-
1
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
Tyson G.W., Chapman J., Hugenholtz P., Allen E.E., Ram R.J., Richardson P.M., Solovyev V.V., Rubin E.M., Rokhsar D.S., Banfield J.F. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004, 428:37-43.
-
(2004)
Nature
, vol.428
, 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
-
2
-
-
33947235074
-
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families
-
Yooseph S., Sutton G., Rusch D.B., Halpern A.L., Williamson S.J., Remington K., Eisen J.A., Heidelberg K.B., Manning G., Li W., et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 2007, 5:e16.
-
(2007)
PLoS Biol
, vol.5
-
-
Yooseph, S.1
Sutton, G.2
Rusch, D.B.3
Halpern, A.L.4
Williamson, S.J.5
Remington, K.6
Eisen, J.A.7
Heidelberg, K.B.8
Manning, G.9
Li, W.10
-
3
-
-
0037010721
-
Metagenome' a challenging source of enzyme discovery
-
Lorenz P., Schleper C. Metagenome' a challenging source of enzyme discovery. J Mol Catal B: Enzymatic 2002, 19-20:13-19.
-
(2002)
J Mol Catal B: Enzymatic
, pp. 13-19
-
-
Lorenz, P.1
Schleper, C.2
-
4
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
Tyson G.W., Chapman J., Hugenholtz P., Allen E.E., Ram R.J., Richardson P.M., Solovyev V.V., Rubin E.M., Rokhsar D.S., Banfield J.F. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004, 428:37-43.
-
(2004)
Nature
, vol.428
, 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
-
5
-
-
52449114817
-
Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities
-
Gilbert J.A., Field D., Huang Y., Edwards R., Li W., Gilna P., Joint I. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE 2008, 3:e3042.
-
(2008)
PLoS ONE
, vol.3
-
-
Gilbert, J.A.1
Field, D.2
Huang, Y.3
Edwards, R.4
Li, W.5
Gilna, P.6
Joint, I.7
-
6
-
-
78649732106
-
The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation
-
Gilbert J.A., Field D., Swift P., Thomas S., Cummings D., Temperton B., Weynberg K., Huse S., Hughes M., Joint I., Somerfield P.J., Mühling M. The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation. PLoS One. 2010, 5:e15545. 10.1371/journal.pone.0015545.
-
(2010)
PLoS One.
, vol.5
-
-
Gilbert, J.A.1
Field, D.2
Swift, P.3
Thomas, S.4
Cummings, D.5
Temperton, B.6
Weynberg, K.7
Huse, S.8
Hughes, M.9
Joint, I.10
Somerfield, P.J.11
Mühling, M.12
-
7
-
-
27444438599
-
The microbial pan-genome
-
Medini D., Donati C., Tettelin H., Masignani V., Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev 2005, 15:589-594.
-
(2005)
Curr Opin Genet Dev
, vol.15
, pp. 589-594
-
-
Medini, D.1
Donati, C.2
Tettelin, H.3
Masignani, V.4
Rappuoli, R.5
-
8
-
-
70249089090
-
Single-molecule sequencing of an individual human genome
-
Pushkarev D., Neff N.F., Quake S.R. Single-molecule sequencing of an individual human genome. Nat Biotechnol 2009, 27:847-850.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 847-850
-
-
Pushkarev, D.1
Neff, N.F.2
Quake, S.R.3
-
9
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., Wu D., Paulsen I., Nelson K.E., Nelson W., et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304:66-74.
-
(2004)
Science
, vol.304
, 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
-
10
-
-
33947238287
-
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific
-
Rusch D.B., Halpern A.L., Sutton G., Heidelberg K.B., Williamson S., Yooseph S., Wu D., Eisen J.A., Hoffman J.M., Remington K., et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 2007, 5:e77.
-
(2007)
PLoS Biol
, vol.5
-
-
Rusch, D.B.1
Halpern, A.L.2
Sutton, G.3
Heidelberg, K.B.4
Williamson, S.5
Yooseph, S.6
Wu, D.7
Eisen, J.A.8
Hoffman, J.M.9
Remington, K.10
-
11
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin J., Li R., Raes J., Arumugam M., Burgdorf K.S., Manichanh C., Nielsen T., Pons N., Levenez F., Yamada T., et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65.
-
(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
-
12
-
-
84856432606
-
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset
-
Larsen P.E., Collart F., Field D., Meyer F., Keegan K.P., Henry C.S., McGrath J., Quinn J., Gilbert J.A. Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. Microb Inform Exp 2011, 1:4.
-
(2011)
Microb Inform Exp
, vol.1
, pp. 4
-
-
Larsen, P.E.1
Collart, F.2
Field, D.3
Meyer, F.4
Keegan, K.P.5
Henry, C.S.6
McGrath, J.7
Quinn, J.8
Gilbert, J.A.9
-
13
-
-
33845957530
-
Accurate phylogenetic classification of variable-length DNA fragments
-
McHardy A.C., Martín H.G., Tsirigos A., Hugenholtz P., Rigoutsos I. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods 2007, 4:63-72.
-
(2007)
Nat Methods
, vol.4
, pp. 63-72
-
-
McHardy, A.C.1
Martín, H.G.2
Tsirigos, A.3
Hugenholtz, P.4
Rigoutsos, I.5
-
14
-
-
57349141505
-
A bioinformatician's guide to metagenomics
-
Kunin V., Copeland A., Lapidus A., Mavromatis K., Hugenholtz P. A bioinformatician's guide to metagenomics. Microbiol Mol Biol Rev 2008, 72:557-578.
-
(2008)
Microbiol Mol Biol Rev
, vol.72
, pp. 557-578
-
-
Kunin, V.1
Copeland, A.2
Lapidus, A.3
Mavromatis, K.4
Hugenholtz, P.5
-
16
-
-
43149115851
-
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
-
Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821-829.
-
(2008)
Genome Res
, vol.18
, pp. 821-829
-
-
Zerbino, D.R.1
Birney, E.2
-
17
-
-
3042615882
-
Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs
-
Chevreux B., Pfisterer T., Drescher B., Driesel A.J., Müller W.E., Wetter T., Suhai S. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 2004, 14:1147-1159.
-
(2004)
Genome Res
, vol.14
, pp. 1147-1159
-
-
Chevreux, B.1
Pfisterer, T.2
Drescher, B.3
Driesel, A.J.4
Müller, W.E.5
Wetter, T.6
Suhai, S.7
-
18
-
-
66449136667
-
AByS.S: a parallel assembler for short read sequence data
-
Simpson J.T., Wong K., Jackman S.D., Schein J.E., Jones S.J., Birol I. AByS.S: a parallel assembler for short read sequence data. Genome Res 2009, 19:1117-1123.
-
(2009)
Genome Res
, vol.19
, pp. 1117-1123
-
-
Simpson, J.T.1
Wong, K.2
Jackman, S.D.3
Schein, J.E.4
Jones, S.J.5
Birol, I.6
-
19
-
-
75349109607
-
ALLPATHS 2 small genomes assembled accurately and with high continuity from short paired reads
-
Maccallum I., Przybylski D., Gnerre S., Burton J., Shlyakhter I., Gnirke A., Malek J., McKernan K., Ranade S., Shea T.P., et al. ALLPATHS 2 small genomes assembled accurately and with high continuity from short paired reads. Genome Biol 2009, 10:R103.
-
(2009)
Genome Biol
, vol.10
-
-
Maccallum, I.1
Przybylski, D.2
Gnerre, S.3
Burton, J.4
Shlyakhter, I.5
Gnirke, A.6
Malek, J.7
McKernan, K.8
Ranade, S.9
Shea, T.P.10
-
20
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
22
-
-
0036226603
-
BLAT - the BLAST-like alignment tool
-
Kent W.J. BLAT - the BLAST-like alignment tool. Genome Res 2002, 12:656-664.
-
(2002)
Genome Res
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
23
-
-
79955877212
-
RAPSearch: a fast protein similarity search tool for short reads
-
Ye Y., Choi J.H., Tang H. RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinform 2011, 12:159.
-
(2011)
BMC Bioinform
, vol.12
, pp. 159
-
-
Ye, Y.1
Choi, J.H.2
Tang, H.3
-
24
-
-
78651326786
-
FragGeneScan: predicting genes in short and error-prone reads
-
Rho M., Tang H., Ye Y. FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res 2010 Nov, 38:e191.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Rho, M.1
Tang, H.2
Ye, Y.3
-
26
-
-
33750976398
-
MetaGene: prokaryotic gene finding from environmental genome shotgun sequences
-
Noguchi H., Park J., Takagi T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res 2006, 34:5623-5630.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 5623-5630
-
-
Noguchi, H.1
Park, J.2
Takagi, T.3
-
27
-
-
59149090570
-
MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes
-
Noguchi H., Taniguchi T., Itoh T. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res 2008, 15:387-396.
-
(2008)
DNA Res
, vol.15
, pp. 387-396
-
-
Noguchi, H.1
Taniguchi, T.2
Itoh, T.3
-
28
-
-
42449162998
-
Phylogenetic classification of short environmental DNA fragments
-
Krause L., Diaz N.N., Goesmann A., Kelley S., Nattkemper T.W., Rohwer F., Edwards R.A., Stoye J. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res 2008, 36:2230-2239.
-
(2008)
Nucleic Acids Res
, vol.36
, 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
-
30
-
-
66149130975
-
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column
-
Shi Y., Tyson G.W., DeLong E.F. Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature 2009, 459:266-269.
-
(2009)
Nature
, vol.459
, pp. 266-269
-
-
Shi, Y.1
Tyson, G.W.2
DeLong, E.F.3
-
31
-
-
34250662138
-
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
-
Grissa I., Vergnaud G., Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinform 2007, 8:172.
-
(2007)
BMC Bioinform
, vol.8
, pp. 172
-
-
Grissa, I.1
Vergnaud, G.2
Pourcel, C.3
-
32
-
-
0037252684
-
Rfam: an RNA family database
-
Griffiths-Jones S., Bateman A., Marshall M., Khanna A., Eddy S.R. Rfam: an RNA family database. Nucleic Acids Res 2003, 31:439-441.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 439-441
-
-
Griffiths-Jones, S.1
Bateman, A.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
-
33
-
-
53549118607
-
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes
-
Meyer F., Paarmann D., D'Souza M., Olson R., Glass E.M., Kubal M., Paczian T., Rodriguez A., Stevens R., Wilke A., et al. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinform [electronic resource] 2008, 9:386.
-
(2008)
BMC Bioinform [electronic resource]
, 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
-
34
-
-
38549139537
-
IMG/M: a data management and analysis system for metagenomes
-
Markowitz V.M., Ivanova N.N., Szeto E., Palaniappan K., Chu K., Dalevi D., Chen I.M., Grechkin Y., Dubchak I., Anderson I., et al. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res 2008, 36:D534-D538.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Markowitz, V.M.1
Ivanova, N.N.2
Szeto, E.3
Palaniappan, K.4
Chu, K.5
Dalevi, D.6
Chen, I.M.7
Grechkin, Y.8
Dubchak, I.9
Anderson, I.10
-
35
-
-
78651266825
-
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource
-
Sun S., Chen J., Li W., Altintas I., Lin A., Peltier S., Stocks K., Allen E.E., Ellisman M., Grethe J., Wooley J. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res 2011, 39:D546-D551.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Sun, S.1
Chen, J.2
Li, W.3
Altintas, I.4
Lin, A.5
Peltier, S.6
Stocks, K.7
Allen, E.E.8
Ellisman, M.9
Grethe, J.10
Wooley, J.11
-
36
-
-
38549092091
-
Database resources of the National Center for Biotechnology Information
-
Wheeler D.L., Barrett T., Benson D.A., Bryant S.H., Canese K., Chetvernin V., Church D.M., Dicuccio M., Edgar R., Federhen S., et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2008, 36:D13-D21.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Wheeler, D.L.1
Barrett, T.2
Benson, D.A.3
Bryant, S.H.4
Canese, K.5
Chetvernin, V.6
Church, D.M.7
Dicuccio, M.8
Edgar, R.9
Federhen, S.10
-
37
-
-
77954526823
-
The case for cloud computing in genome informatics
-
Stein L. The case for cloud computing in genome informatics. Genome Biol 2010, 11:207. 10.1186/gb-2010-11-5-207.
-
(2010)
Genome Biol
, vol.11
, pp. 207
-
-
Stein, L.1
-
38
-
-
79959792587
-
The Genomic Standards Consortium
-
Field D., Amaral-Zettler L., Cochrane G., Cole J.R., Dawyndt P., Garrity G.M., Gilbert J., Glöckner F.O., Hirschman L., Karsch-Mizrachi I., et al. The Genomic Standards Consortium. PLoS Biol 2011, 9:e1001088.
-
(2011)
PLoS Biol
, vol.9
-
-
Field, D.1
Amaral-Zettler, L.2
Cochrane, G.3
Cole, J.R.4
Dawyndt, P.5
Garrity, G.M.6
Gilbert, J.7
Glöckner, F.O.8
Hirschman, L.9
Karsch-Mizrachi, I.10
-
39
-
-
80053436839
-
Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology Meeting in Seattle, WA, August 22-27, 2010
-
Gilbert J.A., Meyer F., Knight R., Field D., Kyrpides N., Yilmaz P., Wooley J. Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology Meeting in Seattle, WA, August 22-27, 2010. Stand Genomic Sci 2010, 3:235-239.
-
(2010)
Stand Genomic Sci
, vol.3
, pp. 235-239
-
-
Gilbert, J.A.1
Meyer, F.2
Knight, R.3
Field, D.4
Kyrpides, N.5
Yilmaz, P.6
Wooley, J.7
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