-
1
-
-
78649773164
-
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
-
Adey, A., Morrison, H.G., Asan, Xun, X., Kitzman, J.O., Turner, E.H., etal. (2010) Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol 11: R119.
-
(2010)
Genome Biol
, vol.11
, pp. R119
-
-
Adey, A.1
Morrison, H.G.A.2
Adey, A.3
Morrison, H.4
Xun, X.5
Kitzman, J.O.6
Turner, E.H.7
-
2
-
-
79951694175
-
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
-
Aird, D., Ross, M.G., Chen, W.S., Danielsson, M., Fennell, T., Russ, C., etal. (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 12: R18.
-
(2011)
Genome Biol
, vol.12
, pp. R18
-
-
Aird, D.1
Ross, M.G.2
Chen, W.S.3
Danielsson, M.4
Fennell, T.5
Russ, C.6
-
3
-
-
84879678051
-
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
-
Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K.L., Tyson, G.W., and Nielsen, P.H. (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31: 533-538.
-
(2013)
Nat Biotechnol
, vol.31
, pp. 533-538
-
-
Albertsen, M.1
Hugenholtz, P.2
Skarshewski, A.3
Nielsen, K.L.4
Tyson, G.W.5
Nielsen, P.H.6
-
4
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders, S., and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106.
-
(2010)
Genome Biol
, vol.11
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
5
-
-
84863292680
-
Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection
-
Biesbroek, G., Sanders, E.A.M., Roeselers, G., Wang, X., Caspers, M.P.M., Trzciński, K., etal. (2012) Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection. PLoS ONE 7: e32942.
-
(2012)
PLoS ONE
, vol.7
, pp. e32942
-
-
Biesbroek, G.1
Sanders, E.A.M.2
Roeselers, G.3
Wang, X.4
Caspers, M.P.M.5
Trzciński, K.6
-
6
-
-
79952298772
-
Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis
-
Bogaert, D., Keijser, B., Huse, S., Rossen, J., Veenhoven, R., van Gils, E., etal. (2011) Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis. PLoS ONE 6: e17035.
-
(2011)
PLoS ONE
, vol.6
, pp. e17035
-
-
Bogaert, D.1
Keijser, B.2
Huse, S.3
Rossen, J.4
Veenhoven, R.5
van Gils, E.6
-
7
-
-
79953023907
-
Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments
-
Bowers, R.M., McLetchie, S., Knight, R., and Fierer, N. (2011) Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments. ISME J 5: 601-612.
-
(2011)
ISME J
, vol.5
, pp. 601-612
-
-
Bowers, R.M.1
McLetchie, S.2
Knight, R.3
Fierer, N.4
-
8
-
-
79955611184
-
PhymmBL expanded: confidence scores, custom databases, parallelization and more
-
Brady, A., and Salzberg, S. (2011) PhymmBL expanded: confidence scores, custom databases, parallelization and more. Nat Methods 8: 367.
-
(2011)
Nat Methods
, vol.8
, pp. 367
-
-
Brady, A.1
Salzberg, S.2
-
9
-
-
69549135124
-
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
-
Brady, A., and Salzberg, S.L. (2009) Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 6: 673-676.
-
(2009)
Nat Methods
, vol.6
, pp. 673-676
-
-
Brady, A.1
Salzberg, S.L.2
-
10
-
-
84868687821
-
Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides
-
Brown, S.D., Utturkar, S.M., Klingeman, D.M., Johnson, C.M., Martin, S.L., Land, M.L., etal. (2012) Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides. J Bacteriol 194: 5991-5993.
-
(2012)
J Bacteriol
, vol.194
, pp. 5991-5993
-
-
Brown, S.D.1
Utturkar, S.M.2
Klingeman, D.M.3
Johnson, C.M.4
Martin, S.L.5
Land, M.L.6
-
11
-
-
84865344067
-
Structure, fluctuation and magnitude of a natural grassland soil metagenome
-
Delmont, T.O., Prestat, E., Keegan, K.P., Faubladier, M., Robe, P., Clark, I.M., etal. (2012) Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J 6: 1677-1687.
-
(2012)
ISME J
, vol.6
, pp. 1677-1687
-
-
Delmont, T.O.1
Prestat, E.2
Keegan, K.P.3
Faubladier, M.4
Robe, P.5
Clark, I.M.6
-
12
-
-
70350015324
-
Community-wide analysis of microbial genome sequence signatures
-
Dick, G.J., Andersson, A.F., Baker, B.J., Simmons, S.L., Thomas, B.C., Yelton, A.P., and Banfield, J.F. (2009) Community-wide analysis of microbial genome sequence signatures. Genome Biol 10: R85.
-
(2009)
Genome Biol
, vol.10
, pp. R85
-
-
Dick, G.J.1
Andersson, A.F.2
Baker, B.J.3
Simmons, S.L.4
Thomas, B.C.5
Yelton, A.P.6
Banfield, J.F.7
-
13
-
-
84887791432
-
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
-
Dillies, M.A., Rau, A., Aubert, J., Hennequet-Antier, C., Jeanmougin, M., Servant, N., etal. (2012) A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinform 14: 671-683.
-
(2012)
Brief Bioinform
, vol.14
, pp. 671-683
-
-
Dillies, M.A.1
Rau, A.2
Aubert, J.3
Hennequet-Antier, C.4
Jeanmougin, M.5
Servant, N.6
-
14
-
-
84865720549
-
Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method
-
Duhaime, M.B., Deng, L., Poulos, B.T., and Sullivan, M.B. (2012) Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method. Environ Microbiol 14: 2526-2537.
-
(2012)
Environ Microbiol
, vol.14
, pp. 2526-2537
-
-
Duhaime, M.B.1
Deng, L.2
Poulos, B.T.3
Sullivan, M.B.4
-
15
-
-
84870829895
-
Reference-independent comparative metagenomics using cross-assembly: crAss
-
Dutilh, B.E., Schmieder, R., Nulton, J., Felts, B., Salamon, P., Edwards, R.A., and Mokili, J.L. (2012) Reference-independent comparative metagenomics using cross-assembly: crAss. Bioinformatics 28: 3225-3231.
-
(2012)
Bioinformatics
, vol.28
, pp. 3225-3231
-
-
Dutilh, B.E.1
Schmieder, R.2
Nulton, J.3
Felts, B.4
Salamon, P.5
Edwards, R.A.6
Mokili, J.L.7
-
16
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
17
-
-
84871826193
-
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
-
Fierer, N., Leff, J.W., Adams, B.J., Nielsen, U.N., Bates, S.T., Lauber, C.L., etal. (2012) Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA 109: 21390-21395.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 21390-21395
-
-
Fierer, N.1
Leff, J.W.2
Adams, B.J.3
Nielsen, U.N.4
Bates, S.T.5
Lauber, C.L.6
-
18
-
-
70350294348
-
Systematic artifacts in metagenomes from complex microbial communities
-
Gomez-Alvarez, V., Teal, T.K., and Schmidt, T.M. (2009) Systematic artifacts in metagenomes from complex microbial communities. ISME J 3: 1314-1317.
-
(2009)
ISME J
, vol.3
, pp. 1314-1317
-
-
Gomez-Alvarez, V.1
Teal, T.K.2
Schmidt, T.M.3
-
19
-
-
66349083859
-
Topographical and temporal diversity of the human skin microbiome
-
Grice, E.A., Kong, H.H., Conlan, S., Deming, C.B., Davis, J., Young, A.C., etal. (2009) Topographical and temporal diversity of the human skin microbiome. Science 324: 1190-1192.
-
(2009)
Science
, vol.324
, 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
-
20
-
-
79959882452
-
Linear amplification for deep sequencing
-
Hoeijmakers, W.A., Bartfai, R., Francoijs, K.J., and Stunnenberg, H.G. (2011) Linear amplification for deep sequencing. Nat Protoc 6: 1026-1036.
-
(2011)
Nat Protoc
, vol.6
, pp. 1026-1036
-
-
Hoeijmakers, W.A.1
Bartfai, R.2
Francoijs, K.J.3
Stunnenberg, H.G.4
-
21
-
-
57149093416
-
Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing
-
Huse, S.M., Dethlefsen, L., Huber, J.A., Mark Welch, D., Relman, D.A., and Sogin, M.L. (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 4: e1000255.
-
(2008)
PLoS Genet
, vol.4
, pp. e1000255
-
-
Huse, S.M.1
Dethlefsen, L.2
Huber, J.A.3
Mark Welch, D.4
Relman, D.A.5
Sogin, M.L.6
-
22
-
-
84867043272
-
Global distribution of microbial abundance and biomass in subseafloor sediment
-
Kallmeyer, J., Pockalny, R., Adhikari, R.R., Smith, D.C., and D'Hondt, S. (2012) Global distribution of microbial abundance and biomass in subseafloor sediment. Proc Natl Acad Sci USA 109: 16213-16216.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 16213-16216
-
-
Kallmeyer, J.1
Pockalny, R.2
Adhikari, R.R.3
Smith, D.C.4
D'Hondt, S.5
-
23
-
-
63949083912
-
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
-
Kozarewa, I., Ning, Z., Quail, M.A., Sanders, M.J., Berriman, M., and Turner, D.J. (2009) Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 6: 291-295.
-
(2009)
Nat Methods
, vol.6
, pp. 291-295
-
-
Kozarewa, I.1
Ning, Z.2
Quail, M.A.3
Sanders, M.J.4
Berriman, M.5
Turner, D.J.6
-
24
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
26
-
-
84903362470
-
Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities
-
e00682-e00613
-
Maignien, L., DeForce, E.A., Chafee, M.E., Eren, A.M., and Simmons, S.L. (2014) Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities. MBio 5(1): e00682-13. doi:10.1128/mBio.00682-13.
-
(2014)
MBio
, vol.5
, Issue.1
-
-
Maignien, L.1
DeForce, E.A.2
Chafee, M.E.3
Eren, A.M.4
Simmons, S.L.5
-
27
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin, M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10-12.
-
(2011)
EMBnet.journal
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
28
-
-
80455126001
-
Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems
-
Minoche, A.E., Dohm, J.C., 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
, pp. R112
-
-
Minoche, A.E.1
Dohm, J.C.2
Himmelbauer, H.3
-
29
-
-
84867397631
-
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
-
Namiki, T., Hachiya, T., Tanaka, H., and Sakakibara, Y. (2012) MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res 40: e155.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. e155
-
-
Namiki, T.1
Hachiya, T.2
Tanaka, H.3
Sakakibara, Y.4
-
30
-
-
84905730761
-
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
-
Nielsen, H.B., Almeida, M., Juncker, A.S., Rasmussen, S., Li, J., Sunagawa, S., etal. (2014) Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotech 32: 822-828.
-
(2014)
Nat Biotech
, vol.32
, pp. 822-828
-
-
Nielsen, H.B.1
Almeida, M.2
Juncker, A.S.3
Rasmussen, S.4
Li, J.5
Sunagawa, S.6
-
31
-
-
84937029478
-
Ovation ultralow library systems: user guide
-
NuGen, Technical Manual.
-
NuGen (2013) Ovation ultralow library systems: user guide. NuGen, Technical Manual.
-
(2013)
-
-
-
32
-
-
84937067863
-
-
vegan: Community Ecology Package. R package version 2.0-10.
-
Oksanen, J., Blanchet, F.G., Kindt, R., Legendre, P., Minchin, P.R., ÓHara, R.B., Simpson, G.L., Solymos, P., Henry, M., Stevens, H., and Wagner, H. (2013) vegan: Community Ecology Package. R package version 2.0-10. http://CRAN.R-project.org/package=vegan.
-
(2013)
-
-
Oksanen, J.1
Blanchet, F.G.2
Kindt, R.3
Legendre, P.4
Minchin, P.R.5
ÓHara, R.B.6
Simpson, G.L.7
Solymos, P.8
Henry, M.9
Stevens, H.10
Wagner, H.11
-
33
-
-
84855306099
-
Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA
-
Parkinson, N.J., Maslau, S., Ferneyhough, B., Zhang, G., Gregory, L., Buck, D., etal. (2012) Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA. Genome Res 22: 125-133.
-
(2012)
Genome Res
, vol.22
, pp. 125-133
-
-
Parkinson, N.J.1
Maslau, S.2
Ferneyhough, B.3
Zhang, G.4
Gregory, L.5
Buck, D.6
-
34
-
-
84873739311
-
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
-
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., etal. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41: D590-D596.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D590-D596
-
-
Quast, C.1
Pruesse, E.2
Yilmaz, P.3
Gerken, J.4
Schweer, T.5
Yarza, P.6
-
35
-
-
84881138595
-
Insights into the phylogeny and coding potential of microbial dark matter
-
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N.N., Anderson, I.J., Cheng, J.F., etal. (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
Cheng, J.F.6
-
36
-
-
84920644670
-
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
-
Salter, S.J., Cox, M.J., Turek, E.M., Calus, S.T., Cookson, W.O., Moffatt, M.F., etal. (2014) Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 12: 87.
-
(2014)
BMC Biol
, vol.12
, pp. 87
-
-
Salter, S.J.1
Cox, M.J.2
Turek, E.M.3
Calus, S.T.4
Cookson, W.O.5
Moffatt, M.F.6
-
37
-
-
84877278609
-
Sequencing platform and library preparation choices impact viral metagenomes
-
Solonenko, S.A., Ignacio-Espinoza, J.C., Alberti, A., Cruaud, C., Hallam, S., Konstantinidis, K., etal. (2013) Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics 14: 320.
-
(2013)
BMC Genomics
, vol.14
, pp. 320
-
-
Solonenko, S.A.1
Ignacio-Espinoza, J.C.2
Alberti, A.3
Cruaud, C.4
Hallam, S.5
Konstantinidis, K.6
-
38
-
-
0036566806
-
Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'
-
Thompson, J.R., Marcelino, L.A., and Polz, M.F. (2002) Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res 30: 2083-2088.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 2083-2088
-
-
Thompson, J.R.1
Marcelino, L.A.2
Polz, M.F.3
-
39
-
-
33745890364
-
ESOM-Maps: tools for clustering, visualization, and classification with Emergent SOM
-
Technical Report Dept. of Mathematics and Computer Science, University of Marburg, Germany, No. 46.
-
Ultsch, A., Moerchen, F. (2005) ESOM-Maps: tools for clustering, visualization, and classification with Emergent SOM, Technical Report Dept. of Mathematics and Computer Science, University of Marburg, Germany, No. 46.
-
(2005)
-
-
Ultsch, A.1
Moerchen, F.2
-
40
-
-
78649317883
-
Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon
-
Wang, Y., Antonopoulos, D.A., Zhu, X., Harrell, L., Hanan, I., Alverdy, J.C., etal. (2010) Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Appl Microbiol Biotechnol 88: 1333-1342.
-
(2010)
Appl Microbiol Biotechnol
, vol.88
, pp. 1333-1342
-
-
Wang, Y.1
Antonopoulos, D.A.2
Zhu, X.3
Harrell, L.4
Hanan, I.5
Alverdy, J.C.6
-
41
-
-
84937067864
-
-
ggplot2: elegant graphics for data analysis.
-
Wickham, H. (2009) ggplot2: elegant graphics for data analysis.
-
(2009)
-
-
Wickham, H.1
-
42
-
-
77955929948
-
The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses
-
Yergeau, E., Hogues, H., Whyte, L.G., and Greer, C.W. (2010) The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. ISME J 4: 1206-1214.
-
(2010)
ISME J
, vol.4
, pp. 1206-1214
-
-
Yergeau, E.1
Hogues, H.2
Whyte, L.G.3
Greer, C.W.4
-
43
-
-
78649707158
-
Multiple displacement amplification compromises quantitative analysis of metagenomes
-
Yilmaz, S., Allgaier, M., and Hugenholtz, P. (2010) Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat Methods 7: 943-944.
-
(2010)
Nat Methods
, vol.7
, pp. 943-944
-
-
Yilmaz, S.1
Allgaier, M.2
Hugenholtz, P.3
-
44
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino, D.R., and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
45
-
-
84898881845
-
Bias from removing read duplication in ultra-deep sequencing experiments
-
Zhou, W., Chen, T., Zhao, H., Eterovic, A.K., Meric-Bernstam, F., Mills, G.B., and Chen, K. (2014) Bias from removing read duplication in ultra-deep sequencing experiments. Bioinformatics 30: 1073-1080.
-
(2014)
Bioinformatics
, vol.30
, pp. 1073-1080
-
-
Zhou, W.1
Chen, T.2
Zhao, H.3
Eterovic, A.K.4
Meric-Bernstam, F.5
Mills, G.B.6
Chen, K.7
|