-
1
-
-
0030982247
-
A molecular view of microbial diversity and the biosphere
-
Pace NR. A molecular view of microbial diversity and the biosphere. Science. 1997;276:734-40.
-
(1997)
Science
, vol.276
, pp. 734-740
-
-
Pace, N.R.1
-
2
-
-
67650021209
-
Microbial community profiling for human microbiome projects: tools, techniques, and challenges
-
Hamady M, Knight R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res. 2009;19:1141-52.
-
(2009)
Genome Res
, vol.19
, pp. 1141-1152
-
-
Hamady, M.1
Knight, R.2
-
3
-
-
2542523843
-
ARB: a software environment for sequence data
-
Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar BA, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüssmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH. ARB: a software environment for sequence data. Nucleic Acids Res. 2004;32:1363-71.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1363-1371
-
-
Ludwig, W.1
Strunk, O.2
Westram, R.3
Richter, L.4
Meier, H.5
Yadhukumar, B.A.6
Lai, T.7
Steppi, S.8
Jobb, G.9
Förster, W.10
Brettske, I.11
Gerber, S.12
Ginhart, A.W.13
Gross, O.14
Grumann, S.15
Hermann, S.16
Jost, R.17
König, A.18
Liss, T.19
Lüssmann, R.20
May, M.21
Nonhoff, B.22
Reichel, B.23
Strehlow, R.24
Stamatakis, A.25
Stuckmann, N.26
Vilbig, A.27
Lenke, M.28
Ludwig, T.29
Bode, A.30
Schleifer, K.H.31
more..
-
4
-
-
33845873289
-
Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation
-
Letunic I, Bork P. Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 2007;23:127-8.
-
(2007)
Bioinformatics
, vol.23
, pp. 127-128
-
-
Letunic, I.1
Bork, P.2
-
5
-
-
67249096511
-
ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences
-
Sun Y, Cai Y, Liu L, Yu F, Farrell ML, McKendree W, Farmerie W. ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res. 2009;37:e76.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Sun, Y.1
Cai, Y.2
Liu, L.3
Yu, F.4
Farrell, M.L.5
McKendree, W.6
Farmerie, W.7
-
6
-
-
70349866695
-
Upcoming challenges for multiple sequence alignment methods in the high-throughput era
-
Kemena C, Notredame C. Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics. 2009;25:2455-65.
-
(2009)
Bioinformatics
, vol.25
, pp. 2455-2465
-
-
Kemena, C.1
Notredame, C.2
-
7
-
-
77953627150
-
VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences
-
Mori H, Maruyama F, Kurokawa K. VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences. BMC Bioinformatics. 2010;11:332.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 332
-
-
Mori, H.1
Maruyama, F.2
Kurokawa, K.3
-
8
-
-
85044250749
-
-
VITCOMIC version 1 web site. Accessed 29 June 2017.
-
VITCOMIC version 1 web site. http://vitcomic1.vitcomic.org / Accessed 29 June 2017.
-
-
-
-
9
-
-
84878812684
-
Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island
-
Somboonna N, Assawamakin A, Wilantho A, Tangphatsornruang S, Tongsima S. Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island. Thailand BMC Genomics. 2012;13:S29.
-
(2012)
Thailand BMC Genomics
, vol.13
, pp. S29
-
-
Somboonna, N.1
Assawamakin, A.2
Wilantho, A.3
Tangphatsornruang, S.4
Tongsima, S.5
-
10
-
-
84870849159
-
Assessment of microbial richness in pelagic sediment of Andaman sea by bacterial tag encoded FLX titanium amplicon pyrosequencing (bTEFAP)
-
Sundarakrishnan B, Pushpanathan M, Jayashree S, Rajendhran J, Sakthivel N, Jayachandran S, Gunasekaran P. Assessment of microbial richness in pelagic sediment of Andaman sea by bacterial tag encoded FLX titanium amplicon pyrosequencing (bTEFAP). Indian J Microbiol. 2012;52:544-50.
-
(2012)
Indian J Microbiol
, vol.52
, pp. 544-550
-
-
Sundarakrishnan, B.1
Pushpanathan, M.2
Jayashree, S.3
Rajendhran, J.4
Sakthivel, N.5
Jayachandran, S.6
Gunasekaran, P.7
-
11
-
-
84884261498
-
Characteristics of microbial communities in crustal fluids in a deep-sea hydrothermal field of the suiyo seamount
-
Kato S, Nakawake M, Kita J, Yamanaka T, Utsumi M, Okamura K, Ishibashi J, Ohkuma M, Yamagishi A. Characteristics of microbial communities in crustal fluids in a deep-sea hydrothermal field of the suiyo seamount. Front Microbiol. 2013;4:85.
-
(2013)
Front Microbiol
, vol.4
, pp. 85
-
-
Kato, S.1
Nakawake, M.2
Kita, J.3
Yamanaka, T.4
Utsumi, M.5
Okamura, K.6
Ishibashi, J.7
Ohkuma, M.8
Yamagishi, A.9
-
12
-
-
84891787231
-
Ribosomal database project: data and tools for high throughput rRNA analysis
-
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42:D633-42.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D633-D642
-
-
Cole, J.R.1
Wang, Q.2
Fish, J.A.3
Chai, B.4
McGarrell, D.M.5
Sun, Y.6
Brown, C.T.7
Porras-Alfaro, A.8
Kuske, C.R.9
Tiedje, J.M.10
-
13
-
-
1942443733
-
Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons
-
Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol. 2004;186:2629-35.
-
(2004)
J Bacteriol
, vol.186
, pp. 2629-2635
-
-
Acinas, S.G.1
Marcelino, L.A.2
Klepac-Ceraj, V.3
Polz, M.F.4
-
14
-
-
84905661514
-
CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction
-
Angly FE, Dennis PG, Skarshewski A, Vanwonterghem I, Hugenholtz P, Tyson GW. CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. Microbiome. 2014;2:11.
-
(2014)
Microbiome
, vol.2
, pp. 11
-
-
Angly, F.E.1
Dennis, P.G.2
Skarshewski, A.3
Vanwonterghem, I.4
Hugenholtz, P.5
Tyson, G.W.6
-
15
-
-
40149103278
-
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
-
Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods. 2008;5:235-7.
-
(2008)
Nat Methods
, vol.5
, pp. 235-237
-
-
Hamady, M.1
Walker, J.J.2
Harris, J.K.3
Gold, N.J.4
Knight, R.5
-
16
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403-10.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
17
-
-
66249114350
-
Effects of experimental choices and analysis noise on surveys of the "rare biosphere"
-
Hamp TJ, Jones WJ, Fodor AA. Effects of experimental choices and analysis noise on surveys of the "rare biosphere". Appl Environ Microbiol. 2009;75:3263-70.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 3263-3270
-
-
Hamp, T.J.1
Jones, W.J.2
Fodor, A.A.3
-
18
-
-
84899117846
-
Design and experimental application of a novel non-degenerate universal primer set that amplifies prokaryotic 16S rRNA genes with a low possibility to amplify eukaryotic rRNA genes
-
Mori H, Maruyama F, Kato H, Toyoda A, Dozono A, Ohtsubo Y, Nagata Y, Fujiyama A, Tsuda M, Kurokawa K. Design and experimental application of a novel non-degenerate universal primer set that amplifies prokaryotic 16S rRNA genes with a low possibility to amplify eukaryotic rRNA genes. DNA Res. 2014;21:217-27.
-
(2014)
DNA Res
, vol.21
, pp. 217-227
-
-
Mori, H.1
Maruyama, F.2
Kato, H.3
Toyoda, A.4
Dozono, A.5
Ohtsubo, Y.6
Nagata, Y.7
Fujiyama, A.8
Tsuda, M.9
Kurokawa, K.10
-
19
-
-
74049108922
-
BLAST+: architecture and applications
-
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
20
-
-
85044180072
-
-
VITCOMIC1 reference 16S rRNA gene sequence database. Accessed 29 June 2017.
-
VITCOMIC1 reference 16S rRNA gene sequence database. http://vitcomic1.vitcomic.org / Accessed 29 June 2017.
-
-
-
-
21
-
-
0030661563
-
Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA
-
Liu WT, Marsh TL, Cheng H, Forney LJ. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol. 1997;63:4516-22.
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 4516-4522
-
-
Liu, W.T.1
Marsh, T.L.2
Cheng, H.3
Forney, L.J.4
-
22
-
-
0016154301
-
The 3' -terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites
-
Shine J, Dalgarno L. The 3' -terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974;71:1342-6.
-
(1974)
Proc Natl Acad Sci U S A
, vol.71
, pp. 1342-1346
-
-
Shine, J.1
Dalgarno, L.2
-
23
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460-1.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
24
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27:2194-200.
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
25
-
-
85044233574
-
-
Accessed 29 June 2017.
-
Reference gold database. http://drive5.com/uchime/gold.fa Accessed 29 June 2017.
-
Reference gold database
-
-
-
26
-
-
78751527447
-
Networks of gene sharing among 329 Proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths
-
Kloesges T, Popa O, Martin W, Dagan T. Networks of gene sharing among 329 Proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol Biol Evol. 2011;28:1057-74.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 1057-1074
-
-
Kloesges, T.1
Popa, O.2
Martin, W.3
Dagan, T.4
-
27
-
-
84934440243
-
MAFFT. Iterative refinement and additional methods
-
Katoh K, Standley DM. MAFFT. Iterative refinement and additional methods. Methods Mol Biol. 2014;1079:131-46.
-
(2014)
Methods Mol Biol.
, vol.1079
, pp. 131-146
-
-
Katoh, K.1
Standley, D.M.2
-
28
-
-
0000122573
-
PHYLIP-phylogeny inference package (version 3.2)
-
Felsenstein J. PHYLIP-phylogeny inference package (version 3.2). Cladistics. 1989;5:164-6.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
29
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980;16:111-20.
-
(1980)
J Mol Evol
, vol.16
, pp. 111-120
-
-
Kimura, M.1
-
30
-
-
84923861788
-
CLAST: CUDA implemented large-scale alignment search tool
-
Yano M, Mori H, Akiyama Y, Yamada T, Kurokawa K. CLAST: CUDA implemented large-scale alignment search tool. BMC Bioinformatics. 2014;15:406.
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 406
-
-
Yano, M.1
Mori, H.2
Akiyama, Y.3
Yamada, T.4
Kurokawa, K.5
-
31
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. A core gut microbiome in obese and lean twins. Nature. 2009;457:480-4.
-
(2009)
Nature
, vol.457
, pp. 480-484
-
-
Turnbaugh, P.J.1
Hamady, M.2
Yatsunenko, T.3
Cantarel, B.L.4
Duncan, A.5
Ley, R.E.6
Sogin, M.L.7
Jones, W.J.8
Roe, B.A.9
Affourtit, J.P.10
Egholm, M.11
Henrissat, B.12
Heath, A.C.13
Knight, R.14
Gordon, J.I.15
-
32
-
-
84868094960
-
Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance
-
Kembel SW, Wu M, Eisen JA, Green JA. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput Biol. 2012;8:e1002743.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Kembel, S.W.1
Wu, M.2
Eisen, J.A.3
Green, J.A.4
-
33
-
-
70449723278
-
Visualization of ribosomal RNA operon copy number distribution
-
Rastogi R, Wu M, Dasgupta I, Fox GE. Visualization of ribosomal RNA operon copy number distribution. BMC Microbiol. 2009;9:208.
-
(2009)
BMC Microbiol
, vol.9
, pp. 208
-
-
Rastogi, R.1
Wu, M.2
Dasgupta, I.3
Fox, G.E.4
-
34
-
-
34250665888
-
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
-
Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35:3100-8.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 3100-3108
-
-
Lagesen, K.1
Hallin, P.2
Rødland, E.A.3
Staerfeldt, H.H.4
Rognes, T.5
Ussery, D.W.6
-
35
-
-
84874022605
-
-
Accessed 29 June 2017.
-
NCBI Genome Database. ftp://ftp.ncbi.nih.gov/genomes/genbank/bacteria/ Accessed 29 June 2017.
-
NCBI Genome Database
-
-
-
36
-
-
84946027595
-
Database resources of the National Center for biotechnology information
-
Resource Coordinators NCBI. Database resources of the National Center for biotechnology information. Nucleic Acids Res. 2015;43:D6-D17.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D6-D17
-
-
-
37
-
-
84988948748
-
Next generation sequencing data of a defined microbial mock community
-
Singer E, Andreopoulos B, Bowers RM, Lee J, Deshpande S, Chiniguy J, Ciobanu D, Klenk HP, Zane M, Daum C, Clum A, Cheng JF, Copeland A, Woyke T. Next generation sequencing data of a defined microbial mock community. Sci Data. 2016;3:160081.
-
(2016)
Sci Data
, vol.3
-
-
Singer, E.1
Andreopoulos, B.2
Bowers, R.M.3
Lee, J.4
Deshpande, S.5
Chiniguy, J.6
Ciobanu, D.7
Klenk, H.P.8
Zane, M.9
Daum, C.10
Clum, A.11
Cheng, J.F.12
Copeland, A.13
Woyke, T.14
-
38
-
-
85040920865
-
MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis
-
Rodrigues JFM, Schmidt TSB, Tackmann J, von Mering C. MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. Bioinformatics. 2017;33:3808-10.
-
(2017)
Bioinformatics
, vol.33
, pp. 3808-3810
-
-
Rodrigues, J.F.M.1
Schmidt, T.S.B.2
Tackmann, J.3
von Mering, C.4
-
39
-
-
84870814915
-
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
-
Kopylova E, Noe L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211-7.
-
(2012)
Bioinformatics
, vol.28
, pp. 3211-3217
-
-
Kopylova, E.1
Noe, L.2
Touzet, H.3
-
40
-
-
85006856675
-
RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
-
Xie C, Goi CL, Huson DH, Little PF, Williams RB. RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys. BMC Bioinformatics. 2016;17:508.
-
(2016)
BMC Bioinformatics
, vol.17
, pp. 508
-
-
Xie, C.1
Goi, C.L.2
Huson, D.H.3
Little, P.F.4
Williams, R.B.5
-
41
-
-
5644227319
-
Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases
-
Clarridge JE 3rd. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev. 2004;17:840-62.
-
(2004)
Clin Microbiol Rev
, vol.17
, pp. 840-862
-
-
Clarridge, J.E.1
-
42
-
-
34548293679
-
Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261-7.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
43
-
-
85044216898
-
-
Accessed 29 June 2017.
-
VITCOMIC2 web server. http://vitcomic.org/vitcomic2/ Accessed 29 June 2017.
-
VITCOMIC2 web server
-
-
-
44
-
-
2942571539
-
The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
-
Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics. 2002;3:2.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 2
-
-
Cannone, J.J.1
Subramanian, S.2
Schnare, M.N.3
Collett, J.R.4
D'Souza, L.M.5
Du, Y.6
Feng, B.7
Lin, N.8
Madabusi, L.V.9
Müller, K.M.10
Pande, N.11
Shang, Z.12
Yu, N.13
Gutell, R.R.14
-
46
-
-
80052226692
-
Sequence-specific error profile of Illumina sequencers
-
Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, Altaf-Ul-Amin M, Ogasawara N, Kanaya S. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res. 2011;39:e90.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Nakamura, K.1
Oshima, T.2
Morimoto, T.3
Ikeda, S.4
Yoshikawa, H.5
Shiwa, Y.6
Ishikawa, S.7
Linak, M.C.8
Hirai, A.9
Takahashi, H.10
Altaf-Ul-Amin, M.11
Ogasawara, N.12
Kanaya, S.13
|