{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,19]],"date-time":"2025-03-19T11:48:18Z","timestamp":1742384898170},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: A metabolic graph represents the connectivity patterns of a metabolic system, and provides a powerful framework within which the organization of metabolic reactions can be analyzed and elucidated. A common practice is to prune (i.e. remove nodes and edges) the metabolic graph prior to any analysis in order to eliminate confounding signals from the representation. Currently, this pruning process is carried out in an ad hoc fashion, resulting in discrepancies and ambiguities across studies.<\/jats:p>\n               <jats:p>Results: We propose a biochemically informative criterion, the strength of chemical linkage (SCL), for a systematic pruning of metabolic graphs. By analyzing the metabolic graph of Escherichia coli, we show that thresholding SCL is powerful in selecting the conventional pathways' connectivity out of the raw network connectivity when the network is restricted to the reactions collected from these pathways. Further, we argue that the root of ambiguity in pruning metabolic graphs is in the continuity of the amount of chemical content that can be conserved in reaction transformation patterns. Finally, we demonstrate how biochemical pathways can be inferred efficiently if the search procedure is guided by SCL.<\/jats:p>\n               <jats:p>Contact: \u00a0wz4@rice.edu; nakhleh@rice.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr271","type":"journal-article","created":{"date-parts":[[2011,5,7]],"date-time":"2011-05-07T00:34:56Z","timestamp":1304728496000},"page":"1957-1963","source":"Crossref","is-referenced-by-count":4,"title":["The strength of chemical linkage as a criterion for pruning metabolic graphs"],"prefix":"10.1093","volume":"27","author":[{"given":"Wanding","family":"Zhou","sequence":"first","affiliation":[]},{"given":"Luay","family":"Nakhleh","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2011,5,5]]},"reference":[{"key":"2023012712452958500_B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/jb\/mvi094","article-title":"Scale-freeness and biological networks","volume":"138","author":"Arita","year":"2005","journal-title":"J. Biochem."},{"key":"2023012712452958500_B2","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1089\/cmb.2008.0044","article-title":"Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks","volume":"15","author":"Blum","year":"2008","journal-title":"J. Comput. Biol."},{"key":"2023012712452958500_B3","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.1021\/ci100061d","article-title":"An open-source java platform for automated reaction mapping","volume":"50","author":"Crabtree","year":"2010","journal-title":"J. Chem. Inform. Model."},{"key":"2023012712452958500_B4","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1016\/j.jmb.2005.09.079","article-title":"Inferring meaningful pathways in weighted metabolic networks","volume":"356","author":"Croes","year":"2006","journal-title":"J. Mol. Biol."},{"key":"2023012712452958500_B5","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1093\/bib\/4.3.246","article-title":"An overview of data models for the analysis of biochemical pathways","volume":"4","author":"Deville","year":"2003","journal-title":"Brief. Bioinform."},{"key":"2023012712452958500_B6","doi-asserted-by":"crossref","first-page":"R26","DOI":"10.1186\/gb-2007-8-2-r26","article-title":"A network perspective on the evolution of metabolism by gene duplication","volume":"8","author":"Diaz-Mejia","year":"2007","journal-title":"Genome Biol."},{"key":"2023012712452958500_B7","first-page":"35","article-title":"Structural analysis of expanding metabolic networks","volume":"15","author":"Ebenhh","year":"2004","journal-title":"Genome Inform."},{"key":"2023012712452958500_B8","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1016\/j.jmb.2009.03.006","article-title":"Metabolic pathfinding using rpair annotation","volume":"388","author":"Faust","year":"2009","journal-title":"J. Mol. Biol."},{"key":"2023012712452958500_B9","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1038\/nbt1492","article-title":"A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology","volume":"26","author":"Herrgard","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"2023012712452958500_B10","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1098\/rsif.2008.0489","article-title":"Model validation of simple-graph representations of metabolism","volume":"6","author":"Holme","year":"2009","journal-title":"J. R. Soc. Inter."},{"key":"2023012712452958500_B11","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1038\/35036627","article-title":"The large-scale organization of metabolic networks","volume":"407","author":"Jeong","year":"2000","journal-title":"Nature"},{"key":"2023012712452958500_B12","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopaedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023012712452958500_B13","first-page":"P062","article-title":"RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions","volume":"15","author":"Kotera","year":"2004","journal-title":"Genome Inform."},{"key":"2023012712452958500_B14","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1186\/1471-2105-7-170","article-title":"Biowarehouse: a bioinformatics database warehouse toolkit","volume":"7","author":"Lee","year":"2006","journal-title":"BMC Bioinformatics"},{"issue":"Suppl. 1","key":"2023012712452958500_B15","doi-asserted-by":"crossref","first-page":"D443","DOI":"10.1093\/nar\/gkh139","article-title":"The aMAZE LightBench: a web interface to a relational database of cellular processes","volume":"32","author":"Lemer","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012712452958500_B16","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1093\/bioinformatics\/19.2.270","article-title":"Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms","volume":"19","author":"Ma","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012712452958500_B17","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1049\/ip-syb:20060012","article-title":"Challenges to be faced in the reconstruction of metabolic networks from public databases","volume":"153","author":"Poolman","year":"2006","journal-title":"IEEE Proc. Sys. Biol."},{"key":"2023012712452958500_B18","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1093\/bioinformatics\/bti116","article-title":"Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)","volume":"21","author":"Rahman","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012712452958500_B19","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1126\/science.1073374","article-title":"Hierarchical organization of modularity in metabolic networks","volume":"297","author":"Ravasz","year":"2002","journal-title":"Science"},{"key":"2023012712452958500_B20","doi-asserted-by":"crossref","first-page":"168101","DOI":"10.1103\/PhysRevLett.94.168101","article-title":"Scale-rich metabolic networks","volume":"94","author":"Tanaka","year":"2005","journal-title":"Phys. Rev. Lett."},{"key":"2023012712452958500_B21","first-page":"245","article-title":"Graph-based analysis of metabolic networks","volume":"38","author":"van Helden","year":"2002","journal-title":"Ernst Schering Res Found Workshop"},{"key":"2023012712452958500_B22","doi-asserted-by":"crossref","first-page":"1803","DOI":"10.1098\/rspb.2001.1711","article-title":"The small world inside large metabolic networks","volume":"268","author":"Wagner","year":"2001","journal-title":"Proc. R. Soc. Lond. Ser. B Biol. Sci."},{"key":"2023012712452958500_B23","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1186\/1471-2105-7-386","article-title":"Hierarchical modularity of nested bow-ties in metabolic networks","volume":"7","author":"Zhao","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023012712452958500_B24","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1186\/1471-2105-8-311","article-title":"Modular co-evolution of metabolic networks","volume":"8","author":"Zhao","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2023012712452958500_B25","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1186\/1471-2105-6-8","article-title":"Structural comparison of metabolic networks in selected single cell organisms","volume":"6","author":"Zhu","year":"2005","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/14\/1957\/48933142\/bioinformatics_27_14_1957.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/14\/1957\/48933142\/bioinformatics_27_14_1957.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:37:46Z","timestamp":1674826666000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/14\/1957\/193850"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,5,5]]},"references-count":25,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2011,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr271","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2011,7]]},"published":{"date-parts":[[2011,5,5]]}}}