-
1
-
-
38849163365
-
Exponential decline of deep-sea ecosystem functioning linked to benthic biodiversity loss
-
Danovaro R., et al. Exponential decline of deep-sea ecosystem functioning linked to benthic biodiversity loss. Curr. Biol. 2008, 18:1-18.
-
(2008)
Curr. Biol.
, vol.18
, pp. 1-18
-
-
Danovaro, R.1
-
2
-
-
33745060740
-
The influence of biotic interactions on soil biodiversity
-
Wardle D.A. The influence of biotic interactions on soil biodiversity. Ecol. Lett. 2006, 9:870-886.
-
(2006)
Ecol. Lett.
, vol.9
, pp. 870-886
-
-
Wardle, D.A.1
-
3
-
-
83755222630
-
Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions
-
Wegner Parfrey L., et al. Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Front. Microbiol. 2011, 2:1-16.
-
(2011)
Front. Microbiol.
, vol.2
, pp. 1-16
-
-
Wegner Parfrey, L.1
-
4
-
-
33646579538
-
2S Gradient in a supersulfidic Anoxic Fjord (Framvaren, Norway)
-
2S Gradient in a supersulfidic Anoxic Fjord (Framvaren, Norway). Appl. Environ. Microbiol. 2006, 72:3626-3636.
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 3626-3636
-
-
Behnke, A.1
-
5
-
-
33646269716
-
Genetic diversity and habitats of two enigmatic marine alveolate lineages
-
Groisillier A., et al. Genetic diversity and habitats of two enigmatic marine alveolate lineages. Aquat. Microb. Ecol. 2006, 42:277-291.
-
(2006)
Aquat. Microb. Ecol.
, vol.42
, pp. 277-291
-
-
Groisillier, A.1
-
6
-
-
20444481378
-
Molecular screening of free-living microbial eukaryotes: diversity and distribution using a meta-analysis
-
Richards T., Bass D. Molecular screening of free-living microbial eukaryotes: diversity and distribution using a meta-analysis. Curr. Opin. Microbiol. 2005, 8:240-252.
-
(2005)
Curr. Opin. Microbiol.
, vol.8
, pp. 240-252
-
-
Richards, T.1
Bass, D.2
-
7
-
-
80051641790
-
Archaeorhizomycetes: unearthing an ancient class of ubiqutous soil fungi
-
Rosling A., et al. Archaeorhizomycetes: unearthing an ancient class of ubiqutous soil fungi. Science 2011, 333:876-879.
-
(2011)
Science
, vol.333
, pp. 876-879
-
-
Rosling, A.1
-
8
-
-
79958294748
-
Discovery of novel intermediate forms redefines the fungal tree of life
-
Jones M.D.M., et al. Discovery of novel intermediate forms redefines the fungal tree of life. Nature 2011, 474:200-203.
-
(2011)
Nature
, vol.474
, pp. 200-203
-
-
Jones, M.D.M.1
-
9
-
-
77951929876
-
Ultrasequencing of the meiofaunal biosphere: practice, pitfalls, and promises
-
Creer S., et al. Ultrasequencing of the meiofaunal biosphere: practice, pitfalls, and promises. Mol. Ecol. 2010, 19:4-20.
-
(2010)
Mol. Ecol.
, vol.19
, pp. 4-20
-
-
Creer, S.1
-
10
-
-
70349915703
-
Evaulating high-throughput sequencing as a method for metagenomic analysis of nematode diversity
-
Porazinska D.L., et al. Evaulating high-throughput sequencing as a method for metagenomic analysis of nematode diversity. Mol. Ecol. Resour. 2009, 9:1439-1450.
-
(2009)
Mol. Ecol. Resour.
, vol.9
, pp. 1439-1450
-
-
Porazinska, D.L.1
-
11
-
-
77951908579
-
Multiple marker parallel tag enviornmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water
-
Stoeck T., et al. Multiple marker parallel tag enviornmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol. Ecol. 2010, 19:21-31.
-
(2010)
Mol. Ecol.
, vol.19
, pp. 21-31
-
-
Stoeck, T.1
-
12
-
-
70749095743
-
Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities
-
Stoeck T., et al. Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities. BMC Biol. 2009, 7:72.
-
(2009)
BMC Biol.
, vol.7
, pp. 72
-
-
Stoeck, T.1
-
13
-
-
0030982247
-
A molecular view of microbial diversity and the biosphere
-
Pace N.R. A molecular view of microbial diversity and the biosphere. Science 1997, 276:734-740.
-
(1997)
Science
, vol.276
, pp. 734-740
-
-
Pace, N.R.1
-
14
-
-
33747073504
-
Microbial diversity in the deep sea and the unexplored 'rare biosphere'
-
Sogin M.L., et al. Microbial diversity in the deep sea and the unexplored 'rare biosphere'. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:12115-12120.
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 12115-12120
-
-
Sogin, M.L.1
-
16
-
-
56649124715
-
The influence of sex, handedness, and washing on the diversity of hand surface bacteria
-
Fierer N., et al. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:17994-17999.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 17994-17999
-
-
Fierer, N.1
-
17
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh P.J., et al. A core gut microbiome in obese and lean twins. Nature 2009, 457:480-484.
-
(2009)
Nature
, vol.457
, pp. 480-484
-
-
Turnbaugh, P.J.1
-
18
-
-
0037310350
-
The correlation between rDNA copy number and genome size in eukaryotes
-
Prokopowich C.D., et al. The correlation between rDNA copy number and genome size in eukaryotes. Genome 2003, 46:48-50.
-
(2003)
Genome
, vol.46
, pp. 48-50
-
-
Prokopowich, C.D.1
-
19
-
-
77953646161
-
Diversity of 16S rRNA genes within individual prokaryotic genomes
-
Pei A.Y., et al. Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl. Environ. Microbiol. 2010, 76:3886-3897.
-
(2010)
Appl. Environ. Microbiol.
, vol.76
, pp. 3886-3897
-
-
Pei, A.Y.1
-
20
-
-
13844317082
-
Mapping of picoeukaryotes in marine ecosystems with a quantitative PCR of the 18S rRNA gene
-
Zhu F., et al. Mapping of picoeukaryotes in marine ecosystems with a quantitative PCR of the 18S rRNA gene. FEMS Microbiol. Ecol. 2005, 52:79-92.
-
(2005)
FEMS Microbiol. Ecol.
, vol.52
, pp. 79-92
-
-
Zhu, F.1
-
21
-
-
21144441817
-
Lateral gene transfer in eukaryotes
-
Andersson J.O. Lateral gene transfer in eukaryotes. Cell. Mol. Life Sci. 2005, 62:1182-1197.
-
(2005)
Cell. Mol. Life Sci.
, vol.62
, pp. 1182-1197
-
-
Andersson, J.O.1
-
22
-
-
35148888609
-
Microbial population structures in the deep marine biosphere
-
Huber J.A., et al. Microbial population structures in the deep marine biosphere. Science 2007, 318:97-100.
-
(2007)
Science
, vol.318
, pp. 97-100
-
-
Huber, J.A.1
-
23
-
-
68149178616
-
A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes
-
Amaral-Zettler L., et al. A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS ONE 2009, 4:e6372.
-
(2009)
PLoS ONE
, vol.4
-
-
Amaral-Zettler, L.1
-
24
-
-
77951889917
-
Diversity in a hidden world: potential an limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms
-
Medinger R., et al. Diversity in a hidden world: potential an limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Mol. Ecol. 2010, 19:32-40.
-
(2010)
Mol. Ecol.
, vol.19
, pp. 32-40
-
-
Medinger, R.1
-
25
-
-
79960558703
-
Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization
-
Orsi W., et al. Protistan microbial observatory in the Cariaco Basin, Caribbean. II. Habitat specialization. ISME J. 2011, 5:1357-1373.
-
(2011)
ISME J.
, vol.5
, pp. 1357-1373
-
-
Orsi, W.1
-
26
-
-
79960560895
-
Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness
-
Edgcomb V., et al. Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness. ISME J. 2011, 5:1344-1356.
-
(2011)
ISME J.
, vol.5
, pp. 1344-1356
-
-
Edgcomb, V.1
-
27
-
-
84857508990
-
Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments
-
Bik H.M., et al. Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments. Mol. Ecol. 2012, 21:1048-1059.
-
(2012)
Mol. Ecol.
, vol.21
, pp. 1048-1059
-
-
Bik, H.M.1
-
28
-
-
77954557093
-
Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity
-
Nolte V., et al. Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Mol. Ecol. 2010, 19:2908-2915.
-
(2010)
Mol. Ecol.
, vol.19
, pp. 2908-2915
-
-
Nolte, V.1
-
29
-
-
77956304094
-
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
-
Reeder J., Knight R. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat. Methods 2010, 7:668-669.
-
(2010)
Nat. Methods
, vol.7
, pp. 668-669
-
-
Reeder, J.1
Knight, R.2
-
30
-
-
84880321899
-
Second-generation environmental sequencing unmasks marine metazoan biodiversity
-
Fonseca V.G., et al. Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat. Commun. 2010, 1:98.
-
(2010)
Nat. Commun.
, vol.1
, pp. 98
-
-
Fonseca, V.G.1
-
31
-
-
79551476785
-
Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions
-
Behnke A., et al. Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environ. Microbiol. 2011, 13:340-349.
-
(2011)
Environ. Microbiol.
, vol.13
, pp. 340-349
-
-
Behnke, A.1
-
32
-
-
80051955306
-
Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments
-
Lecroq B., et al. Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:13177-13182.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 13177-13182
-
-
Lecroq, B.1
-
33
-
-
77953353038
-
Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA
-
Chariton A., et al. Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA. Front. Ecol. Environ. 2010, 8:233-238.
-
(2010)
Front. Ecol. Environ.
, vol.8
, pp. 233-238
-
-
Chariton, A.1
-
34
-
-
79954587407
-
Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos
-
Hajibabaei M., et al. Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE 2011, 6:e17497.
-
(2011)
PLoS ONE
, vol.6
-
-
Hajibabaei, M.1
-
35
-
-
77957984013
-
Assessing macroinvertebrate biodiversity in freshwater ecosystems: advances and challenges in DNA-based approaches
-
Pfrender M.E., et al. Assessing macroinvertebrate biodiversity in freshwater ecosystems: advances and challenges in DNA-based approaches. Q. Rev. Biol. 2010, 85:319-340.
-
(2010)
Q. Rev. Biol.
, vol.85
, pp. 319-340
-
-
Pfrender, M.E.1
-
36
-
-
79960535651
-
Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities
-
Emerson B., et al. Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities. Philos. Trans. R. Soc. B: Biol. Sci. 2011, 366:2391-2402.
-
(2011)
Philos. Trans. R. Soc. B: Biol. Sci.
, vol.366
, pp. 2391-2402
-
-
Emerson, B.1
-
37
-
-
78649244963
-
Systems biology for ecology: from molecules to ecosystems
-
Purdy K.J., et al. Systems biology for ecology: from molecules to ecosystems. Adv. Ecol. Res. 2010, 43:87-149.
-
(2010)
Adv. Ecol. Res.
, vol.43
, pp. 87-149
-
-
Purdy, K.J.1
-
38
-
-
79251565226
-
Removing noise from pyrosequenced amplicons
-
Quince C., et al. Removing noise from pyrosequenced amplicons. BMC Bioinform. 2011, 12:38.
-
(2011)
BMC Bioinform.
, vol.12
, pp. 38
-
-
Quince, C.1
-
39
-
-
77958610660
-
Pplacer: linear time maximum-likelihood Bayesian phyogenetic placement of sequences onto a fixed reference tree
-
Matsen F.A., et al. pplacer: linear time maximum-likelihood Bayesian phyogenetic placement of sequences onto a fixed reference tree. BMC Bioinform. 2010, 11:538.
-
(2010)
BMC Bioinform.
, vol.11
, pp. 538
-
-
Matsen, F.A.1
-
40
-
-
79960414804
-
Aligning short reads to reference alignments and trees
-
Berger S.A., Stamatakis A. Aligning short reads to reference alignments and trees. Bioinformatics 2011, 27:2068-2075.
-
(2011)
Bioinformatics
, vol.27
, pp. 2068-2075
-
-
Berger, S.A.1
Stamatakis, A.2
-
41
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
42
-
-
72949107142
-
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss P.D., et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75:7537-7541.
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
-
43
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li W., Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
44
-
-
80051732979
-
ESPRIT-Tree: hierarchial clustring analysis of millions of 16S rRNA pyrosequences in quasilinear computational time
-
Cai Y., Sun Y. ESPRIT-Tree: hierarchial clustring analysis of millions of 16S rRNA pyrosequences in quasilinear computational time. Nucleic Acids Res. 2011, 39:e95.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Cai, Y.1
Sun, Y.2
-
45
-
-
58149200948
-
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
-
Cole J.R., et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009, 37:D141-D145.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Cole, J.R.1
-
46
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis T., et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 2006, 72:5069-5072.
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.1
-
47
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso J.G., et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 2010, 7:335-336.
-
(2010)
Nat. Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
-
48
-
-
79952082506
-
Host-associated and free-living phage communities differ profoundly in phylogenetic composition
-
Caporaso J.G., et al. Host-associated and free-living phage communities differ profoundly in phylogenetic composition. PLoS ONE 2011, 6:e16900.
-
(2011)
PLoS ONE
, vol.6
-
-
Caporaso, J.G.1
-
49
-
-
79952006773
-
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
-
Haas B.J., et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011, 21:494-504.
-
(2011)
Genome Res.
, vol.21
, pp. 494-504
-
-
Haas, B.J.1
-
50
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar R.C., et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27:2194-2200.
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
-
51
-
-
37549027613
-
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
-
Pruesse E., et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007, 35:7188-7196.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
-
52
-
-
78751575501
-
Unifrac: an effective distance metric for microbial community comparison
-
Lozupone C., et al. Unifrac: an effective distance metric for microbial community comparison. ISME J. 2011, 5:169-172.
-
(2011)
ISME J.
, vol.5
, pp. 169-172
-
-
Lozupone, C.1
-
53
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
Cline M.S., et al. Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2007, 2:2366-2383.
-
(2007)
Nat. Protoc.
, vol.2
, pp. 2366-2383
-
-
Cline, M.S.1
-
55
-
-
75949108066
-
Galaxy: a web-based genome analysis tool for experimentalists
-
19.10.1-21
-
Blankenberg D., et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. 2010, 19.10.1-21.
-
(2010)
Curr. Protoc. Mol. Biol.
-
-
Blankenberg, D.1
-
56
-
-
70349649798
-
GenGIS: a geospatial information system for genomic data
-
Parks D.H., et al. GenGIS: a geospatial information system for genomic data. Genome Res. 2009, 19:1896-1904.
-
(2009)
Genome Res.
, vol.19
, pp. 1896-1904
-
-
Parks, D.H.1
-
58
-
-
84857467562
-
Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison
-
ar Xiv:1107.5095v1101.
-
Matsen, F.A. and Evans, S. (2011) Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison. ar Xiv:1107.5095v1101.
-
(2011)
-
-
Matsen, F.A.1
Evans, S.2
-
59
-
-
77954336858
-
ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases
-
Bellemain E., et al. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol. 2010, 10:189.
-
(2010)
BMC Microbiol.
, vol.10
, pp. 189
-
-
Bellemain, E.1
-
60
-
-
66249131497
-
Global sequencing: a review of current molecular data and new methods available to assess microbial diversity
-
Christen R. Global sequencing: a review of current molecular data and new methods available to assess microbial diversity. Microbes Environ. 2008, 23:253-268.
-
(2008)
Microbes Environ.
, vol.23
, pp. 253-268
-
-
Christen, R.1
-
61
-
-
33947215475
-
CAMERA: a community resource for metagenomics
-
Seshadri R., et al. CAMERA: a community resource for metagenomics. PLoS Biol. 2007, 5:e75.
-
(2007)
PLoS Biol.
, vol.5
-
-
Seshadri, R.1
-
62
-
-
53549118607
-
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
-
Meyer F., et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinform. 2008, 9:386.
-
(2008)
BMC Bioinform.
, vol.9
, pp. 386
-
-
Meyer, F.1
-
63
-
-
79959792587
-
The Genomic Standards Consortium
-
Field D., et al. The Genomic Standards Consortium. PLoS Biol. 2011, 9:e1001088.
-
(2011)
PLoS Biol.
, vol.9
-
-
Field, D.1
-
64
-
-
79955749319
-
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
-
Yilmaz P., et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat. Biotechnol. 2011, 29:415-420.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 415-420
-
-
Yilmaz, P.1
-
65
-
-
34548293679
-
Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang Q., et al. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 2007, 73:5261-5267.
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
-
66
-
-
84355166737
-
Impact of training sets on classification of high-throughput bacerial 16S rRNA gene surveys
-
Werner J.J., et al. Impact of training sets on classification of high-throughput bacerial 16S rRNA gene surveys. ISME J. 2012, 6:94-103.
-
(2012)
ISME J.
, vol.6
, pp. 94-103
-
-
Werner, J.J.1
-
67
-
-
80054886632
-
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata
-
Pirrung M., et al. TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. Bioinformatics 2011, 10.1093/bioinformatics/btr517.
-
(2011)
Bioinformatics
-
-
Pirrung, M.1
-
68
-
-
77958043342
-
Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life
-
Wegener Parfrey L., et al. Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life. Syst. Biol. 2010, 59:518-533.
-
(2010)
Syst. Biol.
, vol.59
, pp. 518-533
-
-
Wegener Parfrey, L.1
-
69
-
-
0020478245
-
Molecular drive: a cohesive mode of species evolution
-
Dover G. Molecular drive: a cohesive mode of species evolution. Nature 1982, 299:111-117.
-
(1982)
Nature
, vol.299
, pp. 111-117
-
-
Dover, G.1
-
70
-
-
33645113551
-
Monitoring the mode and tempo of concerted evolution in Drosophila melanogaster rDNA locus
-
Averbeck K.T., Eickbush T.H. Monitoring the mode and tempo of concerted evolution in Drosophila melanogaster rDNA locus. Genetics 2005, 171:1837-1846.
-
(2005)
Genetics
, vol.171
, pp. 1837-1846
-
-
Averbeck, K.T.1
Eickbush, T.H.2
-
71
-
-
63849198290
-
Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing
-
James S.A., et al. Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing. Genome Res. 2009, 19:626-635.
-
(2009)
Genome Res.
, vol.19
, pp. 626-635
-
-
James, S.A.1
-
72
-
-
0348226830
-
Molecular characterization of nuclear small subunit (18S)-rDNA pseudogenes in a symbiotic dinoflagellate (Symbiodinium, Dinophyta)
-
Santos S.R., et al. Molecular characterization of nuclear small subunit (18S)-rDNA pseudogenes in a symbiotic dinoflagellate (Symbiodinium, Dinophyta). J. Eukaryot. Microbiol. 2003, 50:417-421.
-
(2003)
J. Eukaryot. Microbiol.
, vol.50
, pp. 417-421
-
-
Santos, S.R.1
-
73
-
-
0028500562
-
Chromosomal homogeneity of Drosophila ribosomal DNA arrays suggests intrachromosomal exchanges drive concerted evolution
-
Schlöetterer C., Tautz D. Chromosomal homogeneity of Drosophila ribosomal DNA arrays suggests intrachromosomal exchanges drive concerted evolution. Curr. Biol. 1994, 4:777-783.
-
(1994)
Curr. Biol.
, vol.4
, pp. 777-783
-
-
Schlöetterer, C.1
Tautz, D.2
-
74
-
-
79953695045
-
Eukaryotic richness in the abyss: insights from Pyrotag sequencing
-
Pawlowski J., et al. Eukaryotic richness in the abyss: insights from Pyrotag sequencing. PLoS ONE 2011, 6:e18169.
-
(2011)
PLoS ONE
, vol.6
-
-
Pawlowski, J.1
-
75
-
-
25844519572
-
Extracellular DNA plays a key role in deep-sea ecosystem functioning
-
Dell'Anno A., Danovaro R. Extracellular DNA plays a key role in deep-sea ecosystem functioning. Science 2005, 309:2179.
-
(2005)
Science
, vol.309
, pp. 2179
-
-
Dell'Anno, A.1
Danovaro, R.2
-
76
-
-
34547834963
-
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing
-
Binladen J., et al. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE 2007, 2:e197.
-
(2007)
PLoS ONE
, vol.2
-
-
Binladen, J.1
-
77
-
-
40149103278
-
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
-
Hamady M., et al. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods 2008, 5:235-237.
-
(2008)
Nat. Methods
, vol.5
, pp. 235-237
-
-
Hamady, M.1
-
78
-
-
34447123273
-
Universal primer cocktails for fish DNA barcoding
-
Ivanova N.V., et al. Universal primer cocktails for fish DNA barcoding. Mol. Ecol. 2007, 7:544-548.
-
(2007)
Mol. Ecol.
, vol.7
, pp. 544-548
-
-
Ivanova, N.V.1
-
79
-
-
80052923041
-
Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca)
-
Matzen da Silva J., et al. Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca). PLoS ONE 2011, 6:e19449.
-
(2011)
PLoS ONE
, vol.6
-
-
Matzen da Silva, J.1
-
80
-
-
68549132517
-
Assessment of bias associated with incomplete extraction of microbial DNA from soil
-
Feinstein L.M., et al. Assessment of bias associated with incomplete extraction of microbial DNA from soil. Appl. Environ. Microbiol. 2009, 75:5428-5433.
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, pp. 5428-5433
-
-
Feinstein, L.M.1
-
81
-
-
77951498638
-
Experimental factors affecting PCR-based estimates of microbial species richness and evenness
-
Engelbrektson A., et al. Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J. 2010, 4:642-647.
-
(2010)
ISME J.
, vol.4
, pp. 642-647
-
-
Engelbrektson, A.1
-
82
-
-
72649084530
-
Polymerase chain reaction primers miss half of rRNA microbial diversity
-
Hong S., et al. Polymerase chain reaction primers miss half of rRNA microbial diversity. ISME J. 2009, 3:1365-1373.
-
(2009)
ISME J.
, vol.3
, pp. 1365-1373
-
-
Hong, S.1
-
83
-
-
51449088676
-
A comparative analysis of microscopy and PCR-based detection methods for blood parasites
-
Valkiunas G., et al. A comparative analysis of microscopy and PCR-based detection methods for blood parasites. J. Parasitol. 2008, 94:1395-1401.
-
(2008)
J. Parasitol.
, vol.94
, pp. 1395-1401
-
-
Valkiunas, G.1
-
84
-
-
0037064627
-
Applications of PCR-based tools for detection and identification of animal trypanosomes: a review and perspectives
-
Desquesnes M., Dávila A.M.R. Applications of PCR-based tools for detection and identification of animal trypanosomes: a review and perspectives. Vet. Parasitol. 2002, 109:213-231.
-
(2002)
Vet. Parasitol.
, vol.109
, pp. 213-231
-
-
Desquesnes, M.1
Dávila, A.M.R.2
-
85
-
-
34948842866
-
Accuracy and quality of massively parallel DNA pyrosequencing
-
Huse S.M., et al. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 2007, 8:R143.
-
(2007)
Genome Biol.
, vol.8
-
-
Huse, S.M.1
-
86
-
-
79956044149
-
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing
-
Gilles A., et al. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 2011, 12:245.
-
(2011)
BMC Genomics
, vol.12
, pp. 245
-
-
Gilles, A.1
-
87
-
-
77954015275
-
Linking operational clustered taxonomic units (OCTUs) from parallel ultra sequencing (PUS) to nematode species
-
Porazinska D.L., et al. Linking operational clustered taxonomic units (OCTUs) from parallel ultra sequencing (PUS) to nematode species. Zootaxa 2010, 2427:55-63.
-
(2010)
Zootaxa
, vol.2427
, pp. 55-63
-
-
Porazinska, D.L.1
-
88
-
-
77954025874
-
Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure
-
Porazinska D.L., et al. Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure. Mol. Ecol. Resour. 2009, 10:666-676.
-
(2009)
Mol. Ecol. Resour.
, vol.10
, pp. 666-676
-
-
Porazinska, D.L.1
-
89
-
-
78649448174
-
A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland
-
Pester M., et al. A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland. ISME J. 2010, 4:1591-1602.
-
(2010)
ISME J.
, vol.4
, pp. 1591-1602
-
-
Pester, M.1
-
90
-
-
77954547447
-
Second-generation seequencing derived insights into the temporal biodiversity dynamics of freshwater protists
-
Creer S. Second-generation seequencing derived insights into the temporal biodiversity dynamics of freshwater protists. Mol. Ecol. 2010, 19:2829-2831.
-
(2010)
Mol. Ecol.
, vol.19
, pp. 2829-2831
-
-
Creer, S.1
-
91
-
-
77957882879
-
Reducing chimera formation during PCR amplification to ensure accurate genotyping
-
Smyth R.P., et al. Reducing chimera formation during PCR amplification to ensure accurate genotyping. Gene 2010, 469:45-51.
-
(2010)
Gene
, vol.469
, pp. 45-51
-
-
Smyth, R.P.1
-
92
-
-
69549112742
-
Accurate determination of microbial diversity from 454 pyrosequencing data
-
Quince C., et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 2009, 6:639-641.
-
(2009)
Nat. Methods
, vol.6
, pp. 639-641
-
-
Quince, C.1
-
93
-
-
77955251092
-
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
-
Huse S.M., et al. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 2010, 12:1889-1898.
-
(2010)
Environ. Microbiol.
, vol.12
, pp. 1889-1898
-
-
Huse, S.M.1
-
94
-
-
33748302019
-
Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago
-
Shapiro L.H., et al. Molecular phylogeny of Banza (Orthoptera: Tettigoniidae), the endemic katydids of the Hawaiian Archipelago. Mol. Phylogenet. Evol. 2006, 41:53-63.
-
(2006)
Mol. Phylogenet. Evol.
, vol.41
, pp. 53-63
-
-
Shapiro, L.H.1
-
95
-
-
77949525420
-
CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies
-
Pandey R., et al. CANGS: a user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. BMC Res. Notes 2010, 12:182.
-
(2010)
BMC Res. Notes
, vol.12
, pp. 182
-
-
Pandey, R.1
-
96
-
-
79956216816
-
CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation
-
Kumar S., et al. CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation. BMC Bioinform. 2011, 12:182.
-
(2011)
BMC Bioinform.
, vol.12
, pp. 182
-
-
Kumar, S.1
-
97
-
-
67249096511
-
ESPRIT: estimating species richness uing large collections of 16S rRNA pyrosequences
-
Sun Y., et al. ESPRIT: estimating species richness uing large collections of 16S rRNA pyrosequences. Nucleic Acids Res. 2009, 37:e76.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Sun, Y.1
-
98
-
-
80052549504
-
Integrative analysis of environmental sequences using MEGAN4
-
Huson D.H., et al. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 2011, 21:1552-1560.
-
(2011)
Genome Res.
, vol.21
, pp. 1552-1560
-
-
Huson, D.H.1
-
99
-
-
72749089248
-
Theoretical considerations of lifecycle modeling: an analysis of the Dryad repository demonstrating automatic metadata propagation, inheritance, and value system adoption
-
Greenberg J. Theoretical considerations of lifecycle modeling: an analysis of the Dryad repository demonstrating automatic metadata propagation, inheritance, and value system adoption. Cataloging Classification Q. 2009, 47:380-402.
-
(2009)
Cataloging Classification Q.
, vol.47
, pp. 380-402
-
-
Greenberg, J.1
-
100
-
-
77954055630
-
MetaBar - a tool for consistent contextual data acquisition and standards compliant submission
-
Hankeln W., et al. MetaBar - a tool for consistent contextual data acquisition and standards compliant submission. BMC Bioinform. 2010, 11:358.
-
(2010)
BMC Bioinform.
, vol.11
, pp. 358
-
-
Hankeln, W.1
|