{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,17]],"date-time":"2024-06-17T06:33:11Z","timestamp":1718605991705},"reference-count":37,"publisher":"Springer Science and Business Media LLC","issue":"S6","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2013,12]]},"DOI":"10.1186\/1752-0509-7-s6-s1","type":"journal-article","created":{"date-parts":[[2013,12,13]],"date-time":"2013-12-13T12:07:24Z","timestamp":1386936444000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Identification of key regulators in glycogen utilization in E. coli based on the simulations from a hybrid functional Petri net model"],"prefix":"10.1186","volume":"7","author":[{"given":"Zhongyuan","family":"Tian","sequence":"first","affiliation":[]},{"given":"Adrien","family":"Faur\u00e9","sequence":"additional","affiliation":[]},{"given":"Hirotada","family":"Mori","sequence":"additional","affiliation":[]},{"given":"Hiroshi","family":"Matsuno","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,12,13]]},"reference":[{"issue":"12","key":"1224_CR1","doi-asserted-by":"publisher","first-page":"1442","DOI":"10.1016\/j.bbapap.2012.06.010","volume":"1824","author":"T Yamamotoya","year":"2012","unstructured":"Yamamotoya T, Dose H, Tian Z, Faur\u00e9 A, Toya Y, Honma M, Igarashi K, Nakahigashi K, Soga T, Mori H, Matsuno H: Glycogen is the primary source of glucose during the lag phase of e. coli proliferation. Biochimica et Biophysica Acta - Proteins and Proteomics. 2012, 1824 (12): 1442-1448. 10.1016\/j.bbapap.2012.06.010.","journal-title":"Biochimica et Biophysica Acta - Proteins and Proteomics"},{"issue":"6","key":"1224_CR2","doi-asserted-by":"publisher","first-page":"952","DOI":"10.1111\/j.1574-6976.2010.00220.x","volume":"34","author":"WA Wilson","year":"2010","unstructured":"Wilson WA, Roach PJ, Montero M, Baroja-Fern\u00e1ndez E, Mu\u00f5z FJ, Eydallin G, Viale AM, Pozueta-Romero J: Regulation of glycogen metabolism in yeast and bacteria. FEMS Microbiology Reviews. 2010, 34 (6): 952-985.","journal-title":"FEMS Microbiology Reviews"},{"issue":"6","key":"1224_CR3","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1016\/S1389-1723(01)80308-X","volume":"92","author":"P Kotrba","year":"2001","unstructured":"Kotrba P, Inui M, Yukawa H: Bacterial phosphotransferase system (pts) in carbohydrate uptake and control of carbon metabolism. Journal of Bioscience and Bioengineering. 2001, 92 (6): 502-517.","journal-title":"Journal of Bioscience and Bioengineering"},{"issue":"6","key":"1224_CR4","doi-asserted-by":"publisher","first-page":"1561","DOI":"10.1111\/j.1365-2958.2011.07663.x","volume":"80","author":"AN Edwards","year":"2011","unstructured":"Edwards AN, Patterson-Fortin LM, Vakulskas CA, Mercante JW, Potrykus K, Vinella D, Camacho MI, Fields JA, Thompson SA, Georgellis D, Cashel M, Babitzke P, Romeo T: Circuitry linking the csr and stringent response global regulatory systems. Molecular Microbiology. 2011, 80 (6): 1561-1580. 10.1111\/j.1365-2958.2011.07663.x.","journal-title":"Molecular Microbiology"},{"issue":"6","key":"1224_CR5","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1046\/j.1365-2958.2002.02982.x","volume":"44","author":"CS Baker","year":"2002","unstructured":"Baker CS, Morozov I, Suzuki K, Romeo T, Babitzke P: CsrA regulates glycogen biosynthesis by preventing translation of glgC in escherichia coli. Molecular Microbiology. 2002, 44 (6): 1599-1610. 10.1046\/j.1365-2958.2002.02982.x.","journal-title":"Molecular Microbiology"},{"issue":"3","key":"1224_CR6","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1128\/JB.01214-10","volume":"193","author":"T Shimada","year":"2011","unstructured":"Shimada T, Yamamoto K, Ishihama A: Novel members of the cra regulon involved in carbon metabolism in escherichia coli. Journal of Bacteriology. 2011, 193 (3): 649-659. 10.1128\/JB.01214-10.","journal-title":"Journal of Bacteriology"},{"issue":"2","key":"1224_CR7","doi-asserted-by":"publisher","first-page":"59","DOI":"10.5483\/BMBRep.2012.45.2.59","volume":"45","author":"P Vinuselvi","year":"2012","unstructured":"Vinuselvi P, Kim MK, Lee SK, Ghim CM: Rewiring carbon catabolite repression for microbial cell factory. BMB reports. 2012, 45 (2): 59-70. 10.5483\/BMBRep.2012.45.2.59.","journal-title":"BMB reports"},{"issue":"4","key":"1224_CR8","doi-asserted-by":"publisher","first-page":"939","DOI":"10.1128\/MMBR.00024-06","volume":"70","author":"J Deutscher","year":"2006","unstructured":"Deutscher J, Francke C, Postma PW: How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiology and Molecular Biology Reviews. 2006, 70 (4): 939-1031. 10.1128\/MMBR.00024-06.","journal-title":"Microbiology and Molecular Biology Reviews"},{"issue":"1","key":"1224_CR9","doi-asserted-by":"publisher","first-page":"612","DOI":"10.1016\/S0006-3495(03)74505-6","volume":"85","author":"C Francke","year":"2003","unstructured":"Francke C, Postma PW, Westerhoff HV, Blom JG, Peletier MA: Why the phosphotransferase system of escherichia coli escapes diffusion limitation. Biophysical Journal. 2003, 85 (1): 612-622. 10.1016\/S0006-3495(03)74505-6.","journal-title":"Biophysical Journal"},{"issue":"2","key":"1224_CR10","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1016\/0014-5793(89)80128-0","volume":"243","author":"M Kawamukai","year":"1989","unstructured":"Kawamukai M, Utsumi R, Sakai H, Komano T: Molecular cloning and sequencing of the glycogen phosphorylase gene from escherichia coli. FEBS Letters. 1989, 243 (2): 193-198. 10.1016\/0014-5793(89)80128-0.","journal-title":"FEBS Letters"},{"issue":"1","key":"1224_CR11","first-page":"46","volume":"17","author":"M Nagasaki","year":"2006","unstructured":"Nagasaki M, Yamaguchi R, Yoshida R, Imoto S, Doi A, Tamada Y, Matsuno H, Miyano S, Higuchi T: Genomic data assimilation for estimating hybrid functional petri net from time-course gene expression data. Genome Informatics Series. 2006, 17 (1): 46-","journal-title":"Genome Informatics Series"},{"issue":"1","key":"1224_CR12","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1002\/bit.10288","volume":"79","author":"C Chassagnole","year":"2002","unstructured":"Chassagnole C, Noisommit-Rizzi N, Schmid JW, Mauch K, Reuss M: Dynamic modeling of the central carbon metabolism of escherichia coli. Biotechnology and bioengineering. 2002, 79 (1): 53-73. 10.1002\/bit.10288.","journal-title":"Biotechnology and bioengineering"},{"issue":"45","key":"1224_CR13","doi-asserted-by":"publisher","first-page":"34909","DOI":"10.1074\/jbc.M002461200","volume":"275","author":"JM Rohwer","year":"2000","unstructured":"Rohwer JM, Meadow ND, Roseman S, Westerhoff HV, Postma PW: Understanding glucose transport by the bacterial Phosphoenolpyruvate:Glycose phosphotransferase system on the basis of kinetic measurements in vitro. Journal of Biological Chemistry. 2000, 275 (45): 34909-34921. 10.1074\/jbc.M002461200.","journal-title":"Journal of Biological Chemistry"},{"issue":"42","key":"1224_CR14","doi-asserted-by":"publisher","first-page":"26511","DOI":"10.1074\/jbc.272.42.26511","volume":"272","author":"M Sondej","year":"1997","unstructured":"Sondej M, Badawi P, Lewis MS, Briggs MC, Jaffe H, Peterkofsky A: High affinity binding and allosteric regulation of escherichia coli glycogen phosphorylase by the histidine phosphocarrier protein, HPr. Journal of Biological Chemistry. 1997, 272 (42): 26511-26521. 10.1074\/jbc.272.42.26511.","journal-title":"Journal of Biological Chemistry"},{"issue":"1","key":"1224_CR15","first-page":"24","volume":"39","author":"BM Koo","year":"2001","unstructured":"Koo BM, Seok YJ: Regulation of glycogen concentration by the histidine-containing phosphocarrier protein HPr in escherichia coli. Journal of Microbiology -Seoul. 2001, 39 (1): 24-30.","journal-title":"Journal of Microbiology -Seoul"},{"issue":"3","key":"1224_CR16","first-page":"385","volume":"3","author":"YJ Seok","year":"2001","unstructured":"Seok YJ, Koo BM, Sondej M, Peterkofsky A: Regulation of e. coli glycogen phosphorylase activity by HPr. Journal of molecular microbiology and biotechnology. 2001, 3 (3): 385-394.","journal-title":"Journal of molecular microbiology and biotechnology"},{"issue":"5","key":"1224_CR17","doi-asserted-by":"crossref","first-page":"2773","DOI":"10.1128\/jb.171.5.2773-2782.1989","volume":"171","author":"T Romeo","year":"1989","unstructured":"Romeo T, Preiss J: Genetic regulation of glycogen biosynthesis in escherichia coli: in vitro effects of cyclic AMP and guanosine 5'-diphosphate 3'-diphosphate and analysis of in vivo transcripts. Journal of Bacteriology. 1989, 171 (5): 2773-2782.","journal-title":"Journal of Bacteriology"},{"issue":"9","key":"1224_CR18","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1016\/j.ejcb.2011.04.002","volume":"90","author":"E Gabor","year":"2011","unstructured":"Gabor E, G\u00f6hler AK, Kosfeld A, Staab A, Kremling A, Jahreis K: The phosphoenolpyruvate-dependent glucose-phosphotransferase system from escherichia coli k-12 as the center of a network regulating carbohydrate flux in the cell. European journal of cell biology. 2011, 90 (9): 711-720. 10.1016\/j.ejcb.2011.04.002.","journal-title":"European journal of cell biology"},{"issue":"26","key":"1224_CR19","doi-asserted-by":"publisher","first-page":"17570","DOI":"10.1074\/jbc.M508965200","volume":"281","author":"HV Patel","year":"2006","unstructured":"Patel HV, Vyas KA, Savtchenko R, Roseman S: The Monomer\/Dimer transition of enzyme i of the escherichia coli phosphotransferase system. Journal of Biological Chemistry. 2006, 281 (26): 17570-17578. 10.1074\/jbc.M508965200.","journal-title":"Journal of Biological Chemistry"},{"issue":"21","key":"1224_CR20","doi-asserted-by":"publisher","first-page":"3630","DOI":"10.1038\/emboj.2010.240","volume":"29","author":"L Lopian","year":"2010","unstructured":"Lopian L, Elisha Y, Nussbaum-Shochat A, Amster-Choder O: Spatial and temporal organization of the e. coli pts components. The EMBO Journal. 2010, 29 (21): 3630-3645. 10.1038\/emboj.2010.240.","journal-title":"The EMBO Journal"},{"issue":"1","key":"1224_CR21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1091\/mbc.E05-09-0824","volume":"17","author":"KW Kohn","year":"2006","unstructured":"Kohn KW, Aladjem MI, Weinstein JN, Pommier Y: Molecular interaction maps of bioregulatory networks: A general rubric for systems biology. Molecular Biology of the Cell. 2006, 17 (1): 1-13.","journal-title":"Molecular Biology of the Cell"},{"key":"1224_CR22","unstructured":"GenoBase: Results of Protein Localization References. [http:\/\/ecoli.naist.jp\/GB8-dev\/GFP\/gfp_result.jsp?fword=JW3643]"},{"issue":"5","key":"1224_CR23","doi-asserted-by":"publisher","first-page":"1128","DOI":"10.1111\/j.1365-2958.2008.06229.x","volume":"68","author":"MF Traxler","year":"2008","unstructured":"Traxler MF, Summers SM, Nguyen HT, Zacharia VM, Hightower GA, Smith JT, Conway T: The global, ppGpp-mediated stringent response to amino acid starvation in escherichia coli. Molecular Microbiology. 2008, 68 (5): 1128-1148. 10.1111\/j.1365-2958.2008.06229.x.","journal-title":"Molecular Microbiology"},{"issue":"1","key":"1224_CR24","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1042\/BJ20101186","volume":"433","author":"M Montero","year":"2011","unstructured":"Montero M, Almagro G, Eydallin G, Viale AM, Mun\u00f5z FJ, Bahaji A, Li J, Rahimpour M, Baroja-Fern\u00e1ndez E, Pozueta-Romero J: Escherichia coli glycogen genes are organized in a single glgBXCAP transcriptional unit possessing an alternative suboperonic promoter within glgC that directs glgAP expression. Biochemical Journal. 2011, 433 (1): 107-117. 10.1042\/BJ20101186.","journal-title":"Biochemical Journal"},{"issue":"4","key":"1224_CR25","first-page":"283","volume":"36","author":"APdA Vieira","year":"2006","unstructured":"Vieira APdA, da Silva MAP, Langone MAP: Biodiesel production via esterification reactions catalyzed by lipase. Latin American applied research. 2006, 36 (4): 283-288.","journal-title":"Latin American applied research"},{"issue":"1","key":"1224_CR26","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1016\/j.jbiotec.2010.02.018","volume":"147","author":"Y Usuda","year":"2010","unstructured":"Usuda Y, Nishio Y, Iwatani S, Van Dien SJ, Imaizumi A, Shimbo K, Kageyama N, Iwahata D, Miyano H, Matsui K: Dynamic modeling of escherichia coli metabolic and regulatory systems for amino-acid production. Journal of Biotechnology. 2010, 147 (1): 17-30. 10.1016\/j.jbiotec.2010.02.018.","journal-title":"Journal of Biotechnology"},{"issue":"1","key":"1224_CR27","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1186\/1475-2859-9-88","volume":"9","author":"T Kadir","year":"2010","unstructured":"Kadir T, Mannan A, Kierzek A, McFadden J, Shimizu K: Modeling and simulation of the main metabolism in escherichia coli and its several single-gene knockout mutants with experimental verification. Microbial Cell Factories. 2010, 9 (1): 88-10.1186\/1475-2859-9-88.","journal-title":"Microbial Cell Factories"},{"key":"1224_CR28","unstructured":"BioModels: [http:\/\/www.ebi.ac.uk\/biomodels-main\/BIOMD0000000051]"},{"issue":"6","key":"1224_CR29","doi-asserted-by":"publisher","first-page":"1000812","DOI":"10.1371\/journal.pcbi.1000812","volume":"6","author":"V Baldazzi","year":"2010","unstructured":"Baldazzi V, Ropers D, Markowicz Y, Kahn D, Geiselmann J, de Jong H: The carbon assimilation network in escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes. PLoS computational biology. 2010, 6 (6): 1000812-10.1371\/journal.pcbi.1000812.","journal-title":"PLoS computational biology"},{"issue":"1","key":"1224_CR30","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1016\/j.gene.2012.11.080","volume":"518","author":"Y Tohsato","year":"2013","unstructured":"Tohsato Y, Ikuta K, Shionoya A, Mazaki Y, Ito M: Parameter optimization and sensitivity analysis for large kinetic models using a real-coded genetic algorithm. Gene. 2013, 518 (1): 84-90. 10.1016\/j.gene.2012.11.080.","journal-title":"Gene"},{"issue":"suppl 1","key":"1224_CR31","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1093\/nar\/gkh081","volume":"32","author":"I Schomburg","year":"2004","unstructured":"Schomburg I, Chang A, Ebeling C, Gremse M, Heldt AC, Huhn G: Schomburg D: BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Research. 2004, 32 (suppl 1): 431-433.","journal-title":"Nucleic Acids Research"},{"issue":"D1","key":"1224_CR32","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1093\/nar\/gkr1046","volume":"40","author":"U Wittig","year":"2011","unstructured":"Wittig U, Kania R, Golebiewski M, Rey M, Shi L, Jong L, Algaa E, Weidemann A, Sauer-Danzwith H, Mir S, Krebs O, Bittkowski M, Wetsch E, Rojas I, Muller W: SABIO-RK-database for biochemical reaction kinetics. Nucleic Acids Research. 2011, 40 (D1): 790-796.","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"1224_CR33","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1186\/1752-0509-4-92","volume":"4","author":"C Li","year":"2010","unstructured":"Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Nov\u00e8re NL, Laibe C: BioModels database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology. 2010, 4 (1): 92-10.1186\/1752-0509-4-92.","journal-title":"BMC Systems Biology"},{"issue":"15","key":"1224_CR34","doi-asserted-by":"publisher","first-page":"1895","DOI":"10.1093\/bioinformatics\/btl271","volume":"22","author":"JV Rodr\u00edguez","year":"2006","unstructured":"Rodr\u00edguez JV, Kaandorp JA, Dobrzy\u00f1ski M, Blom JG: Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (pts) pathway in escherichia coli. Bioinformatics. 2006, 22 (15): 1895-1901. 10.1093\/bioinformatics\/btl271.","journal-title":"Bioinformatics"},{"issue":"1","key":"1224_CR35","doi-asserted-by":"crossref","first-page":"5","DOI":"10.3233\/ISB-2010-0415","volume":"10","author":"M Nagasaki","year":"2010","unstructured":"Nagasaki M, Saito A, Jeong E, Li C, Kojima K, Ikeda E, Miyano S: Cell illustrator 4.0: A computational platform for systems biology. In Silico Biology. 2010, 10 (1): 5-26.","journal-title":"In Silico Biology"},{"key":"1224_CR36","unstructured":"Additional Files of this Paper, [http:\/\/genome.ib.sci.yamaguchi-u.ac.jp\/etchp\/GIW2013\/]"},{"key":"1224_CR37","unstructured":"Wikipedia: Pearson Product-moment Correlation Coefficient. [http:\/\/en.wikipedia.org\/wiki\/Pearson_product-moment_correlation_coefficient]"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-7-S6-S1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T02:21:29Z","timestamp":1630549289000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-7-S6-S1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,12]]},"references-count":37,"journal-issue":{"issue":"S6","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["1224"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-7-s6-s1","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,12]]},"assertion":[{"value":"13 December 2013","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S1"}}