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    Results: 1 to 20 of 254

    1.

    Computational prediction of human metabolic pathways from the complete human genome.

    Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD.

    Genome Biol. 2005;6(1):R2. Epub 2004 Dec 22.

    PMID:
    15642094
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases.

    Green ML, Karp PD.

    BMC Bioinformatics. 2004 Jun 9;5:76.

    PMID:
    15189570
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    3.

    MetaCyc and AraCyc. Metabolic pathway databases for plant research.

    Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp PD, Rhee SY.

    Plant Physiol. 2005 May;138(1):27-37.

    PMID:
    15888675
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    4.

    Eco Cyc: encyclopedia of Escherichia coli genes and metabolism.

    Karp PD, Riley M, Paley SM, Pellegrini-Toole A, Krummenacker M.

    Nucleic Acids Res. 1999 Jan 1;27(1):55-8.

    PMID:
    9847140
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    5.

    Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.

    Paley SM, Karp PD.

    Bioinformatics. 2002 May;18(5):715-24.

    PMID:
    12050068
    [PubMed - indexed for MEDLINE]
    Free Article
    6.

    MetaCyc: a multiorganism database of metabolic pathways and enzymes.

    Krieger CJ, Zhang P, Mueller LA, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, Karp PD.

    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D438-42.

    PMID:
    14681452
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    7.

    Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

    Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.

    PLoS Biol. 2004 Jun;2(6):e162. Epub 2004 Apr 20. Erratum in: PLoS Biol. 2004 Jul;2(7):e256.

    PMID:
    15103394
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    9.

    Pathway databases: a case study in computational symbolic theories.

    Karp PD.

    Science. 2001 Sep 14;293(5537):2040-4.

    PMID:
    11557880
    [PubMed - indexed for MEDLINE]
    10.

    LeishCyc: a biochemical pathways database for Leishmania major.

    Doyle MA, MacRae JI, De Souza DP, Saunders EC, McConville MJ, Likić VA.

    BMC Syst Biol. 2009 Jun 5;3:57.

    PMID:
    19497128
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.

    Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Paley S, Popescu L, Pujar A, Shearer AG, Zhang P, Karp PD.

    Nucleic Acids Res. 2010 Jan;38(Database issue):D473-9. Epub 2009 Oct 22.

    PMID:
    19850718
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    12.

    Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.

    Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahrén D, Tsoka S, Darzentas N, Kunin V, López-Bigas N.

    Nucleic Acids Res. 2005 Oct 24;33(19):6083-9. Print 2005.

    PMID:
    16246909
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    13.

    The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.

    Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD.

    Nucleic Acids Res. 2008 Jan;36(Database issue):D623-31. Epub 2007 Oct 27.

    PMID:
    17965431
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    14.

    Reconstruction of metabolic pathways for the cattle genome.

    Seo S, Lewin HA.

    BMC Syst Biol. 2009 Mar 12;3:33.

    PMID:
    19284618
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing.

    Lin J, Qian J, Greenbaum D, Bertone P, Das R, Echols N, Senes A, Stenger B, Gerstein M.

    Nucleic Acids Res. 2002 Oct 15;30(20):4574-82.

    PMID:
    12384605
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    16.

    Genome organization in Arabidopsis thaliana: a survey for genes involved in isoprenoid and chlorophyll metabolism.

    Lange BM, Ghassemian M.

    Plant Mol Biol. 2003 Apr;51(6):925-48.

    PMID:
    12777052
    [PubMed - indexed for MEDLINE]
    17.

    Accelerating the reconstruction of genome-scale metabolic networks.

    Notebaart RA, van Enckevort FH, Francke C, Siezen RJ, Teusink B.

    BMC Bioinformatics. 2006 Jun 13;7:296.

    PMID:
    16772023
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    18.

    Visualizing metabolic activity on a genome-wide scale.

    Luyf AC, de Gast J, van Kampen AH.

    Bioinformatics. 2002 Jun;18(6):813-8.

    PMID:
    12075016
    [PubMed - indexed for MEDLINE]
    Free Article
    19.

    AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis.

    de Oliveira Dal'Molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK.

    Plant Physiol. 2010 Feb;152(2):579-89. Epub 2009 Dec 31.

    PMID:
    20044452
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    20.

    CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences.

    Chen X, Laudeman TW, Rushton PJ, Spraggins TA, Timko MP.

    BMC Bioinformatics. 2007 Apr 19;8:129.

    PMID:
    17445272
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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