-
1
-
-
84858709310
-
Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis
-
22325006
-
Bahl MI, Bergstrom A, Licht TR. 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. 10.1111/j.1574-6968.2012.02523.x, 22325006.
-
(2012)
FEMS Microbiol Lett
, vol.329
, pp. 193-197
-
-
Bahl, M.I.1
Bergstrom, A.2
Licht, T.R.3
-
2
-
-
33645116245
-
Freezing at -800 degrees C distorts the DNA composition of bacterial communities in intestinal samples
-
Molbak L, Sommer HM, Johnsen K, Boye M, Johansen M, Moller K, Leser TD. Freezing at -800 degrees C distorts the DNA composition of bacterial communities in intestinal samples. Curr Issues Intest Microbiol 2006, 7:29-34.
-
(2006)
Curr Issues Intest Microbiol
, vol.7
, pp. 29-34
-
-
Molbak, L.1
Sommer, H.M.2
Johnsen, K.3
Boye, M.4
Johansen, M.5
Moller, K.6
Leser, T.D.7
-
3
-
-
77951941062
-
Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples
-
3148093, 20412303
-
Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N. Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett 2010, 307:80-86. 10.1111/j.1574-6968.2010.01965.x, 3148093, 20412303.
-
(2010)
FEMS Microbiol Lett
, vol.307
, pp. 80-86
-
-
Lauber, C.L.1
Zhou, N.2
Gordon, J.I.3
Knight, R.4
Fierer, N.5
-
4
-
-
0036300743
-
Mucosa-Associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces
-
126800, 12089021
-
Zoetendal EG, Von Wright A, Vilpponen-Salmela T, Ben Amor K, Akkermans AD, de Vos WM. Mucosa-Associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 2002, 68:3401-3407. 10.1128/AEM.68.7.3401-3407.2002, 126800, 12089021.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 3401-3407
-
-
Zoetendal, E.G.1
Von Wright, A.2
Vilpponen-Salmela, T.3
Ben Amor, K.4
Akkermans, A.D.5
de Vos, W.M.6
-
5
-
-
33645471793
-
A microbial world within us
-
16553872
-
Zoetendal EG, Vaughan EE, de Vos WM. A microbial world within us. Mol Microbiol 2006, 59:1639-1650. 10.1111/j.1365-2958.2006.05056.x, 16553872.
-
(2006)
Mol Microbiol
, vol.59
, pp. 1639-1650
-
-
Zoetendal, E.G.1
Vaughan, E.E.2
de Vos, W.M.3
-
6
-
-
84877765843
-
Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing
-
3647099, 22760785
-
Guo F, Zhang T. Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing. Appl Microbiol Biotechnol 2013, 97:4607-4616. 10.1007/s00253-012-4244-4, 3647099, 22760785.
-
(2013)
Appl Microbiol Biotechnol
, vol.97
, pp. 4607-4616
-
-
Guo, F.1
Zhang, T.2
-
7
-
-
84893848394
-
Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities
-
3770609, 24040342
-
Henderson G, Cox F, Kittelmann S, Miri VH, Zethof M, Noel SJ, Waghorn GC, Janssen PH. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLoS One 2013, 8:e74787. 10.1371/journal.pone.0074787, 3770609, 24040342.
-
(2013)
PLoS One
, vol.8
, pp. e74787
-
-
Henderson, G.1
Cox, F.2
Kittelmann, S.3
Miri, V.H.4
Zethof, M.5
Noel, S.J.6
Waghorn, G.C.7
Janssen, P.H.8
-
8
-
-
84891496235
-
Commercial DNA extraction kits impact observed microbial community composition in permafrost samples
-
24102625
-
Vishnivetskaya TA, Layton AC, Lau MC, Chauhan A, Cheng KR, Meyers AJ, Murphy JR, Rogers AW, Saarunya GS, Williams DE, Pfiffner SM, Biggerstaff JP, Stackhouse BT, Phelps TJ, Whyte L, Sayler GS, Onstott TC. Commercial DNA extraction kits impact observed microbial community composition in permafrost samples. FEMS Microbiol Ecol 2014, 87:217-230. 10.1111/1574-6941.12219, 24102625.
-
(2014)
FEMS Microbiol Ecol
, vol.87
, pp. 217-230
-
-
Vishnivetskaya, T.A.1
Layton, A.C.2
Lau, M.C.3
Chauhan, A.4
Cheng, K.R.5
Meyers, A.J.6
Murphy, J.R.7
Rogers, A.W.8
Saarunya, G.S.9
Williams, D.E.10
Pfiffner, S.M.11
Biggerstaff, J.P.12
Stackhouse, B.T.13
Phelps, T.J.14
Whyte, L.15
Sayler, G.S.16
Onstott, T.C.17
-
9
-
-
84938483818
-
-
Human Microbiome Project. http://commonfund.nih.gov/hmp/.
-
-
-
-
10
-
-
84938484164
-
-
MetaHIT. [http://www.metahit.eu/].
-
-
-
-
11
-
-
85027927719
-
Enterotypes of the human gut microbiome
-
3728647, 21508958
-
Arumugam M, Raes J, Pelletier E, Le PD, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, et al. Enterotypes of the human gut microbiome. Nature 2011, 473:174-180. 10.1038/nature09944, 3728647, 21508958.
-
(2011)
Nature
, vol.473
, pp. 174-180
-
-
Arumugam, M.1
Raes, J.2
Pelletier, E.3
Le, P.D.4
Yamada, T.5
Mende, D.R.6
Fernandes, G.R.7
Tap, J.8
Bruls, T.9
Batto, J.M.10
Bertalan, M.11
Borruel, N.12
Casellas, F.13
Fernandez, L.14
Gautier, L.15
Hansen, T.16
Hattori, M.17
Hayashi, T.18
Kleerebezem, M.19
Kurokawa, K.20
Leclerc, M.21
Levenez, F.22
Manichanh, C.23
Nielsen, H.B.24
Nielsen, T.25
Pons, N.26
Poulain, J.27
Qin, J.28
Sicheritz-Ponten, T.29
Tims, S.30
more..
-
12
-
-
84883110880
-
Richness of human gut microbiome correlates with metabolic markers
-
23985870
-
Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, et al. Richness of human gut microbiome correlates with metabolic markers. Nature 2013, 500:541-546. 10.1038/nature12506, 23985870.
-
(2013)
Nature
, vol.500
, pp. 541-546
-
-
Le Chatelier, E.1
Nielsen, T.2
Qin, J.3
Prifti, E.4
Hildebrand, F.5
Falony, G.6
Almeida, M.7
Arumugam, M.8
Batto, J.M.9
Kennedy, S.10
Leonard, P.11
Li, J.12
Burgdorf, K.13
Grarup, N.14
Jørgensen, T.15
Brandslund, I.16
Nielsen, H.B.17
Juncker, A.S.18
Bertalan, M.19
Levenez, F.20
Pons, N.21
Rasmussen, S.22
Sunagawa, S.23
Tap, J.24
Tims, S.25
Zoetendal, E.G.26
Brunak, S.27
Clément, K.28
Doré, J.29
Kleerebezem, M.30
more..
-
13
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
3779803, 20203603
-
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65. 10.1038/nature08821, 3779803, 20203603.
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
Li, R.2
Raes, J.3
Arumugam, M.4
Burgdorf, K.S.5
Manichanh, C.6
Nielsen, T.7
Pons, N.8
Levenez, F.9
Yamada, T.10
Mende, D.R.11
Li, J.12
Xu, J.13
Li, S.14
Li, D.15
Cao, J.16
Wang, B.17
Liang, H.18
Zheng, H.19
Xie, Y.20
Tap, J.21
Lepage, P.22
Bertalan, M.23
Batto, J.M.24
Hansen, T.25
Le Paslier, D.26
Linneberg, A.27
Nielsen, H.B.28
Pelletier, E.29
Renault, P.30
more..
-
14
-
-
70449713952
-
The NIH human microbiome project
-
2792171, 19819907
-
Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C, Baker CC, Di Francesco V, Howcroft TK, Karp RW, Lunsford RD, Wellington CR, Belachew T, Wright M, Giblin C, David H, Mills M, Salomon R, Mullins C, Akolkar B, Begg L, Davis C, Grandison L, Humble M, Khalsa J, Little AR, et al. The NIH human microbiome project. Genome Res 2009, 19:2317-2323. 2792171, 19819907.
-
(2009)
Genome Res
, vol.19
, pp. 2317-2323
-
-
Peterson, J.1
Garges, S.2
Giovanni, M.3
McInnes, P.4
Wang, L.5
Schloss, J.A.6
Bonazzi, V.7
McEwen, J.E.8
Wetterstrand, K.A.9
Deal, C.10
Baker, C.C.11
Di Francesco, V.12
Howcroft, T.K.13
Karp, R.W.14
Lunsford, R.D.15
Wellington, C.R.16
Belachew, T.17
Wright, M.18
Giblin, C.19
David, H.20
Mills, M.21
Salomon, R.22
Mullins, C.23
Akolkar, B.24
Begg, L.25
Davis, C.26
Grandison, L.27
Humble, M.28
Khalsa, J.29
Little, A.R.30
more..
-
15
-
-
35348968286
-
The human microbiome project
-
3709439, 17943116
-
Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature 2007, 449:804-810. 10.1038/nature06244, 3709439, 17943116.
-
(2007)
Nature
, vol.449
, pp. 804-810
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Hamady, M.3
Fraser-Liggett, C.M.4
Knight, R.5
Gordon, J.I.6
-
16
-
-
0030872620
-
Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis
-
168577, 9212428
-
Godon JJ, Zumstein E, Dabert P, Habouzit F, Moletta R. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl Environ Microbiol 1997, 63:2802-2813. 168577, 9212428.
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 2802-2813
-
-
Godon, J.J.1
Zumstein, E.2
Dabert, P.3
Habouzit, F.4
Moletta, R.5
-
17
-
-
84938484203
-
-
FastQC. [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/].
-
-
-
-
18
-
-
84864483625
-
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
-
3394330, 22684630
-
Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res 2012, 40:W622-W627. 10.1093/nar/gks540, 3394330, 22684630.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. W622-W627
-
-
Lohse, M.1
Bolger, A.M.2
Nagel, A.3
Fernie, A.R.4
Lunn, J.E.5
Stitt, M.6
Usadel, B.7
-
19
-
-
77949587649
-
Fast and accurate long-read alignment with Burrows-Wheeler transform
-
2828108, 20080505
-
Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26:589-595. 10.1093/bioinformatics/btp698, 2828108, 20080505.
-
(2010)
Bioinformatics
, vol.26
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
20
-
-
84867634981
-
MOCAT: a metagenomics assembly and gene prediction toolkit
-
3474746, 23082188
-
Kultima JR, Sunagawa S, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P. MOCAT: a metagenomics assembly and gene prediction toolkit. PLoS One 2012, 7:e47656. 10.1371/journal.pone.0047656, 3474746, 23082188.
-
(2012)
PLoS One
, vol.7
, pp. e47656
-
-
Kultima, J.R.1
Sunagawa, S.2
Li, J.3
Chen, W.4
Chen, H.5
Mende, D.R.6
Arumugam, M.7
Pan, Q.8
Liu, B.9
Qin, J.10
Wang, J.11
Bork, P.12
-
21
-
-
33644700003
-
Toward automatic reconstruction of a highly resolved tree of life
-
16513982
-
Ciccarelli FD, Doerks T, Von MC, Creevey CJ, Snel B, Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science 2006, 311:1283-1287. 10.1126/science.1123061, 16513982.
-
(2006)
Science
, vol.311
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
Doerks, T.2
Von, M.C.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
-
22
-
-
84870431038
-
CD-HIT: accelerated for clustering the next-generation sequencing data
-
3516142, 23060610
-
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 2012, 28:3150-3152. 10.1093/bioinformatics/bts565, 3516142, 23060610.
-
(2012)
Bioinformatics
, vol.28
, pp. 3150-3152
-
-
Fu, L.1
Niu, B.2
Zhu, Z.3
Wu, S.4
Li, W.5
-
23
-
-
74049108922
-
BLAST+: architecture and applications
-
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinforma 2009, 10:421.
-
(2009)
BMC Bioinforma
, 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
-
24
-
-
84861203603
-
EggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
-
3245133, 22096231
-
Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P. eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res 2012, 40:D284-D289. 10.1093/nar/gkr1060, 3245133, 22096231.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. D284-D289
-
-
Powell, S.1
Szklarczyk, D.2
Trachana, K.3
Roth, A.4
Kuhn, M.5
Muller, J.6
Arnold, R.7
Rattei, T.8
Letunic, I.9
Doerks, T.10
Jensen, L.J.11
von Mering, C.12
Bork, P.13
-
25
-
-
84938485349
-
-
The R Project for Statistical Computing. [http://www.R-project.org].
-
-
-
-
26
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
17183312
-
Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006, 444:1027-1031. 10.1038/nature05414, 17183312.
-
(2006)
Nature
, vol.444
, pp. 1027-1031
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Mahowald, M.A.3
Magrini, V.4
Mardis, E.R.5
Gordon, J.I.6
-
27
-
-
33845901507
-
Microbial ecology: human gut microbes associated with obesity
-
17183309
-
Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 2006, 444:1022-1023. 10.1038/4441022a, 17183309.
-
(2006)
Nature
, vol.444
, pp. 1022-1023
-
-
Ley, R.E.1
Turnbaugh, P.J.2
Klein, S.3
Gordon, J.I.4
-
28
-
-
84858613358
-
Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study
-
23757280
-
Steven B, Gallegos-Graves LV, Starkenburg SR, Chain PS, Kuske CR. Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study. Environ Microbiol Rep 2012, 4:248-256. 10.1111/j.1758-2229.2012.00328.x, 23757280.
-
(2012)
Environ Microbiol Rep
, vol.4
, pp. 248-256
-
-
Steven, B.1
Gallegos-Graves, L.V.2
Starkenburg, S.R.3
Chain, P.S.4
Kuske, C.R.5
-
29
-
-
84856770811
-
Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample
-
3277595, 22347999
-
Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One 2012, 7:e30087. 10.1371/journal.pone.0030087, 3277595, 22347999.
-
(2012)
PLoS One
, vol.7
, pp. e30087
-
-
Luo, C.1
Tsementzi, D.2
Kyrpides, N.3
Read, T.4
Konstantinidis, K.T.5
-
30
-
-
84860756398
-
Performance comparison of benchtop high-throughput sequencing platforms
-
22522955
-
Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 2012, 30:434-439. 10.1038/nbt.2198, 22522955.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 434-439
-
-
Loman, N.J.1
Misra, R.V.2
Dallman, T.J.3
Constantinidou, C.4
Gharbia, S.E.5
Wain, J.6
Pallen, M.J.7
-
31
-
-
79955724657
-
Comparing de novo genome assembly: the long and short of it
-
3084767, 21559467
-
Narzisi G, Mishra B. Comparing de novo genome assembly: the long and short of it. PLoS One 2011, 6:e19175. 10.1371/journal.pone.0019175, 3084767, 21559467.
-
(2011)
PLoS One
, vol.6
, pp. e19175
-
-
Narzisi, G.1
Mishra, B.2
|