-
1
-
-
85008312194
-
Application of next generation sequencing in clinical microbiology and infection prevention
-
Deurenberg, R.H.; Bathoorn, E.; Chlebowicz, M.A.; Couto, N.; Ferdous, M.; García-Cobos, S.; Kooistra-Smid, A.M.D.; Raangs, E.C.; Rosema, S.; Veloo, A.C.M., et al. Application of next generation sequencing in clinical microbiology and infection prevention. J. Biotechnol. 2017, 243, 16–24.
-
(2017)
J. Biotechnol.
, vol.243
, pp. 16-24
-
-
Deurenberg, R.H.1
Bathoorn, E.2
Chlebowicz, M.A.3
Couto, N.4
Ferdous, M.5
García-Cobos, S.6
Kooistra-Smid, A.M.D.7
Raangs, E.C.8
Rosema, S.9
Veloo, A.C.M.10
-
2
-
-
4344599509
-
Pre-PCR processing of samples: Strategies to generate PCR-compatible samples
-
Rådström, P.; Knutsson, R.; Wolffs, P.; Dahlenborg, M.; Löfström, C. Pre-PCR processing of samples: Strategies to generate PCR-compatible samples. Methods Mol. Biol. 2004, 26, 133–146.
-
(2004)
Methods Mol. Biol.
, vol.26
, pp. 133-146
-
-
Rådström, P.1
Knutsson, R.2
Wolffs, P.3
Dahlenborg, M.4
Löfström, C.5
-
3
-
-
84928734173
-
Microbial food safety: Potential of DNA extraction methods for use in diagnostic metagenomics
-
Josefsen, M.H.; Andersen, S.C.; Christensen, J.; Hoorfar, J. Microbial food safety: Potential of DNA extraction methods for use in diagnostic metagenomics. J. Microbiol. Methods 2015, 114, 30–34.
-
(2015)
J. Microbiol. Methods
, vol.114
, pp. 30-34
-
-
Josefsen, M.H.1
Andersen, S.C.2
Christensen, J.3
Hoorfar, J.4
-
4
-
-
84870491197
-
Overcoming inhibition in real-time diagnostic PCR. Methods Mol
-
Hedman, J.; Rådström, P. Overcoming inhibition in real-time diagnostic PCR. Methods Mol. Biol. 2013, 943, 17–48.
-
(2013)
Biol
, vol.943
, pp. 17-48
-
-
Hedman, J.1
Rådström, P.2
-
5
-
-
84878647680
-
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ
-
Shakya, M.; Quince, C.; Campbell, J.H.; Yang, Z.K.; Schadt, C.W.; Podar, M. Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ. Microbiol. 2013, 15, 1882–1899.
-
(2013)
Microbiol
, vol.15
, pp. 1882-1899
-
-
Shakya, M.1
Quince, C.2
Campbell, J.H.3
Yang, Z.K.4
Schadt, C.W.5
Podar, M.6
-
6
-
-
84858709310
-
Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis
-
Bahl, M.I.; Bergström, A.; Licht, T.R. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol. Lett. 2012, 329, 193–197.
-
(2012)
FEMS Microbiol. Lett.
, vol.329
, pp. 193-197
-
-
Bahl, M.I.1
Bergström, A.2
Licht, T.R.3
-
7
-
-
84893723345
-
Library preparation methods for next-generation sequencing
-
Van Dijk, E.L.; Jaszczyszyn, Y.; Thermes, C. Library preparation methods for next-generation sequencing: Tone down the bias. Exp. Cell Res. 2014, 322, 12–20.
-
(2014)
Tone down the Bias. Exp. Cell Res.
, vol.322
, pp. 12-20
-
-
Van Dijk, E.L.1
Jaszczyszyn, Y.2
Thermes, C.3
-
8
-
-
84921532911
-
Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis
-
Wesolowska-Andersen, A.; Bahl, M.I.; Carvalho, V.; Kristiansen, K.; Sicheritz-Pontén, T.; Gupta, R.; Licht, T.R. Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. Microbiome 2014, 2, 19.
-
(2014)
Microbiome
, vol.2
-
-
Wesolowska-Andersen, A.1
Bahl, M.I.2
Carvalho, V.3
Kristiansen, K.4
Sicheritz-Pontén, T.5
Gupta, R.6
Licht, T.R.7
-
9
-
-
84878869719
-
Comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples
-
Claassen, S.; du Toit, E.; Kaba, M.; Moodley, C.; Zar, H.J.; Nicol, M.P. A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples. J. Microbiol. Methods 2013, 94, 103–110.
-
(2013)
J. Microbiol. Methods
, vol.94
, pp. 103-110
-
-
Claassen, S.1
Du Toit, E.2
Kaba, M.3
Moodley, C.4
Zar, H.J.5
Nicol, M.6
-
10
-
-
84896089558
-
The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing
-
Kennedy, N.A.; Walker, A.W.; Berry, S.H.; Duncan, S.H.; Farquarson, F.M.; Louis, P.; Thomson, J.M.; Satsangi, J.; Flint, H.J.; Parkhill, J., et al. The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing. PLoS ONE 2014, 9, e88982.
-
(2014)
Plos ONE
, vol.9
-
-
Kennedy, N.A.1
Walker, A.W.2
Berry, S.H.3
Duncan, S.H.4
Farquarson, F.M.5
Louis, P.6
Thomson, J.M.7
Satsangi, J.8
Flint, H.J.9
Parkhill, J.10
-
11
-
-
85019322956
-
Pamp, S.J. Impact of sample type and DNA isolation procedure on genomic inference of microbiome composition
-
Knudsen, B.E.; Bergmark, L.; Munk, P.; Lukjancenko, O.; Priemé, A.; Aarestrup, F.M.; Pamp, S.J. Impact of sample type and DNA isolation procedure on genomic inference of microbiome composition. Appl. Environ. Sci. 2016.
-
(2016)
Appl. Environ. Sci.
-
-
Knudsen, B.E.1
Bergmark, L.2
Munk, P.3
Lukjancenko, O.4
Priemé, A.5
Aarestrup, F.M.6
-
12
-
-
77952441809
-
Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens
-
Ariefdjohan, M.W.; Savaiano, D.A.; Nakatsu, C.H. Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens. Nutr. J. 2010, 9, 23.
-
(2010)
Nutr. J.
, vol.9
-
-
Ariefdjohan, M.W.1
Savaiano, D.A.2
Nakatsu, C.H.3
-
13
-
-
38049080602
-
Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces
-
Nechvatal, J.M.; Ram, J.L.; Basson, M.D.; Namprachan, P.; Niec, S.R.; Badsha, K.Z.; Matherly, L.H.; Majumdar, A.P.N.; Kato, I. Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces. J. Microbiol. Methods 2008, 72, 124–132.
-
(2008)
J. Microbiol. Methods
, vol.72
, pp. 124-132
-
-
Nechvatal, J.M.1
Ram, J.L.2
Basson, M.D.3
Namprachan, P.4
Niec, S.R.5
Badsha, K.Z.6
Matherly, L.H.7
Majumdar, A.P.N.8
Kato, I.9
-
14
-
-
84899090573
-
Kraken: Ultrafast metagenomic sequence classification using exact alignments
-
Wood, D.E.; Salzberg, S.L. Kraken: Ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014, 15, R46.
-
(2014)
Genome Biol
, vol.15
-
-
Wood, D.E.1
Salzberg, S.L.2
-
15
-
-
85018755906
-
MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads
-
Petersen, T.N.; Lukjancenko, O.; Thomsen, M.C.F.; Maddalena Sperotto, M.; Lund, O.; Møller Aarestrup, F.; Sicheritz-Pontén, T. MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads. PLoS ONE 2017, 12, e0176469.
-
(2017)
Plos ONE
, vol.12
-
-
Petersen, T.N.1
Lukjancenko, O.2
Thomsen, M.C.F.3
Maddalena Sperotto, M.4
Lund, O.5
Møller Aarestrup, F.6
Sicheritz-Pontén, T.7
-
16
-
-
84929174408
-
CLARK: Fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
-
Ounit, R.; Wanamaker, S.; Close, T.J.; Lonardi, S. CLARK: Fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genom. 2015, 16, 236.
-
(2015)
BMC Genom.
, vol.16
-
-
Ounit, R.1
Wanamaker, S.2
Close, T.J.3
Lonardi, S.4
-
17
-
-
84864440400
-
Metagenomic microbial community profiling using unique clade-specific marker genes
-
Segata, N.; Waldron, L.; Ballarini, A.; Narasimhan, V.; Jousson, O.; Huttenhower, C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 2013, 9, 811–814.
-
(2013)
Nat. Methods
, vol.9
, pp. 811-814
-
-
Segata, N.1
Waldron, L.2
Ballarini, A.3
Narasimhan, V.4
Jousson, O.5
Huttenhower, C.6
-
18
-
-
85020416195
-
Towards diagnostic metagenomics of Campylobacter in fecal samples
-
Andersen, S.C.; Kiil, K.; Harder, C.B.; Josefsen, M.H.; Persson, S.; Nielsen, E.M.; Hoorfar, J. Towards diagnostic metagenomics of Campylobacter in fecal samples. BMC Microbiol. 2017, 17, 33.
-
(2017)
BMC Microbiol
, vol.17
-
-
Andersen, S.C.1
Kiil, K.2
Harder, C.B.3
Josefsen, M.H.4
Persson, S.5
Nielsen, E.M.6
Hoorfar, J.7
-
19
-
-
84901363655
-
Waste not, want not: Why rarefying microbiome data is inadmissible
-
McMurdie, P.J.; Holmes, S. Waste not, want not: Why rarefying microbiome data is inadmissible. PLoS Comput. Biol. 2014, 10, e1003531.
-
(2014)
Plos Comput. Biol.
, vol.10
-
-
McMurdie, P.J.1
Holmes, S.2
-
20
-
-
33747342938
-
Comparative, collaborative, and on-site validation of a TaqMan PCR method as a tool for certified production of fresh, Campylobacter-free chickens
-
Krause, M.; Josefsen, M.H.; Lund, M.; Jacobsen, N.R.; Brorsen, L.; Moos, M.; Stockmarr, A.; Hoorfar, J. Comparative, collaborative, and on-site validation of a TaqMan PCR method as a tool for certified production of fresh, Campylobacter-free chickens. Appl. Environ. Microbiol. 2006, 72, 5463–5468.
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 5463-5468
-
-
Krause, M.1
Josefsen, M.H.2
Lund, M.3
Jacobsen, N.R.4
Brorsen, L.5
Moos, M.6
Stockmarr, A.7
Hoorfar, J.8
-
21
-
-
67649341523
-
Validation of a same-day real-time PCR method for screening of meat and carcass swabs for Salmonella
-
Löfström, C.; Krause, M.; Josefsen, M.H.; Hansen, F.; Hoorfar, J. Validation of a same-day real-time PCR method for screening of meat and carcass swabs for Salmonella. BMC Microbiol. 2009, 9, 85.
-
(2009)
BMC Microbiol
, vol.9
-
-
Löfström, C.1
Krause, M.2
Josefsen, M.H.3
Hansen, F.4
Hoorfar, J.5
-
22
-
-
84914179053
-
-
Vienna, Austria, (accessed on 14 November 2017)
-
R Core Team. R: A Language and environment for statistical computing; Vienna, Austria, 2014. Available online:http://www.R-project.org/(accessed on 14 November 2017).
-
(2014)
R: A Language and Environment for Statistical Computing
-
-
-
23
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M.D.; McCarthy, D.J.; Smyth, G.K. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2009, 26, 139–140.
-
(2009)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
|