메뉴 건너뛰기




Volumn 25, Issue 12, 2009, Pages 1536-1542

Bayesian inference of protein-protein interactions from biological literature

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 66349121774     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp245     Document Type: Article
Times cited : (61)

References (43)
  • 1
    • 13444272070 scopus 로고    scopus 로고
    • The Biomolecular Interaction Network Database and related tools 2005 update
    • Alfarano,C. et al. (2005) The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res., 33 D418-D424.
    • (2005) Nucleic Acids Res , vol.33
    • Alfarano, C.1
  • 2
    • 34547844156 scopus 로고    scopus 로고
    • Manual curation is not sufficient for annotation of genomic databases
    • Baumgartner,W.A. Jr et al. (2007) Manual curation is not sufficient for annotation of genomic databases. Bioinformatics, 23, i41-i48.
    • (2007) Bioinformatics , vol.23
    • Baumgartner Jr, W.A.1
  • 3
    • 15944375458 scopus 로고    scopus 로고
    • PDZBase: A protein-protein interaction database for PDZ-domains
    • Beuming,T. et al. (2005) PDZBase: A protein-protein interaction database for PDZ-domains. Bioinformatics, 21, 827-828.
    • (2005) Bioinformatics , vol.21 , pp. 827-828
    • Beuming, T.1
  • 4
    • 0033292011 scopus 로고    scopus 로고
    • Automatic extraction of biological information from scientific text: Protein-protein interactions
    • Blaschke,C. et al. (1999) Automatic extraction of biological information from scientific text: Protein-protein interactions. Proc. Int. Conf. Intell. Syst. Mol. Biol., 60-67.
    • (1999) Proc. Int. Conf. Intell. Syst. Mol. Biol , pp. 60-67
    • Blaschke, C.1
  • 5
    • 41249090605 scopus 로고    scopus 로고
    • Linking entries in protein interaction database to structured text: The FEBS Letters experiment
    • Ceol,A. et al. (2008) Linking entries in protein interaction database to structured text: The FEBS Letters experiment. FEBS Lett. 582, 1171-1177.
    • (2008) FEBS Lett , vol.582 , pp. 1171-1177
    • Ceol, A.1
  • 6
    • 33846073818 scopus 로고    scopus 로고
    • MINT: The Molecular INTeraction database
    • Chatraryamontri,A. et al. (2007) MINT: The Molecular INTeraction database. Nucleic Acids Res., 35, D572-D574.
    • (2007) Nucleic Acids Res , vol.35
    • Chatraryamontri, A.1
  • 7
    • 0035236048 scopus 로고    scopus 로고
    • GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles
    • Friedman,C. et al. (2001) GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics, 17, S74-S82.
    • (2001) Bioinformatics , vol.17
    • Friedman, C.1
  • 8
    • 0037021407 scopus 로고    scopus 로고
    • Learning anchor verbs for biological interaction patterns from published text articles
    • Hatzivassiloglou,V. and Weng,W. (2002) Learning anchor verbs for biological interaction patterns from published text articles. Int. J. Med. Inform., 67, 19-32.
    • (2002) Int. J. Med. Inform , vol.67 , pp. 19-32
    • Hatzivassiloglou, V.1    Weng, W.2
  • 9
    • 12344282809 scopus 로고    scopus 로고
    • Discovering patterns to extract protein-protein interactions from full texts
    • Huang,M. et al. (2004) Discovering patterns to extract protein-protein interactions from full texts. Bioinformatics, 3604-3612.
    • (2004) Bioinformatics , pp. 3604-3612
    • Huang, M.1
  • 10
    • 31144432293 scopus 로고    scopus 로고
    • Literature mining for the biologist: From information retrieval to biological discovery
    • Jensen,L.J. et al. (2006) Literature mining for the biologist: from information retrieval to biological discovery. Nat. Rev. Genet. 7, 119-129.
    • (2006) Nat. Rev. Genet , vol.7 , pp. 119-129
    • Jensen, L.J.1
  • 11
    • 0035042776 scopus 로고    scopus 로고
    • A literature network of human genes for high-throughput analysis of gene expression
    • Jenssen,T.K. et al. (2001) A literature network of human genes for high-throughput analysis of gene expression. Nat. Genet., 28 21-28.
    • (2001) Nat. Genet , vol.28 , pp. 21-28
    • Jenssen, T.K.1
  • 12
    • 36349010138 scopus 로고    scopus 로고
    • Protein interactions and disease: Computational approaches to uncover the etiology of diseases
    • Kann,M.G. (2007) Protein interactions and disease: Computational approaches to uncover the etiology of diseases. Brief Bioinform., 8, 333-346.
    • (2007) Brief Bioinform , vol.8 , pp. 333-346
    • Kann, M.G.1
  • 13
    • 37549050918 scopus 로고    scopus 로고
    • Kernel approaches for genic interaction extraction
    • Kim,S. et al. (2008a) Kernel approaches for genic interaction extraction. Bioinformatics, 24, 118-126.
    • (2008) Bioinformatics , vol.24 , pp. 118-126
    • Kim, S.1
  • 14
    • 48449105927 scopus 로고    scopus 로고
    • b) PIE: An online prediction system for protein-protein interactions from text
    • Kim,S. et al. (2008b) PIE: An online prediction system for protein-protein interactions from text. Nucleic Acids Res., 36 W411-W415.
    • (2008) Nucleic Acids Res , vol.36
    • Kim, S.1
  • 15
    • 36049040710 scopus 로고    scopus 로고
    • Assessment of the second BioCreative PPI task: Automatic extraction of protein-protein interactions
    • CNIO, Madrid, Spain, pp
    • Krallinger,M. and Valencia,A. (2007) Assessment of the second BioCreative PPI task: Automatic extraction of protein-protein interactions. In Proceedings of the BioCreative Workshop, CNIO, Madrid, Spain, pp. 41-54.
    • (2007) Proceedings of the BioCreative Workshop , pp. 41-54
    • Krallinger, M.1    Valencia, A.2
  • 16
    • 51049088875 scopus 로고    scopus 로고
    • Overview of the protein-protein interaction annotation extraction task of BioCreative II
    • Krallinger,M. et al. (2008a) Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol., 9(Suppl. 2), S4.
    • (2008) Genome Biol , vol.9 , Issue.SUPPL. 2
    • Krallinger, M.1
  • 17
    • 51049084462 scopus 로고    scopus 로고
    • Evaluation of text-mining systems for biology: Overview of the Second BioCreative community challenge
    • Krallinger,M. et al. (2008b) Evaluation of text-mining systems for biology: Overview of the Second BioCreative community challenge. Genome Biol., 9(Suppl. 2), S1.
    • (2008) Genome Biol , vol.9 , Issue.SUPPL. 2
    • Krallinger, M.1
  • 18
    • 41149178971 scopus 로고    scopus 로고
    • A text-mining perspective on the requirements for electronically annotated abstracts
    • Leitner,F. and Valencia,A. (2008) A text-mining perspective on the requirements for electronically annotated abstracts, FEBS Lett., 582, 1178-1181.
    • (2008) FEBS Lett , vol.582 , pp. 1178-1181
    • Leitner, F.1    Valencia, A.2
  • 19
    • 0036371839 scopus 로고    scopus 로고
    • Filling preposition-based templates to capture information from medical abstracts
    • Leroy,G. and Chen,H. (2002) Filling preposition-based templates to capture information from medical abstracts. Pac. Symp. Biocomput., 350-361.
    • (2002) Pac. Symp. Biocomput , pp. 350-361
    • Leroy, G.1    Chen, H.2
  • 20
    • 30344472426 scopus 로고    scopus 로고
    • BioThesaurus: A web-based thesaurus of protein and gene names
    • Liu,H. et al. (2006) BioThesaurus: A web-based thesaurus of protein and gene names. Bioinformatics, 22, 103-105.
    • (2006) Bioinformatics , vol.22 , pp. 103-105
    • Liu, H.1
  • 21
    • 33748656691 scopus 로고    scopus 로고
    • Combination of text-mining algorithms increases the performance
    • Malik,R. et al. (2006) Combination of text-mining algorithms increases the performance. Bioinformatics, 22, 2151-2157.
    • (2006) Bioinformatics , vol.22 , pp. 2151-2157
    • Malik, R.1
  • 22
    • 33644877439 scopus 로고    scopus 로고
    • Human protein reference database - 2006 update
    • Mishra,G.R. et al. (2006) Human protein reference database - 2006 update, Nucleic Acids Res., 34, D411-D414.
    • (2006) Nucleic Acids Res , vol.34
    • Mishra, G.R.1
  • 24
    • 84860538817 scopus 로고    scopus 로고
    • Beyond the clause: Extraction of phosphorylation information from medline abstracts
    • Narayanaswamy,M. et al. (2005) Beyond the clause: Extraction of phosphorylation information from medline abstracts. Bioinformatics 21(Suppl. 1), i319-i327.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Narayanaswamy, M.1
  • 25
    • 34548459831 scopus 로고    scopus 로고
    • A primer on learning in Bayesian networks for computational biology
    • Needham,C.J. et al. (2007) A primer on learning in Bayesian networks for computational biology. PLoS Comput. Biol., 3, e129.
    • (2007) PLoS Comput. Biol , vol.3
    • Needham, C.J.1
  • 26
    • 0001413266 scopus 로고    scopus 로고
    • Toward routine automatic pathway discovery from online scientific text abstracts
    • Ng,S.K. and Wong,M. (1999) Toward routine automatic pathway discovery from online scientific text abstracts. Genome Inform. Ser. Workshop. Genome. Inform., 10, 104-112.
    • (1999) Genome Inform. Ser. Workshop. Genome. Inform , vol.10 , pp. 104-112
    • Ng, S.K.1    Wong, M.2
  • 27
    • 0035104866 scopus 로고    scopus 로고
    • Automated extraction of information on protein-protein interactions from the biological literature
    • Ono,T. et al. (2001) Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics, 17, 155-161.
    • (2001) Bioinformatics , vol.17 , pp. 155-161
    • Ono, T.1
  • 28
    • 20144387067 scopus 로고    scopus 로고
    • The MIPS mammalian protein-protein interaction database
    • Pagel,P. et al. (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics, 21, 832-834.
    • (2005) Bioinformatics , vol.21 , pp. 832-834
    • Pagel, P.1
  • 29
    • 0035230208 scopus 로고    scopus 로고
    • Bidirectional incremental parsing for automatic pathway identification with combinatory categorial grammar
    • Park,J.C. et al. (2001) Bidirectional incremental parsing for automatic pathway identification with combinatory categorial grammar. Pac. Symp. Biocomput., 396-407.
    • (2001) Pac. Symp. Biocomput , pp. 396-407
    • Park, J.C.1
  • 30
    • 0036366650 scopus 로고    scopus 로고
    • Robust relational parsing over biomedical literature: Extracting inhibit relations
    • Pustejovsky,J. et al. (2002) Robust relational parsing over biomedical literature: Extracting inhibit relations. Pac. Symp. Biocomput., 362-373.
    • (2002) Pac. Symp. Biocomput , pp. 362-373
    • Pustejovsky, J.1
  • 31
    • 44649108373 scopus 로고    scopus 로고
    • Comparative analysis of five protein-protein interaction corpora
    • Pyysalo,S. et al. (2008) Comparative analysis of five protein-protein interaction corpora. BMC Bioinformatics, 9 (Suppl. 3), S6.
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 3
    • Pyysalo, S.1
  • 32
    • 0347755535 scopus 로고    scopus 로고
    • The Database of Interacting Proteins: 2004 update
    • Salwinski,L. et al. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res., 32, D449-D451.
    • (2004) Nucleic Acids Res , vol.32
    • Salwinski, L.1
  • 33
    • 33645104154 scopus 로고    scopus 로고
    • Extraction of regulatory gene/protein networks from Medline
    • Saric,J. et al. (2006) Extraction of regulatory gene/protein networks from Medline. Bioinformatics, 22, 645-650.
    • (2006) Bioinformatics , vol.22 , pp. 645-650
    • Saric, J.1
  • 34
    • 27744566307 scopus 로고    scopus 로고
    • Extraction of biological interaction networks from scientific literature
    • Skusa,A. et al. (2005) Extraction of biological interaction networks from scientific literature. Brief Bioinform., 6, 263-276.
    • (2005) Brief Bioinform , vol.6 , pp. 263-276
    • Skusa, A.1
  • 35
    • 0033655017 scopus 로고    scopus 로고
    • Biobibliometrics: Information retrieval and visualization from co-occurrences of gene names in Medline abstracts
    • Stapley,B.J. and Benoit,G. (2000) Biobibliometrics: Information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pac. Symp. Biocomput., 529-540.
    • (2000) Pac. Symp. Biocomput , pp. 529-540
    • Stapley, B.J.1    Benoit, G.2
  • 36
    • 33644873184 scopus 로고    scopus 로고
    • BioGRID: A general repository for interaction datasets
    • Stark,C. et al. (2006) BioGRID: A general repository for interaction datasets. Nucleic Acids Res., 34, D535-D539.
    • (2006) Nucleic Acids Res , vol.34
    • Stark, C.1
  • 37
    • 0242559066 scopus 로고    scopus 로고
    • Extraction of protein interaction information from unstructured text using a context-free grammar
    • Temkin,J.M. and Gilder,M.R. (2003) Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics, 19, 2046-2053.
    • (2003) Bioinformatics , vol.19 , pp. 2046-2053
    • Temkin, J.M.1    Gilder, M.R.2
  • 38
    • 0033657262 scopus 로고    scopus 로고
    • Automatic extraction of protein interactions from scientific abstracts
    • Thomas,J. et al. (2000) Automatic extraction of protein interactions from scientific abstracts. Pac. Symp. Biocomput., 541-552.
    • (2000) Pac. Symp. Biocomput , pp. 541-552
    • Thomas, J.1
  • 39
  • 40
    • 48249123880 scopus 로고    scopus 로고
    • Veretnik,S. et al. (2008) Computational biology resources lack persistence and usability. PLoS Comput. Biol., 4, e1000136.
    • Veretnik,S. et al. (2008) Computational biology resources lack persistence and usability. PLoS Comput. Biol., 4, e1000136.
  • 42
    • 0035228039 scopus 로고    scopus 로고
    • PIES, a protein interaction extraction system
    • Wong,L. (2001) PIES, a protein interaction extraction system. Pac. Symp. Biocomput., 520-531.
    • (2001) Pac. Symp. Biocomput , pp. 520-531
    • Wong, L.1
  • 43
    • 0035236527 scopus 로고    scopus 로고
    • Event extraction from biomedical papers using a full parser
    • Yakushiji,A. et al. (2001) Event extraction from biomedical papers using a full parser. Pac. Symp. Biocomput., 408-419.
    • (2001) Pac. Symp. Biocomput , pp. 408-419
    • Yakushiji, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.