{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T10:40:38Z","timestamp":1773657638992,"version":"3.50.1"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2006,11,16]],"date-time":"2006-11-16T00:00:00Z","timestamp":1163635200000},"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":[[2006,12]]},"DOI":"10.1186\/1471-2105-7-502","type":"journal-article","created":{"date-parts":[[2006,11,16]],"date-time":"2006-11-16T07:17:21Z","timestamp":1163661441000},"source":"Crossref","is-referenced-by-count":30,"title":["A correlated motif approach for finding short linear motifs from protein interaction networks"],"prefix":"10.1186","volume":"7","author":[{"given":"Soon-Heng","family":"Tan","sequence":"first","affiliation":[]},{"given":"Willy","family":"Hugo","sequence":"additional","affiliation":[]},{"given":"Wing-Kin","family":"Sung","sequence":"additional","affiliation":[]},{"given":"See-Kiong","family":"Ng","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2006,11,16]]},"reference":[{"issue":"13","key":"1241_CR1","doi-asserted-by":"publisher","first-page":"3625","DOI":"10.1093\/nar\/gkg545","volume":"31","author":"P Puntervoll","year":"2003","unstructured":"Puntervoll P, Linding R, Gemund C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferre F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Kuster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ: ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res 2003, 31(13):3625\u20133630.","journal-title":"Nucleic Acids Res"},{"issue":"15","key":"1241_CR2","doi-asserted-by":"publisher","first-page":"3342","DOI":"10.1016\/j.febslet.2005.04.005","volume":"579","author":"V Neduva","year":"2005","unstructured":"Neduva V, Russell RB: Linear motifs: evolutionary interaction switches. FEBS Lett 2005, 579(15):3342\u20133345.","journal-title":"FEBS Lett"},{"issue":"5553","key":"1241_CR3","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1126\/science.1064987","volume":"295","author":"AHY Tong","year":"2002","unstructured":"Tong AHY, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G: A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 2002, 295(5553):321\u2013324.","journal-title":"Science"},{"key":"1241_CR4","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1016\/S0014-5793(01)03307-5","volume":"513","author":"G Cesareni","year":"2002","unstructured":"Cesareni G, Cesareni G, Panni S, Nardelli G, Castagnoli L: Can we infer peptide recognition specificity mediated by SH3 domains? FEBS Lett 2002, 513: 38\u201344.","journal-title":"FEBS Lett"},{"issue":"3","key":"1241_CR5","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1002\/pmic.200300632","volume":"4","author":"H Hu","year":"2004","unstructured":"Hu H, Columbus J, Zhang Y, Wu D, Lian L, Yang S, Goodwin J, Luczak C, Carter M, Chen L, James M, Davis R, Sudol M, Rodwell J, Herrero JJ: A map of WW domain family interactions. Proteomics 2004, 4(3):643\u2013655.","journal-title":"Proteomics"},{"issue":"6","key":"1241_CR6","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1016\/j.molcel.2004.09.016","volume":"15","author":"H Goehler","year":"2004","unstructured":"Goehler H, Lalowski M, Stelzl U, Waelter S, Stroedicke M, Worm U, Droege A, Lindenberg KS, Knoblich M, Haenig C, Herbst M, Suopanki J, Scherzinger E, Abraham C, Bauer B, Hasenbank R, Fritzsche A, Ludewig AH, Bussow K, Coleman SH, Gutekunst CA, Landwehrmeyer BG, Lehrach H, Wanker EE: A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Mol Cell 2004, 15(6):853\u2013865.","journal-title":"Mol Cell"},{"issue":"5703","key":"1241_CR7","doi-asserted-by":"publisher","first-page":"1930","DOI":"10.1126\/science.1102452","volume":"306","author":"M Marti","year":"2004","unstructured":"Marti M, Good RT, Rug M, Knuepfer E, Cowman AF: Targeting malaria virulence and remodeling proteins to the host erythrocyte. Science 2004, 306(5703):1930\u20131933.","journal-title":"Science"},{"issue":"5703","key":"1241_CR8","doi-asserted-by":"publisher","first-page":"1934","DOI":"10.1126\/science.1102737","volume":"306","author":"NL Hiller","year":"2004","unstructured":"Hiller NL, Bhattacharjee S, van Ooij C, Liolios K, Harrison T, Lopez-Estrano C, Haldar K: A host-targeting signal in virulence proteins reveals a secretome in malarial infection. Science 2004, 306(5703):1934\u20131937.","journal-title":"Science"},{"key":"1241_CR9","first-page":"28","volume":"2","author":"TL Bailey","year":"1994","unstructured":"Bailey TL, Elkan C: Fitting a mixture model by expectation maximization to discover motifs in biopolymers. ISMB 1994, 2: 28\u201336.","journal-title":"ISMB"},{"issue":"5131","key":"1241_CR10","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1126\/science.8211139","volume":"262","author":"CE Lawrence","year":"1993","unstructured":"Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC: Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 1993, 262(5131):208\u2013214.","journal-title":"Science"},{"issue":"5","key":"1241_CR11","first-page":"509","volume":"13","author":"I Jonassen","year":"1997","unstructured":"Jonassen I: Efficient discovery of conserved patterns using a pattern graph. Comput Appl Biosci 1997, 13(5):509\u2013522.","journal-title":"Comput Appl Biosci"},{"key":"1241_CR12","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1093\/bioinformatics\/14.1.55","volume":"14","author":"I Rigoutsos","year":"1998","unstructured":"Rigoutsos I, Floratos A: Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics 1998, 14: 55\u201367.","journal-title":"Bioinformatics"},{"issue":"20","key":"1241_CR13","doi-asserted-by":"publisher","first-page":"12583","DOI":"10.1073\/pnas.202301299","volume":"99","author":"K-I Goh","year":"2002","unstructured":"Goh K-I, Oh E, Jeong H, Kahng B, Kim D: Classification of scale-free networks. Proc Natl Acad Sci USA 2002, 99(20):12583\u201312588.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"5","key":"1241_CR14","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1016\/S0022-2836(03)00239-0","volume":"327","author":"E Sprinzak","year":"2003","unstructured":"Sprinzak E, Sattath S, Margalit H: How reliable are experimental protein-protein interaction data? J Mol Biol 2003, 327(5):919\u2013923.","journal-title":"J Mol Biol"},{"issue":"Suppl 1","key":"1241_CR15","doi-asserted-by":"publisher","first-page":"I274","DOI":"10.1093\/bioinformatics\/bth922","volume":"20","author":"DJ Reiss","year":"2004","unstructured":"Reiss DJ, Schwikowski B: Predicting protein-peptide interactions via a network-based motif sampler. Bioinformatics 2004, 20(Suppl 1):I274-I282.","journal-title":"Bioinformatics"},{"issue":"12","key":"1241_CR16","doi-asserted-by":"publisher","first-page":"e405","DOI":"10.1371\/journal.pbio.0030405","volume":"3","author":"V Neduva","year":"2005","unstructured":"Neduva V, Linding R, Su-Angrand I, Stark A, de Masi F, Gibson TJ, Lewis J, Serrano L, Russell RB: Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol 2005, 3(12):e405.","journal-title":"PLoS Biol"},{"key":"1241_CR17","first-page":"269","volume-title":"ISMB","author":"PA Pevzner","year":"2000","unstructured":"Pevzner PA, Sze S-H: Combinatorial Approaches to Finding Subtle Signals in DNA Sequences. ISMB 2000, 269\u2013278."},{"key":"1241_CR18","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1145\/369133.369172","volume-title":"RECOMB","author":"J Buhler","year":"2001","unstructured":"Buhler J, Tompa M: Finding motifs using random projections. RECOMB 2001, 69\u201376."},{"issue":"Suppl 1","key":"1241_CR19","doi-asserted-by":"publisher","first-page":"S207","DOI":"10.1093\/bioinformatics\/17.suppl_1.S207","volume":"17","author":"G Pavesi","year":"2001","unstructured":"Pavesi G, Mauri G, Pesole G: An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics 2001, 17(Suppl 1):S207-S214.","journal-title":"Bioinformatics"},{"issue":"1","key":"1241_CR20","first-page":"1","volume":"1","author":"E Eskin","year":"2002","unstructured":"Eskin E, Pevzner PA: Finding composite regulatory patterns in DNA Sequences. Bioinformatics 2002, 1(1):1\u20139.","journal-title":"Bioinformatics"},{"issue":"10","key":"1241_CR21","doi-asserted-by":"publisher","first-page":"1374","DOI":"10.1093\/bioinformatics\/18.10.1374","volume":"18","author":"U Keich","year":"2002","unstructured":"Keich U, Pevzner PA: Finding motifs in the twilight zone. Bioinformatics 2002, 18(10):1374\u20131381.","journal-title":"Bioinformatics"},{"issue":"Suppl 2","key":"1241_CR22","doi-asserted-by":"publisher","first-page":"II149","DOI":"10.1093\/bioinformatics\/btg1072","volume":"19","author":"A Price","year":"2003","unstructured":"Price A, Ramabhadran S, Pevzner PA: Finding Subtle Motifs by Branching from Sample Strings. Bioinformatics 2003, 19(Suppl 2):II149-II155.","journal-title":"Bioinformatics"},{"issue":"5715","key":"1241_CR23","doi-asserted-by":"publisher","first-page":"1621","DOI":"10.1126\/science.1105776","volume":"307","author":"M Barrios-Rodiles","year":"2005","unstructured":"Barrios-Rodiles M, Brown KR, Ozdamar B, Bose R, Liu Z, Donovan RS, Shinjo F, Liu Y, Dembowy J, Taylor IW, Luga V, Przulj N, Robinson M, Suzuki H, Hayashizaki Y, Jurisica I, Wrana JL: High-throughput mapping of a dynamic signaling network in mammalian cells. Science 2005, 307(5715):1621\u20131625.","journal-title":"Science"},{"issue":"10","key":"1241_CR24","doi-asserted-by":"publisher","first-page":"1540","DOI":"10.1101\/gr.153002","volume":"12","author":"M Deng","year":"2002","unstructured":"Deng M, Mehta S, Sun F, Chen T: Inferring domain-domain interactions from protein-protein interactions. Genome Res 2002, 12(10):1540\u20131548.","journal-title":"Genome Res"},{"issue":"4","key":"1241_CR25","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1006\/jmbi.2001.4920","volume":"311","author":"E Sprinzak","year":"2001","unstructured":"Sprinzak E, Margalit H: Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol 2001, 311(4):681\u2013692.","journal-title":"J Mol Biol"},{"issue":"8","key":"1241_CR26","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btg118","volume":"19","author":"S-K Ng","year":"2003","unstructured":"Ng S-K, Zhang Z, Tan S-H: Integrative Approach for Computationally Inferring Protein Domain Interactions. Bioinformatics 2003, 19(8):923\u2013929.","journal-title":"Bioinformatics"},{"key":"1241_CR27","first-page":"1465","volume-title":"NIPS","author":"H-D Wang","year":"2004","unstructured":"Wang H-D, Segal E, Ben-Hur A, Koller D, Brutlag DL: Identifying protein-protein interaction sites on a genome-wide scale. NIPS 2004, 1465\u20131472."},{"issue":"2","key":"1241_CR28","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1096\/fasebj.14.2.231","volume":"14","author":"BK Kay","year":"2000","unstructured":"Kay BK, Williamson MP, Sudol M: The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains. FASEB J 2000, 14(2):231\u2013241.","journal-title":"FASEB J"},{"issue":"5618","key":"1241_CR29","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1126\/science.1083653","volume":"300","author":"T Pawson","year":"2003","unstructured":"Pawson T, Nash P: Assembly of Cell Regulatory Systems Through Protein Interaction Domains. Science 2003, 300(5618):445\u2013452.","journal-title":"Science"},{"key":"1241_CR30","first-page":"D449","volume-title":"NAR","author":"L Salwinski","year":"2004","unstructured":"Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. NAR 2004, (32 Database):D449\u2013451."},{"issue":"10","key":"1241_CR31","doi-asserted-by":"publisher","first-page":"2363","DOI":"10.1101\/gr.1680803","volume":"13","author":"S Peri","year":"2003","unstructured":"Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A: Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003, 13(10):2363\u20132371.","journal-title":"Genome Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-7-502.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-7-502\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-7-502.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T08:34:16Z","timestamp":1548232456000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-7-502"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,11,16]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2006,12]]}},"alternative-id":["1241"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-7-502","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,11,16]]},"article-number":"502"}}