-
1
-
-
0028946084
-
Phylogenetic identification and in situ detection of individual microbial cells without cultivation
-
239358, 7535888
-
Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995, 59(1):143-169. 239358, 7535888.
-
(1995)
Microbiol Rev
, vol.59
, Issue.1
, pp. 143-169
-
-
Amann, R.I.1
Ludwig, W.2
Schleifer, K.H.3
-
2
-
-
55249114699
-
Metagenomics for mining new genetic resources of microbial communities
-
10.1159/000142898, 18957866
-
Ferrer M, Beloqui A, Timmis KN, Golyshin PN. Metagenomics for mining new genetic resources of microbial communities. J Mol Microbiol Biotechnol 2009, 16(1-2):109-123. 10.1159/000142898, 18957866.
-
(2009)
J Mol Microbiol Biotechnol
, vol.16
, Issue.1-2
, pp. 109-123
-
-
Ferrer, M.1
Beloqui, A.2
Timmis, K.N.3
Golyshin, P.N.4
-
3
-
-
65549113872
-
Metagenomics: Concept, methodology, ecological inference and recent advances
-
10.1002/biot.200800201, 19288513
-
Singh J, Behal A, Singla N, Joshi A, Birbian N, Singh S, Bali V, Batra N. Metagenomics: Concept, methodology, ecological inference and recent advances. Biotechnol J 2009, 4(4):480-494. 10.1002/biot.200800201, 19288513.
-
(2009)
Biotechnol J
, vol.4
, Issue.4
, pp. 480-494
-
-
Singh, J.1
Behal, A.2
Singla, N.3
Joshi, A.4
Birbian, N.5
Singh, S.6
Bali, V.7
Batra, N.8
-
4
-
-
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(3):403-410.
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
5
-
-
36248968839
-
Evolutionary optimization of sequence kernels for detection of bacterial gene starts
-
10.1142/S0129065707001214, 18098369
-
Mersch B, Glasmachers T, Meinicke P, Igel C. Evolutionary optimization of sequence kernels for detection of bacterial gene starts. Int J Neural Syst 2007, 17(5):369-381. 10.1142/S0129065707001214, 18098369.
-
(2007)
Int J Neural Syst
, vol.17
, Issue.5
, pp. 369-381
-
-
Mersch, B.1
Glasmachers, T.2
Meinicke, P.3
Igel, C.4
-
6
-
-
34249736359
-
Comprehensive DNA signature discovery and validation
-
10.1371/journal.pcbi.0030098, 1868776, 17511514
-
Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL. Comprehensive DNA signature discovery and validation. PLoS Comput Biol 2007, 3(5):e98. 10.1371/journal.pcbi.0030098, 1868776, 17511514.
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.5
-
-
Phillippy, A.M.1
Mason, J.A.2
Ayanbule, K.3
Sommer, D.D.4
Taviani, E.5
Huq, A.6
Colwell, R.R.7
Knight, I.T.8
Salzberg, S.L.9
-
7
-
-
36048977268
-
On the reliable identification of plant sequences containing a polyadenylation site
-
10.1089/cmb.2007.0058, 17990973
-
Havukkala I, Vanderlooy S. On the reliable identification of plant sequences containing a polyadenylation site. J Comput Biol 2007, 14(9):1229-1245. 10.1089/cmb.2007.0058, 17990973.
-
(2007)
J Comput Biol
, vol.14
, Issue.9
, pp. 1229-1245
-
-
Havukkala, I.1
Vanderlooy, S.2
-
8
-
-
45549107061
-
DNA signatures for detecting genetic engineering in bacteria
-
10.1186/gb-2008-9-3-r56, 2397508, 18348716
-
Allen JE, Gardner SN, Slezak TR. DNA signatures for detecting genetic engineering in bacteria. Genome Biol 2008, 9(3):R56. 10.1186/gb-2008-9-3-r56, 2397508, 18348716.
-
(2008)
Genome Biol
, vol.9
, Issue.3
-
-
Allen, J.E.1
Gardner, S.N.2
Slezak, T.R.3
-
9
-
-
36448948250
-
Extending assembly of short DNA sequences to handle error
-
10.1093/bioinformatics/btm451, 17893086
-
Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, Mardis ER, Dangl JL, Jones CD. Extending assembly of short DNA sequences to handle error. Bioinformatics 2007, 23(21):2942-2944. 10.1093/bioinformatics/btm451, 17893086.
-
(2007)
Bioinformatics
, vol.23
, Issue.21
, pp. 2942-2944
-
-
Jeck, W.R.1
Reinhardt, J.A.2
Baltrus, D.A.3
Hickenbotham, M.T.4
Magrini, V.5
Mardis, E.R.6
Dangl, J.L.7
Jones, C.D.8
-
10
-
-
40549107988
-
Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies
-
Coarfa C, Milosavljevic A. Pash 2.0: scaleable sequence anchoring for next-generation sequencing technologies. Pac Symp Biocomput 2008, 102-113.
-
(2008)
Pac Symp Biocomput
, pp. 102-113
-
-
Coarfa, C.1
Milosavljevic, A.2
-
11
-
-
34447648188
-
SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition
-
10.1186/1471-2105-8-S4-S2, 2230503, 18269696
-
Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C. SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition. BMC Bioinformatics 2007, 8(Suppl 4):S2. 10.1186/1471-2105-8-S4-S2, 2230503, 18269696.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 4
-
-
Melvin, I.1
Ie, E.2
Kuang, R.3
Weston, J.4
Stafford, W.N.5
Leslie, C.6
-
12
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
10.1093/bioinformatics/btl158, 16731699
-
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22(13):1658-1659. 10.1093/bioinformatics/btl158, 16731699.
-
(2006)
Bioinformatics
, vol.22
, Issue.13
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
13
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
10.1128/AEM.03006-05, 1489311, 16820507
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006, 72(7):5069-5072. 10.1128/AEM.03006-05, 1489311, 16820507.
-
(2006)
Appl Environ Microbiol
, vol.72
, Issue.7
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
Huber, T.7
Dalevi, D.8
Hu, P.9
Andersen, G.L.10
-
14
-
-
34548293679
-
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. 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
-
15
-
-
54549106898
-
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
-
10.1093/nar/gkn491, 2566877, 18723574
-
Liu Z, DeSantis TZ, Andersen GL, Knight R. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res 2008, 36(18):e120. 10.1093/nar/gkn491, 2566877, 18723574.
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.18
-
-
Liu, Z.1
DeSantis, T.Z.2
Andersen, G.L.3
Knight, R.4
-
16
-
-
33750576374
-
MICA: desktop software for comprehensive searching of DNA databases
-
10.1186/1471-2105-7-427, 1618866, 17018144
-
Stokes WA, Glick BS. MICA: desktop software for comprehensive searching of DNA databases. BMC Bioinformatics 2006, 7:427. 10.1186/1471-2105-7-427, 1618866, 17018144.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 427
-
-
Stokes, W.A.1
Glick, B.S.2
-
17
-
-
0034764307
-
SSAHA: a fast search method for large DNA databases
-
10.1101/gr.194201, 311141, 11591649
-
Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large DNA databases. Genome Res 2001, 11(10):1725-1729. 10.1101/gr.194201, 311141, 11591649.
-
(2001)
Genome Res
, vol.11
, Issue.10
, pp. 1725-1729
-
-
Ning, Z.1
Cox, A.J.2
Mullikin, J.C.3
-
18
-
-
0027283509
-
The ribosomal database project
-
10.1093/nar/21.13.3021, 309730, 8332524
-
Larsen N, Olsen GJ, Maidak BL, McCaughey MJ, Overbeek R, Macke TJ, Marsh TL, Woese CR. The ribosomal database project. Nucleic Acids Res 1993, 21(13):3021-3023. 10.1093/nar/21.13.3021, 309730, 8332524.
-
(1993)
Nucleic Acids Res
, vol.21
, Issue.13
, pp. 3021-3023
-
-
Larsen, N.1
Olsen, G.J.2
Maidak, B.L.3
McCaughey, M.J.4
Overbeek, R.5
Macke, T.J.6
Marsh, T.L.7
Woese, C.R.8
-
19
-
-
34548338330
-
TIOBE Programming Community Index
-
TIOBE Programming Community Index. , http://www.tiobe.com/index.php/content/paperinfo/tpci
-
-
-
-
20
-
-
34248159346
-
High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment
-
10.1007/s00248-006-9134-9, 17334858
-
DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 2007, 53(3):371-383. 10.1007/s00248-006-9134-9, 17334858.
-
(2007)
Microb Ecol
, vol.53
, Issue.3
, pp. 371-383
-
-
DeSantis, T.Z.1
Brodie, E.L.2
Moberg, J.P.3
Zubieta, I.X.4
Piceno, Y.M.5
Andersen, G.L.6
-
21
-
-
37849012982
-
Short-term temporal variability in airborne bacterial and fungal populations
-
10.1128/AEM.01467-07, 2223228, 17981945
-
Fierer N, Liu Z, Rodriguez-Hernandez M, Knight R, Henn M, Hernandez MT. Short-term temporal variability in airborne bacterial and fungal populations. Appl Environ Microbiol 2008, 74(1):200-207. 10.1128/AEM.01467-07, 2223228, 17981945.
-
(2008)
Appl Environ Microbiol
, vol.74
, Issue.1
, pp. 200-207
-
-
Fierer, N.1
Liu, Z.2
Rodriguez-Hernandez, M.3
Knight, R.4
Henn, M.5
Hernandez, M.T.6
-
22
-
-
54449098594
-
Bacterial community in the crop of the hoatzin, a neotropical folivorous flying bird
-
10.1128/AEM.00574-08, 2565963, 18689523
-
Godoy-Vitorino F, Ley RE, Gao Z, Pei Z, Ortiz-Zuazaga H, Pericchi LR, Garcia-Amado MA, Michelangeli F, Blaser MJ, Gordon JI, et al. Bacterial community in the crop of the hoatzin, a neotropical folivorous flying bird. Appl Environ Microbiol 2008, 74(19):5905-5912. 10.1128/AEM.00574-08, 2565963, 18689523.
-
(2008)
Appl Environ Microbiol
, vol.74
, Issue.19
, pp. 5905-5912
-
-
Godoy-Vitorino, F.1
Ley, R.E.2
Gao, Z.3
Pei, Z.4
Ortiz-Zuazaga, H.5
Pericchi, L.R.6
Garcia-Amado, M.A.7
Michelangeli, F.8
Blaser, M.J.9
Gordon, J.I.10
-
23
-
-
67349105701
-
Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata
-
10.1038/ismej.2008.131, 19129866
-
Sunagawa S, DeSantis TZ, Piceno YM, Brodie EL, DeSalvo MK, Voolstra CR, Weil E, Andersen GL, Medina M. Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata. ISME J 2009, 3(5):512-521. 10.1038/ismej.2008.131, 19129866.
-
(2009)
ISME J
, vol.3
, Issue.5
, pp. 512-521
-
-
Sunagawa, S.1
DeSantis, T.Z.2
Piceno, Y.M.3
Brodie, E.L.4
DeSalvo, M.K.5
Voolstra, C.R.6
Weil, E.7
Andersen, G.L.8
Medina, M.9
-
24
-
-
53649084794
-
Evidence of multiple Treponema phylotypes involved in bovine digital dermatitis as shown by 16S rRNA gene analysis and fluorescence in situ hybridization
-
10.1128/JCM.00670-08, 2546760, 18562583
-
Klitgaard K, Boye M, Capion N, Jensen TK. Evidence of multiple Treponema phylotypes involved in bovine digital dermatitis as shown by 16S rRNA gene analysis and fluorescence in situ hybridization. J Clin Microbiol 2008, 46(9):3012-3020. 10.1128/JCM.00670-08, 2546760, 18562583.
-
(2008)
J Clin Microbiol
, vol.46
, Issue.9
, pp. 3012-3020
-
-
Klitgaard, K.1
Boye, M.2
Capion, N.3
Jensen, T.K.4
-
25
-
-
0034707204
-
Using BLAST for identifying gene and protein names in journal articles
-
10.1016/S0378-1119(00)00431-5, 11163982
-
Krauthammer M, Rzhetsky A, Morozov P, Friedman C. Using BLAST for identifying gene and protein names in journal articles. Gene 2000, 259(1-2):245-252. 10.1016/S0378-1119(00)00431-5, 11163982.
-
(2000)
Gene
, vol.259
, Issue.1-2
, pp. 245-252
-
-
Krauthammer, M.1
Rzhetsky, A.2
Morozov, P.3
Friedman, C.4
-
26
-
-
66349083859
-
Topographical and temporal diversity of the human skin microbiome
-
10.1126/science.1171700, 2805064, 19478181
-
Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Bouffard GG, Blakesley RW, Murray PR, Green ED, et al. Topographical and temporal diversity of the human skin microbiome. Science 2009, 324(5931):1190-1192. 10.1126/science.1171700, 2805064, 19478181.
-
(2009)
Science
, vol.324
, Issue.5931
, pp. 1190-1192
-
-
Grice, E.A.1
Kong, H.H.2
Conlan, S.3
Deming, C.B.4
Davis, J.5
Young, A.C.6
Bouffard, G.G.7
Blakesley, R.W.8
Murray, P.R.9
Green, E.D.10
-
27
-
-
0000122573
-
PHYLIP - Phylogeny Inference Package (Version 3.65)
-
Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.65). Cladistics 1989, 5:164-166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
28
-
-
67649327176
-
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
-
10.1093/molbev/msp077, 2693737, 19377059
-
Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009, 26(7):1641-1650. 10.1093/molbev/msp077, 2693737, 19377059.
-
(2009)
Mol Biol Evol
, vol.26
, Issue.7
, pp. 1641-1650
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
29
-
-
77952254719
-
Alignment and clustering of phylogenetic markers--implications for microbial diversity studies
-
10.1186/1471-2105-11-152, 2859756, 20334679
-
White JR, Navlakha S, Nagarajan N, Ghodsi MR, Kingsford C, Pop M. Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. BMC Bioinformatics 2010, 11:152. 10.1186/1471-2105-11-152, 2859756, 20334679.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 152
-
-
White, J.R.1
Navlakha, S.2
Nagarajan, N.3
Ghodsi, M.R.4
Kingsford, C.5
Pop, M.6
-
30
-
-
27544491192
-
ROCR: visualizing classifier performance in R
-
10.1093/bioinformatics/bti623, 16096348
-
Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: visualizing classifier performance in R. Bioinformatics 2005, 21(20):3940-3941. 10.1093/bioinformatics/bti623, 16096348.
-
(2005)
Bioinformatics
, vol.21
, Issue.20
, pp. 3940-3941
-
-
Sing, T.1
Sander, O.2
Beerenwinkel, N.3
Lengauer, T.4
-
31
-
-
73349110099
-
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
-
10.1111/j.1462-2920.2009.02051.x, 19725865
-
Kunin V, Engelbrektson A, Ochman H, Hugenholtz P. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 2010, 12(1):118-123. 10.1111/j.1462-2920.2009.02051.x, 19725865.
-
(2010)
Environ Microbiol
, vol.12
, Issue.1
, pp. 118-123
-
-
Kunin, V.1
Engelbrektson, A.2
Ochman, H.3
Hugenholtz, P.4
-
32
-
-
77957244650
-
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
-
33
-
-
0025678737
-
Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis
-
10.1016/0022-2836(90)90386-Z, 2258934
-
Michel F, Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol 1990, 216(3):585-610. 10.1016/0022-2836(90)90386-Z, 2258934.
-
(1990)
J Mol Biol
, vol.216
, Issue.3
, pp. 585-610
-
-
Michel, F.1
Westhof, E.2
|