{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T06:09:00Z","timestamp":1778220540866,"version":"3.51.4"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2011,5,4]],"date-time":"2011-05-04T00:00:00Z","timestamp":1304467200000},"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":[[2011,12]]},"DOI":"10.1186\/1471-2105-12-132","type":"journal-article","created":{"date-parts":[[2011,5,4]],"date-time":"2011-05-04T18:25:13Z","timestamp":1304533513000},"source":"Crossref","is-referenced-by-count":40,"title":["Properties of metabolic graphs: biological organization or representation artifacts?"],"prefix":"10.1186","volume":"12","author":[{"given":"Wanding","family":"Zhou","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luay","family":"Nakhleh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,5,4]]},"reference":[{"key":"4487_CR1","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/nrm1570","volume":"6","author":"J Papin","year":"2005","unstructured":"Papin J, Hunter T, Palsson B, Subramaniam S: Reconstruction of Cellular signalling networks and analysis of their properties. Nature Reviews Molecular Cell Biology 2005, 6: 99\u2013111. 10.1038\/nrm1570","journal-title":"Nature Reviews Molecular Cell Biology"},{"issue":"4","key":"4487_CR2","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1109\/TCBB.2008.79","volume":"5","author":"V Lacroix","year":"2008","unstructured":"Lacroix V, Cottret L, Th\u00e9bault P, Sagot M: An introduction to metabolic networks and their structural analysis. IEEE\/ACM Transactions on Computational Biology and Bioinformatics 2008, 5(4):594\u2013617.","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"key":"4487_CR3","doi-asserted-by":"publisher","first-page":"2685","DOI":"10.1073\/pnas.0406811102","volume":"102","author":"KR Patil","year":"2005","unstructured":"Patil KR, Nielsen J: Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Nat Acad Sci USA 2005, 102: 2685\u20132689. 10.1073\/pnas.0406811102","journal-title":"Proc Nat Acad Sci USA"},{"issue":"11","key":"4487_CR4","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1038\/81025","volume":"18","author":"DA Fell","year":"2000","unstructured":"Fell DA, Wagner A: The small world of metabolism. Nature Biotechnology 2000, 18(11):1121\u20131122. [PMID: 11062388] [PMID: 11062388] 10.1038\/81025","journal-title":"Nature Biotechnology"},{"issue":"1478","key":"4487_CR5","doi-asserted-by":"publisher","first-page":"1803","DOI":"10.1098\/rspb.2001.1711","volume":"268","author":"A Wagner","year":"2001","unstructured":"Wagner A, Fell DA: The small world inside large metabolic networks. Proceedings of the Royal Society of London. Series B: Biological Sciences 2001, 268(1478):1803\u20131810. 10.1098\/rspb.2001.1711","journal-title":"Proceedings of the Royal Society of London. Series B: Biological Sciences"},{"issue":"11","key":"4487_CR6","doi-asserted-by":"publisher","first-page":"1423","DOI":"10.1093\/bioinformatics\/btg177","volume":"19","author":"H Ma","year":"2003","unstructured":"Ma H, Zeng A: The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 2003, 19(11):1423\u20131430. 10.1093\/bioinformatics\/btg177","journal-title":"Bioinformatics"},{"key":"4487_CR7","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 Z, Barab\u00e1si A: The large-scale organization of metabolic networks. Nature 2000, 407: 651\u2013654. 10.1038\/35036627","journal-title":"Nature"},{"issue":"6","key":"4487_CR8","doi-asserted-by":"publisher","first-page":"1543","DOI":"10.1073\/pnas.0306458101","volume":"101","author":"M Arita","year":"2004","unstructured":"Arita M: The metabolic network of Escherichia coli is not small. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(6):1543\u20131547. 10.1073\/pnas.0306458101","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"5","key":"4487_CR9","doi-asserted-by":"publisher","first-page":"e1000385","DOI":"10.1371\/journal.pcbi.1000385","volume":"5","author":"S Klamt","year":"2009","unstructured":"Klamt S, Haus UU, Theis F: Hypergraphs and Cellular Networks. PLoS Comput Biol 2009, 5(5):e1000385. 10.1371\/journal.pcbi.1000385","journal-title":"PLoS Comput Biol"},{"key":"4487_CR10","unstructured":"Berge C:Graphs and hypergraphs. English, (Amsterdam, New York): North-Holland Pub. Co., American Elsevier Pub. Co., xiv, 528 p. edition 1976. [ http:\/\/openlibrary.org\/b\/OL14545454M\/Graphs-and-hypergraphs ]"},{"key":"4487_CR11","volume-title":"Hypergraphs","author":"C Berge","year":"1989","unstructured":"Berge C: Hypergraphs. Elsevier; 1989."},{"issue":"40","key":"4487_CR12","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1098\/rsif.2008.0489","volume":"6","author":"P Holme","year":"2009","unstructured":"Holme P: Model validation of simple-graph representations of metabolism. Journal of The Royal Society Interface 2009, 6(40):1027\u20131034. 10.1098\/rsif.2008.0489","journal-title":"Journal of The Royal Society Interface"},{"key":"4487_CR13","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1186\/1471-2105-7-67","volume":"7","author":"CV Forst","year":"2006","unstructured":"Forst CV, Flamm C, Hofacker IL, Stadler PF: Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinformatics 2006, 7: 67. 10.1186\/1471-2105-7-67","journal-title":"BMC Bioinformatics"},{"issue":"14","key":"4487_CR14","doi-asserted-by":"publisher","first-page":"1831","DOI":"10.1093\/bioinformatics\/btp269","volume":"25","author":"A Mithani","year":"2009","unstructured":"Mithani A, Preston GM, Hein J: Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison. Bioinformatics 2009, 25(14):1831\u20131832. 10.1093\/bioinformatics\/btp269","journal-title":"Bioinformatics"},{"issue":"3","key":"4487_CR15","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1089\/cmb.2007.0229","volume":"15","author":"U Haus","year":"2008","unstructured":"Haus U, Klamt S, Stephen T: Computing knock-out strategies in metabolic networks. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology 2008, 15(3):259\u2013268. [ http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/18331197 ]","journal-title":"Journal of Computational Biology: A Journal of Computational Molecular Cell Biology"},{"issue":"4","key":"4487_CR16","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1007\/s00239-005-0027-1","volume":"61","author":"T Handorf","year":"2005","unstructured":"Handorf T, Ebenh\u00f6h O, Heinrich R: Expanding Metabolic Networks: Scopes of Compounds, Robustness, and Evolution. Journal of Molecular Evolution 2005, 61(4):498\u2013512. 10.1007\/s00239-005-0027-1","journal-title":"Journal of Molecular Evolution"},{"issue":"3","key":"4487_CR17","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1142\/S0219720009004163","volume":"7","author":"F Ay","year":"2009","unstructured":"Ay F, Kahveci T, DE Cr\u00e9cy-Lagard V: A fast and accurate algorithm for comparative analysis of metabolic pathways. Journal of bioinformatics and computational biology 2009, 7(3):389. 10.1142\/S0219720009004163","journal-title":"Journal of bioinformatics and computational biology"},{"issue":"10","key":"4487_CR18","doi-asserted-by":"crossref","first-page":"3724","DOI":"10.1128\/AEM.60.10.3724-3731.1994","volume":"60","author":"A Varma","year":"1994","unstructured":"Varma A, Palsson BO: Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 1994, 60(10):3724\u20133731.","journal-title":"Appl Environ Microbiol"},{"issue":"3","key":"4487_CR19","first-page":"323","volume":"3","author":"I Zevedei-Oancea","year":"2003","unstructured":"Zevedei-Oancea I, Schuster S: Topological analysis of metabolic networks based on Petri net theory. In silico biology 2003, 3(3):323\u2013345.","journal-title":"In silico biology"},{"issue":"5","key":"4487_CR20","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1038\/nbt1304","volume":"25","author":"Z Hu","year":"2007","unstructured":"Hu Z, Mellor J, Wu J, Kanehisa M, Stuart J, DeLisi C: Towards zoomable multidimensional maps of the cell. Nature Biotechnology 2007, 25(5):547\u2013554. 10.1038\/nbt1304","journal-title":"Nature Biotechnology"},{"key":"4487_CR21","first-page":"45","volume":"1984","author":"F Bertault","year":"2001","unstructured":"Bertault F, Eades P: Drawing Hypergraphs in the Subset Standard (Short demo Paper). Graph Drawing 2001, 1984: 45\u201376. [ http:\/\/www.springerlink.com\/content\/jmrt8cnw847n0b72\/ ]","journal-title":"Graph Drawing"},{"issue":"2-3","key":"4487_CR22","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1016\/0166-218X(93)90045-P","volume":"42","author":"G Gallo","year":"1993","unstructured":"Gallo G, Longo G, Pallottino S, Nguyen S: Directed hypergraphs and applications. Discrete Appl Math 1993, 42(2\u20133):177\u2013201. 10.1016\/0166-218X(93)90045-P","journal-title":"Discrete Appl Math"},{"key":"4487_CR23","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1186\/1471-2105-5-207","volume":"5","author":"J Nacher","year":"2004","unstructured":"Nacher J, Ueda N, Yamada T, Kanehisa M, Akutsu T: Clustering under the line graph transformation: application to reaction network. BMC Bioinformatics 2004, 5: 207. 10.1186\/1471-2105-5-207","journal-title":"BMC Bioinformatics"},{"key":"4487_CR24","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1016\/j.physa.2005.12.002","volume":"364","author":"E Estrada","year":"2006","unstructured":"Estrada E, Rodr\u00edguez-Vel\u00e1zquez JA: Subgraph centrality and clustering in complex hyper-networks. Physica A: Statistical Mechanics and its Applications 2006, 364: 581\u2013594.","journal-title":"Physica A: Statistical Mechanics and its Applications"},{"key":"4487_CR25","first-page":"290","volume":"Debrecen 6","author":"P Erd\u00f6s","year":"1959","unstructured":"Erd\u00f6s P, R\u00e9nyi A: On random graphs. Publ Math 1959, Debrecen 6: 290\u2013297.","journal-title":"Publ Math"},{"issue":"5439","key":"4487_CR26","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1126\/science.286.5439.509","volume":"286","author":"A Barabasi","year":"1999","unstructured":"Barabasi A, Albert R: Emergence of Scaling in Random Networks. Science 1999, 286(5439):509\u2013512. 10.1126\/science.286.5439.509","journal-title":"Science"},{"issue":"10","key":"4487_CR27","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1038\/nrg2192","volume":"8","author":"M Lynch","year":"2007","unstructured":"Lynch M: The evolution of genetic networks by non-adaptive processes. Nature Reviews Genetics 2007, 8(10):803\u2013813.","journal-title":"Nature Reviews Genetics"},{"issue":"12","key":"4487_CR28","doi-asserted-by":"publisher","first-page":"965","DOI":"10.1038\/nrg2473","volume":"9","author":"A Wagner","year":"2008","unstructured":"Wagner A: Neutralism and selectionism: a network-based reconciliation. Nature Reviews Genetics 2008, 9(12):965\u2013974.","journal-title":"Nature Reviews Genetics"},{"issue":"5586","key":"4487_CR29","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, Barab\u00e0si A: Hierarchical Organization of Modularity in Metabolic Networks. Science 2002, 297(5586):1551\u20131555. 10.1126\/science.1073374","journal-title":"Science"},{"key":"4487_CR30","first-page":"34","volume-title":"International workshop on bioinformatics and systems biology","author":"JC Nacher","year":"2004","unstructured":"Nacher JC, Ueda N, Yamada T, Kanehisa M, Akutsu T: Study on the clustering coefficients in metabolic network using a hierarchical framework. International workshop on bioinformatics and systems biology 2004, 34\u201335. [ http:\/\/www.jsbi.org\/pdfs\/journal1\/IBSB04\/IBSB04P010.pdf ]"},{"key":"4487_CR31","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucl Acids Res 2000, 28: 27\u201330. 10.1093\/nar\/28.1.27","journal-title":"Nucl Acids Res"},{"issue":"6684","key":"4487_CR32","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1038\/30918","volume":"393","author":"DJ Watts","year":"1998","unstructured":"Watts DJ, Strogatz SH: Collective dynamics of 'small-world' networks. Nature 1998, 393(6684):440\u2013442. 10.1038\/30918","journal-title":"Nature"},{"issue":"3","key":"4487_CR33","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1007\/s100510050067","volume":"13","author":"A Barrat","year":"2000","unstructured":"Barrat A, Weigt M: On the properties of small-world network models. The European Physical Journal B - Condensed Matter and Complex Systems 2000, 13(3):547\u2013560. [ http:\/\/www.springerlink.com\/content\/h34804169l475201 ]","journal-title":"The European Physical Journal B - Condensed Matter and Complex Systems"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-132.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-12-132\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-132.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,18]],"date-time":"2020-06-18T21:35:50Z","timestamp":1592516150000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-132"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,5,4]]},"references-count":33,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4487"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-132","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,5,4]]},"article-number":"132"}}