메뉴 건너뛰기




Volumn 28, Issue 16, 2012, Pages 2129-2136

RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; BIOLOGY; COMPUTER PROGRAM; DROSOPHILA MELANOGASTER; GENE REGULATORY NETWORK; HUMAN; METABOLISM; METHODOLOGY; PROBABILITY; PROTEIN ANALYSIS; SACCHAROMYCES CEREVISIAE;

EID: 84865053376     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts341     Document Type: Article
Times cited : (20)

References (43)
  • 1
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. the gene ontology consortium
    • Ashburner, M. et al. (2000) Gene ontology: tool for the unification of biology. the gene ontology consortium. Nat. Genet., 25, 25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 2
    • 79952392096 scopus 로고    scopus 로고
    • SubMAP: aligning metabolic pathways with subnetwork mappings
    • Ay, F. et al. (2011) SubMAP: aligning metabolic pathways with subnetwork mappings. J. Comput. Biol., 18, 219-235.
    • (2011) J. Comput. Biol. , vol.18 , pp. 219-235
    • Ay, F.1
  • 3
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • Barabasi, A.L. and Oltvai, Z.N. (2004) Network biology: understanding the cell's functional organization. Nat. Rev. Genet., 5, 101-113.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 4
    • 78349276794 scopus 로고    scopus 로고
    • GraMoFoNe: a Cytoscape plugin for querying motifs without topology in Protein-Protein Interactions networks
    • Al-Mubaid, H. (ed.), International Society for Computers and their Applications (ISCA), Honolulu, États-Unis
    • Blin, G. et al. (2010a) GraMoFoNe: a Cytoscape plugin for querying motifs without topology in Protein-Protein Interactions networks. In: Al-Mubaid, H. (ed.) 2nd International Conference on Bioinformatics and Computational Biology (BICoB'10), International Society for Computers and their Applications (ISCA), Honolulu, États-Unis, pp. 38-43.
    • (2010) 2nd International Conference on Bioinformatics and Computational Biology (BICoB'10) , pp. 38-43
    • Blin, G.1
  • 5
    • 78149247089 scopus 로고    scopus 로고
    • Querying graphs in protein-protein interactions networks using feedback vertex set
    • Blin, G. et al. (2010b) Querying graphs in protein-protein interactions networks using feedback vertex set. IEEE/ACM Trans. Comput. Biol. Bioinform., 7, 628-635.
    • (2010) IEEE/ACM Trans. Comput. Biol. Bioinform. , vol.7 , pp. 628-635
    • Blin, G.1
  • 6
    • 12344269924 scopus 로고    scopus 로고
    • GO:TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    • Boyle, E.I. et al. (2004) GO:TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics, 20, 3710-3715.
    • (2004) Bioinformatics , vol.20 , pp. 3710-3715
    • Boyle, E.I.1
  • 7
    • 77950844722 scopus 로고    scopus 로고
    • Topology-free querying of protein interaction networks
    • Bruckner, S. et al. (2010) Topology-free querying of protein interaction networks. J. Comput. Biol., 17, 237-252.
    • (2010) J. Comput. Biol. , vol.17 , pp. 237-252
    • Bruckner, S.1
  • 8
    • 27744567556 scopus 로고    scopus 로고
    • Interactome: gateway into systems biology
    • Cusick, M.E. et al. (2005) Interactome: gateway into systems biology. Hum. Mol. Genet., 14 Spec No. 2, R171-R181.
    • (2005) Hum. Mol. Genet. , vol.14 , Issue.SPEC. NO. 2
    • Cusick, M.E.1
  • 9
    • 51349103135 scopus 로고    scopus 로고
    • QNet:Atool for querying protein interaction networks
    • Dost, B. et al. (2008) QNet:Atool for querying protein interaction networks. J. Comput. Biol., 15, 913-925.
    • (2008) J. Comput. Biol. , vol.15 , pp. 913-925
    • Dost, B.1
  • 10
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-based multiple sequence alignment
    • Do, C.B. et al. (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
    • (2005) Genome Res , vol.15 , pp. 330-340
    • Do, C.B.1
  • 11
    • 33644631181 scopus 로고    scopus 로고
    • GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins
    • Durand, P. et al. (2006) GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins. BMC Bioinformatics, 7, 21.
    • (2006) BMC Bioinformatics , vol.7 , pp. 21
    • Durand, P.1
  • 12
    • 34248576314 scopus 로고    scopus 로고
    • NetMatch: a Cytoscape plugin for searching biological networks
    • Ferro, A. et al. (2007) NetMatch: a Cytoscape plugin for searching biological networks. Bioinformatics, 23, 910-912.
    • (2007) Bioinformatics , vol.23 , pp. 910-912
    • Ferro, A.1
  • 13
    • 79957964480 scopus 로고    scopus 로고
    • Asymmetric comparison and querying of biological networks
    • Ferraro, N. et al. (2011) Asymmetric comparison and querying of biological networks. IEEE/ACM Trans. Comput. Biol. Bioinform., 8, 876-889.
    • (2011) IEEE/ACM Trans. Comput. Biol. Bioinform. , vol.8 , pp. 876-889
    • Ferraro, N.1
  • 14
    • 84885714660 scopus 로고    scopus 로고
    • Protein-protein interaction network querying by a 'focus and zoom' approach
    • Elloumi, M., Kung, J., Linial, M., Murphy, R.F., Schneider, K. and Toma, C. (eds.), Springer Berlin Heidelberg
    • Fionda, V. et al. (2008) Protein-protein interaction network querying by a 'focus and zoom' approach. In: Elloumi, M., Kung, J., Linial, M., Murphy, R.F., Schneider, K. and Toma, C. (eds.) Bioinformatics Research and Development, vol. 13 of Communications in Computer and Information Science, Springer Berlin Heidelberg, pp. 331-346.
    • (2008) Bioinformatics Research and Development, vol. 13 of Communications in Computer and Information Science. , pp. 331-346
    • Fionda, V.1
  • 15
    • 79957500684 scopus 로고    scopus 로고
    • Biological network querying techniques: analysis and comparison
    • Fionda, V. and Palopoli, L. (2011) Biological network querying techniques: analysis and comparison. J. Comput. Biol., 18, 595-625.
    • (2011) J. Comput. Biol. , vol.18 , pp. 595-625
    • Fionda, V.1    Palopoli, L.2
  • 16
    • 0034651008 scopus 로고    scopus 로고
    • UPA, a universal protein array system for quantitative detection of protein- protein, protein-DNA, protein-RNA and protein-ligand interactions
    • Ge, H. (2000) UPA, a universal protein array system for quantitative detection of protein- protein, protein-DNA, protein-RNA and protein-ligand interactions. Nucleic Acids Res., 28, e3.
    • (2000) Nucleic Acids Res , vol.28
    • Ge, H.1
  • 17
    • 79959431716 scopus 로고    scopus 로고
    • RINQ: Reference-based Indexing for Network Queries
    • Gulsoy, G. and Kahveci, T. (2011) RINQ: Reference-based Indexing for Network Queries. Bioinformatics, 27, i149-i158.
    • (2011) Bioinformatics , vol.27
    • Gulsoy, G.1    Kahveci, T.2
  • 18
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
    • Ho, Y. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183.
    • (2002) Nature , vol.415 , pp. 180-183
    • Ho, Y.1
  • 19
    • 51049110333 scopus 로고    scopus 로고
    • Mining physical protein-protein interactions from the literature
    • Huang, M. et al. (2008) Mining physical protein-protein interactions from the literature. Genome Biol., 9(Suppl 2), S12.
    • (2008) Genome Biol , vol.9 , Issue.SUPPL. 2
    • Huang, M.1
  • 20
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa, M. and Goto, S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 21
    • 3442886313 scopus 로고    scopus 로고
    • PathBLAST: a tool for alignment of protein interaction networks
    • Kelley, B.P. et al. (2004) PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res., 32, W83-W88.
    • (2004) Nucleic Acids Res , vol.32
    • Kelley, B.P.1
  • 22
    • 58149193222 scopus 로고    scopus 로고
    • Human Protein Reference Database-2009 update
    • Keshava Prasad, T.S. et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res., 37, D767-D772.
    • (2009) Nucleic Acids Res , vol.37
    • Keshava Prasad, T.S.1
  • 23
    • 0002719797 scopus 로고
    • The Hungarian method for the assignment problem
    • Kuhn, H.W. (1955) The Hungarian method for the assignment problem. Naval Res. Log. Quar., 2, 83-97.
    • (1955) Naval Res. Log. Quar. , vol.2 , pp. 83-97
    • Kuhn, H.W.1
  • 24
    • 66349108229 scopus 로고    scopus 로고
    • IsoRankN: spectral methods for global alignment of multiple protein networks
    • Liao, C.S. et al. (2009) IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics, 25, i253-i258.
    • (2009) Bioinformatics , vol.25
    • Liao, C.S.1
  • 25
    • 77951599230 scopus 로고    scopus 로고
    • SIGMA: a set-cover-based inexact graph matching algorithm
    • Mongiovi, M. et al. (2010) SIGMA: a set-cover-based inexact graph matching algorithm. J. Bioinform. Comput. Biol., 8, 199-218.
    • (2010) J. Bioinform. Comput. Biol. , vol.8 , pp. 199-218
    • Mongiovi, M.1
  • 26
    • 78651317907 scopus 로고    scopus 로고
    • IsoBase: a database of functionally related proteins across PPI networks
    • Park, D. et al. (2011) IsoBase: a database of functionally related proteins across PPI networks. Nucleic Acids Res., 39, 295-300.
    • (2011) Nucleic Acids Res , vol.39 , pp. 295-300
    • Park, D.1
  • 27
    • 24044488288 scopus 로고    scopus 로고
    • Alignment of metabolic pathways
    • Pinter, R. et al. (2005) Alignment of metabolic pathways. Bioinformatics, 21, 3401-3408.
    • (2005) Bioinformatics , vol.21 , pp. 3401-3408
    • Pinter, R.1
  • 28
    • 59649104116 scopus 로고    scopus 로고
    • Querying pathways in protein interaction networks based on hidden Markov models
    • Qian, X. et al. (2009) Querying pathways in protein interaction networks based on hidden Markov models. J. Comput. Biol., 16, 145-157.
    • (2009) J. Comput. Biol. , vol.16 , pp. 145-157
    • Qian, X.1
  • 29
    • 77956098140 scopus 로고    scopus 로고
    • PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences
    • Sahraeian, S.M. and Yoon, B.J. (2010) PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences. Nucleic Acids Res., 38, 4917-4928.
    • (2010) Nucleic Acids Res , vol.38 , pp. 4917-4928
    • Sahraeian, S.M.1    Yoon, B.J.2
  • 30
    • 80051619917 scopus 로고    scopus 로고
    • Fast network querying algorithm for searching large-scale biological networks
    • 2011 IEEE International Conference on
    • Sahraeian, S. and Yoon, B.-J. (2011a) Fast network querying algorithm for searching large-scale biological networks. In: Acoustics, Speech and Signal Processing (ICASSP), 2011 IEEE International Conference on, pp. 6008-6011.
    • (2011) Acoustics, Speech and Signal Processing (ICASSP) , pp. 6008-6011
    • Sahraeian, S.1    Yoon, B.-J.2
  • 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
    • 33645732240 scopus 로고    scopus 로고
    • Modeling cellular machinery through biological network comparison
    • Sharan, R. and Ideker, T. (2006) Modeling cellular machinery through biological network comparison. Nat. Biotechnol., 24, 427-433.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 427-433
    • Sharan, R.1    Ideker, T.2
  • 34
    • 33646347364 scopus 로고    scopus 로고
    • QPath: a method for querying pathways in a protein-protein interaction network
    • Shlomi, T. et al. (2006) QPath: a method for querying pathways in a protein-protein interaction network. BMC Bioinformatics, 7.
    • (2006) BMC Bioinformatics , pp. 7
    • Shlomi, T.1
  • 35
    • 51349087811 scopus 로고    scopus 로고
    • Global alignment of multiple protein interaction networks with application to functional orthology detection
    • Singh, R. et al. (2008) Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc. Natl. Acad. Sci. USA, 105, 12763-12768.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 12763-12768
    • Singh, R.1
  • 36
    • 78651328883 scopus 로고    scopus 로고
    • The BioGRID Interaction Database: 2011 update
    • Stark, C. et al. (2011) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res., 39, 698-704.
    • (2011) Nucleic Acids Res , vol.39 , pp. 698-704
    • Stark, C.1
  • 37
    • 33846662155 scopus 로고    scopus 로고
    • SAGA: a subgraph matching tool for biological graphs
    • Tian, Y. et al. (2007) SAGA: a subgraph matching tool for biological graphs. Bioinformatics, 23, 232-239.
    • (2007) Bioinformatics , vol.23 , pp. 232-239
    • Tian, Y.1
  • 38
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • Uetz, P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
    • (2000) Nature , vol.403 , pp. 623-627
    • Uetz, P.1
  • 40
    • 34548141879 scopus 로고    scopus 로고
    • Simple and fast alignment of metabolic pathways by exploiting local diversity
    • Wernicke, S. and Rasche, F. (2007) Simple and fast alignment of metabolic pathways by exploiting local diversity. Bioinformatics, 23, 1978-1985.
    • (2007) Bioinformatics , vol.23 , pp. 1978-1985
    • Wernicke, S.1    Rasche, F.2
  • 41
    • 34047236483 scopus 로고    scopus 로고
    • Path matching and graph matching in biological networks
    • Yang, Q. and Sze, S. (2007) Path matching and graph matching in biological networks. J. Comput. Biol., 14, 56-67.
    • (2007) J. Comput. Biol. , vol.14 , pp. 56-67
    • Yang, Q.1    Sze, S.2
  • 42
    • 85032752217 scopus 로고    scopus 로고
    • Comparative analysis of biological networks: hidden markov model and markov chain-based approach
    • Yoon, B.-J. et al. (2012) Comparative analysis of biological networks: hidden markov model and markov chain-based approach. Signal Process. Mag., IEEE, 29, 22-34.
    • (2012) Signal Process. Mag., IEEE , vol.29 , pp. 22-34
    • Yoon, B.-J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.