메뉴 건너뛰기




Volumn 9781461403203, Issue , 2012, Pages 97-136

Biological network alignment

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY;

EID: 84936777863     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4614-0320-3_5     Document Type: Chapter
Times cited : (6)

References (90)
  • 1
    • 33645732240 scopus 로고    scopus 로고
    • Modeling cellular machinery through biological network comparison
    • Ideker, R.S.T.: Modeling cellular machinery through biological network comparison. Nature Biotechnology 24 (2006) 427-433
    • (2006) Nature Biotechnology , vol.24 , pp. 427-433
    • Ideker, R.S.T.1
  • 2
    • 33748257786 scopus 로고    scopus 로고
    • Graemlin: General and robust alignment of multiple large interaction networks
    • Flannick, J., Novak, A., Srinivasan, B., McAdams, H., Batzoglou, S.: Graemlin: general and robust alignment of multiple large interaction networks. Genome Research 16(9) (2006) 1169-1181
    • (2006) Genome Research , vol.16 , Issue.9 , pp. 1169-1181
    • Flannick, J.1    Novak, A.2    Srinivasan, B.3    McAdams, H.4    Batzoglou, S.5
  • 5
    • 0141593601 scopus 로고    scopus 로고
    • Conserved pathways within bacteria and yeast as revealed by global protein network alignment
    • Kelley, B.P., Sharan, R., Karp, R.M., Sittler, T., Root, D.E., Stockwell, B.R., Ideker, T.: Conserved pathways within bacteria and yeast as revealed by global protein network alignment. PNAS 100(20) (2003)
    • (2003) PNAS , vol.100 , pp. 20
    • Kelley, B.P.1    Sharan, R.2    Karp, R.M.3    Sittler, T.4    Root, D.E.5    Stockwell, B.R.6    Ideker, T.7
  • 6
    • 23844447959 scopus 로고    scopus 로고
    • Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
    • Sharan, R., Ideker, T., Kelley, B.P., Shamir, R., Karp, R.M.: Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. Journal of Computational Biology 12(6) (2005) 835-846
    • (2005) Journal of Computational Biology , vol.12 , Issue.6 , pp. 835-846
    • Sharan, R.1    Ideker, T.2    Kelley, B.P.3    Shamir, R.4    Karp, R.M.5
  • 8
    • 0347473809 scopus 로고    scopus 로고
    • Gaining confidence in high-throughput protein interaction networks
    • Bader, J.S., Chaudhuri, A., Rothberg, J.M., Chant, J.: Gaining confidence in high-throughput protein interaction networks. Nature Biotechnology 22(1) (2003) 78-85
    • (2003) Nature Biotechnology , vol.22 , Issue.1 , pp. 78-85
    • Bader, J.S.1    Chaudhuri, A.2    Rothberg, J.M.3    Chant, J.4
  • 9
    • 26444593028 scopus 로고    scopus 로고
    • Pairwise local alignment of protein interaction networks guided by models of evolution
    • Koyutürk, M., Grama, A., Szpankowski, W.: Pairwise local alignment of protein interaction networks guided by models of evolution. In: RECOMB. (2005) 48-65
    • (2005) RECOMB , pp. 48-65
    • Koyutürk, M.1    Grama, A.2    Szpankowski, W.3
  • 11
    • 0037460091 scopus 로고    scopus 로고
    • Evolving protein interaction networks through gene duplication
    • Pastor-Satorras, R., Smith, E., Solé, R.V.: Evolving protein interaction networks through gene duplication. J Theo. Bio. 222 (2003) 199-210
    • (2003) J Theo. Bio , vol.222 , pp. 199-210
    • Pastor-Satorras, R.1    Smith, E.2    Solé, R.V.3
  • 13
    • 0037423828 scopus 로고    scopus 로고
    • How the global structure of protein interaction networks evolves
    • Wagner, A.: How the global structure of protein interaction networks evolves. Proc. R. Soc. Lond. Biol. Sci. 270(1514) (2003) 457-466
    • (2003) Proc. R. Soc. Lond. Biol. Sci , vol.270 , Issue.1514 , pp. 457-466
    • Wagner, A.1
  • 17
    • 34547666722 scopus 로고    scopus 로고
    • Biological networks: Comparison, conservation, and evolution via relative description length
    • Chor, B., Tuller, T.: Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length. Journal of Computational Biology 14(6) (2007) 817-838
    • (2007) Journal of Computational Biology , vol.14 , Issue.6 , pp. 817-838
    • Chor, B.1    Tuller, T.2
  • 21
    • 54349104506 scopus 로고    scopus 로고
    • NetGrep: Fast network schema searches in interactomes
    • Banks, E., Nabieva, E., Peterson, R., Singh, M.: NetGrep: fast network schema searches in interactomes. Genome Biology 9(9) (2008)
    • (2008) Genome Biology , vol.9 , Issue.9
    • Banks, E.1    Nabieva, E.2    Peterson, R.3    Singh, M.4
  • 22
    • 33644656793 scopus 로고    scopus 로고
    • Systematic identification of functional orthologs based on protein network comparison
    • Bandyopadhyay, S., Sharan, R., Ideker, T.: Systematic identification of functional orthologs based on protein network comparison. Genome Research 16 (2006) 428-435
    • (2006) Genome Research , vol.16 , pp. 428-435
    • Bandyopadhyay, S.1    Sharan, R.2    Ideker, T.3
  • 23
    • 49549096179 scopus 로고    scopus 로고
    • Pairwise global alignment of protein interaction networks by matching neighborhood topology
    • SinghF, R., Xu, J., Berger, B.: Pairwise global alignment of protein interaction networks by matching neighborhood topology. In: RECOMB. (2007) 16-31
    • (2007) RECOMB , pp. 16-31
    • Singhf, R.1    Xu, J.2    Berger, B.3
  • 24
    • 0002719797 scopus 로고
    • The Hungarian method for the assignment problem
    • Kuhn, H.W.: The Hungarian method for the assignment problem. Naval Research Logistic Quarterly 2 (1955) 83-97
    • (1955) Naval Research Logistic Quarterly , vol.2 , pp. 83-97
    • Kuhn, H.W.1
  • 25
    • 40549129437 scopus 로고    scopus 로고
    • Global alignment of multiple protein interaction networks
    • Singh, R., Xu, J., Berger, B.: Global alignment of multiple protein interaction networks. In: Pacific Symposium on Biocomputing. (2008) 303-314
    • (2008) Pacific Symposium on Biocomputing , pp. 303-314
    • Singh, R.1    Xu, J.2    Berger, B.3
  • 26
    • 66349108229 scopus 로고    scopus 로고
    • IsoRankN: Spectral methods for global alignment of multiple protein networks
    • Liao, C.S., Lu, K., Baym, M., Singh, R., Berger, B.: IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics 25(12) (2009) i253-i258
    • (2009) Bioinformatics , vol.25 , Issue.12 , pp. i253-i258
    • Liao, C.S.1    Lu, K.2    Baym, M.3    Singh, R.4    Berger, B.5
  • 29
    • 34547852210 scopus 로고    scopus 로고
    • Alignment of molecular networks by integer quadratic programming
    • Zhenping, L., Zhang, S., Wang, Y., Zhang, X.S., Chen, L.: Alignment of molecular networks by integer quadratic programming. Bioinformatics 23(13) (2007) 1631-1639
    • (2007) Bioinformatics , vol.23 , Issue.13 , pp. 1631-1639
    • Zhenping, L.1    Zhang, S.2    Wang, Y.3    Zhang, X.S.4    Chen, L.5
  • 30
    • 77951152701 scopus 로고    scopus 로고
    • Algorithms for large, sparse network alignment problems
    • Bayati, M., Gerritsen, M., Gleich, D., Saberi, A., Wang, Y.: Algorithms for large, sparse network alignment problems. In: ICDM. (2009) 705-710
    • (2009) ICDM , pp. 705-710
    • Bayati, M.1    Gerritsen, M.2    Gleich, D.3    Saberi, A.4    Wang, Y.5
  • 31
    • 60849107715 scopus 로고    scopus 로고
    • A new graph-based method for pairwise global network alignment
    • Klau, G.W.: A new graph-based method for pairwise global network alignment. BMC Bioinformatics 10(S-1) (2009)
    • (2009) BMC Bioinformatics , vol.10 , Issue.S-1
    • Klau, G.W.1
  • 32
    • 66349109783 scopus 로고    scopus 로고
    • Global alignment of protein-protein interaction networks by graph matching methods
    • Zaslavskiy, M., Bach, F.R., Vert, J.P.: Global alignment of protein-protein interaction networks by graph matching methods. Bioinformatics 25(12) (2009) i259-1267
    • (2009) Bioinformatics , vol.25 , Issue.12 , pp. i259-1267
    • Zaslavskiy, M.1    Bach, F.R.2    Vert, J.P.3
  • 35
    • 47249127315 scopus 로고    scopus 로고
    • Fast and accurate alignment of multiple protein networks
    • Kalaev, M., Bafna, V., Sharan, R.: Fast and accurate alignment of multiple protein networks. In: RECOMB. (2008) 246-256
    • (2008) RECOMB , pp. 246-256
    • Kalaev, M.1    Bafna, V.2    Sharan, R.3
  • 37
    • 0028470228 scopus 로고
    • Nomenclature committee of the international union of biochemistry and molecular biology (NC-IUBMB). Enzyme nomenclature. Recommendations 1992. Supplement: Corrections and additions
    • Tipton, K.F., Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). Enzyme nomenclature. Recommendations 1992. Supplement: corrections and additions. European journal of biochemistry/FEBS, 223(1) (1994) 1-5
    • (1994) European Journal of Biochemistry/FEBS , vol.223 , Issue.1 , pp. 1-5
    • Tipton, K.F.1
  • 41
    • 13444266370 scopus 로고    scopus 로고
    • Online mendelian inheritance in man (omim) a knowledgebase of human genes and genetic disorders
    • Hamosh, A., Scott, A.F., Amberger, J.S., Bocchini, C.A., Mckusick, V.A.: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic acids research 33(Database issue) (2005)
    • (2005) Nucleic Acids Research , vol.33 , Issue.DATABASE ISSUE
    • Hamosh, A.1    Scott, A.F.2    Amberger, J.S.3    Bocchini, C.A.4    McKusick, V.A.5
  • 42
    • 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., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J.M., Sherlock, G.: 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(18) 3710+
    • Bioinformatics , vol.20 , Issue.18 , pp. 3710+
    • Boyle, E.I.1    Weng, S.2    Gollub, J.3    Jin, H.4    Botstein, D.5    Cherry, J.M.6    Sherlock, G.7
  • 49
    • 27244436714 scopus 로고    scopus 로고
    • Expansion of the biocyc collection of pathway/genome databases to 160 genomes
    • Karp, P.D., O.C.M.K.C.G.L.K.: Expansion of the biocyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Research 33 (2005) 6083-9
    • (2005) Nucleic Acids Research , vol.33 , pp. 6083-6089
    • Karp, P.D.1
  • 58
    • 9144234728 scopus 로고    scopus 로고
    • Themouse genome database (mgd): Integrating biology with the genome
    • Bult, C.J., Blake, J.A., Richardson, J.E., Kadin, J.A., Eppig, J.T.: TheMouse Genome Database (MGD): integrating biology with the genome. Nucleic Acids Research 32(Database-Issue) (2004) 476-481
    • (2004) Nucleic Acids Research , vol.32 , Issue.DATABASE-ISSUE , pp. 476-481
    • Bult, C.J.1    Blake, J.A.2    Richardson, J.E.3    Kadin, J.A.4    Eppig, J.T.5
  • 61
    • 44449131125 scopus 로고    scopus 로고
    • Orthology and functional conservation in eukaryotes
    • Dolinski, K., Botstein, D.: Orthology and functional conservation in eukaryotes. Annual Review of Genetics 41(1) (2007) 465-507
    • (2007) Annual Review of Genetics , vol.41 , Issue.1 , pp. 465-507
    • Dolinski, K.1    Botstein, D.2
  • 62
    • 13444256478 scopus 로고    scopus 로고
    • Inparanoid: A comprehensive database of eukaryotic orthologs
    • O'Brien, K.P., Remm, M., Sonnhammer, E.L.L.: Inparanoid: a comprehensive database of eukaryotic orthologs. Nucl. Acids Res. 33 (2005) D476-480
    • (2005) Nucl. Acids Res , vol.33 , pp. D476-480
    • O'brien, K.P.1    Remm, M.2    Sonnhammer, E.L.L.3
  • 63
    • 33646347144 scopus 로고    scopus 로고
    • The origins and evolution of functional modules: Lessons from protein complexes
    • Pereira-Leal, J.B., Levy, E.D., Teichmann, S.A.: The origins and evolution of functional modules: lessons from protein complexes. Phil. Trans. R. Soc. 361(1467) (2006) 507-517
    • (2006) Phil. Trans. R. Soc , vol.361 , Issue.1467 , pp. 507-517
    • Pereira-Leal, J.B.1    Levy, E.D.2    Teichmann, S.A.3
  • 65
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • Spirin, V.,Mirny, L.A.: Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A 100(21) 12123-8+
    • Proc Natl Acad Sci U S A , vol.100 , Issue.21 , pp. 12123-8+
    • Spirin, V.1    Mirny, L.A.2
  • 66
    • 0346156102 scopus 로고    scopus 로고
    • Detection of functional modules from protein interaction networks
    • Pereira-Leal, J., Enright, A., Ouzounis, C.: Detection of functional modules from protein interaction networks. Proteins 54 (2004) 49-57
    • (2004) Proteins , vol.54 , pp. 49-57
    • Pereira-Leal, J.1    Enright, A.2    Ouzounis, C.3
  • 67
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • Ravasz, E., Somera, A.L., Mongru, D.A., Oltvai, Z.N., Barabasi, A.L.: Hierarchical organization of modularity in metabolic networks. Science 297(5586) (2002) 1551-1555
    • (2002) Science , vol.297 , Issue.5586 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3    Oltvai, Z.N.4    Barabasi, A.L.5
  • 68
    • 0036699526 scopus 로고    scopus 로고
    • Revealing modular organization in the yeast transcriptional network
    • Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y., Barkai, N.: Revealing modular organization in the yeast transcriptional network. Nat Genet 31(4) (2002) 370-377
    • (2002) Nat Genet , vol.31 , Issue.4 , pp. 370-377
    • Ihmels, J.1    Friedlander, G.2    Bergmann, S.3    Sarig, O.4    Ziv, Y.5    Barkai, N.6
  • 69
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
    • Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D., Friedman, N.: Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 34(2) (2003) 166-176
    • (2003) Nat Genet , vol.34 , Issue.2 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe'er, D.4    Botstein, D.5    Koller, D.6    Friedman, N.7
  • 70
    • 70450237111 scopus 로고    scopus 로고
    • Phylogenetic analysis of modularity in protein interaction networks
    • Erten, S., Li, X., Bebek, G., Li, J., Koyutürk,M.: Phylogenetic analysis of modularity in protein interaction networks. BMC Bioinformatics 10(1) (2009)
    • (2009) BMC Bioinformatics , vol.10 , Issue.1
    • Erten, S.1    Li, X.2    Bebek, G.3    Li, J.4    Koyutürkm5
  • 71
    • 70349314254 scopus 로고    scopus 로고
    • Evolution in protein interaction networks: Co-evolution, rewiring and the role of duplication
    • Robertson, D.L., Lovell, S.C.: Evolution in protein interaction networks: co-evolution, rewiring and the role of duplication. Biochemical Society transactions 37 (2009) 768-771
    • (2009) Biochemical Society Transactions , vol.37 , pp. 768-771
    • Robertson, D.L.1    Lovell, S.C.2
  • 73
    • 2942744904 scopus 로고    scopus 로고
    • Protein networks, pleiotropy and the evolution of senescence
    • Promislow, D.E.: Protein networks, pleiotropy and the evolution of senescence. In: Proc Biol Sci. Volume 271. (2004) 1225-1234
    • (2004) Proc Biol Sci , vol.271 , pp. 1225-1234
    • Promislow, D.E.1
  • 75
    • 67651177673 scopus 로고    scopus 로고
    • A complex-centric view of protein network evolution
    • Yosef, N., Kupiec, M., Ruppin, E., Sharan, R.: A complex-centric view of protein network evolution. Nucl. Acids Res. 37(12) (2009)
    • (2009) Nucl. Acids Res , vol.37 , Issue.12
    • Yosef, N.1    Kupiec, M.2    Ruppin, E.3    Sharan, R.4
  • 76
    • 70350386642 scopus 로고    scopus 로고
    • Aligning biomolecular networks using modular graph kernels
    • 5724 of Lecture Notes in Computer Science, Springer
    • Towfic, F., Greenlee, M.H.W., Honavar, V.: Aligning biomolecular networks using modular graph kernels. In:WABI. Volume 5724 of Lecture Notes in Computer Science, Springer (2009) 345-361
    • (2009) WABI , pp. 345-361
    • Towfic, F.1    Greenlee, M.H.W.2    Honavar, V.3
  • 77
    • 34447521460 scopus 로고    scopus 로고
    • Human disease classification in the postgenomic era: A complex systems approach to human pathobiology
    • Joseph, L., Isaac, K., Albert-Laszlo, B.: Human disease classification in the postgenomic era: a complex systems approach to human pathobiology. Molecular Systems Biology 3(124) (2007)
    • (2007) Molecular Systems Biology , vol.3 , pp. 124
    • Joseph, L.1    Isaac, K.2    Albert-Laszlo, B.3
  • 78
    • 77952961276 scopus 로고    scopus 로고
    • Network properties of human disease genes with pleiotropic effects
    • Chavali, S., Barrenas, F., Kanduri, K., Benson, M.: Network properties of human disease genes with pleiotropic effects. BMC Systems Biology 4(1) (2010)
    • (2010) BMC Systems Biology , vol.4 , Issue.1
    • Chavali, S.1    Barrenas, F.2    Kanduri, K.3    Benson, M.4
  • 79
    • 84886303119 scopus 로고    scopus 로고
    • Bioinformatics basics: Applications in biological science and medicine
    • Edited by Lukas K. Buehler and Hooman H. Rashidi
    • Lin, Z.: Bioinformatics Basics: Applications in Biological Science and Medicine. Edited by Lukas K. Buehler and Hooman H. Rashidi. Brief Bioinform 9(3) (2008) 256-257
    • (2008) Brief Bioinform , vol.9 , Issue.3 , pp. 256-257
    • Lin, Z.1
  • 80
    • 34247623628 scopus 로고    scopus 로고
    • Getting connected: Analysis and principles of biological networks
    • Zhu, X., Gerstein, M., Snyder, M.: Getting connected: analysis and principles of biological networks. Genes and Development 21(9) (2007) 1010-1024
    • (2007) Genes and Development , vol.21 , Issue.9 , pp. 1010-1024
    • Zhu, X.1    Gerstein, M.2    Snyder, M.3
  • 81
    • 34047110724 scopus 로고    scopus 로고
    • Whole genome molecular phylogeny of large dsdna viruses using composition vector method
    • Lei, G., Ji, Q.: Whole genome molecular phylogeny of large dsdna viruses using composition vector method. BMC Evol Bio 7(41) (2007)
    • (2007) BMC Evol Bio , vol.7 , pp. 41
    • Lei, G.1    Ji, Q.2
  • 84
    • 27744568481 scopus 로고    scopus 로고
    • I.T.: The Plasmodium protein network diverges from those of other eukaryotes
    • Suthram S, Sittler T, I.T.: The Plasmodium protein network diverges from those of other eukaryotes. Nature (2005)
    • (2005) Nature
    • Suthram, S.1    Sittler, T.2
  • 86
    • 58049220319 scopus 로고    scopus 로고
    • Align human interactome with phenome to identify causative genes and networks underlying disease families
    • Wu, X., Liu, Q., Jiang, R.: Align human interactome with phenome to identify causative genes and networks underlying disease families. Bioinformatics 25(1) (2009)
    • (2009) Bioinformatics , vol.25 , pp. 1
    • Wu, X.1    Liu, Q.2    Jiang, R.3
  • 89
    • 85020382362 scopus 로고    scopus 로고
    • Biological network comparison using graphlet degree distribution
    • March 2010
    • Pržulj, N.: Biological network comparison using graphlet degree distribution. Bioinformatics 26 (March 2010) 853-854
    • Bioinformatics , vol.26 , pp. 853-854
    • Pržulj, N.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.