-
1
-
-
33751059692
-
The marine viromes of four oceanic regions
-
Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, et al. (2006) The marine viromes of four oceanic regions. PLoS Biology 4: e368.
-
(2006)
PLoS Biology
, vol.4
-
-
Angly, F.E.1
Felts, B.2
Breitbart, M.3
Salamon, P.4
Edwards, R.A.5
-
2
-
-
51749122921
-
Metagenomics reveals our incomplete knowledge of global diversity
-
Pignatelli M, Aparicio G, Blanquer I, Hernández V, Moya A, et al. (2008) Metagenomics reveals our incomplete knowledge of global diversity. Bioinformatics 24: 2124-2125.
-
(2008)
Bioinformatics
, vol.24
, pp. 2124-2125
-
-
Pignatelli, M.1
Aparicio, G.2
Blanquer, I.3
Hernández, V.4
Moya, A.5
-
3
-
-
35748976529
-
Get the most out of your metagenome: Computational analysis of environmental sequence data
-
Raes J, Foerstner KU, Bork P (2007) Get the most out of your metagenome: computational analysis of environmental sequence data. Curr Opin Microbiol 10: 490-498.
-
(2007)
Curr Opin Microbiol
, vol.10
, pp. 490-498
-
-
Raes, J.1
Foerstner, K.U.2
Bork, P.3
-
5
-
-
0034992826
-
The closest BLAST hit is often not the nearest neighbor
-
Koski LB, Golding GB (2001) The closest BLAST hit is often not the nearest neighbor. J Mol Evol 52: 540-542.
-
(2001)
J Mol Evol
, vol.52
, pp. 540-542
-
-
Koski, L.B.1
Golding, G.B.2
-
6
-
-
41149159700
-
Biodiversity and biogeography of phages in modern stromatolites and thrombolites
-
Desnues C, Rodriguez-Brito B, Rayhawk S, Kelley S, Tran T, et al. (2008) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 452: 340-343.
-
(2008)
Nature
, vol.452
, pp. 340-343
-
-
Desnues, C.1
Rodriguez-Brito, B.2
Rayhawk, S.3
Kelley, S.4
Tran, T.5
-
7
-
-
41649109613
-
Functional metagenomic profiling of nine biomes
-
doi:10.1038/nature06810
-
Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, et al. (2008) Functional metagenomic profiling of nine biomes. Nature 452: 629-632. doi:10.1038/nature06810.
-
(2008)
Nature
, vol.452
, pp. 629-632
-
-
Dinsdale, E.A.1
Edwards, R.A.2
Hall, D.3
Angly, F.4
Breitbart, M.5
-
8
-
-
19144363310
-
PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information
-
doi:10.1186/1471-2105-6-41
-
Angly F, Rodriguez-Brito B, Bangor D, McNairnie P, Breitbart M, et al. (2005) PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics 6: 41. doi:10.1186/1471-2105-6-41.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 41
-
-
Angly, F.1
Rodriguez-Brito, B.2
Bangor, D.3
McNairnie, P.4
Breitbart, M.5
-
9
-
-
0034517760
-
Genome size distributions indicate variability and similarities among marine viral assemblages from diverse environments
-
Steward GF, Montiel JL, Azam F (2000) Genome size distributions indicate variability and similarities among marine viral assemblages from diverse environments. Limnol Oceanogr 45: 1697-1706.
-
(2000)
Limnol Oceanogr
, vol.45
, pp. 1697-1706
-
-
Steward, G.F.1
Montiel, J.L.2
Azam, F.3
-
10
-
-
35948993040
-
Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts
-
Holmfeldt K, Middelboe M, Nybroe O, Riemann L (2007) Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts. Appl Environ Microbiol 73: 6730-6739.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 6730-6739
-
-
Holmfeldt, K.1
Middelboe, M.2
Nybroe, O.3
Riemann, L.4
-
11
-
-
49149087080
-
Burden or benefit? Virus-host interactions in the marine environment
-
Sandaa R (2008) Burden or benefit? Virus-host interactions in the marine environment. Res Microbiol 159: 374-381.
-
(2008)
Res Microbiol
, vol.159
, pp. 374-381
-
-
Sandaa, R.1
-
12
-
-
0842266354
-
Are viruses driving microbial diversification and diversity?
-
Weinbauer MG, Rassoulzadegan F (2004) Are viruses driving microbial diversification and diversity? Environ Microbiol 6: 1-11.
-
(2004)
Environ Microbiol
, vol.6
, pp. 1-11
-
-
Weinbauer, M.G.1
Rassoulzadegan, F.2
-
13
-
-
0035843644
-
PulseNet standardized protocol for subtyping Listeria monocytogenes by macrorestriction and pulsed-field gel electrophoresis
-
Graves LM, Swaminathan B (2001) PulseNet standardized protocol for subtyping Listeria monocytogenes by macrorestriction and pulsed-field gel electrophoresis. Int J Food Microbiol 65: 55-62.
-
(2001)
Int J Food Microbiol
, vol.65
, pp. 55-62
-
-
Graves, L.M.1
Swaminathan, B.2
-
14
-
-
0034265408
-
Pulsed-field gel electrophoresis analysis of virus assemblages present in a hypersaline environment
-
Diez B, Antón J, Guixa-Boixereu N, Pedrós-Alió C, Rodriguez-Valera F (2000) Pulsed-field gel electrophoresis analysis of virus assemblages present in a hypersaline environment. Int Microbiol 3: 159-164.
-
(2000)
Int Microbiol
, vol.3
, pp. 159-164
-
-
Diez, B.1
Antón, J.2
Guixa-Boixereu, N.3
Pedrós-Alió, C.4
Rodriguez-Valera, F.5
-
15
-
-
33847280283
-
Prediction of effective genome size in metagenomic samples
-
Raes J, Korbel J, Lercher M, von Mering C, Bork P (2007) Prediction of effective genome size in metagenomic samples. Genome Biol 8: R10.
-
(2007)
Genome Biol
, vol.8
-
-
Raes, J.1
Korbel, J.2
Lercher, M.3
von Mering, C.4
Bork, P.5
-
16
-
-
3042780438
-
Virioplankton community structure along a salinity gradient in a solar saltern
-
Sandaa R, Foss Skjoldal E, Bratbak G (2003) Virioplankton community structure along a salinity gradient in a solar saltern. Extremophiles 7: 347-351.
-
(2003)
Extremophiles
, vol.7
, pp. 347-351
-
-
Sandaa, R.1
Foss Skjoldal, E.2
Bratbak, G.3
-
17
-
-
0032959665
-
Population dynamics of Chesapeake bay virioplankton: Total-community analysis by pulsedfield gel electrophoresis
-
Wommack KE, Ravel J, Hill RT, Chun J, Colwell RR (1999) Population dynamics of Chesapeake bay virioplankton: total-community analysis by pulsedfield gel electrophoresis. Appl Environ Microbiol 65: 231-40.
-
(1999)
Appl Environ Microbiol
, vol.65
, pp. 231-240
-
-
Wommack, K.E.1
Ravel, J.2
Hill, R.T.3
Chun, J.4
Colwell, R.R.5
-
19
-
-
0036330981
-
The Phage Proteomic Tree: A genome-based taxonomy for phage
-
Rohwer F, Edwards RA (2002) The Phage Proteomic Tree: a genome-based taxonomy for phage. J Bacteriol 184: 4529-35.
-
(2002)
J Bacteriol
, vol.184
, pp. 4529-4535
-
-
Rohwer, F.1
Edwards, R.A.2
-
20
-
-
52949115612
-
Microbiology: Metagenomics
-
Hugenholtz P, Tyson GW (2008) Microbiology: metagenomics. Nature 455: 481-483.
-
(2008)
Nature
, vol.455
, pp. 481-483
-
-
Hugenholtz, P.1
Tyson, G.W.2
-
22
-
-
70350491059
-
Diverse circovirus-like genome architectures revealed by environmental metagenomics
-
doi:10.1099/vir.0.012955-0
-
Rosario K, Duffy S, Breitbart M (2009) Diverse circovirus-like genome architectures revealed by environmental metagenomics. J Gen Virol 90: 2418-2424. doi:10.1099/vir.0.012955-0.
-
(2009)
J Gen Virol
, vol.90
, pp. 2418-2424
-
-
Rosario, K.1
Duffy, S.2
Breitbart, M.3
-
23
-
-
70349458100
-
The genomic basis of trophic strategy in marine bacteria
-
Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, et al. (2009) The genomic basis of trophic strategy in marine bacteria. Proc Nat Acad Sci USA 106: 15527-15533.
-
(2009)
Proc Nat Acad Sci USA
, vol.106
, pp. 15527-15533
-
-
Lauro, F.M.1
McDougald, D.2
Thomas, T.3
Williams, T.J.4
Egan, S.5
-
24
-
-
1542327668
-
Trends between gene content and genome size in prokaryotic species with larger genomes
-
Konstantinidis KT, Tiedje JM (2004) Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Nat Acad Sci USA 101: 3160-3165.
-
(2004)
Proc Nat Acad Sci USA
, vol.101
, pp. 3160-3165
-
-
Konstantinidis, K.T.1
Tiedje, J.M.2
-
25
-
-
67649911268
-
Metagenomic signatures of 86 microbial and viral metagenomes
-
Willner D, Thurber RV, Rohwer F (2009) Metagenomic signatures of 86 microbial and viral metagenomes. Environ Microbiol 11: 1752-1766.
-
(2009)
Environ Microbiol
, vol.11
, pp. 1752-1766
-
-
Willner, D.1
Thurber, R.V.2
Rohwer, F.3
-
26
-
-
33645891993
-
Viral and bacterial assemblage covariance in oligotrophic waters of the West Florida shelf (Gulf of Mexico)
-
Hewson I, Winget DM, Williamson KE, Fuhrman JA, Wommack KE (2006) Viral and bacterial assemblage covariance in oligotrophic waters of the West Florida shelf (Gulf of Mexico). J Mar Biol Assoc UK 86: 591-603.
-
(2006)
J Mar Biol Assoc UK
, vol.86
, pp. 591-603
-
-
Hewson, I.1
Winget, D.M.2
Williamson, K.E.3
Fuhrman, J.A.4
Wommack, K.E.5
-
27
-
-
40149098974
-
-
PLoS
-
Dinsdale EA, Pantos O, Smriga S, Edwards RA, Angly F, et al. (2008) Microbial ecology of four coral atolls in the northern Line Islands. PLoS ONE 3: e1584.
-
(2008)
Microbial ecology of four coral atolls in the northern Line Islands
, vol.ONE 3
-
-
Dinsdale, E.A.1
Pantos, O.2
Smriga, S.3
Edwards, R.A.4
Angly, F.5
-
28
-
-
44449166042
-
On the origin of prokaryotic "species": The taxonomy of halophilic Archaea
-
DasSarma P, DasSarma S (2008) On the origin of prokaryotic "species": the taxonomy of halophilic Archaea. Saline Syst 4: 5.
-
(2008)
Saline Syst
, vol.4
, pp. 5
-
-
DasSarma, P.1
DasSarma, S.2
-
29
-
-
0037716583
-
Haloarchaeal viruses: How diverse are they?
-
Dyall-Smith M, Tang S, Bath C (2003) Haloarchaeal viruses: how diverse are they? Res Microbiol 154: 309-313.
-
(2003)
Res Microbiol
, vol.154
, pp. 309-313
-
-
Dyall-Smith, M.1
Tang, S.2
Bath, C.3
-
30
-
-
57449102600
-
Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa
-
Vega Thurber RL, Barott KL, Hall D, Liu H, Rodriguez-Mueller B, et al. (2008) Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. Proc Nat Acad Sci USA 105: 18413-18418.
-
(2008)
Proc Nat Acad Sci USA
, vol.105
, pp. 18413-18418
-
-
Vega Thurber, R.L.1
Barott, K.L.2
Hall, D.3
Liu, H.4
Rodriguez-Mueller, B.5
-
31
-
-
68249143124
-
Metagenomic analysis of stressed coral holobionts
-
Thurber RV, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, et al. (2009) Metagenomic analysis of stressed coral holobionts. Environ Microbiol 11: 2148-2163.
-
(2009)
Environ Microbiol
, vol.11
, pp. 2148-2163
-
-
Thurber, R.V.1
Willner-Hall, D.2
Rodriguez-Mueller, B.3
Desnues, C.4
Edwards, R.A.5
-
32
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-10.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
33
-
-
13244252316
-
Visualization of comparative genomic analyses by BLAST score ratio
-
Rasko D, Myers G, Ravel J (2005) Visualization of comparative genomic analyses by BLAST score ratio. BMC Bioinformatics 6: 2.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 2
-
-
Rasko, D.1
Myers, G.2
Ravel, J.3
-
34
-
-
0037423702
-
COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance
-
Sadreyev R, Grishin N (2003) COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J Mol Biol 326: 317-336.
-
(2003)
J Mol Biol
, vol.326
, pp. 317-336
-
-
Sadreyev, R.1
Grishin, N.2
-
35
-
-
0025259313
-
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
-
Karlin S, Altschul SF (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Nat Acad Sci USA 87: 2264-2268.
-
(1990)
Proc Nat Acad Sci USA
, vol.87
, pp. 2264-2268
-
-
Karlin, S.1
Altschul, S.F.2
-
36
-
-
33748319353
-
Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae
-
Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, et al. (2006) Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res 5: 2339-2347.
-
(2006)
J Proteome Res
, vol.5
, pp. 2339-2347
-
-
Zybailov, B.1
Mosley, A.L.2
Sardiu, M.E.3
Coleman, M.K.4
Florens, L.5
-
37
-
-
33750699996
-
Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors
-
Florens L, Carozza MJ, Swanson SK, Fournier M, Coleman MK, et al. (2006) Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods 40: 303-311.
-
(2006)
Methods
, vol.40
, pp. 303-311
-
-
Florens, L.1
Carozza, M.J.2
Swanson, S.K.3
Fournier, M.4
Coleman, M.K.5
-
38
-
-
34247642450
-
Quantitative proteomic analysis of distinct mammalian mediator complexes using normalized spectral abundance factors
-
Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, et al. (2006) Quantitative proteomic analysis of distinct mammalian mediator complexes using normalized spectral abundance factors. Proc Nat Acad Sci USA 103: 18928-18933.
-
(2006)
Proc Nat Acad Sci USA
, vol.103
, pp. 18928-18933
-
-
Paoletti, A.C.1
Parmely, T.J.2
Tomomori-Sato, C.3
Sato, S.4
Zhu, D.5
-
39
-
-
10944235924
-
Comparative genomic structure of prokaryotes
-
Bentley SD, Parkhill J (2004) Comparative genomic structure of prokaryotes. Annu Rev Genet 38: 771-92.
-
(2004)
Annu Rev Genet
, vol.38
, pp. 771-792
-
-
Bentley, S.D.1
Parkhill, J.2
-
40
-
-
33845873289
-
Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation
-
Letunic I, Bork P (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23: 127-8.
-
(2007)
Bioinformatics
, vol.23
, pp. 127-128
-
-
Letunic, I.1
Bork, P.2
-
41
-
-
33947215475
-
CAMERA: A community resource for metagenomics
-
Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M (2007) CAMERA: a community resource for metagenomics. PLoS Biol 5: e75.
-
(2007)
PLoS Biol
, vol.5
-
-
Seshadri, R.1
Kravitz, S.A.2
Smarr, L.3
Gilna, P.4
Frazier, M.5
-
42
-
-
0033957466
-
Database resources of the National Center for Biotechnology Information
-
Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, et al. (2000) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 28: 10-4.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 10-14
-
-
Wheeler, D.L.1
Chappey, C.2
Lash, A.E.3
Leipe, D.D.4
Madden, T.L.5
-
43
-
-
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 EM, et al. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 386
-
-
Meyer, F.1
Paarmann, D.2
D'Souza, M.3
Olson, R.4
Glass, E.M.5
-
44
-
-
74549134371
-
-
R Foundation for Statistical Computing, Vienna, Austria n.d, R: A language and environment for statistical computing
-
R Foundation for Statistical Computing, Vienna, Austria (n.d.) R: A language and environment for statistical computing. .
-
-
-
|