메뉴 건너뛰기




Volumn 103, Issue 1, 2014, Pages 1-10

DuctApe: A suite for the analysis and correlation of genomic and OmniLog™ Phenotype Microarray data

Author keywords

Genomics; KEGG; Metabolism; Phenomics; Phenotype Microarray

Indexed keywords

ACINETOBACTER; ARTICLE; BACTERIAL CELL; BACTERIAL GENOME; BACTERIAL STRAIN; CELL METABOLISM; COMPUTER PROGRAM; ESCHERICHIA COLI; GENE SEQUENCE; GENOMICS; MICROARRAY ANALYSIS; PRIORITY JOURNAL; SINORHIZOBIUM MELILOTI; ZYMOMONAS MOBILIS;

EID: 84895898878     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2013.11.005     Document Type: Article
Times cited : (50)

References (48)
  • 1
    • 79951996636 scopus 로고    scopus 로고
    • Phenotype sequencing: identifying the genes that cause a phenotype directly from pooled sequencing of independent mutants
    • Harper M.A., Chen Z., Toy T., Machado I.M., Nelson S.F., Liao J.C., Lee C.J. Phenotype sequencing: identifying the genes that cause a phenotype directly from pooled sequencing of independent mutants. PLoS One 2011, 6:e16517.
    • (2011) PLoS One , vol.6
    • Harper, M.A.1    Chen, Z.2    Toy, T.3    Machado, I.M.4    Nelson, S.F.5    Liao, J.C.6    Lee, C.J.7
  • 3
    • 84860543260 scopus 로고    scopus 로고
    • PhenoLink-a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains
    • Bayjanov J.R., Molenaar D., Tzeneva V., Siezen R.J., van Hijum S.A. PhenoLink-a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains. BMC Genomics 2012, 13:170.
    • (2012) BMC Genomics , vol.13 , pp. 170
    • Bayjanov, J.R.1    Molenaar, D.2    Tzeneva, V.3    Siezen, R.J.4    van Hijum, S.A.5
  • 4
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies: the next generation
    • Metzker M.L. Sequencing technologies: the next generation. Nat. Rev. Genet. 2010, 11:31-46.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 5
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis E.R. The impact of next-generation sequencing technology on genetics. Trends Genet. 2008, 24:133.
    • (2008) Trends Genet. , vol.24 , pp. 133
    • Mardis, E.R.1
  • 6
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa M., Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28:27-30.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 9
    • 76449115656 scopus 로고    scopus 로고
    • Integrating multiple 'omics' analysis for microbial biology: application and methodologies
    • Zhang W., Li F., Nie L. Integrating multiple 'omics' analysis for microbial biology: application and methodologies. Microbiology 2010, 156:287-301.
    • (2010) Microbiology , vol.156 , pp. 287-301
    • Zhang, W.1    Li, F.2    Nie, L.3
  • 10
    • 0034911878 scopus 로고    scopus 로고
    • Phenotype microarrays for high-throughput phenotypic testing and assay of gene function
    • Bochner B.R., Gadzinski P., Panomitros E. Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Res. 2001, 11:1246-1255.
    • (2001) Genome Res. , vol.11 , pp. 1246-1255
    • Bochner, B.R.1    Gadzinski, P.2    Panomitros, E.3
  • 12
    • 24044549351 scopus 로고    scopus 로고
    • PhD: a web database application for phenotype data management
    • Li J.L., Li M.X., Deng H.Y., Duffy P., Deng H.W. PhD: a web database application for phenotype data management. Bioinformatics 2005, 21:3443-3444.
    • (2005) Bioinformatics , vol.21 , pp. 3443-3444
    • Li, J.L.1    Li, M.X.2    Deng, H.Y.3    Duffy, P.4    Deng, H.W.5
  • 15
    • 84859982600 scopus 로고    scopus 로고
    • Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics
    • Vaas L.A.I., Sikorski J., Michael V., Göker M., Klenk H.P. Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS One 2012, 7:e34846.
    • (2012) PLoS One , vol.7
    • Vaas, L.A.I.1    Sikorski, J.2    Michael, V.3    Göker, M.4    Klenk, H.P.5
  • 18
    • 61449098559 scopus 로고    scopus 로고
    • Involvement of the oscA gene in the sulphur starvation response and in Cr(VI) resistance in Pseudomonas corrugata 28
    • Viti C., Decorosi F., Mini A., Tatti E., Giovannetti L. Involvement of the oscA gene in the sulphur starvation response and in Cr(VI) resistance in Pseudomonas corrugata 28. Microbiology 2009, 155:95-105.
    • (2009) Microbiology , vol.155 , pp. 95-105
    • Viti, C.1    Decorosi, F.2    Mini, A.3    Tatti, E.4    Giovannetti, L.5
  • 28
    • 79953315166 scopus 로고    scopus 로고
    • Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes
    • Popa O., Hazkani-Covo E., Landan G., Martin W., Dagan T. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res. 2011, 21:599-609.
    • (2011) Genome Res. , vol.21 , pp. 599-609
    • Popa, O.1    Hazkani-Covo, E.2    Landan, G.3    Martin, W.4    Dagan, T.5
  • 32
    • 79952595565 scopus 로고    scopus 로고
    • The NumPy array: a structure for efficient numerical computation
    • Van Der Walt S., Colbert S.C., Varoquaux G. The NumPy array: a structure for efficient numerical computation. Comput.Sci. Eng. 2011, 13:22-30.
    • (2011) Comput.Sci. Eng. , vol.13 , pp. 22-30
    • Van Der Walt, S.1    Colbert, S.C.2    Varoquaux, G.3
  • 35
    • 34247493236 scopus 로고    scopus 로고
    • Matplotlib: a 2D graphics environment
    • Hunter J.D. Matplotlib: a 2D graphics environment. Comput.Sci. Eng. 2007, 90-95.
    • (2007) Comput.Sci. Eng. , pp. 90-95
    • Hunter, J.D.1
  • 38
    • 0141519279 scopus 로고    scopus 로고
    • OrthoMCL: identification of ortholog groups for eukaryotic genomes
    • Li L., Stoeckert C.J., Roos D.S. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003, 13:2178-2189.
    • (2003) Genome Res. , vol.13 , pp. 2178-2189
    • Li, L.1    Stoeckert, C.J.2    Roos, D.S.3
  • 39
    • 0035861990 scopus 로고    scopus 로고
    • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
    • Remm M., Storm C.E., Sonnhammer E.L. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 2001, 314:1041-1052.
    • (2001) J. Mol. Biol. , vol.314 , pp. 1041-1052
    • Remm, M.1    Storm, C.E.2    Sonnhammer, E.L.3
  • 40
    • 84892506113 scopus 로고    scopus 로고
    • Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals
    • Dalquen D.A., Dessimoz C. Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals. Genome Biol. Evol. 2013, 5:1800-1806.
    • (2013) Genome Biol. Evol. , vol.5 , pp. 1800-1806
    • Dalquen, D.A.1    Dessimoz, C.2
  • 41
    • 0010063566 scopus 로고
    • Who belongs in the family?
    • Thorndike R.L. Who belongs in the family?. Psychometrika 1953, 18:267-276.
    • (1953) Psychometrika , vol.18 , pp. 267-276
    • Thorndike, R.L.1
  • 44
    • 0032514651 scopus 로고    scopus 로고
    • Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli
    • Hubbard B.K., Koch M., Palmer D.R., Babbitt P.C., Gerlt J.A. Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli. Biochemistry 1998, 37:14369-14375.
    • (1998) Biochemistry , vol.37 , pp. 14369-14375
    • Hubbard, B.K.1    Koch, M.2    Palmer, D.R.3    Babbitt, P.C.4    Gerlt, J.A.5
  • 45
    • 80053593606 scopus 로고    scopus 로고
    • Hydrogen-stimulated carbon acquisition and conservation in Salmonella enterica serovar Typhimurium
    • Lamichhane-Khadka R., Frye J.G., Porwollik S., McClelland M., Maier R.J. Hydrogen-stimulated carbon acquisition and conservation in Salmonella enterica serovar Typhimurium. J. Bacteriol. 2011, 193:5824-5832.
    • (2011) J. Bacteriol. , vol.193 , pp. 5824-5832
    • Lamichhane-Khadka, R.1    Frye, J.G.2    Porwollik, S.3    McClelland, M.4    Maier, R.J.5
  • 46
    • 77954038036 scopus 로고    scopus 로고
    • Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing
    • Camarena L., Bruno V., Euskirchen G., Poggio S., Snyder M. Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing. PLoS Pathog. 2010, 6:e1000834.
    • (2010) PLoS Pathog. , vol.6
    • Camarena, L.1    Bruno, V.2    Euskirchen, G.3    Poggio, S.4    Snyder, M.5
  • 47
    • 0029011965 scopus 로고
    • Functional expression of the glucose transporter of Zymomonas mobilis leads to restoration of glucose and fructose uptake in Escherichia coli mutants and provides evidence for its facilitator action
    • Weisser P., Krämer R., Sahm H., Sprenger G.A. Functional expression of the glucose transporter of Zymomonas mobilis leads to restoration of glucose and fructose uptake in Escherichia coli mutants and provides evidence for its facilitator action. J. Bacteriol. 1995, 177:3351-3354.
    • (1995) J. Bacteriol. , vol.177 , pp. 3351-3354
    • Weisser, P.1    Krämer, R.2    Sahm, H.3    Sprenger, G.A.4
  • 48
    • 35948957452 scopus 로고    scopus 로고
    • Metabolic capacity of Bacillus cereus strains ATCC 14579 and ATCC 10987 interlinked with comparative genomics
    • Mols M., De Been M., Zwietering M.H., Moezelaar R., Abee T. Metabolic capacity of Bacillus cereus strains ATCC 14579 and ATCC 10987 interlinked with comparative genomics. Environ. Microbiol. 2007, 9:2933-2944.
    • (2007) Environ. Microbiol. , vol.9 , pp. 2933-2944
    • Mols, M.1    De Been, M.2    Zwietering, M.H.3    Moezelaar, R.4    Abee, T.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.