{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T05:26:57Z","timestamp":1740115617418,"version":"3.37.3"},"publisher-location":"Berlin, Heidelberg","reference-count":30,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642126826"},{"type":"electronic","value":"9783642126833"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010]]},"DOI":"10.1007\/978-3-642-12683-3_2","type":"book-chapter","created":{"date-parts":[[2010,5,4]],"date-time":"2010-05-04T23:00:43Z","timestamp":1273014043000},"page":"15-30","source":"Crossref","is-referenced-by-count":7,"title":["SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings"],"prefix":"10.1007","author":[{"given":"Ferhat","family":"Ay","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tamer","family":"Kahveci","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"2_CR1","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1021\/bp0000712","volume":"16","author":"J.S. Edwards","year":"2000","unstructured":"Edwards, J.S., Palsson, B.O.: Robustness analysis of the Escherichia coli metabolic network. Biotechnology Progress\u00a016, 927\u2013939 (2000)","journal-title":"Biotechnology Progress"},{"key":"2_CR2","doi-asserted-by":"crossref","unstructured":"Ay, F., Xu, F., Kahveci, T.: Scalable Steady State Analysis of Boolean Biological Regulatory Networks. PLoS ONE\u00a04(12), e7992 (2009)","DOI":"10.1371\/journal.pone.0007992"},{"key":"2_CR3","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1093\/bioinformatics\/18.2.351","volume":"18","author":"S. Schuster","year":"2002","unstructured":"Schuster, S., Pfeiffer, T., Koch, I., Moldenhauer, F., Dandekar, T.: Exploring the Pathway Structure of Metabolism: Decomposition into Subnetworks and Application to Mycoplasma pneumoniae. Bioinformatics\u00a018, 351\u2013361 (2002)","journal-title":"Bioinformatics"},{"key":"2_CR4","doi-asserted-by":"crossref","unstructured":"Koyuturk, M., Grama, A., Szpankowski, W.: An efficient algorithm for detecting frequent subgraphs in biological networks. In: ISMB, pp. 200\u2013207 (2004)","DOI":"10.1093\/bioinformatics\/bth919"},{"key":"2_CR5","doi-asserted-by":"crossref","unstructured":"Qian, X., Yoon, B.: Effective Identification of Conserved Pathways in Biological Networks Using Hidden Markov Models. PLoS ONE\u00a04(12), e8070 (2009)","DOI":"10.1371\/journal.pone.0008070"},{"issue":"16","key":"2_CR6","doi-asserted-by":"publisher","first-page":"3401","DOI":"10.1093\/bioinformatics\/bti554","volume":"21","author":"R.Y. Pinter","year":"2005","unstructured":"Pinter, R.Y., Rokhlenko, O., Yeger-Lotem, E., Ziv-Ukelson, M.: Alignment of metabolic pathways. Bioinformatics\u00a021(16), 3401\u20133408 (2005)","journal-title":"Bioinformatics"},{"key":"2_CR7","doi-asserted-by":"crossref","unstructured":"Ay, F., Kahveci, T., de Crecy-Lagard, V.: Consistent alignment of metabolic pathways without abstraction. In: Computational Systems Bioinformatics Conference (CSB), vol.\u00a07, pp. 237\u2013248 (2008)","DOI":"10.1142\/9781848162648_0021"},{"issue":"3","key":"2_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 Crecy-Lagard, V.: A fast and accurate algorithm for comparative analysis of metabolic pathways. Journal of Bioinformatics and Computational Biology (JBCB)\u00a07(3), 389\u2013428 (2009)","journal-title":"Journal of Bioinformatics and Computational Biology (JBCB)"},{"key":"2_CR9","first-page":"191","volume":"3","author":"Y. Tohsato","year":"2008","unstructured":"Tohsato, Y., Nishimura, Y.: Metabolic Pathway Alignment Based on Similarity of Chemical Structures. Information and Media Technologies\u00a03, 191\u2013200 (2008)","journal-title":"Information and Media Technologies"},{"key":"2_CR10","unstructured":"Tohsato, Y., Matsuda, H., Hashimoto, A.: A Multiple Alignment Algorithm for Metabolic Pathway Analysis Using Enzyme Hierarchy. In: ISMB, pp. 376\u2013383 (2000)"},{"issue":"15","key":"2_CR11","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\u00a025(15), 1989\u20131990 (2009)","journal-title":"Bioinformatics"},{"key":"2_CR12","doi-asserted-by":"crossref","unstructured":"Sridhar, P., Kahveci, T., Ranka, S.: An iterative algorithm for metabolic network-based drug target identification. In: Pacific Symposium on Biocomputing (PSB), vol.\u00a012, pp. 88\u201399 (2007)","DOI":"10.1142\/9789812772435_0009"},{"issue":"3","key":"2_CR13","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1016\/j.jmb.2007.05.061","volume":"371","author":"N. Watanabe","year":"2007","unstructured":"Watanabe, N., Cherney, M.M., van Belkum, M.J., Marcus, S.L., Flegel, M.D., Clay, M.D., Deyholos, M.K., Vederas, J.C., James, M.: Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana: a recently discovered enzyme in the biosynthesis of L-lysine by plants and Chlamydia. Journal of Molecular Biology\u00a0371(3), 685\u2013702 (2007)","journal-title":"Journal of Molecular Biology"},{"issue":"11","key":"2_CR14","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, R.J., Teusink, B.: Reconstructing the metabolic network of a bacterium from its genome. Trends in Microbiology\u00a013(11), 550\u2013558 (2005)","journal-title":"Trends in Microbiology"},{"issue":"2","key":"2_CR15","first-page":"45","volume":"16","author":"J.C. Clemente","year":"2005","unstructured":"Clemente, J.C., Satou, K., Valiente, G.: Reconstruction of Phylogenetic Relationships from Metabolic Pathways Based on the Enzyme Hierarchy and the Gene Ontology. Genome Informatics\u00a016(2), 45\u201355 (2005)","journal-title":"Genome Informatics"},{"key":"2_CR16","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1093\/bioinformatics\/btg1018","volume":"19","author":"M. Heymans","year":"2003","unstructured":"Heymans, M., Singh, A.: Deriving phylogenetic trees from the similarity analysis of metabolic pathways. Bioinformatics\u00a019, 138\u2013146 (2003)","journal-title":"Bioinformatics"},{"key":"2_CR17","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 Research\u00a028, 4021\u20134028 (2000)","journal-title":"Nucleic Acids Research"},{"key":"2_CR18","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1186\/1471-2105-5-76","volume":"5","author":"M.L. Green","year":"2004","unstructured":"Green, M.L., Karp, P.: A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics\u00a05, 76 (2004)","journal-title":"BMC Bioinformatics"},{"key":"2_CR19","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1007\/3-540-53832-1_32","volume-title":"Graph-Theoretic Concepts in Computer Science","author":"P. Damaschke","year":"1991","unstructured":"Damaschke, P.: Graph-Theoretic Concepts in Computer Science. In: M\u00f6hring, R.H. (ed.) WG 1990. LNCS, vol.\u00a0484, pp. 72\u201378. Springer, Heidelberg (1991)"},{"key":"2_CR20","volume-title":"Enzyme nomenclature 1992","author":"E.C. Webb","year":"1992","unstructured":"Webb, E.C.: Enzyme nomenclature 1992 . Academic Press, London (1992)"},{"key":"2_CR21","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1007\/978-3-540-71681-5_2","volume-title":"Research in Computational Molecular Biology","author":"R. Singh","year":"2007","unstructured":"Singh, R., Xu, J., Berger, B.: Pairwise global alignment of protein interaction networks by matching neighborhood topology. In: Speed, T., Huang, H. (eds.) RECOMB 2007. LNCS (LNBI), vol.\u00a04453, pp. 16\u201331. Springer, Heidelberg (2007)"},{"key":"2_CR22","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1186\/1752-0509-2-50","volume":"2","author":"D. Deutscher","year":"2008","unstructured":"Deutscher, D., Meilijson, I., Schuster, S., Ruppin, E.: Can single knockouts accurately single out gene functions? BMC Systems Biology\u00a02, 50 (2008)","journal-title":"BMC Systems Biology"},{"issue":"47","key":"2_CR23","doi-asserted-by":"publisher","first-page":"17909","DOI":"10.1073\/pnas.0608643103","volume":"103","author":"A.J. McCoy","year":"2006","unstructured":"McCoy, A.J., Adams, N.E., Hudson, A.O., Gilvarg, C., Leustek, T., Maurelli, A.T.: L,L-diaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate\/lysine. PNAS\u00a0103(47), 17909\u201317914 (2006)","journal-title":"PNAS"},{"issue":"1","key":"2_CR24","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 Research\u00a027(1), 29\u201334 (1999)","journal-title":"Nucleic Acids Research"},{"issue":"39","key":"2_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. Journal of the American Chemical Society (JACS)\u00a0125(39), 11853\u201311865 (2003)","journal-title":"Journal of the American Chemical Society (JACS)"},{"key":"2_CR26","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/0012-365X(92)00057-X","volume":"124","author":"L. LovGasz","year":"1994","unstructured":"LovGasz, L.: Stable set and polynomials. Discrete Mathematics\u00a0124, 137\u2013153 (1994)","journal-title":"Discrete Mathematics"},{"key":"2_CR27","doi-asserted-by":"crossref","unstructured":"Austrin, P., Khot, S., Safra, M.: Inapproximability of Vertex Cover and Independent Set in Bounded Degree Graphs. In: IEEE Conference on Computational Complexity, pp. 74\u201380 (2009)","DOI":"10.1109\/CCC.2009.38"},{"key":"2_CR28","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1016\/S0166-218X(02)00205-6","volume":"126","author":"S. Sakai","year":"2003","unstructured":"Sakai, S., Togasaki, M., Yamazaki, K.: A note on greedy algorithms for the maximum weighted independent set problem. Discrete Applied Mathematics\u00a0126, 313\u2013322 (2003)","journal-title":"Discrete Applied Mathematics"},{"key":"2_CR29","doi-asserted-by":"crossref","first-page":"3435","DOI":"10.1016\/S0021-9258(18)96483-5","volume":"241","author":"P.P. Saunders","year":"1966","unstructured":"Saunders, P.P., Broquist, H.: Saccharopine, an intermediate of aminoadipic acid pathway of lysine biosynthesis. Journal of Biological Chemistry\u00a0241, 3435\u20133440 (1966)","journal-title":"Journal of Biological Chemistry"},{"issue":"6804","key":"2_CR30","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.N., Barabasi, A.: The large-scale organization of metabolic networks. Nature\u00a0407(6804), 651\u2013654 (2000)","journal-title":"Nature"}],"container-title":["Lecture Notes in Computer Science","Research in Computational Molecular Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-12683-3_2.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,20]],"date-time":"2025-02-20T14:54:42Z","timestamp":1740063282000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-12683-3_2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010]]},"ISBN":["9783642126826","9783642126833"],"references-count":30,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-12683-3_2","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2010]]}}}