메뉴 건너뛰기




Volumn 14, Issue SUPPL.1, 2013, Pages

A knowledge-based decision support system in bioinformatics: An application to protein complex extraction

Author keywords

[No Author keywords available]

Indexed keywords

BASIC CONCEPTS; CLUSTERING STRATEGY; COMPLEX EXTRACTION; KNOWLEDGE BASE; KNOWLEDGE BASED DECISION SUPPORT SYSTEMS; NUMERICAL RESULTS; PROTEIN COMPLEXES; PROTEIN-PROTEIN INTERACTIONS; REASONING COMPONENTS; RESEARCH GROUPS; STRATEGIES AND TOOLS; WORK-FLOWS; WORKFLOW MANAGEMENTS;

EID: 84872417708     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S1-S5     Document Type: Article
Times cited : (17)

References (45)
  • 1
    • 0034660322 scopus 로고    scopus 로고
    • Protein function in the post-genomic era
    • 10.1038/35015694, 10866208
    • Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. Protein function in the post-genomic era. Nature 2000, 405:823-826. 10.1038/35015694, 10866208.
    • (2000) Nature , vol.405 , pp. 823-826
    • Eisenberg, D.1    Marcotte, E.M.2    Xenarios, I.3    Yeates, T.O.4
  • 2
    • 84872375985 scopus 로고    scopus 로고
    • Database of interacting proteins
    • Database of interacting proteins. , http://dip.doe-mbi.ucla.edu/
  • 5
    • 77956186383 scopus 로고    scopus 로고
    • Drug discovery and mutant p53
    • 10.1016/j.tcb.2010.06.005, 20656489
    • Maslon MM, Hupp TR. Drug discovery and mutant p53. Trends in Cell Biology 2010, 20(9):542-555. 10.1016/j.tcb.2010.06.005, 20656489.
    • (2010) Trends in Cell Biology , vol.20 , Issue.9 , pp. 542-555
    • Maslon, M.M.1    Hupp, T.R.2
  • 6
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • 10.1186/1471-2105-4-2, 149346, 12525261
    • Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2. 10.1186/1471-2105-4-2, 149346, 12525261.
    • (2003) BMC Bioinformatics , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.2
  • 7
    • 10244264813 scopus 로고    scopus 로고
    • Protein complex prediction via cost-based clustering
    • 10.1093/bioinformatics/bth351, 15180928
    • King AD, Przulj N, Jurisica I. Protein complex prediction via cost-based clustering. Bioinformatics 2004, 20(17):3013-3020. 10.1093/bioinformatics/bth351, 15180928.
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3013-3020
    • King, A.D.1    Przulj, N.2    Jurisica, I.3
  • 8
    • 0005924596 scopus 로고    scopus 로고
    • Graph clustering by flow simulation
    • University of Utrecht, Centers for Mathematics and Computer Science (CWI)
    • Dongen SV. Graph clustering by flow simulation. PhD thesis 2000, University of Utrecht, Centers for Mathematics and Computer Science (CWI).
    • (2000) PhD thesis
    • Dongen, S.V.1
  • 10
    • 0013987194 scopus 로고
    • The centrality index of a graph
    • 10.1007/BF02289527, 5232444
    • Sabidussi G. The centrality index of a graph. Psychometrika 1966, 31(4):581-603. 10.1007/BF02289527, 5232444.
    • (1966) Psychometrika , vol.31 , Issue.4 , pp. 581-603
    • Sabidussi, G.1
  • 11
    • 84865730611 scopus 로고
    • A set of measures of centrality based on betweenness
    • Freeman LC. A set of measures of centrality based on betweenness. Sociometry 1977, 40:35-41.
    • (1977) Sociometry , vol.40 , pp. 35-41
    • Freeman, L.C.1
  • 12
    • 67349128582 scopus 로고    scopus 로고
    • Integration of topological measures for eliminating non-specific interactions in protein interaction networks
    • Bayir MA, Guney TD, Can T. Integration of topological measures for eliminating non-specific interactions in protein interaction networks. Discrete Applied Mathematics 2009, 157:2416-2424.
    • (2009) Discrete Applied Mathematics , vol.157 , pp. 2416-2424
    • Bayir, M.A.1    Guney, T.D.2    Can, T.3
  • 13
    • 33645319955 scopus 로고    scopus 로고
    • Predicting interactions in protein networks by completing defective cliques
    • 10.1093/bioinformatics/btl014, 16455753
    • Yu H, Paccanaro A, Trifonov V, Gerstein M. Predicting interactions in protein networks by completing defective cliques. Bioinformatics 2006, 22(7):823-829. 10.1093/bioinformatics/btl014, 16455753.
    • (2006) Bioinformatics , vol.22 , Issue.7 , pp. 823-829
    • Yu, H.1    Paccanaro, A.2    Trifonov, V.3    Gerstein, M.4
  • 14
    • 46149108150 scopus 로고    scopus 로고
    • Using indirect protein-protein interactions for protein complex prediction
    • 10.1142/S0219720008003497, 18574858
    • Chua HN, Ning K, Sung WK, Leong HW, Wong L. Using indirect protein-protein interactions for protein complex prediction. Journal of Bioinformatics and Computational Biology 2008, 6(3):435-466. 10.1142/S0219720008003497, 18574858.
    • (2008) Journal of Bioinformatics and Computational Biology , vol.6 , Issue.3 , pp. 435-466
    • Chua, H.N.1    Ning, K.2    Sung, W.K.3    Leong, H.W.4    Wong, L.5
  • 15
    • 65449134296 scopus 로고    scopus 로고
    • Clustering algorithms for detecting functional modules in protein interaction networks
    • 10.1142/S0219720009004023, 19226668
    • Gao L, Sun PG, Song J. Clustering algorithms for detecting functional modules in protein interaction networks. Journal of Bioinformatics and Computational Biology 2009, 7:217-242. 10.1142/S0219720009004023, 19226668.
    • (2009) Journal of Bioinformatics and Computational Biology , vol.7 , pp. 217-242
    • Gao, L.1    Sun, P.G.2    Song, J.3
  • 16
    • 34547852262 scopus 로고    scopus 로고
    • An ensemble framework for clustering protein-protein interaction networks
    • 10.1093/bioinformatics/btm212, 17646309
    • Asur S, Ucar D, Parthasarathy S. An ensemble framework for clustering protein-protein interaction networks. Bioinformatics 2007, 23:i29-i40. 10.1093/bioinformatics/btm212, 17646309.
    • (2007) Bioinformatics , vol.23
    • Asur, S.1    Ucar, D.2    Parthasarathy, S.3
  • 17
    • 0027885628 scopus 로고
    • Expert support systems: integrating AI technologies
    • El-Najdawi MK, Stylianou AC. Expert support systems: integrating AI technologies. Commun ACM 1993, 36(12):55-ff.
    • (1993) Commun ACM , vol.36 , Issue.12
    • El-Najdawi, M.K.1    Stylianou, A.C.2
  • 19
    • 38949177447 scopus 로고    scopus 로고
    • ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information
    • 10.1186/1471-2105-8-416, 2222653, 17963510
    • Barthel D, Hirst J, Blazewicz J, Burke E, Krasnogor N. ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information. BMC Bioinformatics 2007, 8:416. 10.1186/1471-2105-8-416, 2222653, 17963510.
    • (2007) BMC Bioinformatics , vol.8 , pp. 416
    • Barthel, D.1    Hirst, J.2    Blazewicz, J.3    Burke, E.4    Krasnogor, N.5
  • 20
    • 78649376401 scopus 로고    scopus 로고
    • The INTERPRET Decision-Support System version 3.0 for evaluation of Magnetic Resonance Spectroscopy data from human brain tumours and other abnormal brain masses
    • 10.1186/1471-2105-11-416, 2928804, 20691091
    • Perez-Ruiz A, Julia-Sape M, Mercadal G, Olier I, Majos C, Arus C. The INTERPRET Decision-Support System version 3.0 for evaluation of Magnetic Resonance Spectroscopy data from human brain tumours and other abnormal brain masses. BMC Bioinformatics 2010, 11:416. 10.1186/1471-2105-11-416, 2928804, 20691091.
    • (2010) BMC Bioinformatics , vol.11 , pp. 416
    • Perez-Ruiz, A.1    Julia-Sape, M.2    Mercadal, G.3    Olier, I.4    Majos, C.5    Arus, C.6
  • 22
  • 23
    • 41949113537 scopus 로고    scopus 로고
    • The Taverna Interaction Service: enabling manual interaction in workflows
    • 10.1093/bioinformatics/btn082, 18337261
    • Lanzen A, Oinn T. The Taverna Interaction Service: enabling manual interaction in workflows. Bioinformatics 2008, 24(8):1118-1120. 10.1093/bioinformatics/btn082, 18337261.
    • (2008) Bioinformatics , vol.24 , Issue.8 , pp. 1118-1120
    • Lanzen, A.1    Oinn, T.2
  • 25
    • 34248198746 scopus 로고    scopus 로고
    • BioWMS: a web-based Workflow Management System for bioinformatics
    • 10.1186/1471-2105-8-S1-S2, 2230503, 18269696
    • Bartocci E, Corradini F, Merelli E, Schortichini L. BioWMS: a web-based Workflow Management System for bioinformatics. BMC Bioinformatics 2007, 8(Suppl 1):S2. 10.1186/1471-2105-8-S1-S2, 2230503, 18269696.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 1
    • Bartocci, E.1    Corradini, F.2    Merelli, E.3    Schortichini, L.4
  • 27
    • 84864067412 scopus 로고    scopus 로고
    • An Intelligent System for Decision Support in Bioinformatics
    • Fiannaca A, La Rosa M, Peri D, Rizzo R. An Intelligent System for Decision Support in Bioinformatics. ERCIM News 2011, 2011(84):35.
    • (2011) ERCIM News , vol.2011 , Issue.84 , pp. 35
    • Fiannaca, A.1    La Rosa, M.2    Peri, D.3    Rizzo, R.4
  • 30
    • 84864032891 scopus 로고    scopus 로고
    • An ontology design methodology for Knowledge-Based systems with application to bioinformatics
    • Fiannaca A, Gaglio S, La Rosa M, Rizzo R, Urso A. An ontology design methodology for Knowledge-Based systems with application to bioinformatics. CIBCB 2012, 85-91.
    • (2012) CIBCB , pp. 85-91
    • Fiannaca, A.1    Gaglio, S.2    La Rosa, M.3    Rizzo, R.4    Urso, A.5
  • 31
    • 85032279305 scopus 로고
    • Tree-maps: a space-filling approach to the visualization of hierarchical information structures
    • Johnson B, Shneiderman B. Tree-maps: a space-filling approach to the visualization of hierarchical information structures. Proceedings of IEEE Conference on Visualization 1991, 284-291.
    • (1991) Proceedings of IEEE Conference on Visualization , pp. 284-291
    • Johnson, B.1    Shneiderman, B.2
  • 32
    • 1442354529 scopus 로고    scopus 로고
    • Jess: the rule engine for the JavaTM platform
    • Jess: the rule engine for the JavaTM platform. , http://herzberg.ca.sandia.gov/jess/
  • 33
    • 0020177941 scopus 로고
    • Rete: a fast algorithm for the many pattern/many object pattern match problem
    • Forgy C. Rete: a fast algorithm for the many pattern/many object pattern match problem. Artificial Intelligence 1982, 19:17-37.
    • (1982) Artificial Intelligence , vol.19 , pp. 17-37
    • Forgy, C.1
  • 34
    • 33244454674 scopus 로고    scopus 로고
    • The protege ontology editor and knowledge acquisition system
    • The protege ontology editor and knowledge acquisition system. , http://protege.stanford.edu/
  • 35
    • 84872393538 scopus 로고    scopus 로고
    • JGraph: leading open source java graph visualization and layout component
    • JGraph: leading open source java graph visualization and layout component. , http://www.jgraph.com/
  • 36
    • 13844264514 scopus 로고    scopus 로고
    • Iterative cluster analysis of protein interaction data
    • Arnau V, Mars S, Martyn I. Iterative cluster analysis of protein interaction data. Bioinformatics 2004, 21(3):364-378.
    • (2004) Bioinformatics , vol.21 , Issue.3 , pp. 364-378
    • Arnau, V.1    Mars, S.2    Martyn, I.3
  • 37
    • 0035817637 scopus 로고    scopus 로고
    • A protein interaction map for cell polarity development
    • 10.1083/jcb.200104057, 2196425, 11489916
    • Drees BL, Sundin B, et al. A protein interaction map for cell polarity development. J Cell Biol 2001, 154:549-571. 10.1083/jcb.200104057, 2196425, 11489916.
    • (2001) J Cell Biol , vol.154 , pp. 549-571
    • Drees, B.L.1    Sundin, B.2
  • 39
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • 10.1038/nrg1272, 14735121
    • Barabasi AL, Oltvail ZN. Network biology: understanding the cell's functional organization. Nature Reviews Genetics 2004, 5:101-113. 10.1038/nrg1272, 14735121.
    • (2004) Nature Reviews Genetics , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvail, Z.N.2
  • 40
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering C, et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417:399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1
  • 41
    • 0035172654 scopus 로고    scopus 로고
    • How useful will functional proteomics data be?
    • 10.1002/cfg.101, 2448398, 18629237
    • Legrain P. How useful will functional proteomics data be?. Comp Funct Genomics 2001, 2(5):301-303. 10.1002/cfg.101, 2448398, 18629237.
    • (2001) Comp Funct Genomics , vol.2 , Issue.5 , pp. 301-303
    • Legrain, P.1
  • 42
    • 33747850574 scopus 로고    scopus 로고
    • Increasing confidence of protein interactomes using network topological metrics
    • 10.1093/bioinformatics/btl335, 16787971
    • Chen J, Hsu W, Lee ML, Ng S. Increasing confidence of protein interactomes using network topological metrics. Bioinformatics 2006, 22(16):1998-2004. 10.1093/bioinformatics/btl335, 16787971.
    • (2006) Bioinformatics , vol.22 , Issue.16 , pp. 1998-2004
    • Chen, J.1    Hsu, W.2    Lee, M.L.3    Ng, S.4
  • 43
    • 33751255087 scopus 로고    scopus 로고
    • Evaluation of clustering algorithms for protein-protein interaction networks
    • 10.1186/1471-2105-7-488, 1637120, 17087821
    • Brohee S, van Helden J. Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 2006, 7:488. 10.1186/1471-2105-7-488, 1637120, 17087821.
    • (2006) BMC Bioinformatics , vol.7 , pp. 488
    • Brohee, S.1    van Helden, J.2
  • 44
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • 10.1101/gr.1239303, 403769, 14597658
    • Shannon P, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
    • (2003) Genome Research , vol.13 , Issue.11 , pp. 2498-2504
    • Shannon, P.1
  • 45
    • 84872388806 scopus 로고    scopus 로고
    • GOTermFinder
    • GOTermFinder. , http://go.princeton.edu/cgi-bin/GOTermFinder/


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.