-
1
-
-
10344227692
-
Metagenomics: Application of genomics to uncultured microorganisms
-
DOI 10.1128/MMBR.68.4.669-685.2004
-
Handelsman J. (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev, 68 (4):669-685. (Pubitemid 39628532)
-
(2004)
Microbiology and Molecular Biology Reviews
, vol.68
, Issue.4
, pp. 669-685
-
-
Handelsman, J.1
-
4
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
DOI 10.1038/nature03959, PII N03959
-
Margulies M, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437:376-380. (Pubitemid 41613494)
-
(2005)
Nature
, vol.437
, Issue.7057
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
Berka, J.7
Braverman, M.S.8
Chen, Y.-J.9
Chen, Z.10
Dewell, S.B.11
Du, L.12
Fierro, J.M.13
Gomes, X.V.14
Godwin, B.C.15
He, W.16
Helgesen, S.17
Ho, C.H.18
Irzyk, G.P.19
Jando, S.C.20
Alenquer, M.L.I.21
Jarvie, T.P.22
Jirage, K.B.23
Kim, J.-B.24
Knight, J.R.25
Lanza, J.R.26
Leamon, J.H.27
Lefkowitz, S.M.28
Lei, M.29
Li, J.30
Lohman, K.L.31
Lu, H.32
Makhijani, V.B.33
McDade, K.E.34
McKenna, M.P.35
Myers, E.W.36
Nickerson, E.37
Nobile, J.R.38
Plant, R.39
Puc, B.P.40
Ronan, M.T.41
Roth, G.T.42
Sarkis, G.J.43
Simons, J.F.44
Simpson, J.W.45
Srinivasan, M.46
Tartaro, K.R.47
Tomasz, A.48
Vogt, K.A.49
Volkmer, G.A.50
Wang, S.H.51
Wang, Y.52
Weiner, M.P.53
Yu, P.54
Begley, R.F.55
Rothberg, J.M.56
more..
-
5
-
-
64849115804
-
Digital PCR provides sensitive and absolute calibration for high throughput sequencing
-
White RA, 3rd, et al. (2009) Digital PCR provides sensitive and absolute calibration for high throughput sequencing. BMC Genomics, 10:116.
-
(2009)
BMC Genomics
, vol.10
, pp. 116
-
-
White Iii, R.A.1
-
6
-
-
33947238287
-
The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific
-
Rusch DB, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol, 5(3):e77.
-
(2007)
PLoS Biol
, vol.5
, Issue.3
-
-
Rusch, D.B.1
-
7
-
-
33947235074
-
The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families
-
Yooseph S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol, 5(3):e16.
-
(2007)
PLoS Biol
, vol.5
, Issue.3
-
-
Yooseph, S.1
-
8
-
-
11144354360
-
Environmental genome shotgun sequencing of the sargasso sea
-
DOI 10.1126/science.1093857
-
Venter JC, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304(5667):66-74. (Pubitemid 38451457)
-
(2004)
Science
, vol.304
, Issue.5667
, pp. 66-74
-
-
Venter, J.C.1
Remington, K.2
Heidelberg, J.F.3
Halpern, A.L.4
Rusch, D.5
Eisen, J.A.6
Wu, D.7
Paulsen, I.8
Nelson, K.E.9
Nelson, W.10
Fouts, D.E.11
Levy, S.12
Knap, A.H.13
Lomas, M.W.14
Nealson, K.15
White, O.16
Peterson, J.17
Hoffman, J.18
Parsons, R.19
Baden-Tillson, H.20
Pfannkoch, C.21
Rogers, Y.-H.22
Smith, H.O.23
more..
-
9
-
-
31544483932
-
Community genomics among stratified microbial assemblages in the ocean's interior
-
DeLong EF, et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science, 311 (5760):496-503.
-
(2006)
Science
, vol.311
, Issue.5760
, pp. 496-503
-
-
Delong, E.F.1
-
10
-
-
0034665853
-
Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea
-
Beja O, et al. (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science, 289(5486):1902-1906.
-
(2000)
Science
, vol.289
, Issue.5486
, pp. 1902-1906
-
-
Beja, O.1
-
11
-
-
68549085316
-
Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre
-
Konstantinidis KT, et al. (2009) Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre. Appl Environ Microbiol, 75 (16):5345-5355.
-
(2009)
Appl Environ Microbiol
, vol.75
, Issue.16
, pp. 5345-5355
-
-
Konstantinidis, K.T.1
-
12
-
-
33744804299
-
Metagenomic analysis of the human distal gut microbiome
-
DOI 10.1126/science.1124234
-
Gill SR, et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science, 312(5778):1355-1359. (Pubitemid 43839542)
-
(2006)
Science
, vol.312
, Issue.5778
, pp. 1355-1359
-
-
Gill, S.R.1
Pop, M.2
DeBoy, R.T.3
Eckburg, P.B.4
Turnbaugh, P.J.5
Samuel, B.S.6
Gordon, J.I.7
Relman, D.A.8
Fraser-Liggett, C.M.9
Nelson, K.E.10
-
13
-
-
34547129847
-
Development of the human infant intestinal microbiota
-
Palmer C, et al. (2007) Development of the human infant intestinal microbiota. PLoS Biol, 5(7):e177.
-
(2007)
PLoS Biol
, vol.5
, Issue.7
-
-
Palmer, C.1
-
14
-
-
69949111703
-
The core gut microbiome, energy balance and obesity
-
Turnbaugh PJ, Gordon JI. (2009) The core gut microbiome, energy balance and obesity. J Physiol, 587(Pt 17):4153-4158.
-
(2009)
J Physiol
, Issue.PART 17
, pp. 4153-4158
-
-
Turnbaugh, P.J.1
Gordon, J.I.2
-
15
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh PJ, et al. (2009) A core gut microbiome in obese and lean twins. Nature, 457(7228):480-484.
-
(2009)
Nature
, vol.457
, Issue.7228
, pp. 480-484
-
-
Turnbaugh, P.J.1
-
16
-
-
52949115612
-
Microbiology: Metagenomics
-
Hugenholtz P, Tyson GW. (2008) Microbiology: metagenomics. Nature, 455 (7212):481-483.
-
(2008)
Nature
, vol.455
, Issue.7212
, pp. 481-483
-
-
Hugenholtz, P.1
Tyson, G.W.2
-
17
-
-
40249095175
-
Something from (almost) nothing: The impact of multiple displacement amplification on microbial ecology
-
DOI 10.1038/ismej.2008.10, PII ISMEJ200810
-
Binga EK, Lasken RS, Neufeld JD. (2008) Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J, 2 (3):233-241. (Pubitemid 351334272)
-
(2008)
ISME Journal
, vol.2
, Issue.3
, pp. 233-241
-
-
Binga, E.K.1
Lasken, R.S.2
Neufeld, J.D.3
-
18
-
-
77955570845
-
Hydroxyapatitemediated separation of dsDNA, ssDNA and RNA genotypes from natural viral assemblages and metagenomic library construction
-
Pfannkoch C, et al. (2010) Hydroxyapatitemediated separation of dsDNA, ssDNA and RNA genotypes from natural viral assemblages and metagenomic library construction. Appl Environ Microbiol, 76 (15):5039-5045.
-
(2010)
Appl Environ Microbiol
, vol.76
, Issue.15
, pp. 5039-5045
-
-
Pfannkoch, C.1
-
19
-
-
84855896008
-
Optimizing the extraction of prokaryotes from soils for highthroughput metagenomic sequencing
-
Submitted
-
Williamson KE, et al. Optimizing the extraction of prokaryotes from soils for highthroughput metagenomic sequencing. Appl Environ Microbiol, Submitted.
-
Appl Environ Microbiol
-
-
Williamson, K.E.1
-
20
-
-
0036092095
-
Quantification, base composition, and fate of extracellular DNA in marine sediments
-
Dell'Anno A, Bompadre S, Danovaro R. (2002) Quantification, base composition, and fate of extracellular DNA in marine sediments. Limnol Oceanogr, 47(3):899-905. (Pubitemid 34527296)
-
(2002)
Limnology and Oceanography
, vol.47
, Issue.3
, pp. 899-905
-
-
Dell'Anno, A.1
Bompadre, S.2
Danovaro, R.3
-
22
-
-
2342470766
-
Extraction of DNA from soil
-
DOI 10.1016/S1164-5563(03)00033-5, PII S1164556303000335
-
Robe P, et al. (2003) Extraction of DNA from soil. Eur J Soil Biol, 39:183-190. (Pubitemid 38592130)
-
(2003)
European Journal of Soil Biology
, vol.39
, Issue.4
, pp. 183-190
-
-
Robe, P.1
Nalin, R.2
Capellano, C.3
Vogel, T.M.4
Simonet, P.5
-
23
-
-
65749105400
-
A perspective: Metatranscriptomics as a tool for the discovery of novel biocatalysts
-
Warnecke F, Hess M. (2009) A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J Biotechnol, 142 (1):91-95.
-
(2009)
J Biotechnol
, vol.142
, Issue.1
, pp. 91-95
-
-
Warnecke, F.1
Hess, M.2
-
24
-
-
66149130975
-
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column
-
Shi Y, Tyson GW, DeLong EF. (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature, 459(7244):266-269.
-
(2009)
Nature
, vol.459
, Issue.7244
, pp. 266-269
-
-
Shi, Y.1
Tyson, G.W.2
Delong, E.F.3
-
25
-
-
80055120631
-
Analyzing gene expression from marine microbial communities using environmental transcriptomics
-
Poretsky RS, et al. (2009) Analyzing gene expression from marine microbial communities using environmental transcriptomics. J Vis Exp, (24).
-
(2009)
J Vis Exp
, Issue.24
-
-
Poretsky, R.S.1
-
26
-
-
52449114817
-
Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities
-
Gilbert JA, et al. (2008) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE, 3(8):e3042.
-
(2008)
PLoS ONE
, vol.3
, Issue.8
-
-
Gilbert, J.A.1
-
27
-
-
1642523441
-
Soil washing improves the recovery of total community DNA from polluted and high organic content sediments
-
DOI 10.1016/j.mimet.2003.10.006
-
Fortin N, et al. (2004) Soil washing improves the recovery of total community DNA from polluted and high organic content sediments. J Microbiol Methods, 56(2):181-191. (Pubitemid 38117177)
-
(2004)
Journal of Microbiological Methods
, vol.56
, Issue.2
, pp. 181-191
-
-
Fortin, N.1
Beaumier, D.2
Lee, K.3
Greer, C.W.4
-
28
-
-
36348995417
-
DNA extraction method affects microbial community profiles from soils and sediment
-
DOI 10.1007/s00253-007-1219-y
-
Carrigg C, et al. (2007) DNA extraction method affects microbial community profiles from soils and sediment. Appl Microbiol Biotechnol, 77(4):955-964. (Pubitemid 350159866)
-
(2007)
Applied Microbiology and Biotechnology
, vol.77
, Issue.4
, pp. 955-964
-
-
Carrigg, C.1
Rice, O.2
Kavanagh, S.3
Collins, G.4
O'Flaherty, V.5
-
29
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
DOI 10.1038/nature02340
-
Tyson GW, et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428(6978):37-43. (Pubitemid 38332350)
-
(2004)
Nature
, vol.428
, Issue.6978
, pp. 37-43
-
-
Tyson, G.W.1
Chapman, J.2
Hugenholtz, P.3
Allen, E.E.4
Ram, R.J.5
Richardson, P.M.6
Solovyev, V.V.7
Rubin, E.M.8
Rokhsar, D.S.9
Banfield, J.F.10
-
30
-
-
53649107122
-
Functional metagenomic profiling of nine biomes
-
Dinsdale EA, et al. (2008) Functional metagenomic profiling of nine biomes. Nature, 455(7214):830.
-
(2008)
Nature
, vol.455
, Issue.7214
, pp. 830
-
-
Dinsdale, E.A.1
-
31
-
-
31144442151
-
Metagenomics to paleogenomics: Large-scale sequencing of mammoth DNA
-
DOI 10.1126/science.1123360
-
Poinar HN, et al. (2006) Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science, 311 (5759):392-394. (Pubitemid 43132666)
-
(2006)
Science
, vol.311
, Issue.5759
, pp. 392-394
-
-
Poinar, H.N.1
Schwarz, C.2
Qi, J.3
Shapiro, B.4
MacPhee, R.D.E.5
Buigues, B.6
Tikhonov, A.7
Huson, D.M.8
Tomsho, L.P.9
Auch, A.10
Rampp, M.11
Miller, W.12
Schuster, S.C.13
-
32
-
-
84855896006
-
-
Products and solutions: System workflow. (2009) [http://www.454.com/ productssolutions/how-it-works/index.asp].
-
(2009)
-
-
-
33
-
-
84855896005
-
-
Products and solutions: Multi span paired end reads. (2009) [http://www.454.com/products-solutions/experimental-designoptions/ multi-span-paired-end-reads.asp].
-
(2009)
-
-
-
34
-
-
0037195156
-
Genomic analysis of uncultured marine viral communities
-
DOI 10.1073/pnas.202488399
-
Breitbart M, et al. (2002) Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A, 99(22):14250-14255. (Pubitemid 35257658)
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.22
, pp. 14250-14255
-
-
Breitbart, M.1
Salamon, P.2
Andresen, B.3
Mahaffy, J.M.4
Segall, A.M.5
Mead, D.6
Azam, F.7
Rohwer, F.8
-
36
-
-
44449119442
-
Metagenomics: Exploring unseen communities
-
Blow N. (2008) Metagenomics: exploring unseen communities. Nature, 453 (7195):687-690.
-
(2008)
Nature
, vol.453
, Issue.7195
, pp. 687-690
-
-
Blow, N.1
-
37
-
-
84855865925
-
-
Publications and resources. (2009) [http://www.454.com/publications-and- resources].
-
(2009)
-
-
-
38
-
-
39649117755
-
The impact of next-generation sequencing technology on genetics
-
Mardis ER. (2008) The impact of next-generation sequencing technology on genetics. Trends Genet, 24(3):133-141.
-
(2008)
Trends Genet
, vol.24
, Issue.3
, pp. 133-141
-
-
Mardis, E.R.1
-
39
-
-
34249794257
-
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
-
DOI 10.1038/nmeth1043, PII NMETH1043
-
Mavromatis K, et al. (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods, 4 (6):495-500. (Pubitemid 46852075)
-
(2007)
Nature Methods
, vol.4
, Issue.6
, 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
-
40
-
-
35748976529
-
Get the most out of your metagenome: Computational analysis of environmental sequence data
-
DOI 10.1016/j.mib.2007.09.001, PII S1369527407001233, Antimicrobials/Genomics
-
Raes J, Foerstner KU, Bork P. (2007) Get the most out of your metagenome: computational analysis of environmental sequence data. Curr Opin Microbiol, 10(5):490-498. (Pubitemid 350052690)
-
(2007)
Current Opinion in Microbiology
, vol.10
, Issue.5
, pp. 490-498
-
-
Raes, J.1
Foerstner, K.U.2
Bork, P.3
-
41
-
-
0033214628
-
Heuristic approach to deriving models for gene finding
-
DOI 10.1093/nar/27.19.3911
-
Besemer J, Borodovsky M. (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res, 27 (19):3911-3920. (Pubitemid 29454440)
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.19
, pp. 3911-3920
-
-
Besemer, J.1
Borodovsky, M.2
-
42
-
-
0035399931
-
Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
-
DOI 10.1016/S0966-842X(01)02079-0, PII S0966842X01020790
-
Karlin S. (2001) Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol, 9 (7):335-343. (Pubitemid 32575278)
-
(2001)
Trends in Microbiology
, vol.9
, Issue.7
, pp. 335-343
-
-
Karlin, S.1
-
43
-
-
33750976398
-
MetaGene: Prokaryotic gene finding from environmental genome shotgun sequences
-
DOI 10.1093/nar/gkl723
-
Noguchi H, Park J, Takagi T. (2006) Meta-Gene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res, 34(19):5623-5630. (Pubitemid 44742449)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.19
, pp. 5623-5630
-
-
Noguchi, H.1
Park, J.2
Takagi, T.3
-
44
-
-
44649090674
-
Gene prediction in metagenomic fragments: A large scale machine learning approach
-
Hoff KJ, et al. (2008) Gene prediction in metagenomic fragments: a large scale machine learning approach. BMC Bioinformatics, 9:217.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 217
-
-
Hoff, K.J.1
-
45
-
-
11144354360
-
Environmental genome shotgun sequencing of the sargasso sea
-
DOI 10.1126/science.1093857
-
Venter J, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304(5667):66-74. (Pubitemid 38451457)
-
(2004)
Science
, vol.304
, Issue.5667
, pp. 66-74
-
-
Venter, J.C.1
Remington, K.2
Heidelberg, J.F.3
Halpern, A.L.4
Rusch, D.5
Eisen, J.A.6
Wu, D.7
Paulsen, I.8
Nelson, K.E.9
Nelson, W.10
Fouts, D.E.11
Levy, S.12
Knap, A.H.13
Lomas, M.W.14
Nealson, K.15
White, O.16
Peterson, J.17
Hoffman, J.18
Parsons, R.19
Baden-Tillson, H.20
Pfannkoch, C.21
Rogers, Y.-H.22
Smith, H.O.23
more..
-
46
-
-
42949114833
-
Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
-
Yooseph S, Li W, Sutton G. (2008) Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering. BMC Bioinformatics, 9:182.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 182
-
-
Yooseph, S.1
Li, W.2
Sutton, G.3
-
47
-
-
33747877444
-
Finding novel genes in bacterial communities isolated from the environment
-
DOI 10.1093/bioinformatics/btl247
-
Krause L, et al. (2006) Finding novel genes in bacterial communities isolated from the environment. Bioinformatics, 22(14): e281-e289. (Pubitemid 44288297)
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Krause, L.1
Diaz, N.N.2
Bartels, D.3
Edwards, R.A.4
Puhler, A.5
Rohwer, F.6
Meyer, F.7
Stoye, J.8
-
48
-
-
38549139537
-
IMG/M: A data management and analysis system for metagenomes
-
DOI 10.1093/nar/gkm869
-
Markowitz VM, et al. (2008) IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res, 36(Database issue):D534-D538. (Pubitemid 351149780)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Markowitz, V.M.1
Ivanova, N.N.2
Szeto, E.3
Palaniappan, K.4
Chu, K.5
Dalevi, D.6
Chen, I.-M.A.7
Grechkin, Y.8
Dubchak, I.9
Anderson, I.10
Lykidis, A.11
Mavromatis, K.12
Hugenholtz, P.13
Kyrpides, N.C.14
-
49
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
DOI 10.1093/nar/gki866
-
Overbeek R, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res, 33(17):5691-5702. (Pubitemid 41548835)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.17
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.-Y.5
Cohoon, M.6
De Crecy-Lagard, V.7
Diaz, N.8
Disz, T.9
Edwards, R.10
Fonstein, M.11
Frank, E.D.12
Gerdes, S.13
Glass, E.M.14
Goesmann, A.15
Hanson, A.16
Iwata-Reuyl, D.17
Jensen, R.18
Jamshidi, N.19
Krause, L.20
Kubal, M.21
Larsen, N.22
Linke, B.23
McHardy, A.C.24
Meyer, F.25
Neuweger, H.26
Olsen, G.27
Olson, R.28
Osterman, A.29
Portnoy, V.30
Pusch, G.D.31
Rodionov, D.A.32
Rul33
ckert, C.34
Steiner, J.35
Stevens, R.36
Thiele, I.37
Vassieva, O.38
Ye, Y.39
Zagnitko, O.40
Vonstein, V.41
more..
-
50
-
-
56249098614
-
The Phaeodactylum genome reveals the evolutionary history of diatom genomes
-
Bowler C, et al. (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature, 456 (7219):239-244.
-
(2008)
Nature
, vol.456
, Issue.7219
, pp. 239-244
-
-
Bowler, C.1
-
51
-
-
42449162998
-
Phylogenetic classification of short environmental DNA fragments
-
DOI 10.1093/nar/gkn038
-
Krause L, et al. (2008) Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res, 36(7):2230-2239. (Pubitemid 351566997)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.7
, pp. 2230-2239
-
-
Krause, L.1
Diaz, N.N.2
Goesmann, A.3
Kelley, S.4
Nattkemper, T.W.5
Rohwer, F.6
Edwards, R.A.7
Stoye, J.8
-
53
-
-
47249139915
-
CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads
-
Chatterji S, et al. (2008) CompostBin: A DNA composition-based algorithm for binning environmental shotgun reads. Res Comput Mol Biol, 17-28.
-
(2008)
Res Comput Mol Biol
, pp. 17-28
-
-
Chatterji, S.1
-
54
-
-
33845957530
-
Accurate phylogenetic classification of variable-length DNA fragments
-
DOI 10.1038/nmeth976, PII NMETH976
-
McHardy AC, et al. (2007) Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods, 4(1):63-72. (Pubitemid 46029478)
-
(2007)
Nature Methods
, vol.4
, Issue.1
, pp. 63-72
-
-
McHardy, A.C.1
Martin, H.G.2
Tsirigos, A.3
Hugenholtz, P.4
Rigoutsos, I.5
-
55
-
-
69549135124
-
Phymm and PhymmBL: Metagenomic phylogenetic classification with interpolated Markov models
-
Brady A, Salzberg SL. (2009) Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods, 6(9):673-676.
-
(2009)
Nat Methods
, vol.6
, Issue.9
, pp. 673-676
-
-
Brady, A.1
Salzberg, S.L.2
-
56
-
-
0025183708
-
Basic local alignment search tool
-
Altschul S, et al. (1990) Basic local alignment search tool. J Mol Biol, 215(3):403-410.
-
(1990)
J Mol Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.1
-
58
-
-
0035133496
-
Fitting multivariate models to community data: A comment on distance-based redundancy analysis
-
McArdle B, Anderson M. (2001) Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology, 82(1):290-297. (Pubitemid 32106404)
-
(2001)
Ecology
, vol.82
, Issue.1
, pp. 290-297
-
-
McArdle, B.H.1
Anderson, M.J.2
-
59
-
-
33845900991
-
Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables
-
Zapala MA, Schork NJ. Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables. Proc Natl Acad Sci U S A, 103(51):19430-19435.
-
Proc Natl Acad Sci USA
, vol.103
, Issue.51
, pp. 19430-19435
-
-
Zapala, M.A.1
Schork, N.J.2
-
60
-
-
60849095134
-
Quantifying environmental adaptation of metabolic pathways in metagenomics
-
Gianoulis TA, et al. (2009) Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A, 106(5):1374-1379.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, Issue.5
, pp. 1374-1379
-
-
Gianoulis, T.A.1
-
61
-
-
54949137701
-
MetaSim: A sequencing simulator for genomics and metagenomics
-
Richter DC, et al. (2008) MetaSim: a sequencing simulator for genomics and metagenomics. PLoS One, 3(10):e3373.
-
(2008)
PLoS One
, vol.3
, Issue.10
-
-
Richter, D.C.1
-
62
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
DOI 10.1038/nature02340
-
Tyson G, et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428(6978):37-43. (Pubitemid 38332350)
-
(2004)
Nature
, vol.428
, Issue.6978
, pp. 37-43
-
-
Tyson, G.W.1
Chapman, J.2
Hugenholtz, P.3
Allen, E.E.4
Ram, R.J.5
Richardson, P.M.6
Solovyev, V.V.7
Rubin, E.M.8
Rokhsar, D.S.9
Banfield, J.F.10
-
64
-
-
26844447711
-
Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community
-
DOI 10.1128/AEM.71.10.6319-6324.2005
-
Tyson GW, et al. (2005) Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community. Appl Environ Microbiol, 71(10):6319-6324. (Pubitemid 41456932)
-
(2005)
Applied and Environmental Microbiology
, vol.71
, Issue.10
, pp. 6319-6324
-
-
Tyson, G.W.1
Lo, I.2
Baker, B.J.3
Allen, E.E.4
Hugenholtz, P.5
Banfield, J.F.6
-
65
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored "rare biosphere"
-
DOI 10.1073/pnas.0605127103
-
Sogin ML, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A, 103 (32):12115-12120. (Pubitemid 44215820)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.32
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
Welch, D.M.4
Huse, S.M.5
Neal, P.R.6
Arrieta, J.M.7
Herndl, G.J.8
-
66
-
-
84855865926
-
-
Genomes OnLine Database: Metagenome Projects
-
Genomes OnLine Database: Metagenome Projects. (2009) [http://www. genomesonline.org/gold.cgi?want=Metagenomes].
-
(2009)
-
-
-
67
-
-
39149124249
-
Metagenomics of the deep Mediterranean, a warm bathypelagic habitat
-
Martin-Cuadrado AB, et al. (2007) Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS ONE, 2(9):e914.
-
(2007)
PLoS ONE
, vol.2
, Issue.9
-
-
Martin-Cuadrado, A.B.1
-
68
-
-
40149098974
-
Microbial ecology of four coral atolls in the Northern Line Islands
-
Dinsdale EA, et al. (2008) Microbial ecology of four coral atolls in the Northern Line Islands. PLoS ONE, 3(2):e1584.
-
(2008)
PLoS ONE
, vol.3
, Issue.2
-
-
Dinsdale, E.A.1
-
69
-
-
41649114407
-
Microbial community gene expression in ocean surface waters
-
DOI 10.1073/pnas.0708897105
-
Frias-Lopez J, et al. (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A, 105 (10):3805-3810. (Pubitemid 351723480)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.10
, pp. 3805-3810
-
-
Frias-Lopez, J.1
Shi, Y.2
Tyson, G.W.3
Coleman, M.L.4
Schuster, S.C.5
Chisholm, S.W.6
DeLong, E.F.7
-
70
-
-
0034665853
-
Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea
-
Beja O, et al. (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science, 289(5486):1902-1906.
-
(2000)
Science
, vol.289
, Issue.5486
, pp. 1902-1906
-
-
Beja, O.1
-
71
-
-
33846238031
-
Light stimulates growth of proteorhodopsin-containing marine Flavobacteria
-
DOI 10.1038/nature05381, PII NATURE05381
-
Gomez-Consarnau L, et al. (2007) Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature, 445 (7124):210-213. (Pubitemid 46095725)
-
(2007)
Nature
, vol.445
, Issue.7124
, pp. 210-213
-
-
Gomez-Consarnau, L.1
Gonzalez, J.M.2
Coll-Llado, M.3
Gourdon, P.4
Pascher, T.5
Neutze, R.6
Pedros-Alio, C.7
Pinhassi, J.8
-
72
-
-
70349286423
-
Soil genomics
-
Singh BK, et al. (2009) Soil genomics. Nat Rev Micro, 7(10):756.
-
(2009)
Nat Rev Micro
, vol.7
, Issue.10
, pp. 756
-
-
Singh, B.K.1
-
73
-
-
34547800097
-
Pyrosequencing enumerates and contrasts soil microbial diversity
-
DOI 10.1038/ismej.2007.53, PII ISMEJ200753
-
Roesch LF, et al. (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J, 1(4):283-290. (Pubitemid 47227850)
-
(2007)
ISME Journal
, vol.1
, Issue.4
, pp. 283-290
-
-
Roesch, L.F.W.1
Fulthorpe, R.R.2
Riva, A.3
Casella, G.4
Hadwin, A.K.M.5
Kent, A.D.6
Daroub, S.H.7
Camargo, F.A.O.8
Farmerie, W.G.9
Triplett, E.W.10
-
74
-
-
23944525404
-
Microbiology: Computational improvements reveal great bacterial diversity and high toxicity in soil
-
DOI 10.1126/science.1112665
-
Gans J, Wolinsky M, Dunbar J. (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science, 309(5739):1387-1390. (Pubitemid 41209368)
-
(2005)
Science
, vol.309
, Issue.5739
, pp. 1387-1390
-
-
Gans, J.1
Wolinsky, M.2
Dunbar, J.3
-
75
-
-
63049092891
-
TerraGenome: A consortium for the sequencing of a soil metagenome
-
Vogel TM, et al. (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. Nat Rev Micro, 7(4):252.
-
(2009)
Nat Rev Micro
, vol.7
, Issue.4
, pp. 252
-
-
Vogel, T.M.1
-
76
-
-
70349292555
-
To sequence or not to sequence the whole-soil metagenome?
-
Baveye PC. (2009) To sequence or not to sequence the whole-soil metagenome? Nat Rev Micro, 7(10):756.
-
(2009)
Nat Rev Micro
, vol.7
, Issue.10
, pp. 756
-
-
Baveye, P.C.1
-
79
-
-
69249118591
-
Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil
-
DOI 10.1128/AEM.00358-07
-
Fierer N, et al. (2007) Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol, 73(21):7059-7066. (Pubitemid 350076828)
-
(2007)
Applied and Environmental Microbiology
, vol.73
, Issue.21
, pp. 7059-7066
-
-
Fierer, N.1
Breitbart, M.2
Nulton, J.3
Salamon, P.4
Lozupone, C.5
Jones, R.6
Robeson, M.7
Edwards, R.A.8
Felts, B.9
Rayhawk, S.10
Knight, R.11
Rohwer, F.12
Jackson, R.B.13
-
80
-
-
60749121732
-
Phylogenetic diversity of Acidobacteria in a former agricultural soil
-
Kielak A, et al. (2009) Phylogenetic diversity of Acidobacteria in a former agricultural soil. ISME J, 3(3):378-382.
-
(2009)
ISME J
, vol.3
, Issue.3
, pp. 378-382
-
-
Kielak, A.1
-
81
-
-
18844481269
-
Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms
-
DOI 10.1128/AEM.66.6.2541-2547.2000
-
Rondon MR, et al. (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol, 66 (6):2541-2547. (Pubitemid 30353963)
-
(2000)
Applied and Environmental Microbiology
, vol.66
, Issue.6
, pp. 2541-2547
-
-
Rondon, M.R.1
August, P.R.2
Bettermann, A.D.3
Brady, S.F.4
Grossman, T.H.5
Liles, M.R.6
Loiacono, K.A.7
Lynch, B.A.8
MacNeil, I.A.9
Minor, C.10
Tiong, C.L.11
Gilman, M.12
Osburne, M.S.13
Clardy, J.14
Handelsman, J.15
Goodman, R.M.16
-
82
-
-
20244376755
-
Comparative metagenomics of microbial communities
-
DOI 10.1126/science.1107851
-
Tringe S, et al. (2005) Comparative metagenomics of microbial communities. Science, 308(5721):554-557. (Pubitemid 40570586)
-
(2005)
Science
, vol.308
, Issue.5721
, pp. 554-557
-
-
Tringe, S.G.1
Von Mering, C.2
Kobayashi, A.3
Salamov, A.A.4
Chen, K.5
Chang, H.W.6
Podar, M.7
Short, J.M.8
Mathur, E.J.9
Detter, J.C.10
Bork, P.11
Hugenholtz, P.12
Rubin, E.M.13
-
83
-
-
53949095625
-
The metagenomics of disease-suppressive soils - Experiences from the METACONTROL project
-
van Elsas JD, et al. (2008) The metagenomics of disease-suppressive soils - experiences from the METACONTROL project. Trends Biotechnol, 26(11):591-601.
-
(2008)
Trends Biotechnol
, vol.26
, Issue.11
, pp. 591-601
-
-
Van Elsas, J.D.1
-
84
-
-
65549136340
-
Identification of cellulase genes from the metagenomes of compost soils and functional characterization of one novel endoglucanase
-
Pang H, et al. (2009) Identification of cellulase genes from the metagenomes of compost soils and functional characterization of one novel endoglucanase. Curr Microbiol, 58 (4):404-408.
-
(2009)
Curr Microbiol
, vol.58
, Issue.4
, pp. 404-408
-
-
Pang, H.1
-
86
-
-
35748929920
-
Expanding the soil antibiotic resistome: exploring environmental diversity
-
DOI 10.1016/j.mib.2007.08.009, PII S136952740700121X, Antimicrobials/Genomics
-
D'Costa VM, Griffiths E, Wright GD. (2007) Expanding the soil antibiotic resistome: exploring environmental diversity. Curr Opin Microbiol, 10(5):481-489. (Pubitemid 350052688)
-
(2007)
Current Opinion in Microbiology
, vol.10
, Issue.5
, pp. 481-489
-
-
D'Costa, V.M.1
Griffiths, E.2
Wright, G.D.3
-
87
-
-
70350530826
-
Identifying natural product biosynthetic genes from a soil metagenome by using T7 phage selection
-
Zhang K, et al. (2009) Identifying natural product biosynthetic genes from a soil metagenome by using T7 phage selection. Chembiochem, 10(16):2599-2606.
-
(2009)
Chembiochem
, vol.10
, Issue.16
, pp. 2599-2606
-
-
Zhang, K.1
-
88
-
-
67349208005
-
A new approach to retrieve full lengths of functional genes from soil by PCR-DGGE and metagenome walking
-
Morimoto S, Fujii T. (2009) A new approach to retrieve full lengths of functional genes from soil by PCR-DGGE and metagenome walking. Appl Microbiol Biotechnol, 83 (2):389-396.
-
(2009)
Appl Microbiol Biotechnol
, vol.83
, Issue.2
, pp. 389-396
-
-
Morimoto, S.1
Fujii, T.2
-
89
-
-
67651249844
-
Isolation and characterization of a novel lysine racemase from a soil metagenomic library
-
Chen IC, et al. (2009) Isolation and characterization of a novel lysine racemase from a soil metagenomic library. Appl Environ Microbiol, 75(15):5161-5166.
-
(2009)
Appl Environ Microbiol
, vol.75
, Issue.15
, pp. 5161-5166
-
-
Chen, I.C.1
-
90
-
-
35348968286
-
The human microbiome project
-
DOI 10.1038/nature06244, PII NATURE06244
-
Turnbaugh PJ, et al. (2007) The human microbiome project. Nature, 449 (7164):804-810. (Pubitemid 47598620)
-
(2007)
Nature
, vol.449
, Issue.7164
, 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
-
93
-
-
20544444045
-
Microbiology: Diversity of the human intestinal microbial flora
-
DOI 10.1126/science.1110591
-
Eckburg PB, et al. (2005) Diversity of the human intestinal microbial flora. Science, 308(5728):1635-1638. (Pubitemid 40807514)
-
(2005)
Science
, vol.308
, Issue.5728
, pp. 1635-1638
-
-
Eckburg, P.B.1
Bik, E.M.2
Bernstein, C.N.3
Purdom, E.4
Dethlefsen, L.5
Sargent, M.6
Gill, S.R.7
Nelson, K.E.8
Relman, D.A.9
-
94
-
-
20344371715
-
Microbes on the human vaginal epithelium
-
DOI 10.1073/pnas.0503236102
-
Hyman RW, et al. (2005) Microbes on the human vaginal epithelium. Proc Natl Acad Sci U S A, 102(22):7952-7957. (Pubitemid 40781044)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.22
, pp. 7952-7957
-
-
Hyman, R.W.1
Fukushima, M.2
Diamond, L.3
Kumm, J.4
Giudice, L.C.5
Davis, R.W.6
-
95
-
-
1642488364
-
Bacterial biota in the human distal esophagus
-
DOI 10.1073/pnas.0306398101
-
Pei Z, et al. (2004) Bacterial biota in the human distal esophagus. Proc Natl Acad Sci U S A, 101(12):4250-4255. (Pubitemid 38405915)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.12
, pp. 4250-4255
-
-
Pei, Z.1
Bini, E.J.2
Yang, L.3
Zhou, M.4
Francois, F.5
Blaser, M.J.6
-
96
-
-
38449088143
-
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
-
Kurokawa K, et al. (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res, 14(4):169-181.
-
(2007)
DNA Res
, vol.14
, Issue.4
, pp. 169-181
-
-
Kurokawa, K.1
-
97
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin J, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464:59-67.
-
(2010)
Nature
, vol.464
, pp. 59-67
-
-
Qin, J.1
-
98
-
-
65449134335
-
Assembling the marine metagenome, one cell at a time
-
Woyke T, et al. (2009) Assembling the marine metagenome, one cell at a time. PLoS ONE, 4(4):e5299.
-
(2009)
PLoS ONE
, vol.4
, Issue.4
-
-
Woyke, T.1
-
99
-
-
35748983784
-
Single-cell genomic sequencing using Multiple Displacement Amplification
-
DOI 10.1016/j.mib.2007.08.005, PII S1369527407001191, Antimicrobials/Genomics
-
Lasken RS. (2007) Single-cell genomic sequencing using multiple displacement amplification. Curr Opin Microbiol, 10 (5):510-516. (Pubitemid 350052686)
-
(2007)
Current Opinion in Microbiology
, vol.10
, Issue.5
, pp. 510-516
-
-
Lasken, R.S.1
-
100
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
Eid J, et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science, 323(5910):133-138.
-
(2009)
Science
, vol.323
, Issue.5910
, pp. 133-138
-
-
Eid, J.1
-
101
-
-
70350294348
-
Systematic artifacts in metagenomes from complex microbial communities
-
Gomez-Alvarez V, Teal TK, Schmidt TM. (2009)Systematic artifacts in metagenomes from complex microbial communities. ISME J, 3(11):1314-1317.
-
(2009)
ISME J
, vol.3
, Issue.11
, pp. 1314-1317
-
-
Gomez-Alvarez, V.1
Teal, T.K.2
Schmidt, T.M.3
-
102
-
-
73349110099
-
Wrinkles in the rare biosphere: Pyrosequencing errors lead to artificial inflation of diversity estimates
-
Kunin V, et al. (2010) Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates. Environ Microbiol, 12(1):118-123.
-
(2010)
Environ Microbiol
, vol.12
, Issue.1
, pp. 118-123
-
-
Kunin, V.1
-
103
-
-
69549138144
-
Metagenomics vs Moore's Law
-
Editorial
-
Editorial. (2009) Metagenomics vs Moore's Law. Nat Methods, 6(9):623.
-
(2009)
Nat Methods
, vol.6
, Issue.9
, pp. 623
-
-
-
104
-
-
73949090104
-
Applications of ultra-high-throughput sequencing
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Humana Press, Clifton, NJ
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Fox S, Filichkin S, Mockler TC. (2009) Applications of Ultra-High-Throughput Sequencing. In Methods Molecular Biology, Humana Press, Clifton, NJ, 79-108.
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(2009)
Methods Molecular Biology
, pp. 79-108
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Fox, S.1
Filichkin, S.2
Mockler, T.C.3
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