-
1
-
-
0033879279
-
Are tropical fungal endophytes hyperdiverse?
-
Arnold AE, Maynard Z, Gilbert GS, et al. 2000. Are tropical fungal endophytes hyperdiverse? Ecol Lett 3: 267-74.
-
(2000)
Ecol Lett
, vol.3
, pp. 267-274
-
-
Arnold, A.E.1
Maynard, Z.2
Gilbert, G.S.3
-
2
-
-
0346103667
-
Fungal endophytes limit pathogen damage in a tropical tree
-
DOI 10.1073/pnas.2533483100
-
Arnold AE, Mejia LC, Kyllo DA, et al. 2003. Fungal endophytes limit pathogen damage in a tropical tree. P Natl Acad Sci USA 100: 15649-54. (Pubitemid 38021044)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.26
, pp. 15649-15654
-
-
Arnold, A.E.1
Mejia, L.C.2
Kyllo, D.3
Rojas, E.I.4
Maynard, Z.5
Robbins, N.6
Herre, E.A.7
-
3
-
-
84876325081
-
Effects of nitrogen addition on soil microbial diversity and methane cycling capacity depend on drainage conditions in a pine forest soil
-
Aronson EL, Dubinsky EA, and Helliker BR. 2013. Effects of nitrogen addition on soil microbial diversity and methane cycling capacity depend on drainage conditions in a pine forest soil. Soil Biol Biochem 62: 119-28.
-
(2013)
Soil Biol Biochem
, vol.62
, pp. 119-128
-
-
Aronson, E.L.1
Dubinsky, E.A.2
Helliker, B.R.3
-
4
-
-
33748799671
-
New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras
-
DOI 10.1128/AEM.00556-06
-
Ashelford KE, Chuzhanova NA, Fry JC, et al. 2006. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microb 72: 5734-41. (Pubitemid 44414595)
-
(2006)
Applied and Environmental Microbiology
, vol.72
, Issue.9
, pp. 5734-5741
-
-
Ashelford, K.E.1
Chuzhanova, N.A.2
Fry, J.C.3
Jones, A.J.4
Weightman, A.J.5
-
5
-
-
20444374146
-
Global change, nitrification, and denitrification: A review
-
Barnard R, Leadley PW, and Hungate BA. 2005. Global change, nitrification, and denitrification: a review. Global Biogeochem Cy 19: GB2007.
-
(2005)
Global Biogeochem Cy
, vol.19
-
-
Barnard, R.1
Leadley, P.W.2
Hungate, B.A.3
-
6
-
-
84874271270
-
NCBI GEO: Archive for functional genomics data sets - Update
-
Barrett T, Wilhite SE, Ledoux P, et al. 2013. NCBI GEO: archive for functional genomics data sets - update. Nucleic Acids Res 41: D991-95.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Barrett, T.1
Wilhite, S.E.2
Ledoux, P.3
-
7
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso JG, Kuczynski J, Stombaugh J, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-36.
-
(2010)
Nat Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
-
8
-
-
84863981120
-
Ultra-highthroughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
-
Caporaso JG, Lauber CL, Walters WA, et al. 2012. Ultra-highthroughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6: 1621-24.
-
(2012)
ISME J
, vol.6
, pp. 1621-1624
-
-
Caporaso, J.G.1
Lauber, C.L.2
Walters, W.A.3
-
9
-
-
64449088698
-
Continuous base identification for single-molecule nanopore DNA sequencing
-
Clarke J, Wu HC, Jayasinghe L, et al. 2009. Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4: 265-70.
-
(2009)
Nat Nanotechnol
, vol.4
, pp. 265-270
-
-
Clarke, J.1
Wu, H.C.2
Jayasinghe, L.3
-
10
-
-
58149200948
-
The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis
-
Cole JR, Wang Q, Cardenas E, et al. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-45.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
-
11
-
-
84887626254
-
The phenomenon of microbial uncultivability
-
Epstein SS. 2013. The phenomenon of microbial uncultivability. Curr Opin Microbiol 16: 636-42.
-
(2013)
Curr Opin Microbiol
, vol.16
, pp. 636-642
-
-
Epstein, S.S.1
-
12
-
-
84871826193
-
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
-
Fierer N, Leff JW, Adams BJ, et al. 2012. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. P Natl Acad Sci USA 109: 21390-95.
-
(2012)
P Natl Acad Sci USA
, vol.109
, pp. 21390-21395
-
-
Fierer, N.1
Leff, J.W.2
Adams, B.J.3
-
13
-
-
33748707177
-
Microarray applications in microbial ecology research
-
DOI 10.1007/s00248-006-9072-6
-
Gentry TJ, Wickham GS, Schadt CW, et al. 2006. Microarray applications in microbial ecology research. Microb Ecol 52: 159-75. (Pubitemid 44392971)
-
(2006)
Microbial Ecology
, vol.52
, Issue.2
, pp. 159-175
-
-
Gentry, T.J.1
Wickham, G.S.2
Schadt, C.W.3
He, Z.4
Zhou, J.5
-
14
-
-
74049132798
-
WebCARMA: A web application for the functional and taxonomic classification of unassembled metagenomic reads
-
Gerlach W, Junemann S, Tille F, et al. 2009. WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics 10: 430.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 430
-
-
Gerlach, W.1
Junemann, S.2
Tille, F.3
-
15
-
-
80051688000
-
Field guide to next-generation DNA sequencers
-
Glenn TC. 2011. Field guide to next-generation DNA sequencers. Mol Ecol Resour 11: 759-69.
-
(2011)
Mol Ecol Resour
, vol.11
, pp. 759-769
-
-
Glenn, T.C.1
-
16
-
-
77955801615
-
Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Goecks J, Nekrutenko A, Taylor J, and Galaxy Team. 2010. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11: R86.
-
(2010)
Genome Biol
, vol.11
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
-
17
-
-
79952006773
-
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
-
Haas BJ, Gevers D, Earl AM, et al. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21: 494-504.
-
(2011)
Genome Res
, vol.21
, pp. 494-504
-
-
Haas, B.J.1
Gevers, D.2
Earl, A.M.3
-
18
-
-
77955803519
-
Plaque microbiology in (periodontal) health and disease
-
Henderson B, Curtis MA, Seymor RM, and Donos N (Eds) . Chichester, UK: Wiley-Blackwell
-
Haffajee AD. 2009. Plaque microbiology in (periodontal) health and disease. In: Henderson B, Curtis MA, Seymor RM, and Donos N (Eds). Periodontal medicine and system biology. Chichester, UK: Wiley-Blackwell.
-
(2009)
Periodontal Medicine and System Biology
-
-
Haffajee, A.D.1
-
19
-
-
77956299931
-
Deep-sea oil plume enriches indigenous oil-degrading bacteria
-
Hazen TC, Dubinsky EA, DeSantis TZ, et al. 2010. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science 330: 204-08.
-
(2010)
Science
, vol.330
, pp. 204-208
-
-
Hazen, T.C.1
Dubinsky, E.A.2
Desantis, T.Z.3
-
20
-
-
78149423315
-
Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function
-
Inskeep WP, Rusch DB, Jay ZJ, et al. 2010. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PLoS ONE 5: e9773.
-
(2010)
PLoS ONE
, vol.5
-
-
Inskeep, W.P.1
Rusch, D.B.2
Jay, Z.J.3
-
21
-
-
83155190998
-
Amplification methods bias metagenomic libraries of uncultured single-stranded and doublestranded DNA viruses
-
Kim K-H and Bae J-W. 2011. Amplification methods bias metagenomic libraries of uncultured single-stranded and doublestranded DNA viruses. Appl Environ Microb 77: 7663-68.
-
(2011)
Appl Environ Microb
, vol.77
, pp. 7663-7668
-
-
Kim, K.-H.1
Bae, J.-W.2
-
22
-
-
84884224944
-
Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments
-
Klatt CG, Inskeep WP, Herrgard MJ, et al. 2013. Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. Front Microbiol 4: 106.
-
(2013)
Front Microbiol
, vol.4
, pp. 106
-
-
Klatt, C.G.1
Inskeep, W.P.2
Herrgard, M.J.3
-
23
-
-
79960560749
-
Community ecology of hot spring cyanobacterial mats: Predominant populations and their functional potential
-
Klatt CG, Wood JM, Rusch DB, et al. 2011. Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential. ISME J 5: 1262-78.
-
(2011)
ISME J
, vol.5
, pp. 1262-1278
-
-
Klatt, C.G.1
Wood, J.M.2
Rusch, D.B.3
-
24
-
-
40649125049
-
Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics
-
DOI 10.1073/pnas.0712205105
-
Koeppel A, Perry EB, Sikorski J, et al. 2008. Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. P Natl Acad Sci USA 105: 2504-09. (Pubitemid 351520543)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.7
, pp. 2504-2509
-
-
Koeppel, A.1
Perry, E.B.2
Sikorski, J.3
Krizanc, D.4
Warner, A.5
Ward, D.M.6
Rooney, A.P.7
Brambilla, E.8
Connor, N.9
Ratcliff, R.M.10
Nevo, E.11
Cohan, F.M.12
-
25
-
-
44649171625
-
Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat
-
Kunin V, Raes J, Harris JK, et al. 2008. Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol 4: 198.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 198
-
-
Kunin, V.1
Raes, J.2
Harris, J.K.3
-
27
-
-
84860756398
-
Performance comparison of benchtop high-throughput sequencing platforms
-
Loman NJ, Misra RV, Dallman TJ, et al. 2012. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30: 434-39.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 434-439
-
-
Loman, N.J.1
Misra, R.V.2
Dallman, T.J.3
-
28
-
-
83555174830
-
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw
-
Mackelprang R, Waldrop MP, Deangelis KM, et al. 2011. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480: 368-71.
-
(2011)
Nature
, vol.480
, pp. 368-371
-
-
Mackelprang, R.1
Waldrop, M.P.2
Deangelis, K.M.3
-
29
-
-
84862024797
-
IMG/M: The integrated metagenome data management and comparative analysis system
-
Markowitz VM, Chen IM, Chu K, et al. 2011. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res 40: D123-29.
-
(2011)
Nucleic Acids Res
, vol.40
-
-
Markowitz, V.M.1
Chen, I.M.2
Chu, K.3
-
30
-
-
31544448331
-
Microbial biogeography: Putting microorganisms on the map
-
DOI 10.1038/nrmicro1341, PII N1341
-
Martiny JBH, Bohannan BJM, Brown JH, et al. 2006. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4: 102-12. (Pubitemid 43158153)
-
(2006)
Nature Reviews Microbiology
, vol.4
, Issue.2
, pp. 102-112
-
-
Martiny, J.B.H.1
Bohannan, B.J.M.2
Brown, J.H.3
Colwell, R.K.4
Fuhrman, J.A.5
Green, J.L.6
Horner-Devine, M.C.7
Kane, M.8
Krumins, J.A.9
Kuske, C.R.10
Morin, P.J.11
Naeem, S.12
Ovreas, L.13
Reysenbach, A.-L.14
Smith, V.H.15
Staley, J.T.16
-
31
-
-
53549118607
-
The metagenomics RAST server - A public resource for the automatic phylogenetic and functional analysis of metagenomes
-
Meyer F, Paarmann D, D'Souza M, 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
-
32
-
-
80455126001
-
Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems
-
Minoche A, Dohm J, and Himmelbauer H. 2011. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems. Genome Biol 12: R112.
-
(2011)
Genome Biol
, vol.12
-
-
Minoche, A.1
Dohm, J.2
Himmelbauer, H.3
-
33
-
-
84884246062
-
Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16S rRNA genes from environmental samples
-
Mosher JJ, Bernberg EL, Shevchenko O, et al. 2013. Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16S rRNA genes from environmental samples. J Microbiol Meth 95: 175-81.
-
(2013)
J Microbiol Meth
, vol.95
, pp. 175-181
-
-
Mosher, J.J.1
Bernberg, E.L.2
Shevchenko, O.3
-
34
-
-
67149109995
-
The ITS region as a target for characterization of fungal communities using emerging sequencing technologies
-
Nilsson RH, Ryberg M, Abarenkov K, et al. 2009. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiol Lett 296: 97-101.
-
(2009)
FEMS Microbiol Lett
, vol.296
, pp. 97-101
-
-
Nilsson, R.H.1
Ryberg, M.2
Abarenkov, K.3
-
35
-
-
63449129221
-
Fungal endophytes: Diversity and functional roles
-
Rodriguez RJ, White Jr JF, Arnold AE, et al. 2009. Fungal endophytes: diversity and functional roles. New Phytol 182: 314-30.
-
(2009)
New Phytol
, vol.182
, pp. 314-330
-
-
Rodriguez, R.J.1
White Jr., J.F.2
Arnold, A.E.3
-
36
-
-
79960597679
-
An integrated semiconductor device enabling non-optical genome sequencing
-
Rothberg JM, Hinz W, Rearick TM, et al. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475: 348-52.
-
(2011)
Nature
, vol.475
, pp. 348-352
-
-
Rothberg, J.M.1
Hinz, W.2
Rearick, T.M.3
-
38
-
-
84881548286
-
Computational meta'omics for microbial community studies
-
Segata N, Boernigen D, Tickle TL, et al. 2013. Computational meta'omics for microbial community studies. Mol Syst Biol 9: 1-15.
-
(2013)
Mol Syst Biol
, vol.9
, pp. 1-15
-
-
Segata, N.1
Boernigen, D.2
Tickle, T.L.3
-
39
-
-
84862162269
-
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples
-
Segata N, Haake SK, Mannon P, et al. 2012. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol 13: R42.
-
(2012)
Genome Biol
, vol.13
-
-
Segata, N.1
Haake, S.K.2
Mannon, P.3
-
40
-
-
79959383523
-
Metagenomic biomarker discovery and explanation
-
Segata N, Izard J, Waldron L, et al. 2011. Metagenomic biomarker discovery and explanation. Genome Biol 12: R60.
-
(2011)
Genome Biol
, vol.12
-
-
Segata, N.1
Izard, J.2
Waldron, L.3
-
41
-
-
84869457261
-
The expanding scope of DNA sequencing
-
Shendure J and Aiden EL. 2012. The expanding scope of DNA sequencing. Nat Biotechnol 30: 1084-94.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 1084-1094
-
-
Shendure, J.1
Aiden, E.L.2
-
42
-
-
70349634435
-
Quantitative phenotyping via deep barcode sequencing
-
Smith AM, Heisler LE, Mellor J, et al. 2009. Quantitative phenotyping via deep barcode sequencing. Genome Res 19: 1836-42.
-
(2009)
Genome Res
, vol.19
, pp. 1836-1842
-
-
Smith, A.M.1
Heisler, L.E.2
Mellor, J.3
-
43
-
-
78651266825
-
Community cyberinfrastructure for advanced microbial ecology research and analysis: The CAMERA resource
-
Sun S, Chen J, Li W, et al. 2010. Community cyberinfrastructure for advanced microbial ecology research and analysis: the CAMERA resource. Nucleic Acids Res 39: D546-51.
-
(2010)
Nucleic Acids Res
, vol.39
-
-
Sun, S.1
Chen, J.2
Li, W.3
-
44
-
-
84859598756
-
Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies
-
Taberlet P, Prud'homme SM, Campione E, et al. 2012. Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Mol Ecol 21: 1816-20.
-
(2012)
Mol Ecol
, vol.21
, pp. 1816-1820
-
-
Taberlet, P.1
Prud'Homme, S.M.2
Campione, E.3
-
45
-
-
84862989346
-
Metagenomics - A guide from sampling to data analysis
-
Thomas T, Gilbert JA, and Meyer F. 2012. Metagenomics - a guide from sampling to data analysis. Microb Inform Exp 2: 3.
-
(2012)
Microb Inform Exp
, vol.2
, pp. 3
-
-
Thomas, T.1
Gilbert, J.A.2
Meyer, F.3
-
46
-
-
84920629237
-
A renaissance for the pioneering 16S rRNA gene
-
Tringe SG and Hugenholtz P. 2008. A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 11: 442-46.
-
(2008)
Curr Opin Microbiol
, vol.11
, pp. 442-446
-
-
Tringe, S.G.1
Hugenholtz, P.2
-
47
-
-
84875162399
-
Fungal community on decomposing leaf litter undergoes rapid successional changes
-
Voriskova J and Baldrian P. 2013. Fungal community on decomposing leaf litter undergoes rapid successional changes. ISME J 7: 477-86.
-
(2013)
ISME J
, vol.7
, pp. 477-486
-
-
Voriskova, J.1
Baldrian, P.2
-
48
-
-
79960557827
-
Reproducibility and quantitation of amplicon sequencing-based detection
-
Zhou J-Z, Wu L-Y, Deng Y, et al. 2011a. Reproducibility and quantitation of amplicon sequencing-based detection. ISME J 5: 1303-13.
-
(2011)
ISME J
, vol.5
, pp. 1303-1313
-
-
Zhou, J.-Z.1
Wu, L.-Y.2
Deng, Y.3
-
49
-
-
84863115440
-
Microbial mediation of carbon- cycle feedbacks to climate warming
-
Zhou J-Z, Xue K, Xie JP, et al. 2011b. Microbial mediation of carbon- cycle feedbacks to climate warming. Nat Clim Change 2: 106-10.
-
(2011)
Nat Clim Change
, vol.2
, pp. 106-110
-
-
Zhou, J.-Z.1
Xue, K.2
Xie, J.P.3
-
50
-
-
84864680957
-
Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape
-
Zimmerman NB and Vitousek PM. 2012. Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape. P Natl Acad Sci USA 109: 13022-27.
-
(2012)
P Natl Acad Sci USA
, vol.109
, pp. 13022-13027
-
-
Zimmerman, N.B.1
Vitousek, P.M.2
|