{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T13:27:33Z","timestamp":1760707653680},"reference-count":63,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2006,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational strategies for identifying such missing genes rely primarily on sequence homology to known enzyme-encoding genes.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We present a novel method for identifying genes encoding for a specific metabolic function based on a local structure of metabolic network and multiple types of functional association evidence, including clustering of genes on the chromosome, similarity of phylogenetic profiles, gene expression, protein fusion events and others. Using <jats:italic>E. coli<\/jats:italic> and <jats:italic>S. cerevisiae<\/jats:italic> metabolic networks, we illustrate predictive ability of each individual type of association evidence and show that significantly better predictions can be obtained based on the combination of all data. In this way our method is able to predict 60% of enzyme-encoding genes of <jats:italic>E. coli<\/jats:italic> metabolism within the top 10 (out of 3551) candidates for their enzymatic function, and as a top candidate within 43% of the cases.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>We illustrate that a combination of genome context and other functional association evidence is effective in predicting genes encoding metabolic enzymes. Our approach does not rely on direct sequence homology to known enzyme-encoding genes, and can be used in conjunction with traditional homology-based metabolic reconstruction methods. The method can also be used to target orphan metabolic activities.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-7-177","type":"journal-article","created":{"date-parts":[[2006,4,6]],"date-time":"2006-04-06T12:52:02Z","timestamp":1144327922000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":78,"title":["Identifying metabolic enzymes with multiple types of association evidence"],"prefix":"10.1186","volume":"7","author":[{"given":"Peter","family":"Kharchenko","sequence":"first","affiliation":[]},{"given":"Lifeng","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Yoav","family":"Freund","sequence":"additional","affiliation":[]},{"given":"Dennis","family":"Vitkup","sequence":"additional","affiliation":[]},{"given":"George M","family":"Church","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,3,29]]},"reference":[{"issue":"6","key":"916_CR1","doi-asserted-by":"publisher","first-page":"820","DOI":"10.1101\/gr.3364705","volume":"15","author":"I Borodina","year":"2005","unstructured":"Borodina I, Krabben P, Nielsen J: Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res 2005, 15(6):820\u2013829. 10.1101\/gr.3364705","journal-title":"Genome Res"},{"issue":"9","key":"916_CR2","doi-asserted-by":"publisher","first-page":"R54","DOI":"10.1186\/gb-2003-4-9-r54","volume":"4","author":"JL Reed","year":"2003","unstructured":"Reed JL, Vo TD, Schilling CH, Palsson BO: An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM\/GPR). Genome Biol 2003, 4(9):R54. 10.1186\/gb-2003-4-9-r54","journal-title":"Genome Biol"},{"issue":"3","key":"916_CR3","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1016\/S0960-9822(02)00478-5","volume":"6","author":"RL Tatusov","year":"1996","unstructured":"Tatusov RL, Mushegian AR, Bork P, Brown NP, Hayes WS, Borodovsky M, Rudd KE, Koonin EV: Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr Biol 1996, 6(3):279\u2013291. 10.1016\/S0960-9822(02)00478-5","journal-title":"Curr Biol"},{"issue":"2","key":"916_CR4","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1016\/S1367-5931(03)00027-9","volume":"7","author":"A Osterman","year":"2003","unstructured":"Osterman A, Overbeek R: Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 2003, 7(2):238\u2013251. 10.1016\/S1367-5931(03)00027-9","journal-title":"Curr Opin Chem Biol"},{"issue":"5","key":"916_CR5","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1007\/s002030050780","volume":"172","author":"SJ Cordwell","year":"1999","unstructured":"Cordwell SJ: Microbial genomes and \"missing\" enzymes: redefining biochemical pathways. Arch Microbiol 1999, 172(5):269\u2013279. 10.1007\/s002030050780","journal-title":"Arch Microbiol"},{"issue":"1","key":"916_CR6","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(1):76. 10.1186\/1471-2105-5-76","journal-title":"BMC Bioinformatics"},{"issue":"28","key":"916_CR7","doi-asserted-by":"publisher","first-page":"25090","DOI":"10.1074\/jbc.M203208200","volume":"277","author":"AC Bishop","year":"2002","unstructured":"Bishop AC, Xu J, Johnson RC, Schimmel P, de Crecy-Lagard V: Identification of the tRNA-dihydrouridine synthase family. J Biol Chem 2002, 277(28):25090\u201325095. 10.1074\/jbc.M203208200","journal-title":"J Biol Chem"},{"issue":"40","key":"916_CR8","doi-asserted-by":"publisher","first-page":"37194","DOI":"10.1074\/jbc.M107232200","volume":"276","author":"TA Bobik","year":"2001","unstructured":"Bobik TA, Rasche ME: Identification of the human methylmalonyl-CoA racemase gene based on the analysis of prokaryotic gene arrangements. Implications for decoding the human genome. J Biol Chem 2001, 276(40):37194\u201337198. 10.1074\/jbc.M107232200","journal-title":"J Biol Chem"},{"issue":"7","key":"916_CR9","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1038\/nbt834","volume":"21","author":"E Morett","year":"2003","unstructured":"Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P: Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol 2003, 21(7):790\u2013795. 10.1038\/nbt834","journal-title":"Nat Biotechnol"},{"issue":"1","key":"916_CR10","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1093\/nar\/gkg034","volume":"31","author":"C von Mering","year":"2003","unstructured":"von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B: STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 2003, 31(1):258\u2013261. 10.1093\/nar\/gkg034","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"916_CR11","doi-asserted-by":"publisher","first-page":"R35","DOI":"10.1186\/gb-2004-5-5-r35","volume":"5","author":"PM Bowers","year":"2004","unstructured":"Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D: Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol 2004, 5(5):R35. 10.1186\/gb-2004-5-5-r35","journal-title":"Genome Biol"},{"issue":"14","key":"916_CR12","doi-asserted-by":"publisher","first-page":"8348","DOI":"10.1073\/pnas.0832373100","volume":"100","author":"OG Troyanskaya","year":"2003","unstructured":"Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D: A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A 2003, 100(14):8348\u20138353. 10.1073\/pnas.0832373100","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5644","key":"916_CR13","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1126\/science.1087361","volume":"302","author":"R Jansen","year":"2003","unstructured":"Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M: A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 2003, 302(5644):449\u2013453. 10.1126\/science.1087361","journal-title":"Science"},{"issue":"6","key":"916_CR14","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1101\/gr.2203804","volume":"14","author":"S Asthana","year":"2004","unstructured":"Asthana S, King OD, Gibbons FD, Roth FP: Predicting protein complex membership using probabilistic network reliability. Genome Res 2004, 14(6):1170\u20131175. 10.1101\/gr.2203804","journal-title":"Genome Res"},{"key":"916_CR15","doi-asserted-by":"publisher","first-page":"I363","DOI":"10.1093\/bioinformatics\/bth910","volume":"20 Suppl 1","author":"Y Yamanishi","year":"2004","unstructured":"Yamanishi Y, Vert JP, Kanehisa M: Protein network inference from multiple genomic data: a supervised approach. Bioinformatics 2004, 20 Suppl 1: I363-I370. 10.1093\/bioinformatics\/bth910","journal-title":"Bioinformatics"},{"issue":"44","key":"916_CR16","doi-asserted-by":"publisher","first-page":"15682","DOI":"10.1073\/pnas.0406614101","volume":"101","author":"SL Wong","year":"2004","unstructured":"Wong SL, Zhang LV, Tong AH, Li Z, Goldberg DS, King OD, Lesage G, Vidal M, Andrews B, Bussey H, Boone C, Roth FP: Combining biological networks to predict genetic interactions. Proc Natl Acad Sci U S A 2004, 101(44):15682\u201315687. 10.1073\/pnas.0406614101","journal-title":"Proc Natl Acad Sci U S A"},{"key":"916_CR17","doi-asserted-by":"publisher","first-page":"i468","DOI":"10.1093\/bioinformatics\/bti1012","volume":"21 Suppl 1","author":"Y Yamanishi","year":"2005","unstructured":"Yamanishi Y, Vert JP, Kanehisa M: Supervised enzyme network inference from the integration of genomic data and chemical information. Bioinformatics 2005, 21 Suppl 1: i468-i477. 10.1093\/bioinformatics\/bti1012","journal-title":"Bioinformatics"},{"issue":"26","key":"916_CR18","doi-asserted-by":"publisher","first-page":"15428","DOI":"10.1073\/pnas.2136809100","volume":"100","author":"C von Mering","year":"2003","unstructured":"von Mering C, Zdobnov EM, Tsoka S, Ciccarelli FD, Pereira-Leal JB, Ouzounis CA, Bork P: Genome evolution reveals biochemical networks and functional modules. Proc Natl Acad Sci U S A 2003, 100(26):15428\u201315433. 10.1073\/pnas.2136809100","journal-title":"Proc Natl Acad Sci U S A"},{"key":"916_CR19","doi-asserted-by":"publisher","first-page":"I178","DOI":"10.1093\/bioinformatics\/bth930","volume":"20 Suppl 1","author":"P Kharchenko","year":"2004","unstructured":"Kharchenko P, Vitkup D, Church GM: Filling gaps in a metabolic network using expression information. Bioinformatics 2004, 20 Suppl 1: I178-I185. 10.1093\/bioinformatics\/bth930","journal-title":"Bioinformatics"},{"key":"916_CR20","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1038\/msb4100023","volume":"1","author":"P Kharchenko","year":"2005","unstructured":"Kharchenko P, Church GM, Vitkup D: Expression dynamics of a cellular metabolic network. Molecular Systems Biology 2005, 1: 74\u201379. 10.1038\/msb4100023","journal-title":"Molecular Systems Biology"},{"key":"916_CR21","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1101\/gr.234503","volume":"13","author":"J Forster","year":"2003","unstructured":"Forster J, Famili I, Fu P, Palsson BO, Nielsen J: Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003, 13: 244\u2013253. 10.1101\/gr.234503","journal-title":"Genome Res"},{"issue":"8","key":"916_CR22","doi-asserted-by":"publisher","first-page":"4285","DOI":"10.1073\/pnas.96.8.4285","volume":"96","author":"M Pellegrini","year":"1999","unstructured":"Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO: Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A 1999, 96(8):4285\u20134288. 10.1073\/pnas.96.8.4285","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"11","key":"916_CR23","doi-asserted-by":"publisher","first-page":"5849","DOI":"10.1073\/pnas.95.11.5849","volume":"95","author":"MA Huynen","year":"1998","unstructured":"Huynen MA, Bork P: Measuring genome evolution. Proc Natl Acad Sci U S A 1998, 95(11):5849\u20135856. 10.1073\/pnas.95.11.5849","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"8","key":"916_CR24","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.1101\/gr.10.8.1204","volume":"10","author":"M Huynen","year":"2000","unstructured":"Huynen M, Snel B, Lathe W, Bork P: Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res 2000, 10(8):1204\u20131210. 10.1101\/gr.10.8.1204","journal-title":"Genome Res"},{"issue":"12","key":"916_CR25","doi-asserted-by":"publisher","first-page":"1524","DOI":"10.1093\/bioinformatics\/btg187","volume":"19","author":"J Wu","year":"2003","unstructured":"Wu J, Kasif S, DeLisi C: Identification of functional links between genes using phylogenetic profiles. Bioinformatics 2003, 19(12):1524\u20131530. 10.1093\/bioinformatics\/btg187","journal-title":"Bioinformatics"},{"issue":"3","key":"916_CR26","doi-asserted-by":"publisher","first-page":"938","DOI":"10.1214\/aoms\/1177700066","volume":"36","author":"WL Harkness","year":"1965","unstructured":"Harkness WL: Properties of the extended hypergeometric distribution. Annals of Mathematical Statistics 1965, 36(3):938\u2013945.","journal-title":"Annals of Mathematical Statistics"},{"issue":"1","key":"916_CR27","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1093\/nar\/29.1.22","volume":"29","author":"RL Tatusov","year":"2001","unstructured":"Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV: The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 2001, 29(1):22\u201328. 10.1093\/nar\/29.1.22","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"916_CR28","first-page":"93","volume":"15","author":"M Itoh","year":"2004","unstructured":"Itoh M, Akutsu T, Kanehisa M: Clustering of database sequences for fast homology search using upper bounds on alignment score. Genome Inform Ser Workshop Genome Inform 2004, 15(1):93\u2013104.","journal-title":"Genome Inform Ser Workshop Genome Inform"},{"issue":"3","key":"916_CR29","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403\u2013410. 10.1006\/jmbi.1990.9999","journal-title":"J Mol Biol"},{"issue":"2","key":"916_CR30","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1093\/jb\/mvi017","volume":"137","author":"N Maltsev","year":"2005","unstructured":"Maltsev N, Glass EM, Ovchinnikova G, Gu Z: Molecular Mechanisms Involved in Robustness of Yeast Central Metabolism against Null Mutations. J Biochem (Tokyo) 2005, 137(2):177\u2013187.","journal-title":"J Biochem (Tokyo)"},{"issue":"10","key":"916_CR31","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1016\/S0167-7799(02)02032-2","volume":"20","author":"SA Teichmann","year":"2002","unstructured":"Teichmann SA, Babu MM: Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends Biotechnol 2002, 20(10):407\u201310; discussion 410. 10.1016\/S0167-7799(02)02032-2","journal-title":"Trends Biotechnol"},{"issue":"5","key":"916_CR32","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1016\/S0168-9525(03)00056-8","volume":"19","author":"V van Noort","year":"2003","unstructured":"van Noort V, Snel B, Huynen MA: Predicting gene function by conserved co-expression. Trends Genet 2003, 19(5):238\u2013242. 10.1016\/S0168-9525(03)00056-8","journal-title":"Trends Genet"},{"issue":"16","key":"916_CR33","doi-asserted-by":"publisher","first-page":"4725","DOI":"10.1093\/nar\/gkh815","volume":"32","author":"B Snel","year":"2004","unstructured":"Snel B, van Noort V, Huynen MA: Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes. Nucleic Acids Res 2004, 32(16):4725\u20134731. 10.1093\/nar\/gkh815","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"916_CR34","doi-asserted-by":"publisher","first-page":"E9","DOI":"10.1371\/journal.pbio.0020009","volume":"2","author":"S Bergmann","year":"2004","unstructured":"Bergmann S, Ihmels J, Barkai N: Similarities and differences in genome-wide expression data of six organisms. PLoS Biol 2004, 2(1):E9. 10.1371\/journal.pbio.0020009","journal-title":"PLoS Biol"},{"issue":"6","key":"916_CR35","doi-asserted-by":"publisher","first-page":"2896","DOI":"10.1073\/pnas.96.6.2896","volume":"96","author":"R Overbeek","year":"1999","unstructured":"Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N: The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A 1999, 96(6):2896\u20132901. 10.1073\/pnas.96.6.2896","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"916_CR36","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1016\/S0168-9525(01)02621-X","volume":"18","author":"I Yanai","year":"2002","unstructured":"Yanai I, Mellor JC, DeLisi C: Identifying functional links between genes using conserved chromosomal proximity. Trends Genet 2002, 18(4):176\u2013179. 10.1016\/S0168-9525(01)02621-X","journal-title":"Trends Genet"},{"issue":"5","key":"916_CR37","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1101\/gr.737703","volume":"13","author":"JM Lee","year":"2003","unstructured":"Lee JM, Sonnhammer EL: Genomic gene clustering analysis of pathways in eukaryotes. Genome Res 2003, 13(5):875\u2013882. 10.1101\/gr.737703","journal-title":"Genome Res"},{"issue":"3-4","key":"916_CR38","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1089\/10665270360688129","volume":"10","author":"D Durand","year":"2003","unstructured":"Durand D, Sankoff D: Tests for gene clustering. J Comput Biol 2003, 10(3\u20134):453\u2013482. 10.1089\/10665270360688129","journal-title":"J Comput Biol"},{"key":"916_CR39","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1038\/47056","volume":"402","author":"AJ Enright","year":"1999","unstructured":"Enright AJ, Illopoulos I, Kyrpides NC, Ouzounis CA: Protein interaction maps for complete genomes based on gene fusion events. Nature 1999, 402: 80\u201383.","journal-title":"Nature"},{"issue":"5428","key":"916_CR40","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1126\/science.285.5428.751","volume":"285","author":"EM Marcotte","year":"1999","unstructured":"Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D: Detecting protein function and protein-protein interactions from genome sequences. Science 1999, 285(5428):751\u2013753. 10.1126\/science.285.5428.751","journal-title":"Science"},{"key":"916_CR41","doi-asserted-by":"publisher","first-page":"7940","DOI":"10.1073\/pnas.141236298","volume":"98","author":"I Yanai","year":"2001","unstructured":"Yanai I, Derti A, DeLisi C: Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Proc Natl Acad Sci 2001, 98: 7940\u20137945. 10.1073\/pnas.141236298","journal-title":"Proc Natl Acad Sci"},{"issue":"2","key":"916_CR42","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1016\/S0378-4347(00)00492-8","volume":"751","author":"S Matic","year":"2001","unstructured":"Matic S, Widell S, Akerlund HE, Johansson G: Interaction between phosphofructokinase and aldolase from Saccharomyces cerevisiae studied by aqueous two-phase partitioning. J Chromatogr B Biomed Sci Appl 2001, 751(2):341\u2013348. 10.1016\/S0378-4347(00)00492-8","journal-title":"J Chromatogr B Biomed Sci Appl"},{"issue":"3","key":"916_CR43","doi-asserted-by":"publisher","first-page":"1143","DOI":"10.1073\/pnas.97.3.1143","volume":"97","author":"T Ito","year":"2000","unstructured":"Ito T, Tashiro K, Muta S, Ozawa R, Chiba T, Nishizawa M, Yamamoto K, Kuhara S, Sakaki Y: Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci U S A 2000, 97(3):1143\u20131147. 10.1073\/pnas.97.3.1143","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6770","key":"916_CR44","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1038\/35001009","volume":"403","author":"P Uetz","year":"2000","unstructured":"Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403(6770):623\u2013627. 10.1038\/35001009","journal-title":"Nature"},{"key":"916_CR45","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/415141a","volume":"415","author":"AC Gavin","year":"2002","unstructured":"Gavin AC, Bosche M, Krause R, Grandi P: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002, 415: 141\u2013147. 10.1038\/415141a","journal-title":"Nature"},{"key":"916_CR46","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/415180a","volume":"415","author":"Y Ho","year":"2002","unstructured":"Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P: Systematic identiifcation of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002, 415: 180\u2013183. 10.1038\/415180a","journal-title":"Nature"},{"key":"916_CR47","first-page":"doi: 10.1038\/ms","volume-title":"Nature Molecular Systems Biology","author":"AM Dudley","year":"2005","unstructured":"Dudley AM, Janse DM, Tanay A, Shamir R, Church GM: A global view of pleiotropy and phenotypically derived gene function in yeast. Nature Molecular Systems Biology 2005, doi: 10.1038\/msb4100004."},{"issue":"5701","key":"916_CR48","doi-asserted-by":"publisher","first-page":"1555","DOI":"10.1126\/science.1099511","volume":"306","author":"I Lee","year":"2004","unstructured":"Lee I, Date SV, Adai AT, Marcotte EM: A probabilistic functional network of yeast genes. Science 2004, 306(5701):1555\u20131558. 10.1126\/science.1099511","journal-title":"Science"},{"issue":"1","key":"916_CR49","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1006\/jcss.1997.1504","volume":"55","author":"Y Freund","year":"1997","unstructured":"Freund Y, Schapire R: A decision-theoretic generalization of on-line learning and an application to boosting. J Computer and System Sci 1997, 55(1):119\u2013139. 10.1006\/jcss.1997.1504","journal-title":"J Computer and System Sci"},{"key":"916_CR50","volume-title":"MSRI Workshop on Nonlinear Estimation and Classification","author":"R Schapire","year":"2002","unstructured":"Schapire R: The boosting approach to machine learning: An overview. MSRI Workshop on Nonlinear Estimation and Classification 2002."},{"key":"916_CR51","first-page":"124","volume-title":"The alternating decision tree learning algorithm","author":"Y Freund","year":"1999","unstructured":"Freund Y, Mason L: The alternating decision tree learning algorithm. 1999, 124\u2013133."},{"issue":"5","key":"916_CR52","first-page":"1651","volume":"26","author":"R Schapire","year":"1997","unstructured":"Schapire R, Freund Y, Barlett P, Lee WS: Boosting the margin: A new explanation for the effectiveness of voting methods. Ann Stat 1997, 26(5):1651\u20131686.","journal-title":"Ann Stat"},{"key":"916_CR53","doi-asserted-by":"publisher","first-page":"I232","DOI":"10.1093\/bioinformatics\/bth923","volume":"20 Suppl 1","author":"M Middendorf","year":"2004","unstructured":"Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C: Predicting genetic regulatory response using classification. Bioinformatics 2004, 20 Suppl 1: I232-I240. 10.1093\/bioinformatics\/bth923","journal-title":"Bioinformatics"},{"key":"916_CR54","first-page":"538","volume-title":"Proc RECOMB","author":"M Middendorf","year":"2005","unstructured":"Middendorf M, Kundaje A, Freund Y, Wiggins C, Leslie C: Motif discovery through predictive modeling of gene regulation. Proc RECOMB 2005, 538\u2013552."},{"issue":"35","key":"916_CR55","doi-asserted-by":"publisher","first-page":"32771","DOI":"10.1074\/jbc.M303661200","volume":"278","author":"TC Meredith","year":"2003","unstructured":"Meredith TC, Woodard RW: Escherichia coli YrbH is a D-arabinose 5-phosphate isomerase. J Biol Chem 2003, 278(35):32771\u201332777. 10.1074\/jbc.M303661200","journal-title":"J Biol Chem"},{"issue":"2","key":"916_CR56","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/S0955-0674(03)00009-7","volume":"15","author":"MA Huynen","year":"2003","unstructured":"Huynen MA, Snel B, von Mering C, Bork P: Function prediction and protein networks. Curr Opin Cell Biol 2003, 15(2):191\u2013198. 10.1016\/S0955-0674(03)00009-7","journal-title":"Curr Opin Cell Biol"},{"issue":"4","key":"916_CR57","first-page":"406","volume":"4","author":"N Saitou","year":"1987","unstructured":"Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4(4):406\u2013425.","journal-title":"Mol Biol Evol"},{"key":"916_CR58","first-page":"1032","volume-title":"Numerical Recipes in C++: The Art of Scientific Computing","author":"WH Press","year":"2002","unstructured":"Press WH, Teukolsky SA, Vetterling WT, Flannery BP: Numerical Recipes in C++: The Art of Scientific Computing. 2nd edition edition. Cambridge, UK, Cambridge University Press; 2002:1032.","edition":"2nd edition"},{"issue":"1","key":"916_CR59","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1093\/nar\/29.1.152","volume":"29","author":"G Sherlock","year":"2001","unstructured":"Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM: The Stanford Microarray Database. Nucleic Acids Res 2001, 29(1):152\u2013155. 10.1093\/nar\/29.1.152","journal-title":"Nucleic Acids Res"},{"key":"916_CR60","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/S0092-8674(00)00015-5","volume":"102","author":"TR Hughes","year":"2000","unstructured":"Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA: Functional discovery via a compendium of expression profiles. Cell 2000, 102: 109\u2013126. 10.1016\/S0092-8674(00)00015-5","journal-title":"Cell"},{"issue":"6","key":"916_CR61","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1016\/j.gde.2003.10.006","volume":"13","author":"D Sankoff","year":"2003","unstructured":"Sankoff D: Rearrangements and chromosomal evolution. Curr Opin Genet Dev 2003, 13(6):583\u2013587. 10.1016\/j.gde.2003.10.006","journal-title":"Curr Opin Genet Dev"},{"key":"916_CR62","unstructured":"Entrez Genome database[http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?db=Genome]"},{"key":"916_CR63","unstructured":"Authors' website[http:\/\/arep.med.harvard.edu\/kharchenko\/identification\/]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-7-177.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T11:02:30Z","timestamp":1630494150000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-7-177"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,3,29]]},"references-count":63,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2006,12]]}},"alternative-id":["916"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-7-177","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,3,29]]},"assertion":[{"value":"3 October 2005","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 March 2006","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 March 2006","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"177"}}