메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

Author keywords

Archetypal analysis; Cystic fibrosis; Gene expression; Hypermutators; Pseudomonas aeruginosa

Indexed keywords

ARCHETYPAL ANALYSIS; CYSTIC FIBROSIS; DNA MICROARRAY ANALYSIS; GENE EXPRESSION PATTERNS; HYPERMUTATORS; INTERPRETATION OF DATA; MATRIX FACTORIZATIONS; PSEUDOMONAS AERUGINOSA;

EID: 84884372193     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-279     Document Type: Article
Times cited : (47)

References (34)
  • 1
    • 61749093225 scopus 로고    scopus 로고
    • A novel methodology for finding the regulation on gene expression data
    • Liu W, Wang B, Glassey J, Martin E, Zhao J. A novel methodology for finding the regulation on gene expression data. Proc Natl Acad Sci U S A 2009, 19:267-272.
    • (2009) Proc Natl Acad Sci U S A , vol.19 , pp. 267-272
    • Liu, W.1    Wang, B.2    Glassey, J.3    Martin, E.4    Zhao, J.5
  • 3
    • 84864054608 scopus 로고    scopus 로고
    • Comprehensive evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data
    • Kim MH, Seo HJ, Joung JG, Kim JH. Comprehensive evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data. BMC bioinformatics 2011, 12(Suppl 1):S8.
    • (2011) BMC bioinformatics , vol.12 , Issue.SUPPL 1
    • Kim, M.H.1    Seo, H.J.2    Joung, J.G.3    Kim, J.H.4
  • 4
    • 0035375137 scopus 로고    scopus 로고
    • Computational analysis of microarray data: nature reviews
    • Quackenbush J. Computational analysis of microarray data: nature reviews. Genetics 2001, 2:418-427.
    • (2001) Genetics , vol.2 , pp. 418-427
    • Quackenbush, J.1
  • 5
    • 84855238658 scopus 로고    scopus 로고
    • Archetypal analysis for machine learning and data mining
    • Mørup M, Hansen LK. Archetypal analysis for machine learning and data mining. Neurocomputing 2012, 80:54-63.
    • (2012) Neurocomputing , vol.80 , pp. 54-63
    • Mørup, M.1    Hansen, L.K.2
  • 7
    • 33846015059 scopus 로고    scopus 로고
    • Archetypes and principal components of an IR image sequence
    • Marinetti S, Finesso L, Marsilio E. Archetypes and principal components of an IR image sequence. Infrared Phys Technol 2007, 49:272-276.
    • (2007) Infrared Phys Technol , vol.49 , pp. 272-276
    • Marinetti, S.1    Finesso, L.2    Marsilio, E.3
  • 9
    • 35649024854 scopus 로고    scopus 로고
    • Toward the human genotope
    • 10.1007/s11538-007-9244-7, 17874271
    • Huggins P, Pachter L, Sturmfels B. Toward the human genotope. Bull Math Biol 2007, 69:2723-2735. 10.1007/s11538-007-9244-7, 17874271.
    • (2007) Bull Math Biol , vol.69 , pp. 2723-2735
    • Huggins, P.1    Pachter, L.2    Sturmfels, B.3
  • 10
    • 76949086352 scopus 로고    scopus 로고
    • Applying unmixing to gene expression data for tumor phylogeny inference
    • Schwartz R, Shackney SE. Applying unmixing to gene expression data for tumor phylogeny inference. BMC Bioinforma 2010, 11:42.
    • (2010) BMC Bioinforma , vol.11 , pp. 42
    • Schwartz, R.1    Shackney, S.E.2
  • 12
    • 84861671055 scopus 로고    scopus 로고
    • Efficiency in evolutionary trade-offs
    • 10.1126/science.1223193, 22654045
    • Noor E, Milo R. Efficiency in evolutionary trade-offs. Science 2012, 336:1114-1115. 10.1126/science.1223193, 22654045.
    • (2012) Science , vol.336 , pp. 1114-1115
    • Noor, E.1    Milo, R.2
  • 16
    • 78751522378 scopus 로고    scopus 로고
    • Parallel evolution in pseudomonas aeruginosa over 39,000 generations in vivo
    • Huse H, Kwon T, Zlosnik J, Speert D. Parallel evolution in pseudomonas aeruginosa over 39,000 generations in vivo. MBio 2010, 1:0-8.
    • (2010) MBio , vol.1 , pp. 0-8
    • Huse, H.1    Kwon, T.2    Zlosnik, J.3    Speert, D.4
  • 17
    • 80051785694 scopus 로고    scopus 로고
    • Bacterial adaptation during chronic infection revealed by independent component analysis of transcriptomic data
    • 10.1186/1471-2180-11-184, 3224102, 21851621
    • Yang L, Rau MH, Yang L, Hoiby N, Molin S, Jelsbak L. Bacterial adaptation during chronic infection revealed by independent component analysis of transcriptomic data. BMC Microbiol 2011, 11:184. 10.1186/1471-2180-11-184, 3224102, 21851621.
    • (2011) BMC Microbiol , vol.11 , pp. 184
    • Yang, L.1    Rau, M.H.2    Yang, L.3    Hoiby, N.4    Molin, S.5    Jelsbak, L.6
  • 18
    • 67650685860 scopus 로고    scopus 로고
    • Dynamics of adaptive microevolution of hypermutable pseudomonas aeruginosa during chronic pulmonary infection in patients with cystic fibrosis
    • 10.1086/599360, 19459782
    • Hoboth C, Hoffmann R, Eichner A, Henke C, Schmoldt S, Imhof A, Heesemann J, Hogardt M. Dynamics of adaptive microevolution of hypermutable pseudomonas aeruginosa during chronic pulmonary infection in patients with cystic fibrosis. J Infect Dis 2009, 200:118-130. 10.1086/599360, 19459782.
    • (2009) J Infect Dis , vol.200 , pp. 118-130
    • Hoboth, C.1    Hoffmann, R.2    Eichner, A.3    Henke, C.4    Schmoldt, S.5    Imhof, A.6    Heesemann, J.7    Hogardt, M.8
  • 19
    • 79954716359 scopus 로고    scopus 로고
    • Mucoid pseudomonas aeruginosa isolates maintain the biofilm formation capacity and the gene expression profiles during the chronic lung infection of CF patients
    • 10.1111/j.1600-0463.2011.02726.x, 21492226
    • Lee B, Schjerling CK, Kirkby N, Hoffmann N, Borup R, Molin S, Høiby N, Ciofu O. Mucoid pseudomonas aeruginosa isolates maintain the biofilm formation capacity and the gene expression profiles during the chronic lung infection of CF patients. APMIS 2011, 119:263-274. 10.1111/j.1600-0463.2011.02726.x, 21492226.
    • (2011) APMIS , vol.119 , pp. 263-274
    • Lee, B.1    Schjerling, C.K.2    Kirkby, N.3    Hoffmann, N.4    Borup, R.5    Molin, S.6    Høiby, N.7    Ciofu, O.8
  • 24
    • 77954645140 scopus 로고    scopus 로고
    • Early adaptive developments of pseudomonas aeruginosa after the transition from life in the environment to persistent colonization in the airways of human cystic fibrosis hosts
    • Rau MH, Hansen SK, Johansen HK, Thomsen LE, Workman CT, Nielsen KF, Jelsbak L, Høiby N, Yang L, Molin S. Early adaptive developments of pseudomonas aeruginosa after the transition from life in the environment to persistent colonization in the airways of human cystic fibrosis hosts. Environ Microbiol 2010, 12:1643-1658.
    • (2010) Environ Microbiol , vol.12 , pp. 1643-1658
    • Rau, M.H.1    Hansen, S.K.2    Johansen, H.K.3    Thomsen, L.E.4    Workman, C.T.5    Nielsen, K.F.6    Jelsbak, L.7    Høiby, N.8    Yang, L.9    Molin, S.10
  • 25
    • 78651267246 scopus 로고    scopus 로고
    • Pseudomonas genome database: improved comparative analysis and population genomics capability for pseudomonas genomes
    • 10.1093/nar/gkq869, 3013766, 20929876
    • Winsor GL, Lam DKW, Fleming L, Lo R, Whiteside MD, Yu NY, Hancock REW, Brinkman FSL. Pseudomonas genome database: improved comparative analysis and population genomics capability for pseudomonas genomes. Nucleic Acids Res 2011, 39:D596-D600. 10.1093/nar/gkq869, 3013766, 20929876.
    • (2011) Nucleic Acids Res , vol.39
    • Winsor, G.L.1    Lam, D.K.W.2    Fleming, L.3    Lo, R.4    Whiteside, M.D.5    Yu, N.Y.6    Hancock, R.E.W.7    Brinkman, F.S.L.8
  • 26
    • 33847264343 scopus 로고    scopus 로고
    • Enrichment or depletion of a GO category within a class of genes: which test?
    • 10.1093/bioinformatics/btl633, 17182697
    • Rivals I, Personnaz L, Taing L, Potier M. Enrichment or depletion of a GO category within a class of genes: which test?. Bioinformatics 2007, 23:401-407. 10.1093/bioinformatics/btl633, 17182697.
    • (2007) Bioinformatics , vol.23 , pp. 401-407
    • Rivals, I.1    Personnaz, L.2    Taing, L.3    Potier, M.4
  • 27
    • 84864390974 scopus 로고    scopus 로고
    • Deletion and acquisition of genomic content during early stage adaptation of pseudomonas aeruginosa to a human host environment
    • 10.1111/j.1462-2920.2012.02795.x, 22672046
    • Rau MH, Marvig RL, Ehrlich GD, Molin S, Jelsbak L. Deletion and acquisition of genomic content during early stage adaptation of pseudomonas aeruginosa to a human host environment. Environ Microbiol 2012, 14:2200-2211. 10.1111/j.1462-2920.2012.02795.x, 22672046.
    • (2012) Environ Microbiol , vol.14 , pp. 2200-2211
    • Rau, M.H.1    Marvig, R.L.2    Ehrlich, G.D.3    Molin, S.4    Jelsbak, L.5
  • 28
    • 0029814366 scopus 로고    scopus 로고
    • Microbial pathogenesis in cystic fibrosis: mucoid pseudomonas aeruginosa and burkholderia cepacia
    • 239456, 8840786
    • Govan JR, Deretic V. Microbial pathogenesis in cystic fibrosis: mucoid pseudomonas aeruginosa and burkholderia cepacia. Microbiological reviews 1996, 60:539-574. 239456, 8840786.
    • (1996) Microbiological reviews , vol.60 , pp. 539-574
    • Govan, J.R.1    Deretic, V.2
  • 30
    • 35748957770 scopus 로고    scopus 로고
    • The microbiology of mutability
    • 10.1111/j.1574-6968.2007.00901.x, 17714481
    • Sundin GW, Weigand MR. The microbiology of mutability. FEMS Microbiol Lett 2007, 277:11-20. 10.1111/j.1574-6968.2007.00901.x, 17714481.
    • (2007) FEMS Microbiol Lett , vol.277 , pp. 11-20
    • Sundin, G.W.1    Weigand, M.R.2
  • 31
    • 57349088170 scopus 로고    scopus 로고
    • Genetic adaptation of pseudomonas aeruginosa to the airways of cystic fibrosis patients is catalyzed by hypermutation
    • 10.1128/JB.01147-08, 2593214, 18849421
    • Mena A, Smith EE, Burns JL, Speert DP, Moskowitz SM, Perez JL, Oliver A. Genetic adaptation of pseudomonas aeruginosa to the airways of cystic fibrosis patients is catalyzed by hypermutation. J Bacteriol 2008, 190:7910-7917. 10.1128/JB.01147-08, 2593214, 18849421.
    • (2008) J Bacteriol , vol.190 , pp. 7910-7917
    • Mena, A.1    Smith, E.E.2    Burns, J.L.3    Speert, D.P.4    Moskowitz, S.M.5    Perez, J.L.6    Oliver, A.7
  • 32
    • 77954644239 scopus 로고    scopus 로고
    • Bacterial hypermutation in cystic fibrosis, not only for antibiotic resistance
    • 10.1111/j.1469-0691.2010.03250.x, 20880409
    • Oliver A, Mena A. Bacterial hypermutation in cystic fibrosis, not only for antibiotic resistance. Clin Microbiol Infect 2010, 16:798-808. 10.1111/j.1469-0691.2010.03250.x, 20880409.
    • (2010) Clin Microbiol Infect , vol.16 , pp. 798-808
    • Oliver, A.1    Mena, A.2
  • 33
    • 79955723729 scopus 로고    scopus 로고
    • Inactivation of the DNA repair genes mutS, mutL or the anti-recombination gene mutS2 leads to activation of vitamin B1 biosynthesis genes
    • 10.1371/journal.pone.0019053, 3084264, 21552516
    • Fukui K, Wakamatsu T, Agari Y, Masui R, Kuramitsu S. Inactivation of the DNA repair genes mutS, mutL or the anti-recombination gene mutS2 leads to activation of vitamin B1 biosynthesis genes. PloS one 2011, 6:e19053. 10.1371/journal.pone.0019053, 3084264, 21552516.
    • (2011) PloS one , vol.6
    • Fukui, K.1    Wakamatsu, T.2    Agari, Y.3    Masui, R.4    Kuramitsu, S.5
  • 34
    • 77949515264 scopus 로고    scopus 로고
    • Simple sequence repeats and mucoid conversion: biased mucA mutagenesis in mismatch repair-deficient pseudomonas aeruginosa
    • 10.1371/journal.pone.0008203, 2781719, 19997602
    • Moyano AJ, Smania AM. Simple sequence repeats and mucoid conversion: biased mucA mutagenesis in mismatch repair-deficient pseudomonas aeruginosa. PloS one 2009, 4:e8203. 10.1371/journal.pone.0008203, 2781719, 19997602.
    • (2009) PloS one , vol.4
    • Moyano, A.J.1    Smania, A.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.