메뉴 건너뛰기




Volumn 33, Issue 19, 2005, Pages 6083-6089

Expansion of the Biocyc collection of pathway/genome databases to 160 genomes

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; GENE EXPRESSION; GENE SEQUENCE; GENETIC CODE; GENETIC CONSERVATION; GENETIC DATABASE; NONHUMAN; PRIORITY JOURNAL; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; ANIMAL; BIOLOGY; GENETICS; GENOME; GENOMICS; HUMAN; METABOLISM;

EID: 27244436714     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki892     Document Type: Article
Times cited : (507)

References (39)
  • 2
    • 0042312609 scopus 로고    scopus 로고
    • PseudoCyc, a pathway-genome database for Pseudomonas aeruginosa
    • Romero,P. and Karp,P. (2003) PseudoCyc, a pathway-genome database for Pseudomonas aeruginosa. J. Mol. Microbiol. Biotechnol., 5, 230-239.
    • (2003) J. Mol. Microbiol. Biotechnol. , vol.5 , pp. 230-239
    • Romero, P.1    Karp, P.2
  • 3
    • 2442636351 scopus 로고    scopus 로고
    • Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery
    • Yeh,I., Hanekamp,T., Tsoka,S., Karp,P.D. and Altman,R.B. (2004) Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery. Genome Res., 14, 917-924.
    • (2004) Genome Res. , vol.14 , pp. 917-924
    • Yeh, I.1    Hanekamp, T.2    Tsoka, S.3    Karp, P.D.4    Altman, R.B.5
  • 5
    • 0037249498 scopus 로고    scopus 로고
    • The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
    • Rhee,S.Y., Beavis,W., Berardini,T.Z., Chen,G., Dixon,D., Doyle,A., Garcia-Hernandez,M., Huala,E., Lander,G., Montoya,M. et al. (2003) The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res., 31, 224-228.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 224-228
    • Rhee, S.Y.1    Beavis, W.2    Berardini, T.Z.3    Chen, G.4    Dixon, D.5    Doyle, A.6    Garcia-Hernandez, M.7    Huala, E.8    Lander, G.9    Montoya, M.10
  • 8
    • 0036175276 scopus 로고    scopus 로고
    • The past, present and future of genome-wide re-annotation
    • COMMENT2001
    • Ouzounis,C.A. and Karp,P.D. (2002) The past, present and future of genome-wide re-annotation. Genome Biol., 3 COMMENT2001.
    • (2002) Genome Biol. , vol.3
    • Ouzounis, C.A.1    Karp, P.D.2
  • 9
    • 0032032781 scopus 로고    scopus 로고
    • Metabolic databases
    • Karp,P.D. (1998) Metabolic databases. Trends Biochem. Sci., 23, 114-116.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 114-116
    • Karp, P.D.1
  • 10
    • 0033168258 scopus 로고    scopus 로고
    • Integrated pathway-genome databases and their role in drug discovery
    • Karp,P.D., Krummenacker,M., Paley,S. and Wagg,J. (1999) Integrated pathway-genome databases and their role in drug discovery. Trends Biotechnol., 17, 275-281.
    • (1999) Trends Biotechnol. , vol.17 , pp. 275-281
    • Karp, P.D.1    Krummenacker, M.2    Paley, S.3    Wagg, J.4
  • 11
    • 0035860545 scopus 로고    scopus 로고
    • Pathway databases: A case study in computational symbolic theories
    • Karp,P.D. (2001) Pathway databases: A case study in computational symbolic theories. Science, 293, 2040-2044.
    • (2001) Science , vol.293 , pp. 2040-2044
    • Karp, P.D.1
  • 12
    • 0030340124 scopus 로고    scopus 로고
    • HinCyc: A knowledge base of the complete genome and metabolic pathways of H. influenzae
    • Karp,P.D., Ouzounis,C. and Paley,S. (1996) HinCyc: A knowledge base of the complete genome and metabolic pathways of H. influenzae. Proc. Int. Conf. Intell. Syst. Mol. Biol., 4, 116-124.
    • (1996) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.4 , pp. 116-124
    • Karp, P.D.1    Ouzounis, C.2    Paley, S.3
  • 14
    • 11244328060 scopus 로고    scopus 로고
    • The Pathway Tools software
    • Karp,P.D., Paley,S. and Romero,P. (eds)
    • The Pathway Tools software. In Karp,P.D., Paley,S. and Romero,P. (eds), Bioinformatics., 18 (Suppl. 1), S225-S232.
    • Bioinformatics , vol.18 , Issue.SUPPL. 1
  • 16
    • 0347132501 scopus 로고    scopus 로고
    • Metabolic database systems for the analysis of genome-wide function
    • Tsoka,S. and Ouzounis,C.A. (2003) Metabolic database systems for the analysis of genome-wide function. Biotechnol. Bioeng., 84, 750-755.
    • (2003) Biotechnol. Bioeng. , vol.84 , pp. 750-755
    • Tsoka, S.1    Ouzounis, C.A.2
  • 17
    • 0034020583 scopus 로고    scopus 로고
    • Global properties of the metabolic map of Escherichia coli
    • Ouzounis,C.A. and Karp,P.D. (2000) Global properties of the metabolic map of Escherichia coli. Genome Res., 10, 568-576.
    • (2000) Genome Res. , vol.10 , pp. 568-576
    • Ouzounis, C.A.1    Karp, P.D.2
  • 18
    • 0034828777 scopus 로고    scopus 로고
    • Functional versatility and molecular diversity of the metabolic map of Escherichia coli
    • Tsoka,S. and Ouzounis,C.A. (2001) Functional versatility and molecular diversity of the metabolic map of Escherichia coli. Genome Res., 11, 1503-1510.
    • (2001) Genome Res. , vol.11 , pp. 1503-1510
    • Tsoka, S.1    Ouzounis, C.A.2
  • 19
    • 0037350415 scopus 로고    scopus 로고
    • The phylogenetic extent of metabolic enzymes and pathways
    • Peregrin-Alvarez,J.M., Tsoka,S. and Ouzounis,C.A. (2003) The phylogenetic extent of metabolic enzymes and pathways. Genome Res., 13, 422-427.
    • (2003) Genome Res. , vol.13 , pp. 422-427
    • Peregrin-Alvarez, J.M.1    Tsoka, S.2    Ouzounis, C.A.3
  • 21
    • 13244268322 scopus 로고    scopus 로고
    • A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
    • Green,M.L. and Karp,P.D. (2004) A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics, 5, 76.
    • (2004) BMC Bioinformatics , vol.5 , pp. 76
    • Green, M.L.1    Karp, P.D.2
  • 22
  • 23
    • 0036086784 scopus 로고    scopus 로고
    • Evaluation of computational metabolic-pathway predictions for Helicobacter pylori
    • Paley,S.M. and Karp,P.D. (2002) Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinformatics, 18, 715-724.
    • (2002) Bioinformatics , vol.18 , pp. 715-724
    • Paley, S.M.1    Karp, P.D.2
  • 30
    • 24044478768 scopus 로고    scopus 로고
    • MagicMatch - Cross-referencing sequence identifiers across databases
    • Smith,M., Kunin,V., Goldovsky,L., Enright,A.J. and Ouzounis,C.A. (2005) MagicMatch - cross-referencing sequence identifiers across databases. Bioinformatics, 21, 3429-3430.
    • (2005) Bioinformatics , vol.21 , pp. 3429-3430
    • Smith, M.1    Kunin, V.2    Goldovsky, L.3    Enright, A.J.4    Ouzounis, C.A.5
  • 32
    • 13444306641 scopus 로고    scopus 로고
    • NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2005) NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33, D501-D504.
    • (2005) Nucleic Acids Res. , vol.33
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 33
    • 1842559849 scopus 로고    scopus 로고
    • Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases
    • Romero,P.R. and Karp,P.D. (2004) Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases. Bioinformatics, 20, 709-717.
    • (2004) Bioinformatics , vol.20 , pp. 709-717
    • Romero, P.R.1    Karp, P.D.2
  • 34
    • 0034040680 scopus 로고    scopus 로고
    • An ontology for biological function based on molecular interactions
    • Karp,P.D. (2000) An ontology for biological function based on molecular interactions. Bioinformatics, 16, 269-285.
    • (2000) Bioinformatics , vol.16 , pp. 269-285
    • Karp, P.D.1
  • 35
    • 0034570532 scopus 로고    scopus 로고
    • MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products
    • Serres,M.H. and Riley,M. (2000) MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. Microb. Comp. Genomics, 5, 205-222.
    • (2000) Microb. Comp. Genomics , vol.5 , pp. 205-222
    • Serres, M.H.1    Riley, M.2
  • 38
    • 23044485115 scopus 로고    scopus 로고
    • Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers
    • Green,M.L. and Karp,P.D. (2005) Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers. Nucleic Acids Res., 33, 4035-4039.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 4035-4039
    • Green, M.L.1    Karp, P.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.