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Volumn 27, Issue 22, 2011, Pages 3173-3178

An efficient network querying method based on conditional random fields

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGY; GENE REGULATORY NETWORK; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; SIGNAL TRANSDUCTION;

EID: 80755144078     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr524     Document Type: Article
Times cited : (13)

References (28)
  • 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
    • 54349104506 scopus 로고    scopus 로고
    • Netgrep: fast network schema searches in interactomes
    • Banks,E. et al. (2008) Netgrep: fast network schema searches in interactomes. Genome Biol., 9, R138.
    • (2008) Genome Biol. , vol.9
    • Banks, E.1
  • 4
    • 78149247089 scopus 로고    scopus 로고
    • Querying graphs in protein-protein interactions networks using feedback vertex set
    • Blin,G. et al. (2010) 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
  • 5
    • 67849118795 scopus 로고    scopus 로고
    • TORQUE: topology-free querying of protein interaction networks
    • Bruckner,S. et al. (2009) TORQUE: topology-free querying of protein interaction networks. Nucleic Acids Res., 37, W106-W108.
    • (2009) Nucleic Acids Res. , vol.37
    • Bruckner, S.1
  • 6
    • 12344265781 scopus 로고    scopus 로고
    • Graphical models for graph matching: approximate models and optimal algorithms
    • Caelli,T. and Caetano,T. (2005) Graphical models for graph matching: approximate models and optimal algorithms. Pattern Recognit. Lett., 26, 339-346.
    • (2005) Pattern Recognit. Lett. , vol.26 , pp. 339-346
    • Caelli, T.1    Caetano, T.2
  • 8
    • 34548390530 scopus 로고    scopus 로고
    • Conrad: gene prediction using conditional random fields
    • DeCaprio,D. et al. (2007) Conrad: gene prediction using conditional random fields. Genome Res., 17, 1389-1398.
    • (2007) Genome Res. , vol.17 , pp. 1389-1398
    • DeCaprio, D.1
  • 9
    • 51349103135 scopus 로고    scopus 로고
    • QNet: a tool for querying protein interaction networks
    • Dost,B. et al. (2008) QNet: a tool for querying protein interaction networks. J. Comput. Biol., 15, 913-925.
    • (2008) J. Comput. Biol. , vol.15 , pp. 913-925
    • Dost, B.1
  • 10
    • 0025022491 scopus 로고
    • Homology of a yeast actin-binding protein to signal transduction proteins and myosin-i
    • Drubin,D.G. et al. (1990) Homology of a yeast actin-binding protein to signal transduction proteins and myosin-i. Nature, 343, 288-290.
    • (1990) Nature , vol.343 , pp. 288-290
    • Drubin, D.G.1
  • 11
    • 0141843591 scopus 로고    scopus 로고
    • Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways
    • Hattori,M. et al. (2003) Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J. Am. Chem. Soc., 125, 11853-11865.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 11853-11865
    • Hattori, M.1
  • 12
    • 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
  • 13
    • 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
  • 14
    • 0032989249 scopus 로고    scopus 로고
    • Aspartate kinase-independent lysine synthesis in an extremely thermophilic bacterium, thermus thermophilus: lysine is synthesized via alphaaminoadipic acid not via diaminopimelic acid
    • Kobashi,N. et al. (1999) Aspartate kinase-independent lysine synthesis in an extremely thermophilic bacterium, thermus thermophilus: lysine is synthesized via alphaaminoadipic acid not via diaminopimelic acid. J. Bacteriol., 181, 1713-1718.
    • (1999) J. Bacteriol. , vol.181 , pp. 1713-1718
    • Kobashi, N.1
  • 15
    • 0142192295 scopus 로고    scopus 로고
    • Conditional random fields: probabilistic models for segmenting and labeling sequence data
    • Morgan Kaufmann, Waltham, MA, USA
    • Lafferty,J. et al. (2001) Conditional random fields: probabilistic models for segmenting and labeling sequence data. In Proceedings of International Conference on Machine Learning (ICML). Morgan Kaufmann, Waltham, MA, USA, pp. 282-289.
    • (2001) Proceedings of International Conference on Machine Learning (ICML) , pp. 282-289
    • Lafferty, J.1
  • 16
    • 0037174671 scopus 로고    scopus 로고
    • Transcriptional regulatory networks in Saccharomyces cerevisiae
    • Lee,T.I. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
    • (2002) Science , vol.298 , pp. 799-804
    • Lee, T.I.1
  • 17
    • 34547852210 scopus 로고    scopus 로고
    • Alignment of molecular networks by integer quadratic programming
    • Li,Z. et al. (2007) Alignment of molecular networks by integer quadratic programming. Bioinformatics, 23, 1631-1639.
    • (2007) Bioinformatics , vol.23 , pp. 1631-1639
    • Li, Z.1
  • 18
    • 24044488288 scopus 로고    scopus 로고
    • Alignment of metabolic pathways
    • Pinter,R.Y. et al. (2005) Alignment of metabolic pathways. Bioinformatics, 21, 3401-3408.
    • (2005) Bioinformatics , vol.21 , pp. 3401-3408
    • Pinter, R.Y.1
  • 19
    • 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
  • 21
    • 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, 199.
    • (2006) BMC Bioinformatics , vol.7 , pp. 199
    • Shlomi, T.1
  • 22
    • 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
  • 23
    • 57149135436 scopus 로고    scopus 로고
    • Feature correspondence via graph matching: Models and global optimization
    • Springer
    • Torresani,L. et al. (2008) Feature correspondence via graph matching: Models and global optimization. In Computer Vision-ECCV 2008. Springer, pp. 596-609.
    • (2008) Computer Vision-ECCV 2008 , pp. 596-609
    • Torresani, L.1
  • 24
    • 84935113569 scopus 로고
    • Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
    • Viterbi,A. (1967) Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. IEEE Trans. Informat. Theory, 13, 260-269.
    • (1967) IEEE Trans. Informat. Theory , vol.13 , pp. 260-269
    • Viterbi, A.1
  • 25
    • 65749118363 scopus 로고    scopus 로고
    • Graphical models, exponential families, and variational inference
    • Wainwright,M.J. and Jordan,M.I. (2008) Graphical models, exponential families, and variational inference. Found. Trends Mach. Learn., 1, 1-305.
    • (2008) Found. Trends Mach. Learn. , vol.1 , pp. 1-305
    • Wainwright, M.J.1    Jordan, M.I.2
  • 26
    • 58049209792 scopus 로고    scopus 로고
    • Conditional random pattern algorithm for LOH inference and segmentation
    • Wu,L.-Y. et al. (2009) Conditional random pattern algorithm for LOH inference and segmentation. Bioinformatics, 25, 61-67.
    • (2009) Bioinformatics , vol.25 , pp. 61-67
    • Wu, L.-Y.1
  • 27
    • 0033971642 scopus 로고    scopus 로고
    • DIP: the database of interacting proteins
    • Xenarios,I. et al. (2000) DIP: the database of interacting proteins. Nucleic Acids Res., 28, 289-291.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 289-291
    • Xenarios, I.1
  • 28
    • 34047236483 scopus 로고    scopus 로고
    • Path matching and graph matching in biological networks
    • Yang,Q. and Sze,S.-H. (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.-H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.