메뉴 건너뛰기




Volumn 14, Issue 6, 2007, Pages 817-838

Biological networks: Comparison, conservation, and evolution via relative description length

Author keywords

Biological networks; Conserved regions; Metabolic networks; Network evolution; Networks comparison; Relative description length; Tree reconstruction

Indexed keywords

BIOLOGY; CALCULATION; CONFERENCE PAPER; CYTOLOGY; EVOLUTION; MATHEMATICAL ANALYSIS; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN INTERACTION;

EID: 34547666722     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2007.R018     Document Type: Conference Paper
Times cited : (11)

References (55)
  • 1
    • 0034830306 scopus 로고    scopus 로고
    • Properties of a thermostable nitrate reductase from the hyperthermophilic archaeon pyrobaculum aerophilum
    • Afshar, S., Johnson, E., Viries, S., et al. 2001. Properties of a thermostable nitrate reductase from the hyperthermophilic archaeon pyrobaculum aerophilum. J. Bact. 183, 5491-5495.
    • (2001) J. Bact , vol.183 , pp. 5491-5495
    • Afshar, S.1    Johnson, E.2    Viries, S.3
  • 2
    • 0025183708 scopus 로고
    • Basic local alignment search tool
    • Altschul, S.F., Gish, W., Miler, W., et al. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
    • (1990) J. Mol. Biol , vol.215 , pp. 403-410
    • Altschul, S.F.1    Gish, W.2    Miler, W.3
  • 3
    • 0025289157 scopus 로고
    • Tetrachloroethene transformation to trichloroethene and cis-1,2-dichloroethene by sulfate-reducing enrichment cultures
    • Bagly, D.M., and Gossett, J.M. 1990. Tetrachloroethene transformation to trichloroethene and cis-1,2-dichloroethene by sulfate-reducing enrichment cultures. Appl. Environ. Microbiol. 56, 2511-2516.
    • (1990) Appl. Environ. Microbiol , vol.56 , pp. 2511-2516
    • Bagly, D.M.1    Gossett, J.M.2
  • 4
    • 6944240088 scopus 로고    scopus 로고
    • Berg, J., and Lassig, M. 2004. Local graph alignment and motif search in biological networks. Proc. Natl. Acad. Sci. USA 101, 14689-146842004.
    • Berg, J., and Lassig, M. 2004. Local graph alignment and motif search in biological networks. Proc. Natl. Acad. Sci. USA 101, 14689-146842004.
  • 5
    • 0035655004 scopus 로고    scopus 로고
    • The actin loci in the genus drosophila: Establishment of chromosomal homologies among five palearctic species of the drosophila obscura group by in situ hybridization
    • Bondinas, G.P., Loukas, M.G., Goulielmos, G.N., et al. 2001. The actin loci in the genus drosophila: establishment of chromosomal homologies among five palearctic species of the drosophila obscura group by in situ hybridization. Chromosoma 110, 441-450.
    • (2001) Chromosoma , vol.110 , pp. 441-450
    • Bondinas, G.P.1    Loukas, M.G.2    Goulielmos, G.N.3
  • 6
    • 33745794991 scopus 로고    scopus 로고
    • Information theoretic approaches to whole genome phytogenies
    • Burstein, D., Ulitsky, I., Tuller, T., et al. 2005. Information theoretic approaches to whole genome phytogenies. RECOMB 2005, 296-310.
    • (2005) RECOMB 2005 , pp. 296-310
    • Burstein, D.1    Ulitsky, I.2    Tuller, T.3
  • 7
    • 0033691587 scopus 로고    scopus 로고
    • A compression algorithm for DNA sequences and its applications in genome comparison
    • Chen, X., Kwong, S., and Li, M. 2000. A compression algorithm for DNA sequences and its applications in genome comparison. RECOMB 2000, 107-117.
    • (2000) RECOMB 2000 , pp. 107-117
    • Chen, X.1    Kwong, S.2    Li, M.3
  • 8
    • 0008758279 scopus 로고
    • 2.5) time algorithms for subgraph homeomorphisem problem on trees
    • 2.5) time algorithms for subgraph homeomorphisem problem on trees. J. Algorithms 8, 106-112.
    • (1987) J. Algorithms , vol.8 , pp. 106-112
    • Chung, M.J.1
  • 10
    • 0033255209 scopus 로고    scopus 로고
    • Ttetrachloroethene-dehalogenating bacteria
    • Damborsky, J. 1999. Ttetrachloroethene-dehalogenating bacteria. Folia Microbiol. 44, 247-262.
    • (1999) Folia Microbiol , vol.44 , pp. 247-262
    • Damborsky, J.1
  • 12
    • 0023239074 scopus 로고
    • Liver metabolism of budesonide in rat, mouse, and man. comparative aspects
    • Edsbacker, S., Andersson, P., Lindberg, C., et al. 1987. Liver metabolism of budesonide in rat, mouse, and man. comparative aspects. Drug Metab. Dispos. 15, 403-411.
    • (1987) Drug Metab. Dispos , vol.15 , pp. 403-411
    • Edsbacker, S.1    Andersson, P.2    Lindberg, C.3
  • 13
    • 26444590958 scopus 로고    scopus 로고
    • Fast neighbor joining
    • Elias, I., and Lagergren, J. 2005. Fast neighbor joining. ICALP, 1263-1274.
    • (2005) ICALP , pp. 1263-1274
    • Elias, I.1    Lagergren, J.2
  • 14
    • 0024248832 scopus 로고
    • Dependence of tetrachloroethylene dechlorination on methanogenic substrate consumption by methanosarcina sp. strain DCM
    • Fathepure, B.Z., and Boyd, S.A. 1988. Dependence of tetrachloroethylene dechlorination on methanogenic substrate consumption by methanosarcina sp. strain DCM. Appl. Environ. Microbiol. 54, 2976-2980.
    • (1988) Appl. Environ. Microbiol , vol.54 , pp. 2976-2980
    • Fathepure, B.Z.1    Boyd, S.A.2
  • 15
    • 34547719384 scopus 로고    scopus 로고
    • Felsenstein, J. 1993. Phylip phylogeny inference package, version 3.5c. Department of Genetics, University of Washington, Seattle
    • Felsenstein, J. 1993. Phylip (phylogeny inference package), version 3.5c. Department of Genetics, University of Washington, Seattle.
  • 16
    • 0037154277 scopus 로고    scopus 로고
    • Genome sequence of the hyperthermophilic crenarchaeon pyrobaculum aerophilum
    • Fitz-Gibbon, S.T., Lander, H., Kim, U.J., et al. 2001. Genome sequence of the hyperthermophilic crenarchaeon pyrobaculum aerophilum. Proc. Natl. Acad. Sci. USA 99, 984-989.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 984-989
    • Fitz-Gibbon, S.T.1    Lander, H.2    Kim, U.J.3
  • 17
    • 0037249406 scopus 로고    scopus 로고
    • The Sybase database of the drosophila genome projects and community literature
    • FlyBase Consortium
    • FlyBase Consortium. 2003. The Sybase database of the drosophila genome projects and community literature. Nucleic Acids Res. 31, 172-175.
    • (2003) Nucleic Acids Res , vol.31 , pp. 172-175
  • 18
    • 0032744302 scopus 로고    scopus 로고
    • Evolution of metabolisms: A new method for the comparison of metabolic pathways using genomics information
    • Forst, C.V., and Schulten, K. 1999. Evolution of metabolisms: a new method for the comparison of metabolic pathways using genomics information. J. Comput. Biol. 6, 343-360.
    • (1999) J. Comput. Biol , vol.6 , pp. 343-360
    • Forst, C.V.1    Schulten, K.2
  • 20
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • Gavin, A.C., et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147.
    • (2002) Nature , vol.415 , pp. 141-147
    • Gavin, A.C.1
  • 21
    • 0345600247 scopus 로고    scopus 로고
    • A protein interaction map of drosophila melanogaster
    • Giot, L., et al. 2003. A protein interaction map of drosophila melanogaster. Science 302, 1727-1736.
    • (2003) Science , vol.302 , pp. 1727-1736
    • Giot, L.1
  • 22
    • 0031038587 scopus 로고    scopus 로고
    • Expressed var genes are found in Plasmodium falciparum subtelomeric regions
    • Hernandez-Rivas, R., Mattei, D., Sterkers, Y., et al. 1997. Expressed var genes are found in Plasmodium falciparum subtelomeric regions. Mol. Cell. Biol. 17, 604-611.
    • (1997) Mol. Cell. Biol , vol.17 , pp. 604-611
    • Hernandez-Rivas, R.1    Mattei, D.2    Sterkers, Y.3
  • 24
    • 0033470181 scopus 로고    scopus 로고
    • Bile acids: The good, the bad, and the ugly
    • Hofmann, A.F. 1999. Bile acids: the good, the bad, and the ugly. News Physiol. Sci. 14, 24-29.
    • (1999) News Physiol. Sci , vol.14 , pp. 24-29
    • Hofmann, A.F.1
  • 26
    • 0034609791 scopus 로고    scopus 로고
    • The large-scale organization of metabolic networks
    • Jeong, H., Tombor, B., Albert, R., et al. 2000. The large-scale organization of metabolic networks. Nature 407, 651-654.
    • (2000) Nature , vol.407 , pp. 651-654
    • Jeong, H.1    Tombor, B.2    Albert, R.3
  • 27
    • 0034093870 scopus 로고    scopus 로고
    • The pharmacokinetics and metabolism of sucralose in the mouse
    • John, B.A., Wood, S.G., and Hawkins, D.R. 2000. The pharmacokinetics and metabolism of sucralose in the mouse. Food Chem. Toxicol. 38, 5107-5110.
    • (2000) Food Chem. Toxicol , vol.38 , pp. 5107-5110
    • John, B.A.1    Wood, S.G.2    Hawkins, D.R.3
  • 28
    • 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
  • 29
    • 33644874819 scopus 로고    scopus 로고
    • From genomics to chemical genomics: New developments in KEGG
    • Kanehisa, M., Goto, S., Hattori, M., et al. 2006. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-D357.
    • (2006) Nucleic Acids Res , vol.34
    • Kanehisa, M.1    Goto, S.2    Hattori, M.3
  • 30
    • 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., et al. 2003. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl. Acad. Sci. USA 100, 11394-11399.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 11394-11399
    • Kelley, B.P.1    Sharan, R.2    Karp, R.M.3
  • 31
    • 14844305006 scopus 로고    scopus 로고
    • An efficient algorithm for detecting frequent subgraphs in biological networks
    • Koyuturk, M., Grama, A., and Szpankowski, W. 2004. An efficient algorithm for detecting frequent subgraphs in biological networks. Bioinformatics 20, i200-i207.
    • (2004) Bioinformatics , vol.20
    • Koyuturk, M.1    Grama, A.2    Szpankowski, W.3
  • 32
    • 0142124263 scopus 로고    scopus 로고
    • Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
    • Krylov, D.M., Wolf, Y.I., Rogozin, I.B., et al. 2003. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13, 2229-2235.
    • (2003) Genome Res , vol.13 , pp. 2229-2235
    • Krylov, D.M.1    Wolf, Y.I.2    Rogozin, I.B.3
  • 33
    • 0035102453 scopus 로고    scopus 로고
    • An information-based sequence distance and its application to whole mitochondrial genome phylogeny
    • Li, M., Badger, J., Chen, X., et al. 2001. An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 17, 149-154.
    • (2001) Bioinformatics , vol.17 , pp. 149-154
    • Li, M.1    Badger, J.2    Chen, X.3
  • 36
    • 0004234375 scopus 로고    scopus 로고
    • John Wiley and Sons. Inc, New York
    • Michal, G. 1999. Biochemical Pathways. John Wiley and Sons. Inc., New York.
    • (1999) Biochemical Pathways
    • Michal, G.1
  • 37
    • 27544480571 scopus 로고    scopus 로고
    • Biotransformation of deramiclane in primary hepatocytes of rat, mouse, rabbit, dog, and human
    • Monostory, K., Khalmy, K., Ludanyi, K., et al. 2005. Biotransformation of deramiclane in primary hepatocytes of rat, mouse, rabbit, dog, and human. Drug. Metab. Dispos. 33, 1708-1716.
    • (2005) Drug. Metab. Dispos , vol.33 , pp. 1708-1716
    • Monostory, K.1    Khalmy, K.2    Ludanyi, K.3
  • 38
    • 0021956427 scopus 로고
    • Species differences in the metabolism of suprofen in laboratory animals and man
    • Mori, Y., Kuroda, N., Sakai, Y., et al. 1985. Species differences in the metabolism of suprofen in laboratory animals and man. Drug Metab. Dispos. 13, 239-245.
    • (1985) Drug Metab. Dispos , vol.13 , pp. 239-245
    • Mori, Y.1    Kuroda, N.2    Sakai, Y.3
  • 39
    • 34547711660 scopus 로고    scopus 로고
    • Available at:, Accessed Oct. 1
    • NCBI. 2007. NCBI Taxonomy Database. 2007. Available at: www.ncbi.nlm.nih.gov/entrez/linkout/tutorial/taxtour.html. Accessed Oct. 1, 2006.
    • (2006) NCBI. 2007. NCBI Taxonomy Database
  • 40
    • 0009353304 scopus 로고
    • Isolation and sequence of the gene for actin in saccharomyces cerevisiae
    • Ng, R., and Abelson, J. 1980. Isolation and sequence of the gene for actin in saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 77, 3912-3916.
    • (1980) Proc. Natl. Acad. Sci. USA , vol.77 , pp. 3912-3916
    • Ng, R.1    Abelson, J.2
  • 41
    • 0034667776 scopus 로고    scopus 로고
    • A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters
    • Ogata, H., Fujibuchi, W., Goto, S., et al. 2000. A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res. 28, 4021-4028.
    • (2000) Nucleic Acids Res , vol.28 , pp. 4021-4028
    • Ogata, H.1    Fujibuchi, W.2    Goto, S.3
  • 43
    • 0026559077 scopus 로고
    • The yeast sua7 gene encodes a homolog of human transcription factor TFIIB and is required for normal start site selection in vivo
    • Pinto, I., Ware, D.E., and Hampsey, M. 1992. The yeast sua7 gene encodes a homolog of human transcription factor TFIIB and is required for normal start site selection in vivo. Cell 68, 977-988.
    • (1992) Cell , vol.68 , pp. 977-988
    • Pinto, I.1    Ware, D.E.2    Hampsey, M.3
  • 44
    • 0035949490 scopus 로고    scopus 로고
    • Introduction of human apolipoprotein e4 "domain interaction" into mouse apolipoprotein E
    • Raffaï, R.L., Dong, L., Farese, Jr, R.V., et al. 2001. Introduction of human apolipoprotein e4 "domain interaction" into mouse apolipoprotein E. Proc. Natl. Acad. Sci. USA 98, 11587-11591.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 11587-11591
    • Raffaï, R.L.1    Dong, L.2    Farese Jr, R.V.3
  • 46
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N., and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
    • (1987) Mol. Biol. Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 47
    • 22144443022 scopus 로고    scopus 로고
    • Comparison of metabolic pathways using constraint graph drawing
    • Schreiber, F. 2003. Comparison of metabolic pathways using constraint graph drawing. APBC 19, 105-110.
    • (2003) APBC , vol.19 , pp. 105-110
    • Schreiber, F.1
  • 48
    • 13844314048 scopus 로고    scopus 로고
    • Conserved patterns of protein interaction in multiple species
    • Sharan, R., Suthram, S., Kelley, R.M., et al. 2005. Conserved patterns of protein interaction in multiple species. Proc. Natl. Acad. Sci. USA 102, 1974-1979.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 1974-1979
    • Sharan, R.1    Suthram, S.2    Kelley, R.M.3
  • 50
    • 27744568481 scopus 로고    scopus 로고
    • The Plasmodium protein network diverges from those of other eukaryotes
    • Suthram, S., Sittler, T., and Ideker, T. 2005. The Plasmodium protein network diverges from those of other eukaryotes. Nature 438, 108-112.
    • (2005) Nature , vol.438 , pp. 108-112
    • Suthram, S.1    Sittler, T.2    Ideker, T.3
  • 51
    • 0033866412 scopus 로고    scopus 로고
    • Evidence for separable functions of srp1p, the yeast homolog of importin alpha (karyopherin alpha): Role for srplp and sts1p in protein degradation
    • Tabb, M.M., Tongaonkar, P., Vu, L., et al. 2000. Evidence for separable functions of srp1p, the yeast homolog of importin alpha (karyopherin alpha): role for srplp and sts1p in protein degradation. Mol. Cell Biol. 20, 6062-6073.
    • (2000) Mol. Cell Biol , vol.20 , pp. 6062-6073
    • Tabb, M.M.1    Tongaonkar, P.2    Vu, L.3
  • 52
    • 0034565517 scopus 로고    scopus 로고
    • A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy
    • Tohsato, Y., Matsuda, H., and Hashimoto, A. 2000. A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy. ISMB 2000, 376-383.
    • (2000) ISMB 2000 , pp. 376-383
    • Tohsato, Y.1    Matsuda, H.2    Hashimoto, A.3
  • 53
    • 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
  • 55
    • 0012584372 scopus 로고    scopus 로고
    • All pairs shortest paths using bridging sets and rectangular matrix multiplication
    • Zwick, U. 2002. All pairs shortest paths using bridging sets and rectangular matrix multiplication. J. ACM 49, 289-317.
    • (2002) J. ACM , vol.49 , pp. 289-317
    • Zwick, U.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.