opin Genet Dev"},{"key":"79_CR48_79","doi-asserted-by":"crossref","unstructured":"Dang CV, O\u2019Donnell KA, Zeller KI, Nguyen T, Osthus RC, Li F (2006) The c-Myc target gene network. Semin Cancer Biol 16:253\u201364","DOI":"10.1016\/j.semcancer.2006.07.014"},{"key":"79_CR49_79","doi-asserted-by":"crossref","first-page":"e1672","DOI":"10.1371\/journal.pone.0001672","volume":"3","author":"MI Davidich","year":"2008","unstructured":"Davidich MI, Bornholdt S (2008) Boolean network model predicts cell cycle sequence of fission yeast. PLoS ONE 3:e1672","journal-title":"PLoS ONE"},{"key":"79_CR50_79","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1126\/science.1113832","volume":"311","author":"EH Davidson","year":"2006","unstructured":"Davidson EH, Erwin DH (2006) Gene regulatory networks and the evolution of animal body plans. Science 311:796\u2013800","journal-title":"Science"},{"key":"79_CR51_79","doi-asserted-by":"crossref","first-page":"3997","DOI":"10.1128\/MCB.25.10.3997-4009.2005","volume":"25","author":"IL de la Serna","year":"2005","unstructured":"de la Serna IL, Ohkawa Y, Berkes CA, Bergstrom DA, Dacwag CS, Tapscott SJ, Imbalzano AN (2005) MyoD targets chromatin remodeling complexes to the myogenin locus prior to forming a\u00a0stable DNA-bound complex. Mol Cell Biol 25:3997\u20134009","journal-title":"Mol Cell Biol"},{"key":"79_CR52_79","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1074\/mcp.M100037-MCP200","volume":"1","author":"CM Deane","year":"2002","unstructured":"Deane CM, Salwinski L, Xenarios I, Eisenberg D (2002) Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics 1:349\u201356","journal-title":"Mol Cell Proteomics"},{"key":"79_CR53_79","unstructured":"Delbr\u00fcck M (1949) Discussion. In: Unit\u00e9s biologiques dou\u00e9es de continuit\u00e9 g\u00e9n\u00e9tique Colloques Internationaux du Centre National de la Recherche Scientifique. CNRS, Paris"},{"key":"79_CR54_79","doi-asserted-by":"crossref","unstructured":"Deplancke B, Mukhopadhyay A, Ao W, Elewa AM, Grove CA, Martinez NJ, Sequerra R, Doucette\u2010Stamm L, Reece-Hoyes JS, Hope IA, Tissenbaum HA, Mango SE, Walhout AJ (2006) A\u00a0gene\u2010centered C. elegans protein\u2010DNA interaction network. Cell 125:1193\u2013205","DOI":"10.1016\/j.cell.2006.04.038"},{"key":"79_CR55_79","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1209\/0295-5075\/1\/2\/001","volume":"1","author":"B Derrida","year":"1986","unstructured":"Derrida B, Pomeau Y (1986) Random networks of automata: a\u00a0simple annealed approximation. Europhys Lett 1:45\u201349","journal-title":"Europhys Lett"},{"key":"79_CR56_79","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1016\/j.cell.2007.02.053","volume":"129","author":"IB Dodd","year":"2007","unstructured":"Dodd IB, Micheelsen MA, Sneppen K, Thon G (2007) Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell 129:813\u201322","journal-title":"Cell"},{"key":"79_CR57_79","doi-asserted-by":"crossref","first-page":"2321","DOI":"10.1093\/bioinformatics\/btg307","volume":"19","author":"GS Eichler","year":"2003","unstructured":"Eichler GS, Huang S, Ingber DE (2003) Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles. Bioinformatics 19:2321\u20132322","journal-title":"Bioinformatics"},{"key":"79_CR58_79","doi-asserted-by":"crossref","first-page":"138701","DOI":"10.1103\/PhysRevLett.91.138701","volume":"91","author":"E Eisenberg","year":"2003","unstructured":"Eisenberg E, Levanon EY (2003) Preferential attachment in the protein network evolution. Phys Rev Lett 91:138701","journal-title":"Phys Rev Lett"},{"key":"79_CR59_79","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1182\/blood.V92.2.348","volume":"92","author":"T Enver","year":"1998","unstructured":"Enver T, Heyworth CM, Dexter TM (1998) Do stem cells play dice? Blood 92:348\u201351; discussion 352","journal-title":"Blood"},{"key":"79_CR60_79","doi-asserted-by":"crossref","unstructured":"Espinosa-Soto C, Padilla\u2010Longoria P, Alvarez-Buylla ER (2004) A\u00a0gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles. Plant Cell 16:2923\u201339","DOI":"10.1105\/tpc.104.021725"},{"key":"79_CR61_79","doi-asserted-by":"crossref","first-page":"e8","DOI":"10.1371\/journal.pbio.0050008","volume":"5","author":"JJ Faith","year":"2007","unstructured":"Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a\u00a0compendium of expression profiles. PLoS Biol 5:e8","journal-title":"PLoS Biol"},{"key":"79_CR62_79","doi-asserted-by":"crossref","first-page":"e124","DOI":"10.1093\/bioinformatics\/btl210","volume":"22","author":"A Faure","year":"2006","unstructured":"Faure A, Naldi A, Chaouiya C, Thieffry D (2006) Dynamical analysis of a\u00a0generic Boolean model for the control of the mammalian cell cycle. Bioinformatics 22:e124\u201331","journal-title":"Bioinformatics"},{"key":"79_CR63_79","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1016\/j.cell.2005.09.023","volume":"123","author":"F Fazi","year":"2005","unstructured":"Fazi F, Rosa A, Fatica A, Gelmetti V, De Marchis ML, Nervi C, Bozzoni I (2005) A\u00a0minicircuitry comprised of microRNA\u2010223 and transcription factors NFI-A\u00a0and C\/EBPalpha regulates human granulopoiesis. Cell 123:819\u201331","journal-title":"Cell"},{"key":"79_CR64_79","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1126\/science.280.5365.895","volume":"280","author":"JE Ferrell Jr.","year":"1998","unstructured":"Ferrell JE Jr., Machleder EM (1998) The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280:895\u20138","journal-title":"Science"},{"key":"79_CR65_79","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1038\/nri958","volume":"2","author":"AG Fisher","year":"2002","unstructured":"Fisher AG (2002) Cellular identity and lineage choice. Nat Rev Immunol 2:977\u201382","journal-title":"Nat Rev Immunol"},{"key":"79_CR66_79","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1063\/1.1414882","volume":"11","author":"JJ Fox","year":"2001","unstructured":"Fox JJ, Hill CC (2001) From topology to dynamics in biochemical networks. Chaos 11:809\u2013815","journal-title":"Chaos"},{"key":"79_CR67_79","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1471-2148-4-13","volume":"4","author":"HB Fraser","year":"2004","unstructured":"Fraser HB, Hirsh AE (2004) Evolutionary rate depends on number of protein\u2013protein interactions independently of gene expression level. BMC Evol Biol 4:13","journal-title":"BMC Evol Biol"},{"key":"79_CR68_79","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1126\/science.1068696","volume":"296","author":"HB Fraser","year":"2002","unstructured":"Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW (2002) Evolutionary rate in the protein interaction network. Science 296:750\u20132","journal-title":"Science"},{"key":"79_CR69_79","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1016\/j.gde.2005.08.002","volume":"15","author":"F Fuks","year":"2005","unstructured":"Fuks F (2005) DNA methylation and histone modifications: teaming up to silence genes. Curr Opin Genet Dev 15:490\u2013495","journal-title":"Curr Opin Genet Dev"},{"key":"79_CR70_79","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1210\/me.2007-0121","volume":"22","author":"H Gao","year":"2007","unstructured":"Gao H, Falt S, Sandelin A, Gustafsson JA, Dahlman-Wright K (2007) Genome\u2010wide identification of estrogen receptor\u00a0\u03b1 binding sites in mouse liver. Mol Endocrinol 22:10\u201322","journal-title":"Mol Endocrinol"},{"key":"79_CR71_79","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1038\/35002131","volume":"403","author":"TS Gardner","year":"2000","unstructured":"Gardner TS, Cantor CR, Collins JJ (2000) Construction of a\u00a0genetic toggle switch in Escherichia coli. Nature 403:339\u2013342","journal-title":"Nature"},{"key":"79_CR72_79","first-page":"1","volume-title":"Artificial life","author":"C Gershenson","year":"2002","unstructured":"Gershenson C (2002) Classification of random Boolean networks. In: Standish RK, Bedau MA, Abbass HA (eds) Artificial life, vol\u00a08. MIT Press, Cambridge, pp\u00a01\u20138"},{"key":"79_CR73_79","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1017\/S1464793101005607","volume":"76","author":"T Gisiger","year":"2001","unstructured":"Gisiger T (2001) Scale invariance in biology: coincidence or footprint of a\u00a0universal mechanism? Biol Rev Camb Philos Soc 76:161\u2013209","journal-title":"Biol Rev Camb Philos Soc"},{"key":"79_CR74_79","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/0022-5193(72)90157-9","volume":"34","author":"L Glass","year":"1972","unstructured":"Glass L, Kauffman SA (1972) Co\u2010operative components, spatial localization and oscillatory cellular dynamics. J\u00a0Theor Biol 34:219\u201337","journal-title":"J Theor Biol"},{"key":"79_CR75_79","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/j.cell.2007.02.006","volume":"128","author":"AD Goldberg","year":"2007","unstructured":"Goldberg AD, Allis CD, Bernstein E (2007) Epigenetics: a\u00a0landscape takes shape. Cell 128:635\u20138","journal-title":"Cell"},{"key":"79_CR76_79","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1140\/epjb\/e2004-00316-5","volume":"41","author":"ML Goldstein","year":"2004","unstructured":"Goldstein ML, Morris SA, Yen GG (2004) Problems with fitting to the power-law distribution. Eur Phys J B 41:255\u2013258","journal-title":"Eur Phys J B"},{"key":"79_CR77_79","first-page":"464","volume":"92","author":"BC Goodwin","year":"1999","unstructured":"Goodwin BC, Webster GC (1999) Rethinking the origin of species by natural selection. Riv Biol 92:464\u20137","journal-title":"Riv Biol"},{"key":"79_CR78_79","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1098\/rspb.1979.0086","volume":"205","author":"SJ Gould","year":"1979","unstructured":"Gould SJ, Lewontin RC (1979) The spandrels of San Marco and the Panglossian paradigm: a\u00a0critique of the adaptationist programme. Proc R Soc Lond B Biol Sci 205:581\u201398","journal-title":"Proc R Soc Lond B Biol Sci"},{"key":"79_CR79_79","doi-asserted-by":"crossref","first-page":"3089","DOI":"10.1182\/blood.V99.9.3089","volume":"99","author":"T Graf","year":"2002","unstructured":"Graf T (2002) Differentiation plasticity of hematopoietic cells. Blood 99:3089\u2013101","journal-title":"Blood"},{"key":"79_CR80_79","doi-asserted-by":"crossref","first-page":"8811","DOI":"10.1073\/pnas.1432147100","volume":"100","author":"JA Grass","year":"2003","unstructured":"Grass JA, Boyer ME, Pal S, Wu J, Weiss MJ, Bresnick EH (2003) GATA-1\u2011dependent transcriptional repression of GATA-2 via disruption of positive autoregulation and domain\u2010wide chromatin remodeling. Proc Natl Acad Sci USA\u00a0100:8811\u20136","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR81_79","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1088\/1367-2630\/9\/10\/373","volume":"9","author":"F Greil","year":"2007","unstructured":"Greil F, Drossel B, Sattler J (2007) Critical Kauffman networks under deterministic asynchronous update. New J Phys 9:373","journal-title":"New J Phys"},{"key":"79_CR82_79","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1038\/ng873","volume":"31","author":"N Guelzim","year":"2002","unstructured":"Guelzim N, Bottani S, Bourgine P, Kepes F (2002) Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 31:60\u20133","journal-title":"Nat Genet"},{"key":"79_CR83_79","first-page":"69141","volume":"2006","author":"Y Guo","year":"2006","unstructured":"Guo Y, Eichler GS, Feng Y, Ingber DE, Huang S (2006) Towards a\u00a0holistic, yet gene\u2010centered analysis of gene expression profiles: a\u00a0case study of human lung cancers. J\u00a0Biomed Biotechnol 2006:69141","journal-title":"J Biomed Biotechnol"},{"key":"79_CR84_79","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1093\/molbev\/msi072","volume":"22","author":"MW Hahn","year":"2005","unstructured":"Hahn MW, Kern AD (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein\u2010interaction networks. Mol Biol Evol 22:803\u20136","journal-title":"Mol Biol Evol"},{"key":"79_CR85_79","doi-asserted-by":"crossref","first-page":"C47","DOI":"10.1038\/35011540","volume":"402","author":"LH Hartwell","year":"1999","unstructured":"Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402:C47\u201352","journal-title":"Nature"},{"key":"79_CR86_79","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1002\/cplx.10022","volume":"7","author":"SE Harris","year":"2002","unstructured":"Harris SE, Sawhill BK, Wuensche A, Kauffman SA (2002) A\u00a0model of transcriptional regulatory networks based on biases in the observed regulation rules. Complexity 7:23\u201340","journal-title":"Complexity"},{"key":"79_CR87_79","doi-asserted-by":"crossref","first-page":"2075","DOI":"10.1073\/pnas.040411297","volume":"97","author":"J Hasty","year":"2000","unstructured":"Hasty J, Pradines J, Dolnik M, Collins JJ (2000) Noise-based switches and amplifiers for gene expression. Proc Natl Acad Sci USA\u00a097:2075\u201380","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR88_79","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1093\/nar\/gkh183","volume":"32","author":"PM Haverty","year":"2004","unstructured":"Haverty PM, Hansen U, Weng Z (2004) Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res 32:179\u201388","journal-title":"Nucleic Acids Res"},{"key":"79_CR89_79","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1038\/nrg1379","volume":"5","author":"L He","year":"2004","unstructured":"He L, Hannon GJ (2004) MicroRNAs: small RNAs with a\u00a0big role in gene regulation. Nat Rev Genet 5:522\u201331","journal-title":"Nat Rev Genet"},{"key":"79_CR90_79","volume-title":"Chaos and nonlinear dynamics: An introduction for scientists and engineers, 2 edn","author":"R Hilborn","year":"1994","unstructured":"Hilborn R (1994) Chaos and nonlinear dynamics: An introduction for scientists and engineers, 2 edn. Oxford University Press, New York"},{"key":"79_CR91_79","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature04955","volume":"441","author":"K Hochedlinger","year":"2006","unstructured":"Hochedlinger K, Jaenisch R (2006) Nuclear reprogramming and pluripotency. Nature 441:1061\u20137","journal-title":"Nature"},{"key":"79_CR92_79","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1101\/gad.11.6.774","volume":"11","author":"M Hu","year":"1997","unstructured":"Hu M, Krause D, Greaves M, Sharkis S, Dexter M, Heyworth C, Enver T (1997) Multilineage gene expression precedes commitment in the hemopoietic system. Genes Dev 11:774\u201385","journal-title":"Genes Dev"},{"key":"79_CR93_79","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1093\/bfgp\/2.4.279","volume":"2","author":"S Huang","year":"2004","unstructured":"Huang S (2004) Back to the biology in systems biology: what can we learn from biomolecular networks. Brief Funct Genomics Proteomics 2:279\u2013297","journal-title":"Brief Funct Genomics Proteomics"},{"key":"79_CR94_79","first-page":"1761","volume-title":"Cell fates as attractors \u2013 stability and flexibility of cellular phenotype. In: Endothelial biomedicine","author":"S Huang","year":"2007","unstructured":"Huang S (2007) Cell fates as attractors\u00a0\u2013 stability and flexibility of cellular phenotype. In: Endothelial biomedicine, 1st edn, Cambridge University Press, New York, pp\u00a01761\u20131779","edition":"1"},{"key":"79_CR95_79","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1006\/excr.2000.5044","volume":"261","author":"S Huang","year":"2000","unstructured":"Huang S, Ingber DE (2000) Shape\u2010dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks. Exp Cell Res 261:91\u2013103","journal-title":"Exp Cell Res"},{"key":"79_CR96_79","doi-asserted-by":"crossref","first-page":"27","DOI":"10.3233\/BD-2007-26104","volume":"26","author":"S Huang","year":"2006","unstructured":"Huang S, Ingber DE (2006) A\u00a0non\u2010genetic basis for cancer progression and metastasis: self\u2010organizing attractors in cell regulatory networks. Breast Dis 26:27\u201354","journal-title":"Breast Dis"},{"key":"79_CR97_79","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1007\/112_0602","volume":"157","author":"S Huang","year":"2006","unstructured":"Huang S, Wikswo J (2006) Dimensions of systems biology. Rev Physiol Biochem Pharmacol 157:81\u2013104","journal-title":"Rev Physiol Biochem Pharmacol"},{"key":"79_CR98_79","doi-asserted-by":"crossref","first-page":"128701","DOI":"10.1103\/PhysRevLett.94.128701","volume":"94","author":"S Huang","year":"2005","unstructured":"Huang S, Eichler G, Bar-Yam Y, Ingber DE (2005) Cell fates as high\u2010dimensional attractor states of a\u00a0complex gene regulatory network. Phys Rev Lett 94:128701","journal-title":"Phys Rev Lett"},{"key":"79_CR99_79","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1016\/j.ydbio.2007.02.036","volume":"305","author":"S Huang","year":"2007","unstructured":"Huang S, Guo YP, May G, Enver T (2007) Bifurcation dynamics of cell fate decision in bipotent progenitor cells. Dev Biol 305:695\u2013713","journal-title":"Dev Biol"},{"key":"79_CR100_79","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/S0092-8674(00)00015-5","volume":"102","author":"TR Hughes","year":"2000","unstructured":"Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH (2000) Functional discovery via a\u00a0compendium of expression profiles. Cell 102:109\u201326","journal-title":"Cell"},{"key":"79_CR101_79","doi-asserted-by":"crossref","first-page":"2323","DOI":"10.1182\/blood.V96.7.2323","volume":"96","author":"DA Hume","year":"2000","unstructured":"Hume DA (2000) Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. Blood 96:2323\u20138","journal-title":"Blood"},{"key":"79_CR102_79","doi-asserted-by":"crossref","first-page":"1993","DOI":"10.1093\/bioinformatics\/bth166","volume":"20","author":"J Ihmels","year":"2004","unstructured":"Ihmels J, Bergmann S, Barkai N (2004) Defining transcription modules using large-scale gene expression data. Bioinformatics 20:1993\u20132003","journal-title":"Bioinformatics"},{"key":"79_CR103_79","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1111\/j.1749-6632.2002.tb04913.x","volume":"981","author":"E Jablonka","year":"2002","unstructured":"Jablonka E, Lamb MJ (2002) The changing concept of epigenetics. Ann N Y Acad Sci 981:82\u201396","journal-title":"Ann N Y Acad Sci"},{"key":"79_CR104_79","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/35075138","volume":"411","author":"H Jeong","year":"2001","unstructured":"Jeong H, Mason SP, Barabasi AL, Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411:41\u201342","journal-title":"Nature"},{"key":"79_CR105_79","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1126\/science.1141319","volume":"316","author":"DS Johnson","year":"2007","unstructured":"Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome\u2010wide mapping of in vivo protein\u2010DNA interactions. Science 316:1497\u2013502","journal-title":"Science"},{"key":"79_CR106_79","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2148-3-1","volume":"3","author":"IK Jordan","year":"2003","unstructured":"Jordan IK, Wolf YI, Koonin EV (2003) No simple dependence between protein evolution rate and the number of protein\u2013protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol Biol 3:1","journal-title":"BMC Evol Biol"},{"key":"79_CR107_79","first-page":"96","volume":"2005","author":"MP Joy","year":"2005","unstructured":"Joy MP, Brock A, Ingber DE, Huang S (2005) High\u2010betweenness proteins in the yeast protein interaction network. J\u00a0Biomed Biotechnol 2005:96\u2013103","journal-title":"J Biomed Biotechnol"},{"key":"79_CR108_79","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/nrg1615","volume":"6","author":"M Kaern","year":"2005","unstructured":"Kaern M, Elston TC, Blake WJ, Collins JJ (2005) Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 6:451\u201364","journal-title":"Nat Rev Genet"},{"key":"79_CR109_79","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4612-0823-5","volume-title":"Understanding Nonlinear Dynamics","author":"D Kaplan","year":"1995","unstructured":"Kaplan D, Glass L (1995) Understanding Nonlinear Dynamics, 1st edn. Springer, New York","edition":"1"},{"key":"79_CR110_79","doi-asserted-by":"crossref","first-page":"e49","DOI":"10.1371\/journal.pone.0000049","volume":"1","author":"K Kashiwagi","year":"2006","unstructured":"Kashiwagi K, Urabe I, Kancko K, Yomo T (2006) Adaptive response of a\u00a0gene network to environmental changes by fitness\u2010induced attractor selection. PLoS One, 1:e49","journal-title":"PLoS One"},{"key":"79_CR111_79","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/224177a0","volume":"224","author":"S Kauffman","year":"1969","unstructured":"Kauffman S (1969) Homeostasis and differentiation in random genetic control networks. Nature 224:177\u20138","journal-title":"Nature"},{"key":"79_CR112_79","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1016\/j.jtbi.2003.12.017","volume":"230","author":"S Kauffman","year":"2004","unstructured":"Kauffman S (2004) A\u00a0proposal for using the ensemble approach to understand genetic regulatory networks. J\u00a0Theor Biol 230:581\u201390","journal-title":"J Theor Biol"},{"key":"79_CR113_79","doi-asserted-by":"crossref","first-page":"14796","DOI":"10.1073\/pnas.2036429100","volume":"100","author":"S Kauffman","year":"2003","unstructured":"Kauffman S, Peterson C, Samuelsson B, Troein C (2003) Random Boolean network models and the yeast transcriptional network. Proc Natl Acad Sci USA\u00a0100:14796\u20139","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR114_79","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/0022-5193(69)90015-0","volume":"22","author":"SA Kauffman","year":"1969","unstructured":"Kauffman SA (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J\u00a0Theor Biol 22:437\u2013467","journal-title":"J Theor Biol"},{"key":"79_CR115_79","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1038\/scientificamerican0891-78","volume":"265","author":"SA Kauffman","year":"1991","unstructured":"Kauffman SA (1991) Antichaos and adaptation. Sci Am 265:78\u201384","journal-title":"Sci Am"},{"key":"79_CR116_79","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780195079517.001.0001","volume-title":"The origins of order","author":"SA Kauffman","year":"1993","unstructured":"Kauffman SA (1993) The origins of order. Oxford University Press, New York"},{"key":"79_CR117_79","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1016\/S0092-8674(04)00044-3","volume":"116","author":"S Khorasanizadeh","year":"2004","unstructured":"Khorasanizadeh S (2004) The nucleosome: from genomic organization to genomic regulation. Cell 116:259\u201372","journal-title":"Cell"},{"key":"79_CR118_79","doi-asserted-by":"crossref","first-page":"e60","DOI":"10.1371\/journal.pcbi.0030060","volume":"3","author":"KY Kim","year":"2007","unstructured":"Kim KY, Wang J (2007) Potential energy landscape and robustness of a\u00a0gene regulatory network: toggle switch. PLoS Comput Biol 3:e60","journal-title":"PLoS Comput Biol"},{"key":"79_CR119_79","doi-asserted-by":"crossref","first-page":"055101","DOI":"10.1103\/PhysRevE.72.055101","volume":"72","author":"K Klemm","year":"2005","unstructured":"Klemm K, Bornholdt S (2005) Stable and unstable attractors in Boolean networks. Phys Rev E Stat Nonlin Soft Matter Phys 72:055101","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"key":"79_CR120_79","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1073\/pnas.0306490101","volume":"101","author":"RR Klevecz","year":"2004","unstructured":"Klevecz RR, Bolen J, Forrest G, Murray DB (2004) A\u00a0genomewide oscillation in transcription gates DNA replication and cell cycle. Proc Natl Acad Sci USA\u00a0101:1200\u20135","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR121_79","doi-asserted-by":"crossref","first-page":"1172","DOI":"10.1093\/bioinformatics\/bti096","volume":"21","author":"M Kloster","year":"2005","unstructured":"Kloster M, Tang C, Wingreen NS (2005) Finding regulatory modules through large-scale gene\u2010expression data analysis. Bioinformatics 21:1172\u20139","journal-title":"Bioinformatics"},{"key":"79_CR122_79","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1016\/j.cell.2007.02.005","volume":"128","author":"T Kouzarides","year":"2007","unstructured":"Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693\u2013705","journal-title":"Cell"},{"key":"79_CR123_79","doi-asserted-by":"crossref","first-page":"9517","DOI":"10.1073\/pnas.0500345102","volume":"102","author":"BP Kramer","year":"2005","unstructured":"Kramer BP, Fussenegger M (2005) Hysteresis in a\u00a0synthetic mammalian gene network. Proc Natl Acad Sci USA 102:9517\u20139522","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR124_79","doi-asserted-by":"crossref","first-page":"158701","DOI":"10.1103\/PhysRevLett.98.158701","volume":"98","author":"P Krawitz","year":"2007","unstructured":"Krawitz P, Shmulevich I (2007) Basin entropy in Boolean network ensembles. Phys Rev Lett 98:158701","journal-title":"Phys Rev Lett"},{"key":"79_CR125_79","doi-asserted-by":"crossref","first-page":"878","DOI":"10.1128\/MCB.01915-06","volume":"27","author":"H Krysinska","year":"2007","unstructured":"Krysinska H, Hoogenkamp M, Ingram R, Wilson N, Tagoh H, Laslo P, Singh H, Bonifer C (2007) A\u00a0two-step, PU.1\u2011dependent mechanism for developmentally regulated chromatin remodeling and transcription of the c-fms gene. Mol Cell Biol 27:878\u201387","journal-title":"Mol Cell Biol"},{"key":"79_CR126_79","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1016\/j.cell.2004.12.006","volume":"119","author":"S Kubicek","year":"2004","unstructured":"Kubicek S, Jenuwein T (2004) A\u00a0crack in histone lysine methylation. Cell 119:903\u20136","journal-title":"Cell"},{"key":"79_CR127_79","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1016\/j.cell.2006.06.052","volume":"126","author":"P Laslo","year":"2006","unstructured":"Laslo P, Spooner CJ, Warmflash A, Lancki DW, Lee HJ, Sciammas R, Gantner BN, Dinner AR, Singh H (2006) Multilineage transcriptional priming and determination of alternate hematopoietic cell fates. Cell 126:755\u201366","journal-title":"Cell"},{"key":"79_CR128_79","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1126\/science.1075090","volume":"298","author":"TI Lee","year":"2002","unstructured":"Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799\u2013804","journal-title":"Science"},{"key":"79_CR129_79","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/S0962-8924(02)00002-8","volume":"13","author":"JM Levsky","year":"2003","unstructured":"Levsky JM, Singer RH (2003) Gene expression and the myth of the average cell. Trends Cell Biol 13:4\u20136","journal-title":"Trends Cell Biol"},{"key":"79_CR130_79","doi-asserted-by":"crossref","first-page":"4781","DOI":"10.1073\/pnas.0305937101","volume":"101","author":"F Li","year":"2004","unstructured":"Li F, Long T, Lu Y, Ouyang Q, Tang C (2004) The yeast cell-cycle network is robustly designed. Proc Natl Acad Sci USA 101:4781\u20136","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR131_79","doi-asserted-by":"crossref","first-page":"263","DOI":"10.2741\/2677","volume":"13","author":"H Li","year":"2008","unstructured":"Li H, Xuan J, Wang Y, Zhan M (2008) Inferring regulatory networks. Front Biosci 13:263\u201375","journal-title":"Front Biosci"},{"key":"79_CR132_79","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/ng1956","volume":"39","author":"HN Lim","year":"2007","unstructured":"Lim HN, van Oudenaarden A (2007) A\u00a0multistep epigenetic switch enables the stable inheritance of DNA methylation states. Nat Genet 39:269\u201375","journal-title":"Nat Genet"},{"key":"79_CR133_79","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/bioinformatics\/btl562","volume":"23","author":"F Luo","year":"2007","unstructured":"Luo F, Yang Y, Chen CF, Chang R, Zhou J, Scheuermann RH (2007) Modular organization of protein interaction networks. Bioinformatics 23:207\u201314","journal-title":"Bioinformatics"},{"key":"79_CR134_79","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1038\/nature02782","volume":"431","author":"NM Luscombe","year":"2004","unstructured":"Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431:308\u201312","journal-title":"Nature"},{"key":"79_CR135_79","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1471-2105-6-11","volume":"6","author":"T MacCarthy","year":"2005","unstructured":"MacCarthy T, Pomiankowski A, Seymour R (2005) Using large-scale perturbations in gene network reconstruction. BMC Bioinformatics 6:11","journal-title":"BMC Bioinformatics"},{"key":"79_CR136_79","doi-asserted-by":"crossref","first-page":"11980","DOI":"10.1073\/pnas.2133841100","volume":"100","author":"S Mangan","year":"2003","unstructured":"Mangan S, Alon U (2003) Structure and function of the feed\u2010forward loop network motif. Proc Natl Acad Sci USA 100:11980\u20135","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR137_79","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1098\/rsif.2006.0140","volume":"3","author":"T Manke","year":"2006","unstructured":"Manke T, Demetrius L, Vingron M (2006) An entropic characterization of protein interaction networks and cellular robustness. JR Soc Interface 3:843\u201350","journal-title":"JR Soc Interface"},{"key":"79_CR138_79","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/90222","volume":"19","author":"EM Marcotte","year":"2001","unstructured":"Marcotte EM (2001) The path not taken. Nat Biotechnol 19:626\u2013627","journal-title":"Nat Biotechnol"},{"key":"79_CR139_79","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1196\/annals.1407.019","volume":"1115","author":"AA Margolin","year":"2007","unstructured":"Margolin AA, Califano A (2007) Theory and limitations of genetic network inference from microarray data. Ann N Y Acad Sci 1115:51\u201372","journal-title":"Ann N Y Acad Sci"},{"key":"79_CR140_79","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1126\/science.1065103","volume":"296","author":"S Maslov","year":"2002","unstructured":"Maslov S, Sneppen K (2002) Specificity and stability in topology of protein networks. Science 296:910\u20133","journal-title":"Science"},{"key":"79_CR141_79","doi-asserted-by":"crossref","first-page":"1526","DOI":"10.1242\/jeb.005017","volume":"210","author":"JS Mattick","year":"2007","unstructured":"Mattick JS (2007) A\u00a0new paradigm for developmental biology. J\u00a0Exp Biol 210:1526\u201347","journal-title":"J Exp Biol"},{"key":"79_CR142_79","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/238413a0","volume":"238","author":"RM May","year":"1972","unstructured":"May RM (1972) Will a\u00a0large complex system be stable? Nature 238:413\u2013414","journal-title":"Nature"},{"key":"79_CR143_79","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1038\/nbt1335","volume":"25","author":"A Meissner","year":"2007","unstructured":"Meissner A, Wernig M, Jaenisch R (2007) Direct reprogramming of genetically unmodified fibroblasts into pluripotent stem cells. Nat Biotechnol 25:1177\u20131181","journal-title":"Nat Biotechnol"},{"key":"79_CR144_79","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/j.tig.2006.03.008","volume":"22","author":"J Mellor","year":"2006","unstructured":"Mellor J (2006) Dynamic nucleosomes and gene transcription. Trends Genet 22:320\u20139","journal-title":"Trends Genet"},{"key":"79_CR145_79","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1016\/j.gde.2006.08.013","volume":"16","author":"E Metzger","year":"2006","unstructured":"Metzger E, Wissmann M, Schule R (2006) Histone demethylation and androgen\u2010dependent transcription. Curr Opin Genet Dev 16:513\u20137","journal-title":"Curr Opin Genet Dev"},{"key":"79_CR146_79","doi-asserted-by":"crossref","first-page":"2715","DOI":"10.1038\/sj.emboj.7600749","volume":"24","author":"H Mikkers","year":"2005","unstructured":"Mikkers H, Frisen J (2005) Deconstructing stemness. Embo J 24:2715\u20139","journal-title":"Embo J"},{"key":"79_CR147_79","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1126\/science.298.5594.824","volume":"298","author":"R Milo","year":"2002","unstructured":"Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U (2002) Network motifs: simple building blocks of complex networks. Science 298:824\u20137","journal-title":"Science"},{"key":"79_CR148_79","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1101\/SQB.1961.026.01.048","volume":"26","author":"J Monod","year":"1961","unstructured":"Monod J, Jacob F (1961) Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harb Symp Quant Biol 26:389\u2013401","journal-title":"Cold Spring Harb Symp Quant Biol"},{"key":"79_CR149_79","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1196\/annals.1329.064","volume":"1030","author":"F Morceau","year":"2004","unstructured":"Morceau F, Schnekenburger M, Dicato M, Diederich M (2004) GATA-1: friends, brothers, and coworkers. Ann N Y Acad Sci 1030:537\u201354","journal-title":"Ann N Y Acad Sci"},{"key":"79_CR150_79","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1146\/annurev.cb.11.110195.000343","volume":"11","author":"SJ Morrison","year":"1995","unstructured":"Morrison SJ, Uchida N, Weissman IL (1995) The biology of hematopoietic stem cells. Annu Rev Cell Dev Biol 11:35\u201371","journal-title":"Annu Rev Cell Dev Biol"},{"key":"79_CR151_79","volume-title":"Mathematical biology, 2nd edn (1993)","author":"JD Murray","year":"1989","unstructured":"Murray JD (1989) Mathematical biology, 2nd edn (1993). Springer, Berlin"},{"key":"79_CR152_79","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1137\/S003614450342480","volume":"45","author":"MEJ Newman","year":"2003","unstructured":"Newman MEJ (2003) The structure and function of complex networks. SIAM Review 45:167\u2013256","journal-title":"SIAM Review"},{"key":"79_CR153_79","doi-asserted-by":"crossref","first-page":"1897","DOI":"10.1073\/pnas.0711525105","volume":"105","author":"M Nykter","year":"2008","unstructured":"Nykter M, Price ND, Aldana M, Ramsey SA, Kauffman SA, Hood L, Yli-Harja O, Shmulevich I (2008) Gene expression dynamics in the macrophage exhibit criticality. Proc Natl Acad Sci USA 105:1897\u2013900","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR154_79","doi-asserted-by":"crossref","first-page":"058702","DOI":"10.1103\/PhysRevLett.100.058702","volume":"100","author":"M Nykter","year":"2008","unstructured":"Nykter M, Price ND, Larjo A, Aho T, Kauffman SA, Yli-Harja O, Shmulevich I (2008) Critical networks exhibit maximal information diversity in structure\u2010dynamics relationships. Phys Rev Lett 100:058702","journal-title":"Phys Rev Lett"},{"key":"79_CR155_79","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1126\/science.1089769","volume":"303","author":"DT Odom","year":"2004","unstructured":"Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, Murray HL, Volkert TL, Schreiber J, Rolfe PA, Gifford DK, Fraenkel E, Bell GI, Young RA (2004) Control of pancreas and liver gene expression by HNF transcription factors. Science 303:1378\u201381","journal-title":"Science"},{"key":"79_CR156_79","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/nature05934","volume":"448","author":"K Okita","year":"2007","unstructured":"Okita K, Ichisaka T, Yamanaka S (2007) Generation of germline\u2010competent induced pluripotent stem cells. Nature 448:313\u20137","journal-title":"Nature"},{"key":"79_CR157_79","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/nature02298","volume":"427","author":"EM Ozbudak","year":"2004","unstructured":"Ozbudak EM, Thattai M, Lim HN, Shraiman BI, Van Oudenaarden A (2004) Multistability in the lactose utilization network of Escherichia coli. Nature 427:737\u2013740","journal-title":"Nature"},{"key":"79_CR158_79","doi-asserted-by":"crossref","first-page":"1484","DOI":"10.1126\/science.300.5625.1484b","volume":"300","author":"E Pennisi","year":"2003","unstructured":"Pennisi E (2003) Human genome. A\u00a0low number wins the GeneSweep Pool. Science 300:1484","journal-title":"Science"},{"key":"79_CR159_79","volume-title":"Mut zur utopie","author":"P Picht","year":"1969","unstructured":"Picht P (1969) Mut zur utopie. Piper, M\u00fcnchen"},{"key":"79_CR160_79","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1016\/j.tree.2005.04.004","volume":"20","author":"SR Proulx","year":"2005","unstructured":"Proulx SR, Promislow DE, Phillips PC (2005) Network thinking in ecology and evolution. Trends Ecol Evol 20:345\u201353","journal-title":"Trends Ecol Evol"},{"key":"79_CR161_79","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1146\/annurev.cellbio.19.111301.143037","volume":"19","author":"M Raff","year":"2003","unstructured":"Raff M (2003) Adult stem cell plasticity: fact or artifact? Annu Rev Cell Dev Biol 19:1\u201322","journal-title":"Annu Rev Cell Dev Biol"},{"key":"79_CR162_79","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1111\/j.1399-0004.2005.00478.x","volume":"68","author":"A Ralston","year":"2005","unstructured":"Ralston A\u00a0and Rossant J (2005) Genetic regulation of stem cell origins in the mouse embryo. Clin Genet 68:106\u201312","journal-title":"Clin Genet"},{"key":"79_CR163_79","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/j.jtbi.2006.02.011","volume":"242","author":"P Ramo","year":"2006","unstructured":"Ramo P, Kesseli J, Yli-Harja O (2006) Perturbation avalanches and criticality in gene regulatory networks. J\u00a0Theor Biol 242:164\u201370","journal-title":"J Theor Biol"},{"key":"79_CR164_79","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1126\/science.1073374","volume":"297","author":"E Ravasz","year":"2002","unstructured":"Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL (2002) Hierarchical organization of modularity in metabolic networks. Science 297:1551\u20135","journal-title":"Science"},{"key":"79_CR165_79","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1038\/420127a","volume":"420","author":"W Reik","year":"2002","unstructured":"Reik W, Dean W (2002) Back to the beginning. Nature 420:127","journal-title":"Nature"},{"key":"79_CR166_79","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.tig.2004.11.010","volume":"21","author":"O Resendis-Antonio","year":"2005","unstructured":"Resendis-Antonio O, Freyre-Gonzalez JA, Menchaca-Mendez R, Gutierrez-Rios RM, Martinez-Antonio A, Avila-Sanchez C, Collado-Vides J (2005) Modular analysis of the transcriptional regulatory network of E. coli. Trends Genet 21:16\u201320","journal-title":"Trends Genet"},{"key":"79_CR167_79","doi-asserted-by":"crossref","first-page":"8370","DOI":"10.1128\/JB.187.24.8370-8374.2005","volume":"187","author":"H Robins","year":"2005","unstructured":"Robins H, Krasnitz M, Barak H, Levine AJ (2005) A\u00a0relative\u2010entropy algorithm for genomic fingerprinting captures host-phage similarities. J\u00a0Bacteriol 187:8370\u20134","journal-title":"J Bacteriol"},{"key":"79_CR168_79","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1016\/j.jtbi.2006.01.021","volume":"241","author":"I Roeder","year":"2006","unstructured":"Roeder I, Glauche I (2006) Towards an understanding of lineage specification in hematopoietic stem cells: a\u00a0mathematical model for the interaction of transcription factors GATA-1 and PU.1. J\u00a0Theor Biol 241:852\u201365","journal-title":"J Theor Biol"},{"key":"79_CR169_79","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1471-2105-7-5","volume":"7","author":"H Salgado","year":"2006","unstructured":"Salgado H, Santos-Zavaleta A, Gama-Castro S, Peralta-Gil M, Penaloza-Spinola MI, Martinez-Antonio A, Karp PD, Collado-Vides J (2006) The comprehensive updated regulatory network of Escherichia coli K-12. BMC Bioinformatics 7:5","journal-title":"BMC Bioinformatics"},{"key":"79_CR170_79","doi-asserted-by":"crossref","unstructured":"Samonte RV, Eichler EE (2002) Segmental duplications and the evolution of the primate genome. Nat Rev Genet 3:65\u201372","DOI":"10.1038\/nrg705"},{"key":"79_CR171_79","doi-asserted-by":"crossref","first-page":"2052","DOI":"10.1073\/pnas.0408105102","volume":"102","author":"R Sandberg","year":"2005","unstructured":"Sandberg R, Ernberg I (2005) Assessment of tumor characteristic gene expression in cell lines using a\u00a0tissue similarity index (TSI). Proc Natl Acad Sci USA 102:2052\u20137","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR172_79","doi-asserted-by":"crossref","first-page":"3646","DOI":"10.1182\/blood-2006-01-030015","volume":"108","author":"RA Shivdasani","year":"2006","unstructured":"Shivdasani RA (2006) MicroRNAs: regulators of gene expression and cell differentiation. Blood 108:3646\u201353","journal-title":"Blood"},{"key":"79_CR173_79","doi-asserted-by":"crossref","first-page":"048701","DOI":"10.1103\/PhysRevLett.93.048701","volume":"93","author":"I Shmulevich","year":"2004","unstructured":"Shmulevich I, Kauffman SA (2004) Activities and sensitivities in boolean network models. Phys Rev Lett 93:048701","journal-title":"Phys Rev Lett"},{"key":"79_CR174_79","doi-asserted-by":"crossref","first-page":"13439","DOI":"10.1073\/pnas.0506771102","volume":"102","author":"I Shmulevich","year":"2005","unstructured":"Shmulevich I, Kauffman SA, Aldana M (2005) Eukaryotic cells are dynamically ordered or critical but not chaotic. Proc Natl Acad Sci USA 102:13439\u201344","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR175_79","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/s10709-006-0035-0","volume":"129","author":"ML Siegal","year":"2007","unstructured":"Siegal ML, Promislow DE, Bergman A (2007) Functional and evolutionary inference in gene networks: does topology matter? Genetica 129:83\u2013103","journal-title":"Genetica"},{"key":"79_CR176_79","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1111\/j.1365-2958.2007.05951.x","volume":"66","author":"MC Smith","year":"2007","unstructured":"Smith MC, Sumner ER, Avery SV (2007) Glutathione and Gts1p drive beneficial variability in the cadmium resistances of individual yeast cells. Mol Microbiol 66:699\u2013712","journal-title":"Mol Microbiol"},{"key":"79_CR177_79","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1093\/bfgp\/elm013","volume":"6","author":"TD Southall","year":"2007","unstructured":"Southall TD, Brand AH (2007) Chromatin profiling in model organisms. Brief Funct Genomic Proteomic 6:133\u201340","journal-title":"Brief Funct Genomic Proteomic"},{"key":"79_CR178_79","doi-asserted-by":"crossref","first-page":"1712","DOI":"10.1002\/pmic.200300700","volume":"4","author":"C Southan","year":"2004","unstructured":"Southan C (2004) Has the yo-yo stopped? An assessment of human protein\u2010coding gene number. Proteomics 4:1712\u201326","journal-title":"Proteomics"},{"key":"79_CR179_79","first-page":"15","volume":"44","author":"CD Stern","year":"2000","unstructured":"Stern CD (2000) Conrad H. Waddington\u2019s contributions to avian and mammalian development, 1930\u20131940. Int J Dev Biol 44:15\u201322","journal-title":"Int J Dev Biol"},{"key":"79_CR180_79","first-page":"156","volume":"12","author":"R Strohman","year":"1994","unstructured":"Strohman R (1994) Epigenesis: the missing beat in biotechnology? Biotechnology (N Y) 12:156\u201364","journal-title":"Biotechnology (N Y)"},{"key":"79_CR181_79","doi-asserted-by":"crossref","first-page":"4221","DOI":"10.1073\/pnas.0501179102","volume":"102","author":"MP Stumpf","year":"2005","unstructured":"Stumpf MP, Wiuf C, May RM (2005) Subnets of scale-free networks are not scale-free: sampling properties of networks. Proc Natl Acad Sci USA 102:4221\u20134","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR182_79","doi-asserted-by":"crossref","first-page":"2477","DOI":"10.1038\/sj.onc.1209272","volume":"25","author":"M Suzuki","year":"2006","unstructured":"Suzuki M, Yamada T, Kihara-Negishi F, Sakurai T, Hara E, Tenen DG, Hozumi N, Oikawa T (2006) Site\u2010specific DNA methylation by a\u00a0complex of PU.1 and Dnmt3a\/b. Oncogene 25:2477\u201388","journal-title":"Oncogene"},{"key":"79_CR183_79","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1016\/j.ydbio.2006.02.051","volume":"294","author":"G Swiers","year":"2006","unstructured":"Swiers G, Patient R, Loose M (2006) Genetic regulatory networks programming hematopoietic stem cells and erythroid lineage specification. Dev Biol 294:525\u201340","journal-title":"Dev Biol"},{"key":"79_CR184_79","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1016\/j.cell.2006.07.024","volume":"126","author":"K Takahashi","year":"2006","unstructured":"Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126:663\u201376","journal-title":"Cell"},{"key":"79_CR185_79","doi-asserted-by":"crossref","first-page":"2685","DOI":"10.1242\/dev.01874","volume":"132","author":"SJ Tapscott","year":"2005","unstructured":"Tapscott SJ (2005) The circuitry of a\u00a0master switch: Myod and the regulation of skeletal muscle gene transcription. Development 132:2685\u201395","journal-title":"Development"},{"key":"79_CR186_79","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1146\/annurev.genet.38.072902.092831","volume":"38","author":"JS Taylor","year":"2004","unstructured":"Taylor JS, Raes J (2004) Duplication and divergence: The evolution of new genes and old ideas. Annu Rev Genet 38:615\u2013643","journal-title":"Annu Rev Genet"},{"key":"79_CR187_79","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1038\/ng1340","volume":"36","author":"SA Teichmann","year":"2004","unstructured":"Teichmann SA, Babu MM (2004) Gene regulatory network growth by duplication. Nat Genet 36:492\u20136","journal-title":"Nat Genet"},{"key":"79_CR188_79","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1002\/(SICI)1521-1878(199805)20:5<433::AID-BIES10>3.0.CO;2-2","volume":"20","author":"D Thieffry","year":"1998","unstructured":"Thieffry D, Huerta AM, Perez-Rueda E, Collado-Vides J (1998) From specific gene regulation to genomic networks: a\u00a0global analysis of transcriptional regulation in Escherichia coli. Bioessays 20:433\u201340","journal-title":"Bioessays"},{"key":"79_CR189_79","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1086\/398642","volume":"27","author":"N Tinbergen","year":"1952","unstructured":"Tinbergen N (1952) Derived activities; their causation, biological significance, origin, and emancipation during evolution. Q Rev Biol 27:1\u201332","journal-title":"Q Rev Biol"},{"key":"79_CR190_79","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1093\/bioinformatics\/18.2.287","volume":"18","author":"H Toh","year":"2002","unstructured":"Toh H, Horimoto K (2002) Inference of a\u00a0genetic network by a\u00a0combined approach of cluster analysis and graphical Gaussian modeling. Bioinformatics 18:287\u201397","journal-title":"Bioinformatics"},{"key":"79_CR191_79","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.cell.2006.04.003","volume":"125","author":"P Trojer","year":"2006","unstructured":"Trojer P, Reinberg D (2006) Histone lysine demethylases and their impact on epigenetics. Cell 125:213\u20137","journal-title":"Cell"},{"key":"79_CR192_79","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/S0955-0674(03)00017-6","volume":"15","author":"JJ Tyson","year":"2003","unstructured":"Tyson JJ, Chen KC, Novak B (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15:221\u2013231","journal-title":"Curr Opin Cell Biol"},{"key":"79_CR193_79","doi-asserted-by":"crossref","unstructured":"van Helden J, Wernisch L, Gilbert D, Wodak SJ (2002) Graph-based analysis of metabolic networks. Ernst Schering Res Found Workshop:245\u201374","DOI":"10.1007\/978-3-662-04747-7_12"},{"key":"79_CR194_79","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1016\/S0168-9525(03)00203-8","volume":"19","author":"E van Nimwegen","year":"2003","unstructured":"van Nimwegen E (2003) Scaling laws in the functional content of genomes. Trends Genet 19:479\u201384","journal-title":"Trends Genet"},{"key":"79_CR195_79","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1126\/science.302.5644.371a","volume":"302","author":"G Vogel","year":"2003","unstructured":"Vogel G (2003) Stem cells. \u2018Stemness\u2019 genes still elusive. Science 302:371","journal-title":"Science"},{"key":"79_CR196_79","volume-title":"Organisers and genes","author":"CH Waddington","year":"1940","unstructured":"Waddington CH (1940) Organisers and genes. Cambridge University Press, Cambridge"},{"key":"79_CR197_79","doi-asserted-by":"crossref","DOI":"10.5962\/bhl.title.7217","volume-title":"Principles of embryology","author":"CH Waddington","year":"1956","unstructured":"Waddington CH (1956) Principles of embryology. Allen and Unwin Ltd, London"},{"key":"79_CR198_79","volume-title":"The strategy of the genes","author":"CH Waddington","year":"1957","unstructured":"Waddington CH (1957) The strategy of the genes. Allen and Unwin, London"},{"key":"79_CR199_79","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1146\/annurev.soc.30.020404.104342","volume":"20","author":"DJ Watts","year":"2004","unstructured":"Watts DJ (2004) The \u201cnew\u201d science of networks. Ann Rev Sociol 20:243\u2013270","journal-title":"Ann Rev Sociol"},{"key":"79_CR200_79","first-page":"495","volume":"92","author":"G Webster","year":"1999","unstructured":"Webster G, Goodwin BC (1999) A\u00a0structuralist approach to morphology. Riv Biol 92:495\u20138","journal-title":"Riv Biol"},{"key":"79_CR201_79","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1038\/nature05944","volume":"448","author":"M Wernig","year":"2007","unstructured":"Wernig M, Meissner A, Foreman R, Brambrink T, Ku M, Hochedlinger K, Bernstein BE, Jaenisch R (2007) In vitro reprogramming of fibroblasts into a\u00a0pluripotent ES-cell-like state. Nature 448:318\u201324","journal-title":"Nature"},{"key":"79_CR202_79","doi-asserted-by":"crossref","first-page":"1977","DOI":"10.1091\/mbc.02-02-0030","volume":"13","author":"ML Whitfield","year":"2002","unstructured":"Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D (2002) Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell 13:1977\u20132000","journal-title":"Mol Biol Cell"},{"issue":"Suppl 1","key":"79_CR203_79","doi-asserted-by":"crossref","first-page":"8590","DOI":"10.1073\/pnas.0701044104","volume":"104","author":"AS Wilkins","year":"2007","unstructured":"Wilkins AS (2007) Colloquium Papers: Between \u201cdesign\u201d and \u201cbricolage\u201d: Genetic networks, levels of selection, and adaptive evolution. Proc Natl Acad Sci USA 104 Suppl 1:8590\u20136","journal-title":"Proc Natl Acad Sci USA"},{"key":"79_CR204_79","unstructured":"Wuensche A (1998) Genomic regulation modeled as a\u00a0network with basins of attraction. Pac Symp Biocomput:89\u2013102"},{"key":"79_CR205_79","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1038\/nature02089","volume":"426","author":"W Xiong","year":"2003","unstructured":"Xiong W, Ferrell JE Jr. (2003) A\u00a0positive\u2010feedback\u2010based bistable \u2018memory module\u2019 that governs a\u00a0cell fate decision. Nature 426:460\u2013465","journal-title":"Nature"},{"key":"79_CR206_79","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.febslet.2004.11.019","volume":"578","author":"X Xu","year":"2004","unstructured":"Xu X, Wang L, Ding D (2004) Learning module networks from genome\u2010wide location and expression data. FEBS Lett 578:297\u2013304","journal-title":"FEBS Lett"},{"key":"79_CR207_79","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.tig.2004.04.008","volume":"20","author":"H Yu","year":"2004","unstructured":"Yu H, Greenbaum D, Xin Lu H, Zhu X, Gerstein M (2004) Genomic analysis of essentiality within protein networks. Trends Genet 20:227\u201331","journal-title":"Trends Genet"},{"key":"79_CR208_79","doi-asserted-by":"crossref","first-page":"e59","DOI":"10.1371\/journal.pcbi.0030059","volume":"3","author":"H Yu","year":"2007","unstructured":"Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M (2007) The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 3:e59","journal-title":"PLoS Comput Biol"},{"key":"79_CR209_79","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1242\/dev.128.5.617","volume":"128","author":"CH Yuh","year":"2001","unstructured":"Yuh CH, Bolouri H, Davidson EH (2001) Cis\u2010regulatory logic in the endo16 gene: switching from a\u00a0specification to a\u00a0differentiation mode of control. Development 128:617\u201329","journal-title":"Development"},{"key":"79_CR210_79","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1093\/bfgp\/2.4.279","volume":"2","author":"S Huang","year":"2004","unstructured":"Huang S (2004) Back to the biology in systems biology: what can we learn from biomolecular networks. Brief Funct Genomics Proteomics 2:279\u2013297","journal-title":"Brief Funct Genomics Proteomics"},{"key":"79_CR211_79","first-page":"1761","volume-title":"Endothelial biomedicine","author":"S Huang","year":"2007","unstructured":"Huang S (2007) Cell fates as attractors\u00a0\u2013 stability and flexibility of cellular phenotype. In: Endothelial biomedicine, 1st edn. Cambridge University Press, New York, pp\u00a01761\u20131779","edition":"1"},{"key":"79_CR212_79","doi-asserted-by":"crossref","first-page":"27","DOI":"10.3233\/BD-2007-26104","volume":"26","author":"S Huang","year":"2006","unstructured":"Huang S, Ingber DE (2006) A\u00a0non\u2010genetic basis for cancer progression and metastasis: self\u2010organizing attractors in cell regulatory networks. Breast Dis 26:27\u201354","journal-title":"Breast Dis"},{"key":"79_CR213_79","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-540-32667-0","volume-title":"Life: An introduction to complex systems biology, 1edn","author":"K Kaneko","year":"2006","unstructured":"Kaneko K (2006) Life: An introduction to complex systems biology, 1edn. Springer, Berlin"},{"key":"79_CR214_79","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1038\/scientificamerican0891-78","volume":"265","author":"SA Kauffman","year":"1991","unstructured":"Kauffman SA (1991) Antichaos and adaptation. Sci Am 265:78\u201384","journal-title":"Sci Am"},{"key":"79_CR215_79","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780195079517.001.0001","volume-title":"The origins of order","author":"SA Kauffman","year":"1993","unstructured":"Kauffman SA (1993) The origins of order. Oxford University Press, New York"},{"key":"79_CR216_79","volume-title":"At home in the universe: the search for the laws of self\u2010organization and complexity","author":"SA Kauffman","year":"1996","unstructured":"Kauffman SA (1996) At home in the universe: the search for the laws of self\u2010organization and complexity. Oxford University Press, New York"},{"key":"79_CR217_79","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1016\/S0968-0004(99)01473-5","volume":"24","author":"M Laurent","year":"1999","unstructured":"Laurent M, Kellershohn N (1999) Multistability: a\u00a0major means of differentiation and evolution in biological systems. Trends Biochem Sci 24:418\u2013422","journal-title":"Trends Biochem Sci"},{"issue":"Suppl 1","key":"79_CR218_79","doi-asserted-by":"crossref","first-page":"8590","DOI":"10.1073\/pnas.0701044104","volume":"104","author":"AS Wilkins","year":"2007","unstructured":"Wilkins AS (2007) Colloquium papers: Between \u201cdesign\u201d and \u201cbricolage\u201d: Genetic networks, levels of selection, and adaptive evolution. Proc Natl Acad Sci USA 104 Suppl 1:8590\u20136","journal-title":"Proc Natl Acad Sci USA"}],"container-title":["Encyclopedia of Complexity and Systems Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-0-387-30440-3_79","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,22]],"date-time":"2024-08-22T04:20:01Z","timestamp":1724300401000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-0-387-30440-3_79"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009]]},"ISBN":["9780387758886","9780387304403"],"references-count":218,"URL":"https:\/\/doi.org\/10.1007\/978-0-387-30440-3_79","relation":{},"subject":[],"published":{"date-parts":[[2009]]}}}