-
1
-
-
77649200259
-
A primer on metagenomics
-
10.1371/journal.pcbi.1000667, 2829047, 20195499
-
Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLoS Comput Biol 2010, 6:e1000667. 10.1371/journal.pcbi.1000667, 2829047, 20195499.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Wooley, J.C.1
Godzik, A.2
Friedberg, I.3
-
2
-
-
84860672197
-
A comparative evaluation of sequence classification programs
-
10.1186/1471-2105-13-92, 3428669, 22574964
-
Bazinet AL, Cummings MP. A comparative evaluation of sequence classification programs. BMC Bioinformatics 2012, 13:92. 10.1186/1471-2105-13-92, 3428669, 22574964.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 92
-
-
Bazinet, A.L.1
Cummings, M.P.2
-
3
-
-
79959326732
-
Discovering the unknown: improving detection of novel species and genera from short reads
-
3085467, 21541181
-
Rosen GL, Polikar R, Caseiro DA, Essinger SD, Sokhansanj BA. Discovering the unknown: improving detection of novel species and genera from short reads. J Biomed Biotechnol 2011, 2011:495849. 3085467, 21541181.
-
(2011)
J Biomed Biotechnol
, vol.2011
, pp. 495849
-
-
Rosen, G.L.1
Polikar, R.2
Caseiro, D.A.3
Essinger, S.D.4
Sokhansanj, B.A.5
-
4
-
-
53549118607
-
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
-
10.1186/1471-2105-9-386, 2563014, 18803844
-
Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008, 9:386. 10.1186/1471-2105-9-386, 2563014, 18803844.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 386
-
-
Meyer, F.1
Paarmann, D.2
D'Souza, M.3
Olson, R.4
Glass, E.M.5
Kubal, M.6
Paczian, T.7
Rodriguez, A.8
Stevens, R.9
Wilke, A.10
Wilkening, J.11
Edwards, R.A.12
-
5
-
-
33847702910
-
MEGAN analysis of metagenomic data
-
10.1101/gr.5969107, 1800929, 17255551
-
Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res 2007, 17:377-386. 10.1101/gr.5969107, 1800929, 17255551.
-
(2007)
Genome Res
, vol.17
, pp. 377-386
-
-
Huson, D.H.1
Auch, A.F.2
Qi, J.3
Schuster, S.C.4
-
6
-
-
79961139783
-
Classifying short genomic fragments from novel lineages using composition and homology
-
10.1186/1471-2105-12-328, 3173459, 21827705
-
Parks DH, MacDonald NJ, Beiko RG. Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinformatics 2011, 12:328. 10.1186/1471-2105-12-328, 3173459, 21827705.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 328
-
-
Parks, D.H.1
MacDonald, N.J.2
Beiko, R.G.3
-
7
-
-
69549135124
-
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
-
10.1038/nmeth.1358, 2762791, 19648916
-
Brady A, Salzberg SL. Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 2009, 6:673-676. 10.1038/nmeth.1358, 2762791, 19648916.
-
(2009)
Nat Methods
, vol.6
, pp. 673-676
-
-
Brady, A.1
Salzberg, S.L.2
-
8
-
-
34249794257
-
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
-
10.1038/nmeth1043, 17468765
-
Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, Mchardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P, Kyrpides NC. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods 2007, 4:495-500. 10.1038/nmeth1043, 17468765.
-
(2007)
Nat Methods
, vol.4
, pp. 495-500
-
-
Mavromatis, K.1
Ivanova, N.2
Barry, K.3
Shapiro, H.4
Goltsman, E.5
Mchardy, A.C.6
Rigoutsos, I.7
Salamov, A.8
Korzeniewski, F.9
Land, M.10
Lapidus, A.11
Grigoriev, I.12
Richardson, P.13
Hugenholtz, P.14
Kyrpides, N.C.15
-
9
-
-
84355161776
-
The oral metagenome in health and disease
-
10.1038/ismej.2011.85, 3246241, 21716308
-
Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, Simón-Soro A, Pignatelli M, Mira A. The oral metagenome in health and disease. ISME J 2012, 6:46-56. 10.1038/ismej.2011.85, 3246241, 21716308.
-
(2012)
ISME J
, vol.6
, pp. 46-56
-
-
Belda-Ferre, P.1
Alcaraz, L.D.2
Cabrera-Rubio, R.3
Romero, H.4
Simón-Soro, A.5
Pignatelli, M.6
Mira, A.7
-
10
-
-
79952937941
-
Variation in tropical reef symbiont metagenomes defined by secondary metabolism
-
10.1371/journal.pone.0017897, 3062557, 21445351
-
Donia MS, Fricke WF, Ravel J, Schmidt EW. Variation in tropical reef symbiont metagenomes defined by secondary metabolism. PLoS One 2011, 6:e17897. 10.1371/journal.pone.0017897, 3062557, 21445351.
-
(2011)
PLoS One
, vol.6
-
-
Donia, M.S.1
Fricke, W.F.2
Ravel, J.3
Schmidt, E.W.4
-
11
-
-
78049420498
-
An insect herbivore microbiome with high plant biomass-degrading capacity
-
10.1371/journal.pgen.1001129, 2944797, 20885794
-
Suen G, Scott JJ, Aylward FO, Adams SM, Tringe SG, Pinto-Tomás AA, Foster CE, Pauly M, Weimer PJ, Barry KW, Goodwin LA, Bouffard P, Li L, Osterberger J, Harkins TT, Slater SC, Donohue TJ, Currie CR. An insect herbivore microbiome with high plant biomass-degrading capacity. PLoS Genet 2010, 6(9):e1001129. 10.1371/journal.pgen.1001129, 2944797, 20885794.
-
(2010)
PLoS Genet
, vol.6
, Issue.9
-
-
Suen, G.1
Scott, J.J.2
Aylward, F.O.3
Adams, S.M.4
Tringe, S.G.5
Pinto-Tomás, A.A.6
Foster, C.E.7
Pauly, M.8
Weimer, P.J.9
Barry, K.W.10
Goodwin, L.A.11
Bouffard, P.12
Li, L.13
Osterberger, J.14
Harkins, T.T.15
Slater, S.C.16
Donohue, T.J.17
Currie, C.R.18
-
12
-
-
79953025661
-
Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice
-
10.1038/ismej.2010.162, 3105739, 20962874
-
Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, Barry KA, Nelson KE, Torralba M, Henrissat B, Coutinho PM, Cann IKO, White BA, Fahey GC. Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. ISME J 2011, 5:639-649. 10.1038/ismej.2010.162, 3105739, 20962874.
-
(2011)
ISME J
, vol.5
, pp. 639-649
-
-
Swanson, K.S.1
Dowd, S.E.2
Suchodolski, J.S.3
Middelbos, I.S.4
Vester, B.M.5
Barry, K.A.6
Nelson, K.E.7
Torralba, M.8
Henrissat, B.9
Coutinho, P.M.10
Cann, I.K.O.11
White, B.A.12
Fahey, G.C.13
-
13
-
-
54949137701
-
MetaSim: a sequencing simulator for genomics and metagenomics
-
10.1371/journal.pone.0003373, 2556396, 18841204
-
Richter DC, Ott F, Auch AF, Schmid R, Huson DH. MetaSim: a sequencing simulator for genomics and metagenomics. PLoS One 2008, 3:e3373. 10.1371/journal.pone.0003373, 2556396, 18841204.
-
(2008)
PLoS One
, vol.3
-
-
Richter, D.C.1
Ott, F.2
Auch, A.F.3
Schmid, R.4
Huson, D.H.5
-
14
-
-
40549141418
-
Metagenomics: read length matters
-
10.1128/AEM.02181-07, 2258652, 18192407
-
Wommack KE, Bhavsar J, Ravel J. Metagenomics: read length matters. Appl Environ Microbiol 2008, 74:1453-1463. 10.1128/AEM.02181-07, 2258652, 18192407.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 1453-1463
-
-
Wommack, K.E.1
Bhavsar, J.2
Ravel, J.3
-
15
-
-
78651266519
-
Combining gene prediction methods to improve metagenomic gene annotation
-
10.1186/1471-2105-12-20, 3042383, 21232129
-
Yok NG, Rosen GL. Combining gene prediction methods to improve metagenomic gene annotation. BMC Bioinformatics 2011, 12:20. 10.1186/1471-2105-12-20, 3042383, 21232129.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 20
-
-
Yok, N.G.1
Rosen, G.L.2
-
16
-
-
84884470145
-
A new method for extracting skin microbes allows metagenomic analysis of whole-deep skin
-
10.1371/journal.pone.0074914, 3779245, 24073227
-
Garcia-Garcerà M, Garcia-Etxebarria K, Coscollà M, Latorre A, Calafell F. A new method for extracting skin microbes allows metagenomic analysis of whole-deep skin. PLoS One 2013, 8:e74914. 10.1371/journal.pone.0074914, 3779245, 24073227.
-
(2013)
PLoS One
, vol.8
-
-
Garcia-Garcerà, M.1
Garcia-Etxebarria, K.2
Coscollà, M.3
Latorre, A.4
Calafell, F.5
-
17
-
-
80052425126
-
Titration-free 454 sequencing using Y adapters
-
10.1038/nprot.2011.369, 21886102
-
Zheng Z, Advani A, Melefors T, Glavas S, Nordström H, Ye W, Engstrand L, Andersson AF. Titration-free 454 sequencing using Y adapters. Nat Protoc 2011, 6:1367-1376. 10.1038/nprot.2011.369, 21886102.
-
(2011)
Nat Protoc
, vol.6
, pp. 1367-1376
-
-
Zheng, Z.1
Advani, A.2
Melefors, T.3
Glavas, S.4
Nordström, H.5
Ye, W.6
Engstrand, L.7
Andersson, A.F.8
-
18
-
-
77953050946
-
A catalog of reference genomes from the human microbiome
-
2940224, 20489017
-
Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, et al. A catalog of reference genomes from the human microbiome. Science 2010, 328:994-999. 2940224, 20489017.
-
(2010)
Science
, vol.328
, pp. 994-999
-
-
Nelson, K.E.1
Weinstock, G.M.2
Highlander, S.K.3
Worley, K.C.4
Creasy, H.H.5
Wortman, J.R.6
Rusch, D.B.7
Mitreva, M.8
Sodergren, E.9
Chinwalla, A.T.10
Feldgarden, M.11
Gevers, D.12
Haas, B.J.13
Madupu, R.14
Ward, D.V.15
Birren, B.W.16
Gibbs, R.A.17
Methe, B.18
Petrosino, J.F.19
Strausberg, R.L.20
Sutton, G.G.21
White, O.R.22
Wilson, R.K.23
Durkin, S.24
Giglio, M.G.25
Gujja, S.26
Howarth, C.27
Kodira, C.D.28
Kyrpides, N.29
Mehta, T.30
more..
-
19
-
-
79952390994
-
Fast identification and removal of sequence contamination from genomic and metagenomic datasets
-
10.1371/journal.pone.0017288, 3052304, 21408061
-
Schmieder R, Edwards R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One 2011, 6:e17288. 10.1371/journal.pone.0017288, 3052304, 21408061.
-
(2011)
PLoS One
, vol.6
-
-
Schmieder, R.1
Edwards, R.2
-
20
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
10.1093/nar/25.17.3389, 146917, 9254694
-
Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.H.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
21
-
-
84863304598
-
-
Vienna, Austria: R Foundation for Statistical Computing, R Core team
-
R Core team R: A Language and Environment for Statistical Computing 2012, Vienna, Austria: R Foundation for Statistical Computing, R Core team.
-
(2012)
R: A Language and Environment for Statistical Computing
-
-
|