{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T09:35:51Z","timestamp":1789032951378,"version":"build-2803163510"},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2007,3,13]],"date-time":"2007-03-13T00:00:00Z","timestamp":1173744000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,12]]},"DOI":"10.1186\/1471-2105-8-88","type":"journal-article","created":{"date-parts":[[2007,3,13]],"date-time":"2007-03-13T02:30:31Z","timestamp":1173753031000},"source":"Crossref","is-referenced-by-count":26,"title":["Regulation of metabolic networks by small molecule metabolites"],"prefix":"10.1186","volume":"8","author":[{"given":"Alex","family":"Gutteridge","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minoru","family":"Kanehisa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susumu","family":"Goto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2007,3,13]]},"reference":[{"issue":"2","key":"1460_CR1","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/nrg1272","volume":"5","author":"AL Barabasi","year":"2004","unstructured":"Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5(2):101\u2013113. 10.1038\/nrg1272","journal-title":"Nat Rev Genet"},{"issue":"5","key":"1460_CR2","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1016\/S0968-0004(03)00064-1","volume":"28","author":"JA Papin","year":"2003","unstructured":"Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO: Metabolic pathways in the post-genome era. Trends Biochem Sci 2003, 28(5):250\u2013258. 10.1016\/S0968-0004(03)00064-1","journal-title":"Trends Biochem Sci"},{"issue":"6804","key":"1460_CR3","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1038\/35036627","volume":"407","author":"H Jeong","year":"2000","unstructured":"Jeong H, Tombor B, Albert R, Oltvai ZN, Barabsi AL: The large-scale organization of metabolic networks. Nature 2000, 407(6804):651\u2013654. 10.1038\/35036627","journal-title":"Nature"},{"key":"1460_CR4","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1186\/1471-2105-7-332","volume":"7","author":"C-H Yeang","year":"2006","unstructured":"Yeang C-H, Vingron M: A joint model of regulatory and metabolic networks. BMC Bioinformatics 2006, 7: 332. 10.1186\/1471-2105-7-332","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"1460_CR5","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1006\/abbi.2001.2637","volume":"397","author":"P Reichard","year":"2002","unstructured":"Reichard P: Ribonucleotide reductases: the evolution of allosteric regulation. Arch Biochem Biophys 2002, 397(2):149\u2013155. 10.1006\/abbi.2001.2637","journal-title":"Arch Biochem Biophys"},{"issue":"3","key":"1460_CR6","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1007\/s00203-005-0758-9","volume":"183","author":"WC Winkler","year":"2005","unstructured":"Winkler WC: Metabolic monitoring by bacterial mrnas. Arch Microbiol 2005, 183(3):151\u2013159. 10.1007\/s00203-005-0758-9","journal-title":"Arch Microbiol"},{"issue":"2","key":"1460_CR7","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1016\/j.mib.2004.02.003","volume":"7","author":"P Babitzke","year":"2004","unstructured":"Babitzke P: Regulation of transcription attenuation and translation initiation by allosteric control of an rna-binding protein: the bacillus subtilis trap protein. Curr Opin Microbiol 2004, 7(2):132\u2013139. 10.1016\/j.mib.2004.02.003","journal-title":"Curr Opin Microbiol"},{"issue":"6","key":"1460_CR8","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1016\/j.cbpa.2005.09.016","volume":"9","author":"WC Winkler","year":"2005","unstructured":"Winkler WC: Riboswitches and the role of noncoding rnas in bacterial metabolic control. Curr Opin Chem Biol 2005, 9(6):594\u2013602. 10.1016\/j.cbpa.2005.09.016","journal-title":"Curr Opin Chem Biol"},{"issue":"15","key":"1460_CR9","doi-asserted-by":"publisher","first-page":"3264","DOI":"10.1016\/j.febslet.2005.03.089","volume":"579","author":"GS Baillie","year":"2005","unstructured":"Baillie GS, Scott JD, Houslay MD: Compartmentalisation of phosphodiesterases and protein kinase a: opposites attract. FEBS Lett 2005, 579(15):3264\u20133270. 10.1016\/j.febslet.2005.03.089","journal-title":"FEBS Lett"},{"issue":"1\u20133","key":"1460_CR10","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1016\/S0014-5793(04)00310-2","volume":"563","author":"KV Venkatesh","year":"2004","unstructured":"Venkatesh KV, Bhartiya S, Ruhela A: Multiple feedback loops are key to a robust dynamic performance of tryptophan regulation in escherichia coli. FEBS Lett 2004, 563(1\u20133):234\u2013240. 10.1016\/S0014-5793(04)00310-2","journal-title":"FEBS Lett"},{"key":"1460_CR11","doi-asserted-by":"crossref","unstructured":"Simao E, Remy E, Thieffry D, Chaouiya C: Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in e. coli. Bioinformatics 21(Suppl 2):","DOI":"10.1093\/bioinformatics\/bti1130"},{"issue":"52","key":"1460_CR12","doi-asserted-by":"publisher","first-page":"19103","DOI":"10.1073\/pnas.0505231102","volume":"102","author":"CL Barrett","year":"2005","unstructured":"Barrett CL, Herring CD, Reed JL, Palsson BO: The global transcriptional regulatory network for metabolism in escherichia coli exhibits few dominant functional states. Proc Natl Acad Sci USA 2005, 102(52):19103\u201319108. 10.1073\/pnas.0505231102","journal-title":"Proc Natl Acad Sci USA"},{"issue":"6987","key":"1460_CR13","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1038\/nature02456","volume":"429","author":"MW Covert","year":"2004","unstructured":"Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO: Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004, 429(6987):92\u201396. 10.1038\/nature02456","journal-title":"Nature"},{"issue":"5439","key":"1460_CR14","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1126\/science.286.5439.509","volume":"286","author":"AL Barabasi","year":"1999","unstructured":"Barabasi AL, Albert R: Emergence of scaling in random networks. Science 1999, 286(5439):509\u2013512. 10.1126\/science.286.5439.509","journal-title":"Science"},{"issue":"4","key":"1460_CR15","doi-asserted-by":"publisher","first-page":"928","DOI":"10.1002\/pmic.200300636","volume":"4","author":"SH Yook","year":"2004","unstructured":"Yook SH, Oltvai ZN, Barabsi AL: Functional and topological characterization of protein interaction networks. Proteomics 2004, 4(4):928\u2013942. 10.1002\/pmic.200300636","journal-title":"Proteomics"},{"issue":"6","key":"1460_CR16","doi-asserted-by":"publisher","first-page":"1543","DOI":"10.1073\/pnas.0306458101","volume":"101","author":"M Arita","year":"2004","unstructured":"Arita M: The metabolic world of escherichia coli is not small. Proc Natl Acad Sci USA 2004, 101(6):1543\u20131547. 10.1073\/pnas.0306458101","journal-title":"Proc Natl Acad Sci USA"},{"issue":"9","key":"1460_CR17","doi-asserted-by":"publisher","first-page":"991","DOI":"10.2174\/1568026043388529","volume":"4","author":"F Rodriguez-Barrios","year":"2004","unstructured":"Rodriguez-Barrios F, Gago F: Hiv protease inhibition: limited recent progress and advances in understanding current pitfalls. Curr Top Med Chem 2004, 4(9):991\u20131007. 10.2174\/1568026043388529","journal-title":"Curr Top Med Chem"},{"issue":"Pt 5","key":"1460_CR18","doi-asserted-by":"publisher","first-page":"980","DOI":"10.1042\/bst0310980","volume":"31","author":"RT Kroemer","year":"2003","unstructured":"Kroemer RT: Molecular modelling probes: docking and scoring. Biochem Soc Trans 2003, 31(Pt 5):980\u2013984.","journal-title":"Biochem Soc Trans"},{"key":"1460_CR19","unstructured":"May A, Zacharias M: Accounting for global protein deformability during protein-protein and protein-ligand docking. Biochim Biophys Acta"},{"key":"1460_CR20","doi-asserted-by":"crossref","unstructured":"Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D: Brenda, the enzyme database: updates and major new developments. Nucleic Acids Res (32 Database):","DOI":"10.1093\/nar\/gkh081"},{"key":"1460_CR21","doi-asserted-by":"crossref","unstructured":"Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen IT, Peralta-Gil M, Karp PD: Ecocyc: a comprehensive database resource for escherichia coli. Nucleic Acids Res (33 Database):","DOI":"10.1093\/nar\/gki108"},{"key":"1460_CR22","doi-asserted-by":"crossref","unstructured":"Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M: From genomics to chemical genomics: new developments in kegg. Nucleic Acids Res (34 Database):","DOI":"10.1093\/nar\/gkj102"},{"issue":"12","key":"1460_CR23","doi-asserted-by":"publisher","first-page":"1870","DOI":"10.1093\/bioinformatics\/bth167","volume":"20","author":"HW Ma","year":"2004","unstructured":"Ma HW, Zhao XM, Yuan YJ, Zeng AP: Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. Bioinformatics 2004, 20(12):1870\u20131876. 10.1093\/bioinformatics\/bth167","journal-title":"Bioinformatics"},{"issue":"5586","key":"1460_CR24","doi-asserted-by":"publisher","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: Hierarchical organization of modularity in metabolic networks. Science 2002, 297(5586):1551\u20131555. 10.1126\/science.1073374","journal-title":"Science"},{"issue":"39","key":"1460_CR25","doi-asserted-by":"publisher","first-page":"11853","DOI":"10.1021\/ja036030u","volume":"125","author":"M Hattori","year":"2003","unstructured":"Hattori M, Okuno Y, Goto S, Kanehisa M: Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J Am Chem Soc 2003, 125(39):11853\u201311865. 10.1021\/ja036030u","journal-title":"J Am Chem Soc"},{"key":"1460_CR26","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1038\/2605","volume":"4","author":"D Koshland","year":"1998","unstructured":"Koshland D: Conformational changes: how small is big enough? Nat Med 1998, 4: 1112\u20134. 10.1038\/2605","journal-title":"Nat Med"},{"key":"1460_CR27","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1016\/j.jmb.2004.11.013","volume":"346","author":"A Gutteridge","year":"2005","unstructured":"Gutteridge A, Thornton J: Conformational changes observed in enzyme crystal structures upon substrate binding. J Mol Biol 2005, 346: 21\u20138. 10.1016\/j.jmb.2004.11.013","journal-title":"J Mol Biol"},{"issue":"1","key":"1460_CR28","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1093\/nar\/30.1.402","volume":"30","author":"S Goto","year":"2002","unstructured":"Goto S, Okuno Y, Hattori M, Nishioka T, Kanehisa M: Ligand: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res 2002, 30(1):402\u2013404. 10.1093\/nar\/30.1.402","journal-title":"Nucleic Acids Res"},{"issue":"2\u20133","key":"1460_CR29","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1016\/0005-2760(92)90305-F","volume":"1128","author":"H Jansen","year":"1992","unstructured":"Jansen H, van Tol A, Auwerx J, Skretting G, Staels B: Opposite regulation of hepatic lipase and lecithin: cholesterol acyltransferase by glucocorticoids in rats. Biochim Biophys Acta 1992, 1128(2\u20133):181\u2013185.","journal-title":"Biochim Biophys Acta"},{"issue":"1C","key":"1460_CR30","doi-asserted-by":"publisher","first-page":"1017","DOI":"10.1016\/0022-4731(83)90048-1","volume":"19","author":"GS Boyd","year":"1983","unstructured":"Boyd GS, McNamara B, Suckling KE, Tocher DR: Cholesterol metabolism in the adrenal cortex. J Steroid Biochem 1983, 19(1C):1017\u20131027. 10.1016\/0022-4731(83)90048-1","journal-title":"J Steroid Biochem"},{"issue":"9","key":"1460_CR31","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1038\/sj.cgt.7700358","volume":"8","author":"CM Beausejour","year":"2001","unstructured":"Beausejour CM, Eliopoulos N, Momparler L, Le NL, Momparler RL: Selection of drug-resistant transduced cells with cytosine nucleoside analogs using the human cytidine deaminase gene. Cancer Gene Ther 2001, 8(9):669\u2013676. 10.1038\/sj.cgt.7700358","journal-title":"Cancer Gene Ther"},{"issue":"8","key":"1460_CR32","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1038\/sj.mp.4001518","volume":"9","author":"TD Gould","year":"2004","unstructured":"Gould TD, Quiroz JA, Singh J, Zarate CA, Manji HK: Emerging experimental therapeutics for bipolar disorder: insights from the molecular and cellular actions of current mood stabilizers. Mol Psychiatry 2004, 9(8):734\u2013755. 10.1038\/sj.mp.4001518","journal-title":"Mol Psychiatry"},{"issue":"4","key":"1460_CR33","first-page":"133","volume":"37","author":"CB Nemeroff","year":"2003","unstructured":"Nemeroff CB: The role of gaba in the pathophysiology and treatment of anxiety disorders. Psychopharmacol Bull 2003, 37(4):133\u2013146.","journal-title":"Psychopharmacol Bull"},{"issue":"7","key":"1460_CR34","first-page":"593","volume":"154","author":"AC Sewell","year":"1995","unstructured":"Sewell AC, Bhles HJ, Herwig J, Demirkol M: Neurological deterioration in patients with urea cycle disorders under valproate therapy-a cause for concern. Eur J Pediatr 1995, 154(7):593\u2013594.","journal-title":"Eur J Pediatr"},{"issue":"12","key":"1460_CR35","first-page":"764","volume":"146","author":"D Christmann","year":"1990","unstructured":"Christmann D, Hirsch E, Mutschler V, Collard M, Marescaux C, Colombo JP: [late diagnosis of congenital argininemia during administration of sodium valproate]. Rev Neurol (Paris) 1990, 146(12):764\u2013766.","journal-title":"Rev Neurol (Paris)"},{"issue":"8","key":"1460_CR36","doi-asserted-by":"publisher","first-page":"2455","DOI":"10.1093\/nar\/gkl140","volume":"34","author":"S Krishna","year":"2006","unstructured":"Krishna S, Andersson AM, Semsey S, Sneppen K: Structure and function of negative feedback loops at the interface of genetic and metabolic networks. Nucleic Acids Res 2006, 34(8):2455\u20132462. 10.1093\/nar\/gkl140","journal-title":"Nucleic Acids Res"},{"issue":"5594","key":"1460_CR37","doi-asserted-by":"publisher","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: Network motifs: simple building blocks of complex networks. Science 2002, 298(5594):824\u2013827. 10.1126\/science.298.5594.824","journal-title":"Science"},{"issue":"3","key":"1460_CR38","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403\u2013410.","journal-title":"J Mol Biol"},{"key":"1460_CR39","unstructured":"The igraph library[ http:\/\/cneurocvs.rmki.kfki.hu\/igraph ]"},{"key":"1460_CR40","unstructured":"BioRuby[ http:\/\/bioruby.org ]"},{"key":"1460_CR41","unstructured":"RSRuby[ http:\/\/web.kuicr.kyoto-u.ac.jp\/~alexg\/ ]"},{"key":"1460_CR42","unstructured":"Tioga[ http:\/\/www.kitp.ucsb.edu\/paxton\/tioga.html ]"},{"issue":"1","key":"1460_CR43","doi-asserted-by":"publisher","first-page":"71","DOI":"10.2165\/00822942-200504010-00009","volume":"4","author":"L Goldovsky","year":"2005","unstructured":"Goldovsky L, Cases I, Enright AJ, Ouzounis CA: Biolayout(java): versatile network visualisation of structural and functional relationships. Appl Bioinformatics 2005, 4(1):71\u201374. 10.2165\/00822942-200504010-00009","journal-title":"Appl Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-88.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-8-88\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-88.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,4,25]],"date-time":"2019-04-25T22:37:36Z","timestamp":1556231856000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-88"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,3,13]]},"references-count":43,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1460"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-88","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,3,13]]},"article-number":"88"}}