메뉴 건너뛰기




Volumn 5541 LNBI, Issue , 2009, Pages 400-417

Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information

Author keywords

Clustering; Hierarchical tree decompositions; Metagenomics; OTUs; Protein interaction networks; Variation of information

Indexed keywords

CLUSTERING; HIERARCHICAL TREE DECOMPOSITIONS; METAGENOMICS; OTUS; PROTEIN INTERACTION NETWORKS; VARIATION OF INFORMATION;

EID: 67650456399     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-02008-7_29     Document Type: Conference Paper
Times cited : (16)

References (52)
  • 1
    • 13844264514 scopus 로고    scopus 로고
    • Iterative cluster analysis of protein interaction data
    • Arnau, V., Mars, S., Marín, I.: Iterative cluster analysis of protein interaction data. Bioinformatics 21(3), 364-378 (2005)
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 364-378
    • Arnau, V.1    Mars, S.2    Marín, I.3
  • 2
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • Bader, G.D., Hogue, C.W.V.: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4, 2 (2003)
    • (2003) BMC Bioinformatics , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.V.2
  • 3
    • 34547473549 scopus 로고    scopus 로고
    • Bernard, A., Vaughn, D.S., Hartemink, A.J.: Reconstructing the topology of protein complexes. In: Speed, T., Huang, H. (eds.) RECOMB 2007. LNCS (LNBI),4453, pp. 32-46. Springer, Heidelberg (2007)
    • Bernard, A., Vaughn, D.S., Hartemink, A.J.: Reconstructing the topology of protein complexes. In: Speed, T., Huang, H. (eds.) RECOMB 2007. LNCS (LNBI),vol. 4453, pp. 32-46. Springer, Heidelberg (2007)
  • 5
    • 33751255087 scopus 로고    scopus 로고
    • Brohee, S., van Helden, J.: Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7, 488+ (2006)
    • Brohee, S., van Helden, J.: Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7, 488+ (2006)
  • 6
    • 1442329655 scopus 로고    scopus 로고
    • Functional classification of proteins for the prediction of cellular function from a proteinprotein interaction network
    • Brun, C., Chevenet, F., Martin, D., Wojcik, J., Guenoche, A., Jacq, B.: Functional classification of proteins for the prediction of cellular function from a proteinprotein interaction network. Genome Biol. 5(1), R6 (2003)
    • (2003) Genome Biol , vol.5 , Issue.1
    • Brun, C.1    Chevenet, F.2    Martin, D.3    Wojcik, J.4    Guenoche, A.5    Jacq, B.6
  • 7
    • 10244264786 scopus 로고    scopus 로고
    • The CRASSS plug-in for integrating annotation data with hierarchical clustering results
    • Buehler, E.C., Sachs, J.R., Shao, K., Bagchi, A., Ungar, L.H.: The CRASSS plug-in for integrating annotation data with hierarchical clustering results. Bioinformatics 20(17), 3266-3269 (2004)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3266-3269
    • Buehler, E.C.1    Sachs, J.R.2    Shao, K.3    Bagchi, A.4    Ungar, L.H.5
  • 9
    • 34249897253 scopus 로고    scopus 로고
    • Geographical distribution and diversity of bacteria associated with natural populations of Drosophila melanogaster
    • Corby-Harris, V., et al.: Geographical distribution and diversity of bacteria associated with natural populations of Drosophila melanogaster. Appl. Environ. Microbiol. 73, 3470-3479 (2007)
    • (2007) Appl. Environ. Microbiol , vol.73 , pp. 3470-3479
    • Corby-Harris, V.1
  • 10
    • 33747827586 scopus 로고    scopus 로고
    • DeSantis, T.Z., Hugenholtz, P., Keller, K., Brodie, E.L., Larsen, N., Piceno, Y.M.,Phan, R., Andersen, G.L.: NAST: a multiple sequence alignment server for comparative analysis of 16s rRNA genes. Nucleic Acids Res. 34(Web Server issue), W394-W399 (2006)
    • DeSantis, T.Z., Hugenholtz, P., Keller, K., Brodie, E.L., Larsen, N., Piceno, Y.M.,Phan, R., Andersen, G.L.: NAST: a multiple sequence alignment server for comparative analysis of 16s rRNA genes. Nucleic Acids Res. 34(Web Server issue), W394-W399 (2006)
  • 11
    • 34548748711 scopus 로고    scopus 로고
    • Weighted graph cuts without eigenvectors a multilevel approach
    • Dhillon, I.S., Guan, Y., Kulis, B.: Weighted graph cuts without eigenvectors a multilevel approach. IEEE Trans. Pattern Anal. Mach. Intell. 29(11), 1944-1957 (2007)
    • (2007) IEEE Trans. Pattern Anal. Mach. Intell , vol.29 , Issue.11 , pp. 1944-1957
    • Dhillon, I.S.1    Guan, Y.2    Kulis, B.3
  • 12
    • 36949014067 scopus 로고    scopus 로고
    • Hierarchical tree snipping: Clustering guided by prior knowledge
    • Dotan-Cohen, D., Melkman, A.A., Kasif, S.: Hierarchical tree snipping: Clustering guided by prior knowledge. Bioinformatics 23(24), 3335-3342 (2007)
    • (2007) Bioinformatics , vol.23 , Issue.24 , pp. 3335-3342
    • Dotan-Cohen, D.1    Melkman, A.A.2    Kasif, S.3
  • 14
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C.: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5), 1792-1797 (2004)
    • (2004) Nucleic Acids Res , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 15
    • 67650419425 scopus 로고    scopus 로고
    • Felsenstein, J, PHYLIP: Phylogeny inference package (version 3.2, Cladistics 5, 164-166 1989
    • Felsenstein, J.: PHYLIP: Phylogeny inference package (version 3.2). Cladistics 5, 164-166 (1989)
  • 16
    • 51449115465 scopus 로고    scopus 로고
    • Fulthorpe, R.R., Roesch, L.F.W., Riva, A., Triplett, E.W.: Distantly sampled soils carry few species in common. ISME J. 2, 901-910 (2008)
    • Fulthorpe, R.R., Roesch, L.F.W., Riva, A., Triplett, E.W.: Distantly sampled soils carry few species in common. ISME J. 2, 901-910 (2008)
  • 18
    • 0030807655 scopus 로고    scopus 로고
    • BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
    • Gascuel, O.: BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14(7), 685-695 (1997)
    • (1997) Mol. Biol. Evol , vol.14 , Issue.7 , pp. 685-695
    • Gascuel, O.1
  • 19
    • 13444306676 scopus 로고    scopus 로고
    • 364+ (2005)
    • 364+ (2005)
  • 20
    • 33847744247 scopus 로고    scopus 로고
    • Hart, T.G., Ramani, A.K., Marcotte, E.M.: How complete are current yeast and human protein-interaction networks? Genome Biol. 7, 120+ (2006)
    • Hart, T.G., Ramani, A.K., Marcotte, E.M.: How complete are current yeast and human protein-interaction networks? Genome Biol. 7, 120+ (2006)
  • 24
    • 0032131147 scopus 로고    scopus 로고
    • A fast and high quality multilevel scheme for partitioning irregular graphs
    • Karypis, G., Kumar, V.: A fast and high quality multilevel scheme for partitioning irregular graphs. SIAM J. Sci. Comput. 20(1), 359-392 (1998)
    • (1998) SIAM J. Sci. Comput , vol.20 , Issue.1 , pp. 359-392
    • Karypis, G.1    Kumar, V.2
  • 25
    • 44849090313 scopus 로고    scopus 로고
    • Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome
    • Kennedy, J., et al.: Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome. Environ. Microbiol. 10, 1888-1902 (2008)
    • (2008) Environ. Microbiol , vol.10 , pp. 1888-1902
    • Kennedy, J.1
  • 26
    • 33846047770 scopus 로고    scopus 로고
    • Kerrien, S., Alam-Faruque, Y., Aranda, B., Bancarz, I., Bridge, A., Derow, C., Dimmer, E., Feuermann, M., Friedrichsen, A., Huntley, R., Kohler, C., Khadake, J., Leroy, C., Liban, A., Lieftink, C., Montecchi-Palazzi, L., Orchard, S., Risse, J., Robbe, K., Roechert, B., Thorneycroft, D., Zhang, Y., Apweiler, R., Hermjakob,H.: IntAct-open source resource for molecular interaction data. Nucleic Acids Res. 35(Database issue), D561-D565 (2007)
    • Kerrien, S., Alam-Faruque, Y., Aranda, B., Bancarz, I., Bridge, A., Derow, C., Dimmer, E., Feuermann, M., Friedrichsen, A., Huntley, R., Kohler, C., Khadake, J., Leroy, C., Liban, A., Lieftink, C., Montecchi-Palazzi, L., Orchard, S., Risse, J., Robbe, K., Roechert, B., Thorneycroft, D., Zhang, Y., Apweiler, R., Hermjakob,H.: IntAct-open source resource for molecular interaction data. Nucleic Acids Res. 35(Database issue), D561-D565 (2007)
  • 27
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura, M.: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120 (1980)
    • (1980) J. Mol. Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 28
    • 10244264813 scopus 로고    scopus 로고
    • Protein complex prediction via cost-based clustering
    • King, A.D., Przulj, N., Jurisica, I.: Protein complex prediction via cost-based clustering. Bioinformatics 20(17), 3013-3020 (2004)
    • (2004) Bioinformatics , vol.20 , Issue.17 , pp. 3013-3020
    • King, A.D.1    Przulj, N.2    Jurisica, I.3
  • 29
    • 38449114820 scopus 로고    scopus 로고
    • Discovering protein complexes in dense reliable neighborhoods of protein interaction networks
    • Li, X.L., Foo, C.S., Ng, S.K.: Discovering protein complexes in dense reliable neighborhoods of protein interaction networks. In: Comp. Syst. Bioinformatics Conference, vol. 6, pp. 157-168 (2007)
    • (2007) Comp. Syst. Bioinformatics Conference , vol.6 , pp. 157-168
    • Li, X.L.1    Foo, C.S.2    Ng, S.K.3
  • 30
    • 34249794257 scopus 로고    scopus 로고
    • Mavromatis, K., Ivanova, N., Barry, K., Shapiro, H., Goltsman, E., McHardy, A.C.C., Rigoutsos, I., Salamov, A., Korzeniewski, F., Land, M., Lapidus, A., Grigoriev, I., Richardson, P., Hugenholtz, P., Kyrpides, N.C.C.: Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat. Methods,495-500 (2007)
    • Mavromatis, K., Ivanova, N., Barry, K., Shapiro, H., Goltsman, E., McHardy, A.C.C., Rigoutsos, I., Salamov, A., Korzeniewski, F., Land, M., Lapidus, A., Grigoriev, I., Richardson, P., Hugenholtz, P., Kyrpides, N.C.C.: Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat. Methods,495-500 (2007)
  • 31
    • 33947156744 scopus 로고    scopus 로고
    • Comparing clustering-san information based distance
    • Meila, M.: Comparing clustering-san information based distance. J. Multivariate Anal. 98(5), 873-895 (2007)
    • (2007) J. Multivariate Anal , vol.98 , Issue.5 , pp. 873-895
    • Meila, M.1
  • 32
    • 47949097158 scopus 로고    scopus 로고
    • Mathematical classification and clustering
    • Mirkin, B.: Mathematical classification and clustering. J. Global Optim. 12(1), 105-108 (1998)
    • (1998) J. Global Optim , vol.12 , Issue.1 , pp. 105-108
    • Mirkin, B.1
  • 34
    • 59649120244 scopus 로고    scopus 로고
    • Revealing biological modules via graph summarization
    • Navlakha, S., Schatz, M.C., Kingsford, C.: Revealing biological modules via graph summarization. J. Comp. Biol. 16(2), 253-264 (2009)
    • (2009) J. Comp. Biol , vol.16 , Issue.2 , pp. 253-264
    • Navlakha, S.1    Schatz, M.C.2    Kingsford, C.3
  • 35
    • 33745012299 scopus 로고    scopus 로고
    • Modularity and community structure in networks
    • Newman, M.E.J.: Modularity and community structure in networks. Proc. Natl. Acad. Sci. USA 103(23), 8577-8582 (2006)
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , Issue.23 , pp. 8577-8582
    • Newman, M.E.J.1
  • 37
    • 43249113326 scopus 로고    scopus 로고
    • Qiu, J., Noble, W.S.: Predicting co-complexed protein pairs from heterogeneous data. PLoS Comp. Biol. 4(4) (2008)
    • Qiu, J., Noble, W.S.: Predicting co-complexed protein pairs from heterogeneous data. PLoS Comp. Biol. 4(4) (2008)
  • 38
    • 84950632109 scopus 로고
    • Objective criteria for the evaluation of clustering methods
    • Rand, W.M.: Objective criteria for the evaluation of clustering methods. J. Am. Stat. Assoc. 66(336), 846-850 (1971)
    • (1971) J. Am. Stat. Assoc , vol.66 , Issue.336 , pp. 846-850
    • Rand, W.M.1
  • 39
    • 0037417817 scopus 로고    scopus 로고
    • Modular organization of cellular networks
    • Rives, A.W., Galitski, T.: Modular organization of cellular networks. Proc. Natl. Acad. Sci. USA 100(3), 1128-1133 (2003)
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , Issue.3 , pp. 1128-1133
    • Rives, A.W.1    Galitski, T.2
  • 40
    • 0242268461 scopus 로고    scopus 로고
    • Predicting protein functions from redundancies in largescale protein interaction networks
    • Samanta, M.P., Liang, S.: Predicting protein functions from redundancies in largescale protein interaction networks. Proc. Natl. Acad. Sci. USA 100(22), 12579-12583 (2003)
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , Issue.22 , pp. 12579-12583
    • Samanta, M.P.1    Liang, S.2
  • 41
    • 15444362001 scopus 로고    scopus 로고
    • Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness
    • Schloss, P.D., Handelsman, J.: Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71(3), 1501-1506 (2005)
    • (2005) Appl. Environ. Microbiol , vol.71 , Issue.3 , pp. 1501-1506
    • Schloss, P.D.1    Handelsman, J.2
  • 42
    • 33746639717 scopus 로고    scopus 로고
    • Toward a census of bacteria in soil. PLoS
    • Schloss, P.D., Handelsman, J.: Toward a census of bacteria in soil. PLoS Comp.Biol. 2(7), e92 (2006)
    • (2006) Comp.Biol , vol.2 , Issue.7
    • Schloss, P.D.1    Handelsman, J.2
  • 45
    • 46649092734 scopus 로고    scopus 로고
    • Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures
    • Tan, M., Smith, E., Broach, J., Floudas, C.: Microarray data mining: A novel optimization-based approach to uncover biologically coherent structures. BMC Bioinformatics 9(1), 268 (2008)
    • (2008) BMC Bioinformatics , vol.9 , Issue.1 , pp. 268
    • Tan, M.1    Smith, E.2    Broach, J.3    Floudas, C.4
  • 46
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22),4673-4680 (1994)
    • (1994) Nucleic Acids Res , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 47
    • 2942601249 scopus 로고    scopus 로고
    • Selection of informative clusters from hierarchical cluster tree with gene classes
    • Toronen, P.: Selection of informative clusters from hierarchical cluster tree with gene classes. BMC Bioinformatics 5, 32 (2004)
    • (2004) BMC Bioinformatics , vol.5 , pp. 32
    • Toronen, P.1
  • 48
    • 23744454242 scopus 로고    scopus 로고
    • A cluster algorithm for graphs
    • Technical Report INS-R0010, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam
    • Van Dongen, S.: A cluster algorithm for graphs. Technical Report INS-R0010, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam (2000)
    • (2000)
    • Van Dongen, S.1
  • 49
    • 34548293679 scopus 로고    scopus 로고
    • Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    • Wang, Q., Garrity, G.M., Tiedje, J.M., Cole, J.R.: Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73(16), 5261-5267 (2007)
    • (2007) Appl. Environ. Microbiol , vol.73 , Issue.16 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 50
    • 36549000721 scopus 로고    scopus 로고
    • Warnecke, F., Luginbühl, P., Ivanova, N., Ghassemian, M., Richardson, T.H., Stege, J.T., Cayouette, M., Mchardy, A.C., Djordjevic, G., Aboushadi, N., Sorek, R., Tringe, S.G., Podar, M., Martin, H.G., Kunin, V., Dalevi, D., Madejska, J., Kirton, E., Platt, D., Szeto, E., Salamov, A., Barry, K., Mikhailova, N., Kyrpides, N.C., Matson, E.G., Ottesen, E.A., Zhang, X., Hernández, M., Murillo, C., Acosta, L.G., Rigoutsos, I., Tamayo, G., Green, B.D., Chang, C., Rubin, E.M., Mathur, E.J., Robertson, D.E., Hugenholtz, P., Leadbetter, J.R.: Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450(7169), 560-565 (2007)
    • Warnecke, F., Luginbühl, P., Ivanova, N., Ghassemian, M., Richardson, T.H., Stege, J.T., Cayouette, M., Mchardy, A.C., Djordjevic, G., Aboushadi, N., Sorek, R., Tringe, S.G., Podar, M., Martin, H.G., Kunin, V., Dalevi, D., Madejska, J., Kirton, E., Platt, D., Szeto, E., Salamov, A., Barry, K., Mikhailova, N., Kyrpides, N.C., Matson, E.G., Ottesen, E.A., Zhang, X., Hernández, M., Murillo, C., Acosta, L.G., Rigoutsos, I., Tamayo, G., Green, B.D., Chang, C., Rubin, E.M., Mathur, E.J., Robertson, D.E., Hugenholtz, P., Leadbetter, J.R.: Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450(7169), 560-565 (2007)
  • 51
    • 33645319955 scopus 로고    scopus 로고
    • Predicting interactions in protein networks by completing defective cliques
    • Yu, H., Paccanaro, A., Trifonov, V., Gerstein, M.: Predicting interactions in protein networks by completing defective cliques. Bioinformatics 22(7), 823-829 (2006)
    • (2006) Bioinformatics , vol.22 , Issue.7 , pp. 823-829
    • Yu, H.1    Paccanaro, A.2    Trifonov, V.3    Gerstein, M.4
  • 52
    • 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 Dev. 21(9), 1010-1024 (2007)
    • (2007) Genes Dev , vol.21 , Issue.9 , pp. 1010-1024
    • Zhu, X.1    Gerstein, M.2    Snyder, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.