메뉴 건너뛰기




Volumn 15, Issue 1, 2014, Pages

VAMPS: A website for visualization and analysis of microbial population structures

Author keywords

Bacteria; Data visualization; Microbial diversity; Microbial ecology; Microbiome; Next generation sequencing; SSU rRNA; Website

Indexed keywords

MICROBIAL DIVERSITY; MICROBIAL ECOLOGY; MICROBIOME; NEXT-GENERATION SEQUENCING; SSU RRNA;

EID: 84893161170     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-41     Document Type: Article
Times cited : (155)

References (27)
  • 1
    • 79251565226 scopus 로고    scopus 로고
    • Removing noise from pyrosequenced amplicons
    • 10.1186/1471-2105-12-38, 3045300, 21276213
    • Quince C, Lanzen A, Davenport R, Turnbaugh P. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 2011, 12(1):38. 10.1186/1471-2105-12-38, 3045300, 21276213.
    • (2011) BMC Bioinformatics , vol.12 , Issue.1 , pp. 38
    • Quince, C.1    Lanzen, A.2    Davenport, R.3    Turnbaugh, P.4
  • 2
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • 10.1093/bioinformatics/btq461, 20709691
    • Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26(19):2460-2461. 10.1093/bioinformatics/btq461, 20709691.
    • (2010) Bioinformatics , vol.26 , Issue.19 , pp. 2460-2461
    • Edgar, R.C.1
  • 3
    • 34548293679 scopus 로고    scopus 로고
    • A naive bayesian classifier for rapid assignment of rrna sequences into the new bacterial taxonomy
    • 10.1128/AEM.00062-07, 1950982, 17586664
    • Wang Q, Garrity GM, Tiedje JM, Cole JR. A naive bayesian classifier for rapid assignment of rrna sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007, 73(16):5261-5267. 10.1128/AEM.00062-07, 1950982, 17586664.
    • (2007) Appl Environ Microbiol , vol.73 , Issue.16 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 4
    • 37549027613 scopus 로고    scopus 로고
    • SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • 10.1093/nar/gkm864, 2175337, 17947321
    • Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl Acids Res 2007, 35(21):7188-7196. 10.1093/nar/gkm864, 2175337, 17947321.
    • (2007) Nucl Acids Res , vol.35 , Issue.21 , pp. 7188-7196
    • Pruesse, E.1    Quast, C.2    Knittel, K.3    Fuchs, B.M.4    Ludwig, W.5    Peplies, J.6    Glockner, F.O.7
  • 5
    • 53549118607 scopus 로고    scopus 로고
    • The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
    • 10.1186/1471-2105-9-386, 2563014, 18803844
    • Meyer F, Paarmann D, D'Souza M, Olson R, Glass E, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008, 9(1):386. 10.1186/1471-2105-9-386, 2563014, 18803844.
    • (2008) BMC Bioinformatics , vol.9 , Issue.1 , pp. 386
    • Meyer, F.1    Paarmann, D.2    D'Souza, M.3    Olson, R.4    Glass, E.5    Kubal, M.6    Paczian, T.7    Rodriguez, A.8    Stevens, R.9    Wilke, A.10
  • 8
    • 79951482388 scopus 로고    scopus 로고
    • Changing the equation on scientific data visualization
    • 10.1126/science.1197654, 21311008
    • Fox P, Hendler J. Changing the equation on scientific data visualization. Science 2011, 331(6018):705-708. 10.1126/science.1197654, 21311008.
    • (2011) Science , vol.331 , Issue.6018 , pp. 705-708
    • Fox, P.1    Hendler, J.2
  • 9
    • 34948842866 scopus 로고    scopus 로고
    • Accuracy and quality of massively parallel DNA pyrosequencing
    • 10.1186/gb-2007-8-7-r143, 2323236, 17659080
    • Huse S, Huber J, Morrison H, Sogin M, Mark Welch D. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 2007, 8(7):R143. 10.1186/gb-2007-8-7-r143, 2323236, 17659080.
    • (2007) Genome Biol , vol.8 , Issue.7
    • Huse, S.1    Huber, J.2    Morrison, H.3    Sogin, M.4    Mark Welch, D.5
  • 10
  • 12
    • 77955251092 scopus 로고    scopus 로고
    • Ironing out the wrinkles in the rare biosphere through improved OTU clustering
    • 10.1111/j.1462-2920.2010.02193.x, 2909393, 20236171
    • Huse SM, Mark Welch D, Morrison HG, Sogin ML. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 2010, 12(7):1889-1898. 10.1111/j.1462-2920.2010.02193.x, 2909393, 20236171.
    • (2010) Environ Microbiol , vol.12 , Issue.7 , pp. 1889-1898
    • Huse, S.M.1    Mark Welch, D.2    Morrison, H.G.3    Sogin, M.L.4
  • 13
    • 79952001955 scopus 로고    scopus 로고
    • Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering
    • Hao X, Jiang R, Chen T. Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinformatics 2011,
    • (2011) Bioinformatics
    • Hao, X.1    Jiang, R.2    Chen, T.3
  • 14
    • 84863304598 scopus 로고    scopus 로고
    • Vienna, Austria: R Foundation for Statistical Computing, R Core Team
    • R Core Team R: A Language and Environment for Statistical Computing 2012, Vienna, Austria: R Foundation for Statistical Computing, R Core Team.
    • (2012) R: A Language and Environment for Statistical Computing
  • 15
    • 80055041479 scopus 로고    scopus 로고
    • Exploring the diversity of Gardnerella vaginalis in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation
    • 10.1371/journal.pone.0026732, 3201972, 22046340
    • Eren AM, Zozaya M, Taylor CM, Dowd SE, Martin DH, Ferris MJ. Exploring the diversity of Gardnerella vaginalis in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation. PLoS ONE 2011, 6(10):e26732. 10.1371/journal.pone.0026732, 3201972, 22046340.
    • (2011) PLoS ONE , vol.6 , Issue.10
    • Eren, A.M.1    Zozaya, M.2    Taylor, C.M.3    Dowd, S.E.4    Martin, D.H.5    Ferris, M.J.6
  • 16
    • 84858617141 scopus 로고    scopus 로고
    • Sequencing our way towards understanding global eukaryotic biodiversity
    • 10.1016/j.tree.2011.11.010, 3311718, 22244672
    • Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK. Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol 2012, 27(4):233-243. 10.1016/j.tree.2011.11.010, 3311718, 22244672.
    • (2012) Trends Ecol Evol , vol.27 , Issue.4 , pp. 233-243
    • Bik, H.M.1    Porazinska, D.L.2    Creer, S.3    Caporaso, J.G.4    Knight, R.5    Thomas, W.K.6
  • 18
    • 84856085997 scopus 로고    scopus 로고
    • The Human Microbiome Project
    • The Human Microbiome Project. http://commonfund.nih.gov/hmp.
  • 19
    • 84893848189 scopus 로고    scopus 로고
    • International Census of Marine Microbes
    • International Census of Marine Microbes. http://icomm.mbl.edu.
  • 20
    • 84893827880 scopus 로고    scopus 로고
    • Microbial Inventory of Aquatic Long Term Ecological Research Stations
    • Microbial Inventory of Aquatic Long Term Ecological Research Stations. http://amarallab.mbl.edu/mirada/mirada.html.
  • 21
    • 84893841611 scopus 로고    scopus 로고
    • Census of Deep Life
    • Census of Deep Life. https://dco.gl.ciw.edu.
  • 22
    • 84893823872 scopus 로고    scopus 로고
    • Microbiology of the Built Environment
    • Microbiology of the Built Environment. http://www.sloan.org/major-program-areas/basic-research/microbiology-of-the-built-environment.
  • 23
    • 84893842046 scopus 로고    scopus 로고
    • Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis
    • 10.1186/2049-2618-1-9, 24451366
    • Young V, Raffals L, Huse S, Vital M, Dai D, Schloss P, Brulc J, Antonopoulos D, Arrieta R, Kwon J, et al. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome 2013, 1(1):9. 10.1186/2049-2618-1-9, 24451366.
    • (2013) Microbiome , vol.1 , Issue.1 , pp. 9
    • Young, V.1    Raffals, L.2    Huse, S.3    Vital, M.4    Dai, D.5    Schloss, P.6    Brulc, J.7    Antonopoulos, D.8    Arrieta, R.9    Kwon, J.10
  • 25
    • 84873437771 scopus 로고    scopus 로고
    • Marine bacteria exhibit a bipolar distribution
    • 10.1073/pnas.1212424110, 3568360, 23324742
    • Sul WJ, Oliver TA, Ducklow HW, Amaral-Zettler LA, Sogin ML. Marine bacteria exhibit a bipolar distribution. Proc Natl Acad Sci 2013, 110(6):2342-2347. 10.1073/pnas.1212424110, 3568360, 23324742.
    • (2013) Proc Natl Acad Sci , vol.110 , Issue.6 , pp. 2342-2347
    • Sul, W.J.1    Oliver, T.A.2    Ducklow, H.W.3    Amaral-Zettler, L.A.4    Sogin, M.L.5
  • 26
    • 84867741260 scopus 로고    scopus 로고
    • Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates
    • 10.1038/ismej.2012.47, 3475368, 22739491
    • Bowen JL, Morrison HG, Hobbie JE, Sogin ML. Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates. ISME J 2012, 6(11):2014-2023. 10.1038/ismej.2012.47, 3475368, 22739491.
    • (2012) ISME J , vol.6 , Issue.11 , pp. 2014-2023
    • Bowen, J.L.1    Morrison, H.G.2    Hobbie, J.E.3    Sogin, M.L.4
  • 27
    • 84857121817 scopus 로고    scopus 로고
    • Diversity and dynamics of rare and of resident bacterial populations in coastal sands
    • 10.1038/ismej.2011.132, 3280144, 21975598
    • Gobet A, Boer SI, Huse SM, van Beusekom JEE, Quince C, Sogin ML, Boetius A, Ramette A. Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME J 2012, 6(3):542-553. 10.1038/ismej.2011.132, 3280144, 21975598.
    • (2012) ISME J , vol.6 , Issue.3 , pp. 542-553
    • Gobet, A.1    Boer, S.I.2    Huse, S.M.3    van Beusekom, J.E.E.4    Quince, C.5    Sogin, M.L.6    Boetius, A.7    Ramette, A.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.