-
1
-
-
71449100076
-
Mapping the tree of life: progress and prospects
-
Pace NR, (2009) Mapping the tree of life: progress and prospects. Microbiol Mol Biol Rev 73: 565–576.
-
(2009)
Microbiol Mol Biol Rev
, vol.73
, pp. 565-576
-
-
Pace, N.R.1
-
2
-
-
43849089834
-
Microbial diversity and the genetic nature of microbial species
-
Achtman M, Wagner M, (2008) Microbial diversity and the genetic nature of microbial species. Nature Rev Microbiol 6: 431–440.
-
(2008)
Nature Rev Microbiol
, vol.6
, pp. 431-440
-
-
Achtman, M.1
Wagner, M.2
-
3
-
-
0030982247
-
A molecular view of microbial diversity and the biosphere
-
Pace NR, (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734–740.
-
(1997)
Science
, vol.276
, pp. 734-740
-
-
Pace, N.R.1
-
5
-
-
0035252640
-
Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton
-
López-García P, Rodríguez-Valera F, Pedrós-Alió C, Moreira D, (2001) Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409: 603–607.
-
(2001)
Nature
, vol.409
, pp. 603-607
-
-
López-García, P.1
Rodríguez-Valera, F.2
Pedrós-Alió, C.3
Moreira, D.4
-
6
-
-
0028946084
-
Phylogenetic identification and in situ detection of individual microbial cells without cultivation
-
Amann RI, Ludwig W, Schleifer KH, (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143–169.
-
(1995)
Microbiol Rev
, vol.59
, pp. 143-169
-
-
Amann, R.I.1
Ludwig, W.2
Schleifer, K.H.3
-
7
-
-
0036181778
-
Exploring prokaryotic diversity in the genomic era
-
Hugenholtz P, (2002) Exploring prokaryotic diversity in the genomic era. Genome Biol 3: reviews0003.
-
(2002)
Genome Biol
, vol.3
-
-
Hugenholtz, P.1
-
9
-
-
67650447476
-
Fifteen Years of Microbial Genomics: Meeting the Challenges and Fulfilling the Dream
-
Kyrpides NC, (2009) Fifteen Years of Microbial Genomics: Meeting the Challenges and Fulfilling the Dream. Nature Biotech 27: 627–632.
-
(2009)
Nature Biotech
, vol.27
, pp. 627-632
-
-
Kyrpides, N.C.1
-
11
-
-
0032488048
-
A manifesto for microbial genomics
-
Woese CR, (1998) A manifesto for microbial genomics. Curr Biol 8: R781.
-
(1998)
Curr Biol
, vol.8
, pp. R781
-
-
Woese, C.R.1
-
12
-
-
84956475952
-
-
Dolgin E (2009 November 17) Biologists rally to sequence ‘neglected’ microbes. Available: http://www.nature.com/news/2009/091117/full/news.2009.1093.html. Accessed 1 July 2014.
-
-
-
-
13
-
-
84859165788
-
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
-
Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, et al. (2012) The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 40: D571–D579.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D571-D579
-
-
Pagani, I.1
Liolios, K.2
Jansson, J.3
Chen, I.M.4
Smirnova, T.5
-
14
-
-
84956515594
-
-
Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seeliger HPR, et al. (1990) International Code of Nomenclature of Bacteria. Washington, D.C.: ASM Press.
-
-
-
-
15
-
-
0000685441
-
Holt JG (2001) The Road Map to the Manual
-
Garrity GM, Holt JG (2001) The Road Map to the Manual. In: Bergey's Manual of Systematic Bacteriology. New York: Springer. pp. 119–169.
-
-
-
Garrity, G.M.1
-
16
-
-
76849088617
-
Notes on the characterization of prokaryote strains for taxonomic purposes
-
Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P, (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60: 249–266.
-
(2010)
Int J Syst Evol Microbiol
, vol.60
, pp. 249-266
-
-
Tindall, B.J.1
Rosselló-Móra, R.2
Busse, H.J.3
Ludwig, W.4
Kämpfer, P.5
-
17
-
-
70349326017
-
International Code of Nomenclature of Prokaryotes. Appendix 9: Orthography Int
-
Trüper HG, Euzéby JP, (2009) International Code of Nomenclature of Prokaryotes. Appendix 9: Orthography Int. J Syst Evol Microbiol 59: 2107.
-
(2009)
J Syst Evol Microbiol
, vol.59
, pp. 2107
-
-
Trüper, H.G.1
Euzéby, J.P.2
-
18
-
-
33751221612
-
Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice
-
Tindall BJ, Kämpfer P, Euzéby JP, Oren A, (2006) Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice. Int J Syst Evol Microbiol 56: 2715–2720.
-
(2006)
Int J Syst Evol Microbiol
, vol.56
, pp. 2715-2720
-
-
Tindall, B.J.1
Kämpfer, P.2
Euzéby, J.P.3
Oren, A.4
-
19
-
-
54749093614
-
Proposals to clarify how type strains are deposited and made available to the scientific community for the purpose of systematic
-
Tindall BJ, Garrity GM, (2008) Proposals to clarify how type strains are deposited and made available to the scientific community for the purpose of systematic. Int J Syst Evol Microbiol 58: 1987–1990.
-
(2008)
Int J Syst Evol Microbiol
, vol.58
, pp. 1987-1990
-
-
Tindall, B.J.1
Garrity, G.M.2
-
20
-
-
70349866672
-
Genomics. Genome project standards in a new era of sequencing
-
Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, (2009) Genomics. Genome project standards in a new era of sequencing. Science 326: 236.
-
(2009)
Science
, vol.326
, pp. 236
-
-
Chain, P.S.1
Grafham, D.V.2
Fulton, R.S.3
Fitzgerald, M.G.4
Hostetler, J.5
-
21
-
-
84879351437
-
Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects
-
Göker M, Klenk HP, (2013) Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects. Stand Genomic Sci 8: 360–374.
-
(2013)
Stand Genomic Sci
, vol.8
, pp. 360-374
-
-
Göker, M.1
Klenk, H.P.2
-
22
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, et al. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056–1060.
-
(2009)
Nature
, vol.462
, pp. 1056-1060
-
-
Wu, D.1
Hugenholtz, P.2
Mavromatis, K.3
Pukall, R.4
Dalin, E.5
-
23
-
-
84872589843
-
Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing
-
Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, et al. (2013) Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci U S A 110: 1053–1058.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 1053-1058
-
-
Shih, P.M.1
Wu, D.2
Latifi, A.3
Axen, S.D.4
Fewer, D.P.5
-
24
-
-
84881138595
-
Insights into the phylogeny and coding potential of microbial dark matter
-
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, et al. (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431–437.
-
(2013)
Nature
, vol.499
, pp. 431-437
-
-
Rinke, C.1
Schwientek, P.2
Sczyrba, A.3
Ivanova, N.N.4
Anderson, I.J.5
-
25
-
-
77953050946
-
A Catalog of Reference Genomes from the Human Microbiome
-
Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, et al. (2010) A Catalog of Reference Genomes from the Human Microbiome. Science 328: 994–999.
-
(2010)
Science
, vol.328
, pp. 994-999
-
-
Nelson, K.E.1
Weinstock, G.M.2
Highlander, S.K.3
Worley, K.C.4
Creasy, H.H.5
-
26
-
-
79959792587
-
The Genomic Standards Consortium
-
Field D, Amaral-Zettler L, Cochrane G, Cole JR, Dawyndt P, et al. (2011) The Genomic Standards Consortium. PLoS Biol 9: e1001088.
-
(2011)
PLoS Biol
, vol.9
, pp. e1001088
-
-
Field, D.1
Amaral-Zettler, L.2
Cochrane, G.3
Cole, J.R.4
Dawyndt, P.5
-
27
-
-
43449108562
-
Towards a richer description of our complete collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification
-
Field D, Garrity G, Gray T, Morrison N, Selengut J, et al. (2008) Towards a richer description of our complete collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification. Nature Biotech 26: 541.
-
(2008)
Nature Biotech
, vol.26
, pp. 541
-
-
Field, D.1
Garrity, G.2
Gray, T.3
Morrison, N.4
Selengut, J.5
-
28
-
-
70349882123
-
Megascience. ‘Omics data sharing
-
Field D, Sansone SA, Collis A, Booth T, Dukes P, et al. (2009) Megascience. ‘Omics data sharing. Science 326: 234.
-
(2009)
Science
, vol.326
, pp. 234
-
-
Field, D.1
Sansone, S.A.2
Collis, A.3
Booth, T.4
Dukes, P.5
-
29
-
-
79955749319
-
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
-
Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, et al. (2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol 29: 415–420.
-
(2011)
Nat Biotechnol
, vol.29
, pp. 415-420
-
-
Yilmaz, P.1
Kottmann, R.2
Field, D.3
Knight, R.4
Cole, J.R.5
-
30
-
-
84892646831
-
Adding genomic ‘foliage’ to the tree of life
-
Walker A, (2014) Adding genomic ‘foliage’ to the tree of life. Nat Rev Microbiol 12: 78.
-
(2014)
Nat Rev Microbiol
, vol.12
, pp. 78
-
-
Walker, A.1
-
31
-
-
77952889628
-
En route to a genome-based taxonomy of Archaea and Bacteria?
-
Göker M, Klenk HP, (2010) En route to a genome-based taxonomy of Archaea and Bacteria? Syst Appl Microbiol 33: 175–182.
-
(2010)
Syst Appl Microbiol
, vol.33
, pp. 175-182
-
-
Göker, M.1
Klenk, H.P.2
-
32
-
-
84886206473
-
Reconciling microbial systematics and genomics
-
Buckley M, Roberts RJ, (2007) Reconciling microbial systematics and genomics. American Academy of Microbiology Available: http://academy.asm.org/index.php/genetics-genomics-molecular-microbiology/454-reconciling-microbial-systematics-and-genomics. Accessed 1 July 2014.
-
(2007)
American Academy of Microbiology
-
-
Buckley, M.1
Roberts, R.J.2
-
33
-
-
45749093727
-
Toward a standards-compliant genomic and metagenomic publication record
-
Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, et al. (2008) Toward a standards-compliant genomic and metagenomic publication record. Omics 12: 157–160.
-
(2008)
Omics
, vol.12
, pp. 157-160
-
-
Garrity, G.M.1
Field, D.2
Kyrpides, N.3
Hirschman, L.4
Sansone, S.A.5
-
34
-
-
84857066362
-
The state of standards in genomic sciences
-
Garrity GM, (2011) The state of standards in genomic sciences. Stand Genomic Sci 5: 262–268.
-
(2011)
Stand Genomic Sci
, vol.5
, pp. 262-268
-
-
Garrity, G.M.1
-
35
-
-
84862503319
-
The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools
-
Wilke A, Harrison T, Wilkening J, Field D, Glass EM, et al. (2012) The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics 13: 141.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 141
-
-
Wilke, A.1
Harrison, T.2
Wilkening, J.3
Field, D.4
Glass, E.M.5
-
36
-
-
52149085893
-
The All-Species Living Tree Project: a 16S rRNA-based phylogenetic tree of all sequenced type strains
-
Yarza P, Richter M, Peplies J, Euzeby J, Amann R, et al. (2008) The All-Species Living Tree Project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31: 241–250.
-
(2008)
Syst Appl Microbiol
, vol.31
, pp. 241-250
-
-
Yarza, P.1
Richter, M.2
Peplies, J.3
Euzeby, J.4
Amann, R.5
-
38
-
-
84956468881
-
Special issue on microbial research commons: from strain isolation to practical use
-
Dedeurwaerdere T, DeVos P, Dijkshoorn L, (2010) Special issue on microbial research commons: from strain isolation to practical use. Research in Microbiology 161: 407–514.
-
(2010)
Research in Microbiology
, vol.161
, pp. 407-514
-
-
Dedeurwaerdere, T.1
DeVos, P.2
Dijkshoorn, L.3
-
39
-
-
0036324056
-
High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates
-
Connon SA, Giovannoni SJ, (2002) High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68: 3878–3885.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 3878-3885
-
-
Connon, S.A.1
Giovannoni, S.J.2
-
40
-
-
0021779934
-
Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats
-
Staley JT, Konopka A, (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39: 321–346.
-
(1985)
Annu Rev Microbiol
, vol.39
, pp. 321-346
-
-
Staley, J.T.1
Konopka, A.2
-
41
-
-
0026499429
-
Conservation evaluation and phylogenetic diversity
-
Faith DP, (1992) Conservation evaluation and phylogenetic diversity. Biol Conservation 61: 1–10.
-
(1992)
Biol Conservation
, vol.61
, pp. 1-10
-
-
Faith, D.P.1
-
42
-
-
84956559638
-
The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet
-
Handelsman J (2007) The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, D.C.: The National Academies Press. 170 p.
-
(2007)
Washington, D.C.: The National Academies Press.
, pp. 170
-
-
Handelsman, J.1
-
43
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59–65.
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
Li, R.2
Raes, J.3
Arumugam, M.4
Burgdorf, K.S.5
-
44
-
-
79959794996
-
The Earth Microbiome Project: Meeting report of the “1 EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6 2010
-
Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, et al. (2010) The Earth Microbiome Project: Meeting report of the “1 EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6 2010. Stand Genomic Sci 3: 249–253.
-
(2010)
Stand Genomic Sci
, vol.3
, pp. 249-253
-
-
Gilbert, J.A.1
Meyer, F.2
Jansson, J.3
Gordon, J.4
Pace, N.5
|