{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,28]],"date-time":"2025-03-28T01:56:05Z","timestamp":1743126965154,"version":"3.40.3"},"publisher-location":"New York, NY","reference-count":87,"publisher":"Springer New York","isbn-type":[{"type":"print","value":"9780387758886"},{"type":"electronic","value":"9780387304403"}],"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_34","type":"book-chapter","created":{"date-parts":[[2009,6,17]],"date-time":"2009-06-17T16:33:26Z","timestamp":1245256406000},"page":"511-524","source":"Crossref","is-referenced-by-count":0,"title":["Biological Data Integration and Model Building"],"prefix":"10.1007","author":[{"given":"James A.","family":"Eddy","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathan D.","family":"Price","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"issue":"1","key":"34_CR1_34","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0022-5193(03)00035-3","volume":"223","author":"R Albert","year":"2003","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):1\u201318","journal-title":"J Theor Biol"},{"issue":"2","key":"34_CR2_34","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/S0959-440X(03)00031-9","volume":"13","author":"E Alm","year":"2003","unstructured":"Alm E, Arkin AP (2003) Biological networks. Curr Opin Struct Biol 13(2):193\u2013202","journal-title":"Curr Opin Struct Biol"},{"issue":"6977","key":"34_CR3_34","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1038\/nature02289","volume":"427","author":"E Almaas","year":"2004","unstructured":"Almaas E, Kovacs B et al (2004) Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427(6977):839\u201343","journal-title":"Nature"},{"issue":"4","key":"34_CR4_34","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1038\/ng1532","volume":"37","author":"K Basso","year":"2005","unstructured":"Basso K, Margolin AA et al (2005) Reverse engineering of regulatory networks in human B cells. Nat Genet 37(4):382\u201390","journal-title":"Nat Genet"},{"issue":"3","key":"34_CR5_34","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/j.jtbi.2004.01.008","volume":"228","author":"DA Beard","year":"2004","unstructured":"Beard DA, Babson E et al (2004) Thermodynamic constraints for biochemical networks. J\u00a0Theor Biol 228(3):327\u201333","journal-title":"J Theor Biol"},{"issue":"1","key":"34_CR6_34","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/S0006-3495(02)75150-3","volume":"83","author":"DA Beard","year":"2002","unstructured":"Beard DA, Liang SD et al (2002) Energy balance for analysis of complex metabolic networks. Biophys J 83(1):79\u201386","journal-title":"Biophys J"},{"issue":"5","key":"34_CR7_34","doi-asserted-by":"crossref","first-page":"R36","DOI":"10.1186\/gb-2006-7-5-r36","volume":"7","author":"R Bonneau","year":"2006","unstructured":"Bonneau R, Reiss DJ et al (2006) The Inferelator: an algorithm for learning parsimonious regulatory networks from systems\u2010biology data sets de novo. Genome Biol 7(5):R36","journal-title":"Genome Biol"},{"issue":"6","key":"34_CR8_34","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1002\/bit.10803","volume":"84","author":"AP Burgard","year":"2003","unstructured":"Burgard AP, Pharkya P et al (2003) Optknock: a\u00a0bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84(6):647\u201357","journal-title":"Biotechnol Bioeng"},{"key":"34_CR9_34","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1196\/annals.1310.014","volume":"1020","author":"R Christopher","year":"2004","unstructured":"Christopher R, Dhiman A et al (2004) Data-driven computer simulation of human cancer cell. Ann NY Acad Sci 1020:132\u201353","journal-title":"Ann NY Acad Sci"},{"issue":"12","key":"34_CR10_34","doi-asserted-by":"crossref","first-page":"e439","DOI":"10.1371\/journal.pbio.0020439","volume":"2","author":"JE Cohen","year":"2004","unstructured":"Cohen JE (2004) Mathematics is biology's next microscope, only better; biology is mathematics' next physics, only better. PLoS Biol 2(12):e439","journal-title":"PLoS Biol"},{"issue":"6987","key":"34_CR11_34","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1038\/nature02456","volume":"429","author":"MW Covert","year":"2004","unstructured":"Covert MW, Knight EM et al (2004) Integrating high\u2010throughput and computational data elucidates bacterial networks. Nature 429(6987):92\u20136","journal-title":"Nature"},{"issue":"5742","key":"34_CR12_34","doi-asserted-by":"crossref","first-page":"1854","DOI":"10.1126\/science.1112304","volume":"309","author":"MW Covert","year":"2005","unstructured":"Covert MW, Leung TH et al (2005) Achieving stability of lipopolysaccharide\u2010induced NF-kappaB activation. Science 309(5742):1854\u20131857","journal-title":"Science"},{"key":"34_CR13_34","doi-asserted-by":"crossref","first-page":"D233","DOI":"10.1093\/nar\/gki057","volume":"33","author":"N Deshpande","year":"2005","unstructured":"Deshpande N, Addess KJ et al (2005) The RCSB Protein Data Bank: a\u00a0redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res (Database issue) 33:D233\u20137","journal-title":"Nucleic Acids Res (Database issue)"},{"issue":"6","key":"34_CR14_34","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1073\/pnas.0610772104","volume":"104","author":"NC Duarte","year":"2007","unstructured":"Duarte NC, Becker SA et al (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci USA 104(6):1777\u201382","journal-title":"Proc Natl Acad Sci USA"},{"issue":"7","key":"34_CR15_34","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1101\/gr.2250904","volume":"14","author":"NC Duarte","year":"2004","unstructured":"Duarte NC, Herrgard MJ et al (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a\u00a0fully compartmentalized genome-scale metabolic model. Genome Res 14(7):1298\u2013309","journal-title":"Genome Res"},{"issue":"2","key":"34_CR16_34","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/84379","volume":"19","author":"JS Edwards","year":"2001","unstructured":"Edwards JS, Ibarra RU et al (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19(2):125\u201330","journal-title":"Nat Biotechnol"},{"issue":"6","key":"34_CR17_34","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1021\/bp0000712","volume":"16","author":"JS Edwards","year":"2000","unstructured":"Edwards JS, Palsson BO (2000) Robustness analysis of the Escherichia coli metabolic network. Biotechnol Prog 16(6):927\u201339","journal-title":"Biotechnol Prog"},{"issue":"1","key":"34_CR18_34","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 et al (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a\u00a0compendium of expression profiles. PLoS Biol 5(1):e8","journal-title":"PLoS Biol"},{"issue":"23","key":"34_CR19_34","doi-asserted-by":"crossref","first-page":"13134","DOI":"10.1073\/pnas.2235812100","volume":"100","author":"I Famili","year":"2003","unstructured":"Famili I, Forster J et al (2003) Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a\u00a0genome-scale reconstructed metabolic network. Proc Natl Acad Sci USA 100(23):13134\u201313139","journal-title":"Proc Natl Acad Sci USA"},{"issue":"14","key":"34_CR20_34","doi-asserted-by":"crossref","first-page":"e124","DOI":"10.1093\/bioinformatics\/btl210","volume":"22","author":"A Faure","year":"2006","unstructured":"Faure A, Naldi A et al (2006) Dynamical analysis of a\u00a0generic Boolean model for the control of the mammalian cell cycle. Bioinformatics 22(14):e124\u2013e131","journal-title":"Bioinformatics"},{"issue":"2","key":"34_CR21_34","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1089\/153623103322246584","volume":"7","author":"J Forster","year":"2003","unstructured":"Forster J, Famili I et al (2003) Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. Omics 7(2):193\u2013202","journal-title":"Omics"},{"issue":"11","key":"34_CR22_34","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1016\/j.tim.2005.09.001","volume":"13","author":"C Francke","year":"2005","unstructured":"Francke C, Siezen RJ et al (2005) Reconstructing the metabolic network of a\u00a0bacterium from its genome. Trends Microbiol 13(11):550\u2013558","journal-title":"Trends Microbiol"},{"issue":"5659","key":"34_CR23_34","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1126\/science.1094068","volume":"303","author":"N Friedman","year":"2004","unstructured":"Friedman N (2004) Inferring cellular networks using probabilistic graphical models. Science 303(5659):799\u2013805","journal-title":"Science"},{"issue":"8","key":"34_CR24_34","doi-asserted-by":"crossref","first-page":"e101","DOI":"10.1371\/journal.pcbi.0020101","volume":"2","author":"EP Gianchandani","year":"2006","unstructured":"Gianchandani EP, Papin JA et al (2006) Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol 2(8):e101","journal-title":"PLoS Comput Biol"},{"issue":"6995","key":"34_CR25_34","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/nature02555","volume":"430","author":"JD Han","year":"2004","unstructured":"Han JD, Bertin N et al (2004) Evidence for dynamically organized modularity in the yeast protein\u2010protein interaction network. Nature 430(6995):88\u201393","journal-title":"Nature"},{"issue":"8","key":"34_CR26_34","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1093\/bioinformatics\/bth074","volume":"20","author":"RF Hashimoto","year":"2004","unstructured":"Hashimoto RF, Kim S et al (2004) Growing genetic regulatory networks from seed genes. Bioinformatics 20(8):1241\u20137","journal-title":"Bioinformatics"},{"issue":"7","key":"34_CR27_34","doi-asserted-by":"crossref","first-page":"850","DOI":"10.1002\/bit.20663","volume":"92","author":"M Heinemann","year":"2005","unstructured":"Heinemann M, Kummel A et al (2005) In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. Biotechnol Bioeng 92(7):850\u2013864","journal-title":"Biotechnol Bioeng"},{"issue":"4","key":"34_CR28_34","doi-asserted-by":"crossref","first-page":"2732","DOI":"10.1016\/S0006-3495(03)74696-7","volume":"85","author":"BS Hendriks","year":"2003","unstructured":"Hendriks BS, Wiley HS et al (2003) HER2-mediated effects on EGFR endosomal sorting: analysis of biophysical mechanisms. Biophys J 85(4):2732\u20132745","journal-title":"Biophys J"},{"issue":"2","key":"34_CR29_34","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/jbiol26","volume":"4","author":"MJ Herrgard","year":"2005","unstructured":"Herrgard MJ, Palsson BO (2005) Untangling the web of functional and physical interactions in yeast. J\u00a0Biol 4(2):5","journal-title":"J Biol"},{"issue":"5596","key":"34_CR30_34","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1126\/science.1071914","volume":"298","author":"A Hoffmann","year":"2002","unstructured":"Hoffmann A, Levchenko A et al (2002) The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science 298(5596):1241\u20131245","journal-title":"Science"},{"issue":"5696","key":"34_CR31_34","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1126\/science.1104635","volume":"306","author":"L Hood","year":"2004","unstructured":"Hood L, Heath JR et al (2004) Systems biology and new technologies enable predictive and preventative medicine. Science 306(5696):640\u2013643","journal-title":"Science"},{"issue":"5","key":"34_CR32_34","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1002\/bit.21073","volume":"95","author":"Q Hua","year":"2006","unstructured":"Hua Q, Joyce AR et al (2006) Metabolic analysis of adaptive evolution for in silico\u2010designed lactate\u2010producing strains. Biotechnol Bioeng 95(5):992\u20131002","journal-title":"Biotechnol Bioeng"},{"issue":"48","key":"34_CR33_34","doi-asserted-by":"crossref","first-page":"17296","DOI":"10.1073\/pnas.0508647102","volume":"102","author":"D Hwang","year":"2005","unstructured":"Hwang D, Rust AG et al (2005) A\u00a0data integration methodology for systems biology. Proc Natl Acad Sci USA 102(48):17296\u201317301","journal-title":"Proc Natl Acad Sci USA"},{"issue":"48","key":"34_CR34_34","doi-asserted-by":"crossref","first-page":"17302","DOI":"10.1073\/pnas.0508649102","volume":"102","author":"D Hwang","year":"2005","unstructured":"Hwang D, Smith JJ et al (2005) A\u00a0data integration methodology forsystems biology: experimental verification. Proc Natl Acad Sci USA 102(48):17302\u201317307","journal-title":"Proc Natl Acad Sci USA"},{"issue":"6912","key":"34_CR35_34","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/nature01149","volume":"420","author":"RU Ibarra","year":"2002","unstructured":"Ibarra RU, Edwards JS et al (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420(6912):186\u2013189","journal-title":"Nature"},{"key":"34_CR36_34","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1007\/978-1-4419-8861-4_3","volume":"547","author":"T Ideker","year":"2004","unstructured":"Ideker T (2004) A\u00a0systems approach to discovering signaling and regulatory pathways\u2013or, how to digest large interaction networks into relevant pieces. Adv Exp Med Biol 547:21\u201330","journal-title":"Adv Exp Med Biol"},{"key":"34_CR37_34","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1146\/annurev.genom.2.1.343","volume":"2","author":"T Ideker","year":"2001","unstructured":"Ideker T, Galitski T et al (2001) A\u00a0new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2:343\u2013372","journal-title":"Annu Rev Genomics Hum Genet"},{"issue":"1","key":"34_CR38_34","doi-asserted-by":"crossref","first-page":"S233","DOI":"10.1093\/bioinformatics\/18.suppl_1.S233","volume":"18","author":"T Ideker","year":"2002","unstructured":"Ideker T, Ozier O et al (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics (Suppl) 18(1):S233\u2013S2340","journal-title":"Bioinformatics (Suppl)"},{"issue":"3","key":"34_CR39_34","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1093\/bioinformatics\/17.3.286","volume":"17","author":"N Jamshidi","year":"2001","unstructured":"Jamshidi N, Edwards JS et al (2001) Dynamic simulation of the human red blood cell metabolic network. Bioinformatics 17(3):286\u2013287","journal-title":"Bioinformatics"},{"key":"34_CR40_34","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780195079517.001.0001","volume-title":"The origins of order : self organization and selection in evolution","author":"SA Kauffman","year":"1993","unstructured":"Kauffman SA (1993) The origins of order : self organization and selection in evolution. Oxford University Press, New York"},{"key":"34_CR41_34","doi-asserted-by":"crossref","first-page":"W83","DOI":"10.1093\/nar\/gkh411","volume":"32","author":"BP Kelley","year":"2004","unstructured":"Kelley BP, Yuan B et al (2004) PathBLAST: a\u00a0tool for alignment of protein interaction networks. Nucleic Acids Res (Web Server issue) 32:W83\u2013W88","journal-title":"Nucleic Acids Res (Web Server issue)"},{"issue":"3","key":"34_CR42_34","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1093\/bib\/4.3.228","volume":"4","author":"SY Kim","year":"2003","unstructured":"Kim SY, Imoto S et al (2003) Inferring gene networks from time series microarray data using dynamic Bayesian networks. Brief Bioinform 4(3):228\u2013235","journal-title":"Brief Bioinform"},{"issue":"4","key":"34_CR43_34","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1016\/j.cell.2005.05.005","volume":"121","author":"MW Kirschner","year":"2005","unstructured":"Kirschner MW (2005) The meaning of systems biology. Cell 121(4):503\u2013504","journal-title":"Cell"},{"issue":"6912","key":"34_CR44_34","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1038\/nature01254","volume":"420","author":"H Kitano","year":"2002","unstructured":"Kitano H (2002) Computational systems biology. Nature 420(6912):206\u2013210","journal-title":"Nature"},{"key":"34_CR45_34","volume-title":"The singularity is near: when humans transcend biology","author":"R Kurzweil","year":"2005","unstructured":"Kurzweil R (2005) The singularity is near: when humans transcend biology. Penguin, London"},{"issue":"4","key":"34_CR46_34","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1016\/j.sigpro.2005.06.008","volume":"86","author":"H Lahdesmaki","year":"2006","unstructured":"Lahdesmaki H, Hautaniemi S et al (2006) Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Processing 86(4):814\u2013834","journal-title":"Signal Processing"},{"issue":"1\u20132","key":"34_CR47_34","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1023\/A:1023905711304","volume":"52","author":"H Lahdesmaki","year":"2003","unstructured":"Lahdesmaki H, Shmulevich I et al (2003) On Learning Gene Regulatory Networks Under the Boolean Network Model. Machine Learning 52(1\u20132):147\u2013167","journal-title":"Machine Learning"},{"issue":"10","key":"34_CR48_34","doi-asserted-by":"crossref","first-page":"e254","DOI":"10.1371\/journal.pbio.0050254","volume":"5","author":"S Levy","year":"2007","unstructured":"Levy S, Sutton G et al (2007) The Diploid Genome Sequence of an Individual Human. PLoS Biol 5(10):e254","journal-title":"PLoS Biol"},{"issue":"14","key":"34_CR49_34","doi-asserted-by":"crossref","first-page":"4781","DOI":"10.1073\/pnas.0305937101","volume":"101","author":"F Li","year":"2004","unstructured":"Li F, Long T et al (2004) The yeast cell-cycle network is robustly designed. Proc Natl Acad Sci USA 101(14):4781\u20134786","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"34_CR50_34","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1093\/bioinformatics\/bti752","volume":"22","author":"H Li","year":"2006","unstructured":"Li H, Zhan M (2006) Systematic intervention of transcription for identifying network response to disease and cellular phenotypes. Bioinformatics 22(1):96\u2013102","journal-title":"Bioinformatics"},{"issue":"4","key":"34_CR51_34","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1016\/j.ymben.2003.09.002","volume":"5","author":"R Mahadevan","year":"2003","unstructured":"Mahadevan R, Schilling CH (2003) The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng 5(4):264\u2013276","journal-title":"Metab Eng"},{"issue":"2","key":"34_CR52_34","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1038\/nprot.2006.106","volume":"1","author":"AA Margolin","year":"2006","unstructured":"Margolin AA, Wang K et al (2006) Reverse engineering cellular networks. Nat Protoc 1(2):662\u2013671","journal-title":"Nat Protoc"},{"key":"34_CR53_34","doi-asserted-by":"crossref","DOI":"10.1201\/9780203503935","volume-title":"Modelling metabolism with Mathematica, detailed examples including erythrocyte metabolism","author":"PJ Mulquiney","year":"2003","unstructured":"Mulquiney PJ, Kuchel PW (2003) Modelling metabolism with Mathematica, detailed examples including erythrocyte metabolism. CRC Press, Boca Raton"},{"issue":"7","key":"34_CR54_34","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1093\/bioinformatics\/bti131","volume":"21","author":"R Pal","year":"2005","unstructured":"Pal R, Datta A et al (2005) Intervention in context\u2010sensitive probabilistic Boolean networks. Bioinformatics 21(7):1211\u20131218","journal-title":"Bioinformatics"},{"issue":"10","key":"34_CR55_34","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.1038\/nbt1004-1218","volume":"22","author":"B Palsson","year":"2004","unstructured":"Palsson B (2004) Two\u2010dimensional annotation of genomes. Nat Biotechnol 22(10):1218\u20131219","journal-title":"Nat Biotechnol"},{"issue":"2","key":"34_CR56_34","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nrm1570","volume":"6","author":"JA Papin","year":"2005","unstructured":"Papin JA, Hunter T et al (2005) Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol 6(2):99\u2013111","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"1","key":"34_CR57_34","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1529\/biophysj.103.029884","volume":"87","author":"JA Papin","year":"2004","unstructured":"Papin JA, Palsson BO (2004) The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. Biophys J 87(1):37\u201346","journal-title":"Biophys J"},{"issue":"2","key":"34_CR58_34","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.jtbi.2003.11.016","volume":"227","author":"JA Papin","year":"2004","unstructured":"Papin JA, Palsson BO (2004) Topological analysis of mass-balanced signaling networks: a\u00a0framework to obtain network properties including crosstalk. J\u00a0Theor Biol 227(2):283\u2013297","journal-title":"J Theor Biol"},{"issue":"1","key":"34_CR59_34","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1006\/jtbi.2001.2499","volume":"215","author":"JA Papin","year":"2002","unstructured":"Papin JA, Price ND et al (2002) The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. J\u00a0Theor Biol 215(1):67\u201382","journal-title":"J Theor Biol"},{"issue":"7","key":"34_CR60_34","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1002\/bit.10857","volume":"84","author":"P Pharkya","year":"2003","unstructured":"Pharkya P, Burgard AP et al (2003) Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock. Biotechnol Bioeng 84(7):887\u2013899","journal-title":"Biotechnol Bioeng"},{"issue":"11","key":"34_CR61_34","doi-asserted-by":"crossref","first-page":"2367","DOI":"10.1101\/gr.2872004","volume":"14","author":"P Pharkya","year":"2004","unstructured":"Pharkya P, Burgard AP et al (2004) OptStrain: a\u00a0computational framework for redesign of microbial production systems. Genome Res 14(11):2367\u201376","journal-title":"Genome Res"},{"issue":"17","key":"34_CR62_34","doi-asserted-by":"crossref","first-page":"2934","DOI":"10.1093\/bioinformatics\/bth337","volume":"20","author":"I Pournara","year":"2004","unstructured":"Pournara I, Wernisch L (2004) Reconstruction of gene networks using Bayesian learning and manipulation experiments. Bioinformatics 20(17):2934\u20132942","journal-title":"Bioinformatics"},{"issue":"5","key":"34_CR63_34","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1101\/gr.218002","volume":"12","author":"ND Price","year":"2002","unstructured":"Price ND, Papin JA et al (2002) Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res 12(5):760\u2013769","journal-title":"Genome Res"},{"issue":"11","key":"34_CR64_34","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1038\/nrmicro1023","volume":"2","author":"ND Price","year":"2004","unstructured":"Price ND, Reed JL et al (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2(11):886\u2013897","journal-title":"Nat Rev Microbiol"},{"issue":"4","key":"34_CR65_34","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1529\/biophysj.104.043000","volume":"87","author":"ND Price","year":"2004","unstructured":"Price ND, Schellenberger J et al (2004) Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophys J 87(4):2172\u20132186","journal-title":"Biophys J"},{"issue":"9","key":"34_CR66_34","doi-asserted-by":"crossref","first-page":"2692","DOI":"10.1128\/JB.185.9.2692-2699.2003","volume":"185","author":"JL Reed","year":"2003","unstructured":"Reed JL, Palsson BO (2003) Thirteen years of building constraint-based in silico models of Escherichia coli. J\u00a0Bacteriol 185(9):2692\u20132699","journal-title":"J Bacteriol"},{"issue":"9","key":"34_CR67_34","doi-asserted-by":"crossref","first-page":"1797","DOI":"10.1101\/gr.2546004","volume":"14","author":"JL Reed","year":"2004","unstructured":"Reed JL, Palsson BO (2004) Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. Genome Res 14(9):1797\u20131805","journal-title":"Genome Res"},{"issue":"9","key":"34_CR68_34","doi-asserted-by":"crossref","first-page":"R54","DOI":"10.1186\/gb-2003-4-9-r54","volume":"4","author":"JL Reed","year":"2003","unstructured":"Reed JL, Vo TD et al (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM\/GPR). Genome Biol 4(9):R54","journal-title":"Genome Biol"},{"key":"34_CR69_34","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1186\/1471-2105-7-280","volume":"7","author":"DJ Reiss","year":"2006","unstructured":"Reiss DJ, Baliga NS et al (2006) Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics 7:280","journal-title":"BMC Bioinformatics"},{"issue":"7062","key":"34_CR70_34","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1038\/nature04209","volume":"437","author":"JF Rual","year":"2005","unstructured":"Rual JF, Venkatesan K et al (2005) Towards a\u00a0proteome-scale map of the human protein\u2010protein interaction network. Nature 437(7062):1173\u20131178","journal-title":"Nature"},{"issue":"5721","key":"34_CR71_34","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1126\/science.1105809","volume":"308","author":"K Sachs","year":"2005","unstructured":"Sachs K, Perez O et al (2005) Causal protein\u2010signaling networks derived from multiparameter single-cell data. Science 308(5721):523\u2013529","journal-title":"Science"},{"issue":"1","key":"34_CR72_34","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1016\/j.copbio.2003.11.001","volume":"15","author":"U Sauer","year":"2004","unstructured":"Sauer U (2004) High\u2010throughput phenomics: experimental methods for mapping fluxomes. Curr Opin Biotechnol 15(1):58\u201363","journal-title":"Curr Opin Biotechnol"},{"issue":"11","key":"34_CR73_34","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A et al (2003) Cytoscape: a\u00a0software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498\u2013504","journal-title":"Genome Res"},{"issue":"2","key":"34_CR74_34","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1093\/bioinformatics\/18.2.261","volume":"18","author":"I Shmulevich","year":"2002","unstructured":"Shmulevich I, Dougherty ER et al (2002) Probabilistic Boolean Networks: a\u00a0rule-based uncertainty model for gene regulatory networks. Bioinformatics 18(2):261\u2013274","journal-title":"Bioinformatics"},{"issue":"11","key":"34_CR75_34","doi-asserted-by":"crossref","first-page":"1778","DOI":"10.1109\/JPROC.2002.804686","volume":"90","author":"I Shmulevich","year":"2002","unstructured":"Shmulevich I, Dougherty ER et al (2002) From Boolean to probabilistic Boolean networks as models of genetic regulatory networks. Proceedings of the IEEE 90(11):1778\u20131792","journal-title":"Proceedings of the IEEE"},{"issue":"10","key":"34_CR76_34","doi-asserted-by":"crossref","first-page":"1319","DOI":"10.1093\/bioinformatics\/18.10.1319","volume":"18","author":"I Shmulevich","year":"2002","unstructured":"Shmulevich I, Dougherty ER et al (2002) Gene perturbation and intervention in probabilistic Boolean networks. Bioinformatics 18(10):1319\u20131331","journal-title":"Bioinformatics"},{"issue":"5223","key":"34_CR77_34","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1126\/science.7542802","volume":"269","author":"HO Smith","year":"1995","unstructured":"Smith HO, Tomb JF et al (1995) Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome. Science 269(5223):538\u2013540","journal-title":"Science"},{"issue":"6","key":"34_CR78_34","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1016\/j.cell.2005.08.029","volume":"122","author":"U Stelzl","year":"2005","unstructured":"Stelzl U, Worm U et al (2005) A\u00a0human protein\u2010protein interaction network: a\u00a0resource for annotating the proteome. Cell 122(6):957\u2013968","journal-title":"Cell"},{"issue":"6","key":"34_CR79_34","doi-asserted-by":"crossref","first-page":"e109","DOI":"10.1371\/journal.pcbi.0030109","volume":"3","author":"J Thakar","year":"2007","unstructured":"Thakar J, Pillione M et al (2007) Modelling Systems-Level Regulation of Host Immune Responses. PloS Comput Biol 3(6):e109","journal-title":"PloS Comput Biol"},{"issue":"12","key":"34_CR80_34","doi-asserted-by":"crossref","first-page":"11683","DOI":"10.1074\/jbc.M409072200","volume":"280","author":"I Thiele","year":"2005","unstructured":"Thiele I, Price ND et al (2005) Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. J\u00a0Biol Chem 280(12):11683\u201311695","journal-title":"J Biol Chem"},{"issue":"16","key":"34_CR81_34","doi-asserted-by":"crossref","first-page":"5818","DOI":"10.1128\/JB.187.16.5818-5830.2005","volume":"187","author":"I Thiele","year":"2005","unstructured":"Thiele I, Vo TD et al (2005) Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM\/GPR): an in silico genome-scale characterization of single- and double\u2010deletion mutants. J\u00a0Bacteriol 187(16):5818\u20135830","journal-title":"J Bacteriol"},{"issue":"5659","key":"34_CR82_34","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1126\/science.1091317","volume":"303","author":"AH Tong","year":"2004","unstructured":"Tong AH, Lesage G et al (2004) Global mapping of the yeast genetic interaction network. Science 303(5659):808\u2013813","journal-title":"Science"},{"issue":"6792","key":"34_CR83_34","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1038\/35018085","volume":"406","author":"G von Dassow","year":"2000","unstructured":"von Dassow G, Meir E et al (2000) The segment polarity network is a\u00a0robust developmental module. Nature 406(6792):188\u2013192","journal-title":"Nature"},{"issue":"5742","key":"34_CR84_34","doi-asserted-by":"crossref","first-page":"1857","DOI":"10.1126\/science.1113319","volume":"309","author":"SL Werner","year":"2005","unstructured":"Werner SL, Barken D et al (2005) Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science 309(5742):1857\u20131861","journal-title":"Science"},{"issue":"1","key":"34_CR85_34","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1093\/nar\/30.1.245","volume":"30","author":"J Westbrook","year":"2002","unstructured":"Westbrook J, Feng Z et al (2002) The Protein Data Bank: unifying the archive. Nucleic Acids Res 30(1):245\u2013248","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"34_CR86_34","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.1038\/nbt1020","volume":"22","author":"HV Westerhoff","year":"2004","unstructured":"Westerhoff HV, Palsson BO (2004) The evolution of molecular biology into systems biology. Nat Biotechnol 22(10):1249\u20131252","journal-title":"Nat Biotechnol"},{"issue":"1","key":"34_CR87_34","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1093\/bioinformatics\/bth463","volume":"21","author":"M Zou","year":"2005","unstructured":"Zou M, Conzen SD (2005) A\u00a0new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data. Bioinformatics 21(1):71\u201379","journal-title":"Bioinformatics"}],"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_34","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,10]],"date-time":"2025-02-10T05:53:27Z","timestamp":1739166807000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-0-387-30440-3_34"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009]]},"ISBN":["9780387758886","9780387304403"],"references-count":87,"URL":"https:\/\/doi.org\/10.1007\/978-0-387-30440-3_34","relation":{},"subject":[],"published":{"date-parts":[[2009]]}}}