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Volumn 5, Issue 8, 2009, Pages

A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCES; GENES; MAPPING; PROTEINS; QUERY PROCESSING;

EID: 70049085269     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000465     Document Type: Article
Times cited : (448)

References (28)
  • 1
    • 53649088131 scopus 로고    scopus 로고
    • Applications of next-generation sequencing technologies in functional genomics
    • Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92: 255-264.
    • (2008) Genomics , vol.92 , pp. 255-264
    • Morozova, O.1    Marra, M.A.2
  • 2
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30. (Pubitemid 30047706)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 6
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server - A public resource for the automatic phylogenetic and functional analysis of metagenomes
    • Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, et al. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
    • (2008) BMC Bioinformatics , vol.9 , pp. 386
    • Meyer, F.1    Paarmann, D.2    D'Souza, M.3    Olson, R.4    Glass, E.M.5
  • 7
    • 0037398732 scopus 로고    scopus 로고
    • Missing genes in metabolic pathways: A comparative genomics approach
    • DOI 10.1016/S1367-5931(03)00027-9
    • Osterman A, Overbeek R (2003) Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 7: 238-251. (Pubitemid 36514956)
    • (2003) Current Opinion in Chemical Biology , vol.7 , Issue.2 , pp. 238-251
    • Osterman, A.1    Overbeek, R.2
  • 8
    • 27144524216 scopus 로고    scopus 로고
    • Automatic detection of subsystem/pathway variants in genome analysis
    • DOI 10.1093/bioinformatics/bti1052
    • Ye Y, Osterman A, Overbeek R, Godzik A (2005) Automatic detection of subsystem/pathway variants in genome analysis. Bioinformatics 21 Suppl 1: i478-486. (Pubitemid 41794522)
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Ye, Y.1    Osterman, A.2    Overbeek, R.3    Godzik, A.4
  • 9
    • 67650657332 scopus 로고    scopus 로고
    • Functional annotation of hypothetical proteins - A review
    • Sivashankari S, Shanmughavel P (2006) Functional annotation of hypothetical proteins - A review. Bioinformation 1: 335-338.
    • (2006) Bioinformation , vol.1 , pp. 335-338
    • Sivashankari, S.1    Shanmughavel, P.2
  • 10
    • 33744471138 scopus 로고    scopus 로고
    • New avenues in protein function prediction
    • DOI 10.1110/ps.062158406
    • Friedberg I, Jambon M, Godzik A (2006) New avenues in protein function prediction. Protein Sci 15: 1527-1529. (Pubitemid 43800026)
    • (2006) Protein Science , vol.15 , Issue.6 , pp. 1527-1529
    • Friedberg, I.1    Jambon, M.2    Godzik, A.3
  • 11
    • 56449115108 scopus 로고    scopus 로고
    • Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut
    • Hongoh Y, Sharma VK, Prakash T, Noda S, Toh H, et al. (2008) Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut. Science 322: 1108-1109.
    • (2008) Science , vol.322 , pp. 1108-1109
    • Hongoh, Y.1    Sharma, V.K.2    Prakash, T.3    Noda, S.4    Toh, H.5
  • 14
    • 2642558991 scopus 로고    scopus 로고
    • Metagenomics: From acid mine to shining sea
    • Galperin M (2004) Metagenomics: from acid mine to shining sea. Environ Microbiol 6: 543-545.
    • (2004) Environ Microbiol , vol.6 , pp. 543-545
    • Galperin, M.1
  • 15
    • 67651173106 scopus 로고    scopus 로고
    • Proteomics by Mass Spectrometry: Approaches, Advances, and Applications
    • Epub ahead of print
    • Yates J, Ruse CI, Nakorchevsky A (2009) Proteomics by Mass Spectrometry: Approaches, Advances, and Applications. Annu Rev Biomed Eng Epub ahead of print.
    • (2009) Annu Rev Biomed Eng
    • Yates, J.1    Ruse, C.I.2    Nakorchevsky, A.3
  • 19
    • 27644480801 scopus 로고    scopus 로고
    • Moonlighting vacuolar protease: Multiple jobs for a busy protein
    • DOI 10.1016/j.tplants.2005.09.002, PII S1360138505002232
    • Rosin FM, Watanabe N, Lam E (2005) Moonlighting vacuolar protease: multiple jobs for a busy protein. Trends Plant Sci 10: 516-518. (Pubitemid 41566272)
    • (2005) Trends in Plant Science , vol.10 , Issue.11 , pp. 516-518
    • Rosin, F.M.1    Watanabe, N.2    Lam, E.3
  • 20
    • 27144533653 scopus 로고    scopus 로고
    • Reconstructing the metabolic network of a bacterium from its genome
    • DOI 10.1016/j.tim.2005.09.001, PII S0966842X05002490
    • Francke C, Siezen RJ, Teusink B (2005) Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol 13: 550-558. (Pubitemid 41506897)
    • (2005) Trends in Microbiology , vol.13 , Issue.11 , pp. 550-558
    • Francke, C.1    Siezen, R.J.2    Teusink, B.3
  • 21
    • 41149163825 scopus 로고    scopus 로고
    • Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1
    • Oberhardt MA, Puchalka J, Fryer KE, Martins dos Santos VA, Papin JA (2008) Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. J Bacteriol 190: 2790-2803.
    • (2008) J Bacteriol , vol.190 , pp. 2790-2803
    • Oberhardt, M.A.1    Puchalka, J.2    Fryer, K.E.3    Martins Dos Santos, V.A.4    Papin, J.A.5
  • 22
    • 34547830859 scopus 로고    scopus 로고
    • SPINE: A framework for signaling-regulatory pathway inference from cause-effect experiments
    • DOI 10.1093/bioinformatics/btm170
    • Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R (2007) SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics 23: i359-366. (Pubitemid 47244421)
    • (2007) Bioinformatics , vol.23 , Issue.13
    • Ourfali, O.1    Shlomi, T.2    Ideker, T.3    Ruppin, E.4    Sharan, R.5
  • 26
    • 1842451398 scopus 로고    scopus 로고
    • 1001 Optimal PDB structure alignments: Integer programming methods for finding the maximum contact map overlap
    • DOI 10.1089/106652704773416876
    • Caprara A, Carr R, Istrail S, Lancia G, Walenz B (2004) 1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap. J Comput Biol 11: 27-52. (Pubitemid 38429362)
    • (2004) Journal of Computational Biology , vol.11 , Issue.1 , pp. 27-52
    • Caprara, A.1    Carr, R.2    Istrail, S.3    Lancia, G.4    Walenz, B.5
  • 27
    • 0242369082 scopus 로고    scopus 로고
    • RAPTOR: Optimal protein threading by linear programming
    • Xu J, Li M, Kim D, Xu Y (2004) RAPTOR: optimal protein threading by linear programming. J Bioinform Comput Biol 1: 95-117.
    • (2004) J Bioinform Comput Biol , vol.1 , pp. 95-117
    • Xu, J.1    Li, M.2    Kim, D.3    Xu, Y.4
  • 28
    • 24044492038 scopus 로고    scopus 로고
    • Optimal robust non-unique probe selection using Integer Linear Programming
    • DOI 10.1093/bioinformatics/bth936
    • Klau GW, Rahmann S, Schliep A, Vingron M, Reinert K (2004) Optimal robust non-unique probe selection using Integer Linear Programming. Bioinformatics 20: i186-i193. (Pubitemid 41296688)
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Klau, G.W.1    Rahmann, S.2    Schliep, A.3    Vingron, M.4    Reinert, K.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.