{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T15:56:44Z","timestamp":1687795004887},"reference-count":29,"publisher":"Springer Science and Business Media LLC","issue":"S3","license":[{"start":{"date-parts":[[2012,3,21]],"date-time":"2012-03-21T00:00:00Z","timestamp":1332288000000},"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":[[2012,12]]},"DOI":"10.1186\/1471-2105-13-s3-s2","type":"journal-article","created":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T09:44:41Z","timestamp":1548150281000},"source":"Crossref","is-referenced-by-count":8,"title":["Metabolic network alignment in large scale by network compression"],"prefix":"10.1186","volume":"13","author":[{"given":"Ferhat","family":"Ay","sequence":"first","affiliation":[]},{"given":"Michael","family":"Dang","sequence":"additional","affiliation":[]},{"given":"Tamer","family":"Kahveci","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,3,21]]},"reference":[{"issue":"2","key":"5080_CR1","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1089\/cmb.2008.11TT","volume":"16","author":"S Navlakha","year":"2009","unstructured":"Navlakha S, Schatz M, Kingsford C: Revealing biological modules via graph summarization. J Comput Biol. 2009, 16 (2): 253-264. 10.1089\/cmb.2008.11TT.","journal-title":"J Comput Biol"},{"key":"5080_CR2","first-page":"557","volume":"6","author":"E Segal","year":"2005","unstructured":"Segal E, Pe'er D, Regev A, Koller D, Friedman N: Learning module networks. Journal of Machine Learning Research. 2005, 6: 557-88.","journal-title":"Journal of Machine Learning Research"},{"key":"5080_CR3","first-page":"136","volume-title":"IEEE International Conference on Bioinformatics and Bioengineering (BIBE)","author":"F Ay","year":"2010","unstructured":"Ay F, Dinh T, Thai M, Kahveci T: Dynamic modular structure of regulatory networks. IEEE International Conference on Bioinformatics and Bioengineering (BIBE). 2010, 136-143."},{"issue":"13","key":"5080_CR4","doi-asserted-by":"publisher","first-page":"i149","DOI":"10.1093\/bioinformatics\/btm194","volume":"23","author":"J Dutkowski","year":"2007","unstructured":"Dutkowski J, Tiuryn J: Identification of functional modules from conserved ancestral protein protein interactions. Bioinformatics. 2007, 23 (13): i149-i158. 10.1093\/bioinformatics\/btm194.","journal-title":"Bioinformatics"},{"key":"5080_CR5","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1042\/bj3430115","volume":"343 Pt 1","author":"T Dandekar","year":"1999","unstructured":"Dandekar T, Schuster S, Snel B, Huynen M, Bork P: Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem J. 1999, 343 Pt 1: 115-124. 10.1042\/0264-6021:3430115.","journal-title":"Biochem J"},{"key":"5080_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-3-540-71681-5_1","volume-title":"International Conference on Research in Computational Molecular Biology (RECOMB)","author":"B Dost","year":"2007","unstructured":"Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R: QNet: a tool for querying protein interaction networks. International Conference on Research in Computational Molecular Biology (RECOMB). 2007, 1-15."},{"key":"5080_CR7","doi-asserted-by":"publisher","first-page":"1390","DOI":"10.1093\/bioinformatics\/btr127","volume":"27","author":"O Kuchaiev","year":"2011","unstructured":"Kuchaiev O, Przulj N: Integrative network alignment reveals large regions of global network similarity in yeast and human. Bioinformatics. 2011, 27: 1390-1396. 10.1093\/bioinformatics\/btr127.","journal-title":"Bioinformatics"},{"issue":"3","key":"5080_CR8","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. J Bioinform Comput Biol. 2009, 7 (3): 389-428. 10.1142\/S0219720009004163.","journal-title":"J Bioinform Comput Biol"},{"key":"5080_CR9","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1007\/978-3-642-12683-3_2","volume":"LNCS-6044","author":"F Ay","year":"2010","unstructured":"Ay F, Kahveci T: SubMAP: aligning metabolic pathways with subnetwork mappings. International Conference on Research in Computational Molecular Biology (RECOMB). 2010, LNCS-6044: 15-30.","journal-title":"International Conference on Research in Computational Molecular Biology (RECOMB)"},{"issue":"3","key":"5080_CR10","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1089\/cmb.2010.0280","volume":"18","author":"F Ay","year":"2011","unstructured":"Ay F, Kellis M, Kahveci T: SubMAP: aligning metabolic pathways with subnetwork mappings. J Comput Biol. 2011, 18 (3): 219-235. 10.1089\/cmb.2010.0280.","journal-title":"J Comput Biol"},{"issue":"12","key":"5080_CR11","doi-asserted-by":"publisher","first-page":"i253","DOI":"10.1093\/bioinformatics\/btp203","volume":"25","author":"CS Liao","year":"2009","unstructured":"Liao CS, Lu K, Baym M, Singh R, Berger B: IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics. 2009, 25 (12): i253-i258. 10.1093\/bioinformatics\/btp203.","journal-title":"Bioinformatics"},{"key":"5080_CR12","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1007\/11415770_4","volume-title":"International Conference on Research in Computational Molecular Biology (RECOMB)","author":"M Koyuturk","year":"2005","unstructured":"Koyuturk M, Grama A, Szpankowski W: Pairwise local alignment of protein interaction networks guided by models of evolution. International Conference on Research in Computational Molecular Biology (RECOMB). 2005, 48-65."},{"issue":"15","key":"5080_CR13","doi-asserted-by":"publisher","first-page":"1989","DOI":"10.1093\/bioinformatics\/btp287","volume":"25","author":"Q Cheng","year":"2009","unstructured":"Cheng Q, Harrison R, Zelikovsky A: MetNetAligner: a web service tool for metabolic network alignments. Bioinformatics. 2009, 25 (15): 1989-90. 10.1093\/bioinformatics\/btp287.","journal-title":"Bioinformatics"},{"key":"5080_CR14","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1089\/cmb.2009.0136","volume":"16","author":"M Kalaev","year":"2009","unstructured":"Kalaev M, Bafna V, Sharan R: Fast and accurate alignment of multiple protein networks. J Comput Biol. 2009, 16: 989-99. 10.1089\/cmb.2009.0136.","journal-title":"J Comput Biol"},{"issue":"4","key":"5080_CR15","doi-asserted-by":"publisher","first-page":"241","DOI":"10.2165\/00822942-200403040-00006","volume":"3","author":"M Chen","year":"2004","unstructured":"Chen M, Hofestadt R: PathAligner: metabolic pathway retrieval and alignment. Appl Bioinformatics. 2004, 3 (4): 241-252. 10.2165\/00822942-200403040-00006.","journal-title":"Appl Bioinformatics"},{"issue":"13","key":"5080_CR16","doi-asserted-by":"publisher","first-page":"1631","DOI":"10.1093\/bioinformatics\/btm156","volume":"23","author":"Z Li","year":"2007","unstructured":"Li Z, Zhang S, Wang Y, Zhang XS, Chen L: Alignment of molecular networks by integer quadratic programming. Bioinformatics. 2007, 23 (13): 1631-1639. 10.1093\/bioinformatics\/btm156.","journal-title":"Bioinformatics"},{"key":"5080_CR17","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1186\/1752-0509-2-111","volume":"2","author":"Y Li","year":"2008","unstructured":"Li Y, de Ridder D, de Groot MJL, Reinders MJT: Metabolic pathway alignment between species using a comprehensive and flexible similarity measure. BMC Syst Biol. 2008, 2: 111-10.1186\/1752-0509-2-111.","journal-title":"BMC Syst Biol"},{"key":"5080_CR18","doi-asserted-by":"publisher","first-page":"1341","DOI":"10.1098\/rsif.2010.0063","volume":"7","author":"O Kuchaiev","year":"2010","unstructured":"Kuchaiev O, Milenkovic T, Memisevic V, Hayes W, Przulj N: Topological network alignment uncovers biological function and phylogeny. J R Soc Interface. 2010, 7: 1341-1354. 10.1098\/rsif.2010.0063.","journal-title":"J R Soc Interface"},{"issue":"6","key":"5080_CR19","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1089\/cmb.2007.R018","volume":"14","author":"B Chor","year":"2007","unstructured":"Chor B, Tuller T: Biological networks: comparison, conservation, and evolution via relative description length. J Comput Biol. 2007, 14 (6): 817-838. 10.1089\/cmb.2007.R018.","journal-title":"J Comput Biol"},{"issue":"16","key":"5080_CR20","doi-asserted-by":"publisher","first-page":"3401","DOI":"10.1093\/bioinformatics\/bti554","volume":"21","author":"RY Pinter","year":"2005","unstructured":"Pinter RY, Rokhlenko O, Yeger-Lotem E, Ziv-Ukelson M: Alignment of metabolic pathways. Bioinformatics. 2005, 21 (16): 3401-3408. 10.1093\/bioinformatics\/bti554.","journal-title":"Bioinformatics"},{"key":"5080_CR21","doi-asserted-by":"publisher","first-page":"12763","DOI":"10.1073\/pnas.0806627105","volume":"105","author":"R Singh","year":"2008","unstructured":"Singh R, Xu J, Berger B: Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc Natl Acad Sci USA. 2008, 105: 12763-12768. 10.1073\/pnas.0806627105.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"11","key":"5080_CR22","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1016\/j.tim.2005.09.001","volume":"13","author":"C Francke","year":"2005","unstructured":"Francke C, Siezen RJ, Teusink B: Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol. 2005, 13 (11): 550-558. 10.1016\/j.tim.2005.09.001.","journal-title":"Trends Microbiol"},{"key":"5080_CR23","first-page":"88","volume":"12","author":"P Sridhar","year":"2007","unstructured":"Sridhar P, Kahveci T, Ranka S: An iterative algorithm for metabolic network-based drug target identification. Pac Symp Biocomput. 2007, 12: 88-99.","journal-title":"Pac Symp Biocomput"},{"key":"5080_CR24","doi-asserted-by":"publisher","first-page":"4021","DOI":"10.1093\/nar\/28.20.4021","volume":"28","author":"H Ogata","year":"2000","unstructured":"Ogata H, Fujibuchi W, Goto S, Kanehisa M: A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res. 2000, 28: 4021-4028. 10.1093\/nar\/28.20.4021.","journal-title":"Nucleic Acids Res"},{"key":"5080_CR25","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1186\/1471-2105-5-76","volume":"5","author":"ML Green","year":"2004","unstructured":"Green ML, Karp PD: A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics. 2004, 5: 76-10.1186\/1471-2105-5-76.","journal-title":"BMC Bioinformatics"},{"key":"5080_CR26","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1093\/nar\/27.1.29","volume":"27","author":"H Ogata","year":"1999","unstructured":"Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999, 27: 29-34. 10.1093\/nar\/27.1.29.","journal-title":"Nucleic Acids Res"},{"issue":"6804","key":"5080_CR27","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, Barabasi AL: The large-scale organization of metabolic networks. Nature. 2000, 407 (6804): 651-654. 10.1038\/35036627.","journal-title":"Nature"},{"issue":"7","key":"5080_CR28","doi-asserted-by":"publisher","first-page":"e228","DOI":"10.1371\/journal.pbio.0030228","volume":"3","author":"T Pfeiffer","year":"2005","unstructured":"Pfeiffer T, Soyer OS, Bonhoeffer S: The evolution of connectivity in metabolic networks. PLoS Biol. 2005, 3 (7): e228-10.1371\/journal.pbio.0030228.","journal-title":"PLoS Biol"},{"issue":"5586","key":"5080_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, Barabasi AL: Hierarchical organization of modularity in metabolic networks. Science. 2002, 297 (5586): 1551-1555. 10.1126\/science.1073374.","journal-title":"Science"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S3-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-13-S3-S2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S3-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T09:47:46Z","timestamp":1548150466000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-S3-S2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,3,21]]},"references-count":29,"journal-issue":{"issue":"S3","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["5080"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-s3-s2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,3,21]]},"article-number":"S2"}}