-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
77949569493
-
Antibiotic resistance and its cost: Is it possible to reverse resistance?
-
Andersson, D.I., and Hughes, D. (2010) Antibiotic resistance and its cost: Is it possible to reverse resistance? Nat Rev Microbiol 8: 260-271.
-
(2010)
Nat Rev Microbiol
, vol.8
, pp. 260-271
-
-
Andersson, D.I.1
Hughes, D.2
-
3
-
-
67649133907
-
The GC skew index: A measure of genomic compositional asymmetry and the degree of replicational selection
-
Arakawa, K., and Tomita, M. (2007) The GC skew index: A measure of genomic compositional asymmetry and the degree of replicational selection. Evol Bioinform Online 3: 159-168.
-
(2007)
Evol Bioinform Online
, vol.3
, pp. 159-168
-
-
Arakawa, K.1
Tomita, M.2
-
4
-
-
40549120596
-
The RAST Server: Rapid annotations using subsystems technology
-
Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., etal. (2008) The RAST Server: Rapid annotations using subsystems technology. BMC Genomics 9: 75.
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
Bartels, D.2
Best, A.A.3
DeJongh, M.4
Disz, T.5
Edwards, R.A.6
-
5
-
-
84880712059
-
Exploring the costs of horizontal gene transfer
-
Baltrus, D.A. (2013) Exploring the costs of horizontal gene transfer. Trends Ecol Evol 28: 489-495.
-
(2013)
Trends Ecol Evol
, vol.28
, pp. 489-495
-
-
Baltrus, D.A.1
-
6
-
-
79960944810
-
Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 pseudomonas syringae isolates
-
Baltrus, D.A., Nishimura, M.T., Romanchuk, A., Chang, J.H., Mukhtar, M.S., Cherkis, K., etal. (2011) Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 pseudomonas syringae isolates. PLoS Pathog 7: e1002132.
-
(2011)
PLoS Pathog
, vol.7
, pp. e1002132
-
-
Baltrus, D.A.1
Nishimura, M.T.2
Romanchuk, A.3
Chang, J.H.4
Mukhtar, M.S.5
Cherkis, K.6
-
7
-
-
84860771820
-
SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
-
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., etal. (2012) SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455-477.
-
(2012)
J Comput Biol
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
Nurk, S.2
Antipov, D.3
Gurevich, A.A.4
Dvorkin, M.5
Kulikov, A.S.6
-
8
-
-
78249274906
-
A thermophilic bacterial origin and subsequent constraints by redox, light and salinity on the evolution of the microbial mercuric reductase
-
Barkay, T., Kritee, K., Boyd, E., and Geesey, G. (2010) A thermophilic bacterial origin and subsequent constraints by redox, light and salinity on the evolution of the microbial mercuric reductase. Environ Microbiol 12: 2904-2917.
-
(2010)
Environ Microbiol
, vol.12
, pp. 2904-2917
-
-
Barkay, T.1
Kritee, K.2
Boyd, E.3
Geesey, G.4
-
9
-
-
0033899751
-
Natural selection, infectious transfer and the existence conditions for bacterial plasmids
-
Bergstrom, C.T., Lipsitch, M., and Levin, B.R. (2000) Natural selection, infectious transfer and the existence conditions for bacterial plasmids. Genetics 155: 1505-1519.
-
(2000)
Genetics
, vol.155
, pp. 1505-1519
-
-
Bergstrom, C.T.1
Lipsitch, M.2
Levin, B.R.3
-
10
-
-
84886671563
-
Diverse broad-host-range plasmids from freshwater carry few accessory genes
-
Brown, C.J., Sen, D., Yano, H., Bauer, M.L., Rogers, L.M., Van der Auwera, G.A., and Top, E.M. (2013) Diverse broad-host-range plasmids from freshwater carry few accessory genes. Appl Environ Microbiol 79: 7684-7695.
-
(2013)
Appl Environ Microbiol
, vol.79
, pp. 7684-7695
-
-
Brown, C.J.1
Sen, D.2
Yano, H.3
Bauer, M.L.4
Rogers, L.M.5
Van der Auwera, G.A.6
Top, E.M.7
-
11
-
-
84859474080
-
Insights into the bovine rumen plasmidome
-
Brown Kav, A., Sasson, G., Jami, E., Doron-Faigenboim, A., Benhar, I., and Mizrahi, I. (2012) Insights into the bovine rumen plasmidome. PNAS 109: 5452-5457.
-
(2012)
PNAS
, vol.109
, pp. 5452-5457
-
-
Brown Kav, A.1
Sasson, G.2
Jami, E.3
Doron-Faigenboim, A.4
Benhar, I.5
Mizrahi, I.6
-
12
-
-
84997610790
-
Draft genome sequence of pseudomonas stutzeri strain B1SMN1, a nitrogen-fixing and naphthalene-degrading strain isolated from wastewater
-
Busquets, A., Pena, A., Gomila, M., Mayol, J., Bosch, R., Nogales, B., etal. (2013) Draft genome sequence of pseudomonas stutzeri strain B1SMN1, a nitrogen-fixing and naphthalene-degrading strain isolated from wastewater. Genome Announc 1: e00584-13.
-
(2013)
Genome Announc
, vol.1
, pp. e00584-e00613
-
-
Busquets, A.1
Pena, A.2
Gomila, M.3
Mayol, J.4
Bosch, R.5
Nogales, B.6
-
13
-
-
84901691210
-
How context dependent are species interactions?
-
Chamberlain, S.A., Bronstein, J.L., and Rudgers, J.A. (2014) How context dependent are species interactions? Ecol Lett 17: 881-890.
-
(2014)
Ecol Lett
, vol.17
, pp. 881-890
-
-
Chamberlain, S.A.1
Bronstein, J.L.2
Rudgers, J.A.3
-
14
-
-
0347992016
-
Amelioration of the cost of conjugative plasmid carriage in Escherichia coli K12
-
Dahlberg, C., and Chao, L. (2003) Amelioration of the cost of conjugative plasmid carriage in Escherichia coli K12. Genetics 165: 1641-1649.
-
(2003)
Genetics
, vol.165
, pp. 1641-1649
-
-
Dahlberg, C.1
Chao, L.2
-
15
-
-
33847231339
-
Stability of a promiscuous plasmid in different hosts: No guarantee for a long-term relationship
-
De Gelder, L., Ponciano, J.M., Joyce, P., and Top, E.M. (2007) Stability of a promiscuous plasmid in different hosts: No guarantee for a long-term relationship. Microbiology 153: 452-463.
-
(2007)
Microbiology
, vol.153
, pp. 452-463
-
-
De Gelder, L.1
Ponciano, J.M.2
Joyce, P.3
Top, E.M.4
-
16
-
-
84861750651
-
The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution
-
Eikmeyer, F., Hadiati, A., Szczepanowski, R., Wibberg, D., Schneiker-Bekel, S., Rogers, L.M., etal. (2012) The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution. Plasmid 68: 13-24.
-
(2012)
Plasmid
, vol.68
, pp. 13-24
-
-
Eikmeyer, F.1
Hadiati, A.2
Szczepanowski, R.3
Wibberg, D.4
Schneiker-Bekel, S.5
Rogers, L.M.6
-
17
-
-
34248206797
-
Frequency-dependent advantages of plasmid carriage by Pseudomonas in homogeneous and spatially structured environments
-
Ellis, R.J., Lilley, A.K., Lacey, S.J., Murrell, D., and Godfray, H.C.J. (2007) Frequency-dependent advantages of plasmid carriage by Pseudomonas in homogeneous and spatially structured environments. ISME J 1: 92-95.
-
(2007)
ISME J
, vol.1
, pp. 92-95
-
-
Ellis, R.J.1
Lilley, A.K.2
Lacey, S.J.3
Murrell, D.4
Godfray, H.C.J.5
-
18
-
-
23344451933
-
Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000
-
Feil, H., Feil, W.S., Chain, P., Larimer, F., DiBartolo, G., Copeland, A., etal. (2005) Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc Natl Acad Sci USA 102: 11064-11069.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 11064-11069
-
-
Feil, H.1
Feil, W.S.2
Chain, P.3
Larimer, F.4
DiBartolo, G.5
Copeland, A.6
-
19
-
-
53849090616
-
Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations
-
Fox, R.E., Zhong, X., Krone, S.M., and Top, E.M. (2008) Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations. ISME J 2: 1024-1039.
-
(2008)
ISME J
, vol.2
, pp. 1024-1039
-
-
Fox, R.E.1
Zhong, X.2
Krone, S.M.3
Top, E.M.4
-
20
-
-
23944506044
-
Mobile genetic elements: The agents of open source evolution
-
Frost, L.S., Leplae, R., Summers, A.O., and Toussaint, A. (2005) Mobile genetic elements: The agents of open source evolution. Nat Rev Microbiol 3: 722-732.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 722-732
-
-
Frost, L.S.1
Leplae, R.2
Summers, A.O.3
Toussaint, A.4
-
21
-
-
23944499633
-
Horizontal gene transfer, genome innovation and evolution
-
Gogarten, J.P., and Townsend, J.P. (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3: 679-687.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 679-687
-
-
Gogarten, J.P.1
Townsend, J.P.2
-
22
-
-
79953281735
-
Bacteria-phage antagonistic coevolution in soil
-
Gomez, P., and Buckling, A. (2011) Bacteria-phage antagonistic coevolution in soil. Science 332: 106-109.
-
(2011)
Science
, vol.332
, pp. 106-109
-
-
Gomez, P.1
Buckling, A.2
-
23
-
-
0026500023
-
Rate of plasmid transfer among Escherichia coli strains isolated from natural populations
-
Gordon, D.M. (1992) Rate of plasmid transfer among Escherichia coli strains isolated from natural populations. Microbiology 138: 17-21.
-
(1992)
Microbiology
, vol.138
, pp. 17-21
-
-
Gordon, D.M.1
-
24
-
-
84908406441
-
Selection of a multidrug resistance plasmid by sublethal levels of antibiotics and heavy metals
-
Gullberg, E., Albrecht, L.M., Karlsson, C., Sandegren, L., and Andersson, D.I. (2014) Selection of a multidrug resistance plasmid by sublethal levels of antibiotics and heavy metals. MBio 5: e01918-14.
-
(2014)
MBio
, vol.5
, pp. e01918-e02014
-
-
Gullberg, E.1
Albrecht, L.M.2
Karlsson, C.3
Sandegren, L.4
Andersson, D.I.5
-
25
-
-
84861666352
-
Plasmid-mediated horizontal gene transfer is a coevolutionary process
-
Harrison, E., and Brockhurst, M.A. (2012) Plasmid-mediated horizontal gene transfer is a coevolutionary process. Trends Microbiol 20: 262-267.
-
(2012)
Trends Microbiol
, vol.20
, pp. 262-267
-
-
Harrison, E.1
Brockhurst, M.A.2
-
26
-
-
36248981481
-
Multimetal resistance and tolerance in microbial biofilms
-
Harrison, J.J., Ceri, H., and Turner, R.J. (2007) Multimetal resistance and tolerance in microbial biofilms. Nat Rev Microbiol 5: 928-938.
-
(2007)
Nat Rev Microbiol
, vol.5
, pp. 928-938
-
-
Harrison, J.J.1
Ceri, H.2
Turner, R.J.3
-
27
-
-
84866919992
-
Plasmids foster diversification and adaptation of bacterial populations in soil
-
Heuer, H., and Smalla, K. (2012) Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol Rev 36: 1083-1104.
-
(2012)
FEMS Microbiol Rev
, vol.36
, pp. 1083-1104
-
-
Heuer, H.1
Smalla, K.2
-
28
-
-
33749526666
-
Aerobiology and the global transport of desert dust
-
Kellogg, C.A., and Griffin, D.W. (2006) Aerobiology and the global transport of desert dust. Trends Ecol Evol 21: 638-644.
-
(2006)
Trends Ecol Evol
, vol.21
, pp. 638-644
-
-
Kellogg, C.A.1
Griffin, D.W.2
-
29
-
-
69649109364
-
Circos: An information aesthetic for comparative genomics
-
Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., etal. (2009) Circos: An information aesthetic for comparative genomics. Genome Res 19: 1639-1645.
-
(2009)
Genome Res
, vol.19
, pp. 1639-1645
-
-
Krzywinski, M.1
Schein, J.2
Birol, I.3
Connors, J.4
Gascoyne, R.5
Horsman, D.6
-
30
-
-
2942538300
-
Versatile and open software for comparing large genomes
-
Kurtz, S., Phillippy, A., Delcher, A.L., Smoot, M., Shumway, M., Antonescu, C., and Salzberg, S.L. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.
-
(2004)
Genome Biol
, vol.5
, pp. R12
-
-
Kurtz, S.1
Phillippy, A.2
Delcher, A.L.3
Smoot, M.4
Shumway, M.5
Antonescu, C.6
Salzberg, S.L.7
-
31
-
-
3042786311
-
Mini-Tn7 transposons for site-specific tagging of bacteria with fluorescent proteins
-
Lambertsen, L., Sternberg, C., and Molin, S. (2004) Mini-Tn7 transposons for site-specific tagging of bacteria with fluorescent proteins. Environ Microbiol 6: 726-732.
-
(2004)
Environ Microbiol
, vol.6
, pp. 726-732
-
-
Lambertsen, L.1
Sternberg, C.2
Molin, S.3
-
32
-
-
84895426677
-
Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli
-
Leiby, N., and Marx, C.J. (2014) Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli. PLoS Biol 12: e1001789.
-
(2014)
PLoS Biol
, vol.12
, pp. e1001789
-
-
Leiby, N.1
Marx, C.J.2
-
33
-
-
0026279651
-
Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations
-
Lenski, R.E., Rose, M.R., Simpson, S.C., and Tadler, S.C. (1991) Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2, 000 generations. Am Nat 138: 1315-1341.
-
(1991)
Am Nat
, vol.138
, pp. 1315-1341
-
-
Lenski, R.E.1
Rose, M.R.2
Simpson, S.C.3
Tadler, S.C.4
-
34
-
-
0030613336
-
The acquisition of indigenous plasmids by a genetically marked pseudomonad population colonizing the sugar beet phytosphere is related to local environmental conditions
-
Lilley, A.K., and Bailey, M.J. (1997a) The acquisition of indigenous plasmids by a genetically marked pseudomonad population colonizing the sugar beet phytosphere is related to local environmental conditions. Appl Environ Microbiol 63: 1577-1583.
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 1577-1583
-
-
Lilley, A.K.1
Bailey, M.J.2
-
35
-
-
0030908980
-
Impact of plasmid pQBR103 acquisition and carriage on the phytosphere fitness of pseudomonas fluorescens SBW25: Burden and benefit
-
Lilley, A.K., and Bailey, M.J. (1997b) Impact of plasmid pQBR103 acquisition and carriage on the phytosphere fitness of pseudomonas fluorescens SBW25: Burden and benefit. Appl Environ Microbiol 63: 1584-1587.
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 1584-1587
-
-
Lilley, A.K.1
Bailey, M.J.2
-
36
-
-
0036850768
-
The transfer dynamics of Pseudomonas sp. plasmid pQBR11 in biofilms
-
Lilley, A.K., and Bailey, M.J. (2002) The transfer dynamics of Pseudomonas sp. plasmid pQBR11 in biofilms. FEMS Microbiol Ecol 42: 243-250.
-
(2002)
FEMS Microbiol Ecol
, vol.42
, pp. 243-250
-
-
Lilley, A.K.1
Bailey, M.J.2
-
37
-
-
0028158675
-
In situ transfer of an exogenously isolated plasmid between Pseudomonas spp. in sugar beet rhizosphere
-
Lilley, A.K., Fry, J.C., Day, M.J., and Bailey, M.J. (1994) In situ transfer of an exogenously isolated plasmid between Pseudomonas spp. in sugar beet rhizosphere. Microbiology 140: 27-33.
-
(1994)
Microbiology
, vol.140
, pp. 27-33
-
-
Lilley, A.K.1
Fry, J.C.2
Day, M.J.3
Bailey, M.J.4
-
38
-
-
0030219776
-
Diversity of mercury resistance plasmids obtained by exogenous isolation from the bacteria of sugar beet in three successive years
-
Lilley, A.K., Bailey, M.J., Day, M.J., and Fry, J.C. (1996) Diversity of mercury resistance plasmids obtained by exogenous isolation from the bacteria of sugar beet in three successive years. FEMS Microbiol Ecol 20: 211-227.
-
(1996)
FEMS Microbiol Ecol
, vol.20
, pp. 211-227
-
-
Lilley, A.K.1
Bailey, M.J.2
Day, M.J.3
Fry, J.C.4
-
39
-
-
0024424430
-
Survival of Pseudomonas putida UWC1 containing cloned catabolic genes in a model activated-sludge unit
-
McClure, N.C., Weightman, A.J., and Fry, J.C. (1989) Survival of Pseudomonas putida UWC1 containing cloned catabolic genes in a model activated-sludge unit. Appl Environ Microbiol 55: 2627-2634.
-
(1989)
Appl Environ Microbiol
, vol.55
, pp. 2627-2634
-
-
McClure, N.C.1
Weightman, A.J.2
Fry, J.C.3
-
40
-
-
3142748120
-
Where does bacterial replication start? Rules for predicting the oriC region
-
Mackiewicz, P. (2004) Where does bacterial replication start? Rules for predicting the oriC region. Nucleic Acids Res 32: 3781-3791.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 3781-3791
-
-
Mackiewicz, P.1
-
41
-
-
2542635754
-
The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens
-
MacLean, R.C., Bell, G., and Rainey, P.B. (2004) The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proc Natl Acad Sci USA 101: 8072-8077.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 8072-8077
-
-
MacLean, R.C.1
Bell, G.2
Rainey, P.B.3
-
42
-
-
0037423746
-
Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676
-
Maeda, K., Nojiri, H., Shintani, M., Yoshida, T., Habe, H., and Omori, T. (2003) Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676. J Mol Biol 326: 21-33.
-
(2003)
J Mol Biol
, vol.326
, pp. 21-33
-
-
Maeda, K.1
Nojiri, H.2
Shintani, M.3
Yoshida, T.4
Habe, H.5
Omori, T.6
-
43
-
-
28444479147
-
Present-day mercury resistance transposons are common in bacteria preserved in permafrost grounds since the Upper Pleistocene
-
Mindlin, S., Minakhin, L., Petrova, M., Kholodii, G., Minakhina, S., Gorlenko, Z., and Nikiforov, V. (2005) Present-day mercury resistance transposons are common in bacteria preserved in permafrost grounds since the Upper Pleistocene. Res Microbiol 156: 994-1004.
-
(2005)
Res Microbiol
, vol.156
, pp. 994-1004
-
-
Mindlin, S.1
Minakhin, L.2
Petrova, M.3
Kholodii, G.4
Minakhina, S.5
Gorlenko, Z.6
Nikiforov, V.7
-
44
-
-
77956181661
-
-
Environment Agency Science. Bristol, UK: Environment Agency.
-
Morgan, H., De Búrca, R., Martin, I., and Jeffries, J. (2009) Soil Guideline Values for Mercury in Soil, Environment Agency Science Report SC050021. Bristol, UK: Environment Agency.
-
(2009)
Soil Guideline Values for Mercury in Soil
-
-
Morgan, H.1
De Búrca, R.2
Martin, I.3
Jeffries, J.4
-
45
-
-
84902668698
-
Non-additive costs and interactions alter the competitive dynamics of co-occurring ecologically distinct plasmids
-
Morton, E.R., Platt, T.G., Fuqua, C., and Bever, J.D. (2014) Non-additive costs and interactions alter the competitive dynamics of co-occurring ecologically distinct plasmids. Proc Biol Sci 281: 20132173.
-
(2014)
Proc Biol Sci
, vol.281
, pp. 20132173
-
-
Morton, E.R.1
Platt, T.G.2
Fuqua, C.3
Bever, J.D.4
-
46
-
-
84898621981
-
Complete nucleotide sequence and analysis of two conjugative broad host range plasmids from a marine microbial biofilm
-
Norberg, P., Bergström, M., and Hermansson, M. (2014) Complete nucleotide sequence and analysis of two conjugative broad host range plasmids from a marine microbial biofilm. PLoS ONE 9: e92321.
-
(2014)
PLoS ONE
, vol.9
, pp. e92321
-
-
Norberg, P.1
Bergström, M.2
Hermansson, M.3
-
47
-
-
67651033667
-
Conjugative plasmids: vessels of the communal gene pool
-
Norman, A., Hansen, L.H., and Sorensen, S.J. (2009) Conjugative plasmids: vessels of the communal gene pool. Philos Trans R Soc Lond B Biol Sci 364: 2275-2289.
-
(2009)
Philos Trans R Soc Lond B Biol Sci
, vol.364
, pp. 2275-2289
-
-
Norman, A.1
Hansen, L.H.2
Sorensen, S.J.3
-
48
-
-
0023575486
-
Plasmid incompatibility
-
Novick, R.P. (1987) Plasmid incompatibility. Microbiol Rev 51: 381-395.
-
(1987)
Microbiol Rev
, vol.51
, pp. 381-395
-
-
Novick, R.P.1
-
49
-
-
66749102064
-
Gene cassettes and cassette arrays in mobile resistance integrons
-
Partridge, S.R., Tsafnat, G., Coiera, E., and Iredell, J.R. (2009) Gene cassettes and cassette arrays in mobile resistance integrons. FEMS Microbiol Rev 33: 757-784.
-
(2009)
FEMS Microbiol Rev
, vol.33
, pp. 757-784
-
-
Partridge, S.R.1
Tsafnat, G.2
Coiera, E.3
Iredell, J.R.4
-
50
-
-
84858773498
-
A cooperative virulence plasmid imposes a high fitness cost under conditions that induce pathogenesis
-
Platt, T.G., Bever, J.D., and Fuqua, C. (2012) A cooperative virulence plasmid imposes a high fitness cost under conditions that induce pathogenesis. Proc Biol Sci 279: 1691-1699.
-
(2012)
Proc Biol Sci
, vol.279
, pp. 1691-1699
-
-
Platt, T.G.1
Bever, J.D.2
Fuqua, C.3
-
51
-
-
84863304598
-
-
R Foundation for Statistical Computing, Vienna, Austria..
-
R Development Core Team (2014) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/.
-
(2014)
R: A language and environment for statistical computing
-
-
-
52
-
-
0030052873
-
Physical and genetic map of the Pseudomonas fluorescens SBW25 chromosome
-
521biol
-
Rainey, P.B., and Bailey, M.J. (1996) Physical and genetic map of the Pseudomonas fluorescens SBW25 chromosome. Mol Microbiol 19: 521biol.
-
(1996)
Mol Microbiol
, vol.19
-
-
Rainey, P.B.1
Bailey, M.J.2
-
53
-
-
33644905904
-
Characterization of the Pseudomonas putida Mobile Genetic Element ISPpu10: an occupant of repetitive extragenic palindromic sequences
-
Ramos-Gonzalez, M.I., Campos, M.J., Ramos, J.L., and Espinosa-Urgel, M. (2005) Characterization of the Pseudomonas putida Mobile Genetic Element ISPpu10: an occupant of repetitive extragenic palindromic sequences. Journal of Bacteriology 188: 37-44.
-
(2005)
Journal of Bacteriology
, vol.188
, pp. 37-44
-
-
Ramos-Gonzalez, M.I.1
Campos, M.J.2
Ramos, J.L.3
Espinosa-Urgel, M.4
-
54
-
-
84929503836
-
Modeling and quantifying frequency-dependent fitness in microbial populations with cross-feeding interactions
-
Ribeck, N., and Lenski, R.E. (2015) Modeling and quantifying frequency-dependent fitness in microbial populations with cross-feeding interactions. Evolution 69: 1313-1320.
-
(2015)
Evolution
, vol.69
, pp. 1313-1320
-
-
Ribeck, N.1
Lenski, R.E.2
-
55
-
-
46049106335
-
Chromosomal toxin-antitoxin systems may act as antiaddiction modules
-
Saavedra De Bast, M., Mine, N., and Van Melderen, L. (2008) Chromosomal toxin-antitoxin systems may act as antiaddiction modules. J Bacteriol 190: 4603-4609.
-
(2008)
J Bacteriol
, vol.190
, pp. 4603-4609
-
-
Saavedra De Bast, M.1
Mine, N.2
Van Melderen, L.3
-
56
-
-
0003903343
-
-
Cold Spring Harbor Laboratory Press.
-
Sambrook, J., Fritsch, E.F., Maniatis, T. (1989) Molecular Cloning: a Laboratory Manual, 2nd Edition. Cold Spring Harbor Laboratory Press.
-
(1989)
Molecular Cloning: a Laboratory Manual, 2nd Edition
-
-
Sambrook, J.1
Fritsch, E.F.2
Maniatis, T.3
-
57
-
-
84923368060
-
Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids
-
San Millan, A., Peña-Miller, R., Toll-Riera, M., Halbert, Z.V., McLean, A.R., Cooper, B.S., and MacLean, R.C. (2014) Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids. Nat Commun 5: 5208.
-
(2014)
Nat Commun
, vol.5
, pp. 5208
-
-
San Millan, A.1
Peña-Miller, R.2
Toll-Riera, M.3
Halbert, Z.V.4
McLean, A.R.5
Cooper, B.S.6
MacLean, R.C.7
-
58
-
-
9344256546
-
-
Soil and Groundwater Research Report IV Tech. Rep. EUR 14666 EN. Luxembourg: Commission of the European Communities.
-
Schlüter, K. (1993) The Fate of Mercury in Soil. A Review of Current Knowledge, Soil and Groundwater Research Report IV Tech. Rep. EUR 14666 EN. Luxembourg: Commission of the European Communities.
-
(1993)
The Fate of Mercury in Soil. A Review of Current Knowledge
-
-
Schlüter, K.1
-
59
-
-
83055188823
-
Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes
-
Sen, D., Van der Auwera, G.A., Rogers, L.M., Thomas, C.M., Brown, C.J., and Top, E.M. (2011) Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes. Appl Environ Microbiol 77: 7975-7983.
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 7975-7983
-
-
Sen, D.1
Van der Auwera, G.A.2
Rogers, L.M.3
Thomas, C.M.4
Brown, C.J.5
Top, E.M.6
-
60
-
-
84878275176
-
Community-wide plasmid gene mobilization and selection
-
Sentchilo, V., Mayer, A.P., Guy, L., Miyazaki, R., Tringe, S.G., Barry, K., etal. (2013) Community-wide plasmid gene mobilization and selection. ISME J 7: 1173-1186.
-
(2013)
ISME J
, vol.7
, pp. 1173-1186
-
-
Sentchilo, V.1
Mayer, A.P.2
Guy, L.3
Miyazaki, R.4
Tringe, S.G.5
Barry, K.6
-
61
-
-
0025065314
-
Estimating the rate of plasmid transfer: an end-point method
-
Simonsen, L., Gordon, D.M., Stewart, F.M., and Levin, B.R. (1990) Estimating the rate of plasmid transfer: an end-point method. J Gen Microbiol 136: 2319-2325.
-
(1990)
J Gen Microbiol
, vol.136
, pp. 2319-2325
-
-
Simonsen, L.1
Gordon, D.M.2
Stewart, F.M.3
Levin, B.R.4
-
62
-
-
44249091885
-
Heterogeneous selection in a spatially structured environment affects fitness tradeoffs of plasmid carriage in pseudomonads
-
Slater, F.R., Bruce, K.D., Ellis, R.J., Lilley, A.K., and Turner, S.L. (2008) Heterogeneous selection in a spatially structured environment affects fitness tradeoffs of plasmid carriage in pseudomonads. Appl Environ Microbiol 74: 3189-3197.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 3189-3197
-
-
Slater, F.R.1
Bruce, K.D.2
Ellis, R.J.3
Lilley, A.K.4
Turner, S.L.5
-
63
-
-
77957976940
-
Mobility of plasmids
-
Smillie, C., Garcillan-Barcia, M.P., Francia, M.V., Rocha, E.P.C., and de la Cruz, F. (2010) Mobility of plasmids. Microbiol Mol Biol Rev 74: 434-452.
-
(2010)
Microbiol Mol Biol Rev
, vol.74
, pp. 434-452
-
-
Smillie, C.1
Garcillan-Barcia, M.P.2
Francia, M.V.3
Rocha, E.P.C.4
de la Cruz, F.5
-
64
-
-
0035282866
-
Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: Functional characterization using new analysis and information visualization methods
-
Sofia, H.J., Chen, G., Hetzler, B.G., Reyes-Spindola, J.F., and Miller, N.E. (2001) Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: Functional characterization using new analysis and information visualization methods. Nucleic Acids Res 29: 1097-1106.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 1097-1106
-
-
Sofia, H.J.1
Chen, G.2
Hetzler, B.G.3
Reyes-Spindola, J.F.4
Miller, N.E.5
-
65
-
-
23944484031
-
Studying plasmid horizontal transfer in situ: A critical review
-
Sørensen, S.J., Bailey, M., Hansen, L.H., Kroer, N., and Wuertz, S. (2005) Studying plasmid horizontal transfer in situ: A critical review. Nat Rev Microbiol 3: 700-710.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 700-710
-
-
Sørensen, S.J.1
Bailey, M.2
Hansen, L.H.3
Kroer, N.4
Wuertz, S.5
-
66
-
-
24944465764
-
The Pseudomonas fluorescens SBW25 wrinkly spreader biofilm requires attachment factor, cellulose fibre and LPS interactions to maintain strength and integrity
-
Spiers, A.J., and Rainey, P.B. (2005) The Pseudomonas fluorescens SBW25 wrinkly spreader biofilm requires attachment factor, cellulose fibre and LPS interactions to maintain strength and integrity. J Gen Microbiol 151: 2829-2839.
-
(2005)
J Gen Microbiol
, vol.151
, pp. 2829-2839
-
-
Spiers, A.J.1
Rainey, P.B.2
-
67
-
-
79961209180
-
Sequencing and comparative analysis of IncP-1α antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions
-
Szczepanowski, R., Eikmeyer, F., Harfmann, J., Blom, J., Rogers, L.M., Top, E.M., and Schlüter, A. (2011) Sequencing and comparative analysis of IncP-1α antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions. J Biotechnol 155: 95-103.
-
(2011)
J Biotechnol
, vol.155
, pp. 95-103
-
-
Szczepanowski, R.1
Eikmeyer, F.2
Harfmann, J.3
Blom, J.4
Rogers, L.M.5
Top, E.M.6
Schlüter, A.7
-
68
-
-
0035827349
-
Mutualists and parasites: How to paint yourself into a (metabolic) corner
-
Tamas, I., Klasson, L.M., Sandström, J.P., and Andersson, S.G. (2001) Mutualists and parasites: How to paint yourself into a (metabolic) corner. FEBS Lett 498: 135-139.
-
(2001)
FEBS Lett
, vol.498
, pp. 135-139
-
-
Tamas, I.1
Klasson, L.M.2
Sandström, J.P.3
Andersson, S.G.4
-
69
-
-
79956048989
-
Aquatic systems: Maintaining, mixing and mobilising antimicrobial resistance?
-
Taylor, N.G.H., Verner-Jeffreys, D.W., and Baker-Austin, C. (2011) Aquatic systems: Maintaining, mixing and mobilising antimicrobial resistance? Trends Ecol Evol 26: 278-284.
-
(2011)
Trends Ecol Evol
, vol.26
, pp. 278-284
-
-
Taylor, N.G.H.1
Verner-Jeffreys, D.W.2
Baker-Austin, C.3
-
70
-
-
34547760719
-
Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet
-
Tett, A., Spiers, A.J., Crossman, L.C., Ager, D., Ciric, L., Dow, J.M., etal. (2007) Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet. ISME J 1: 331-340.
-
(2007)
ISME J
, vol.1
, pp. 331-340
-
-
Tett, A.1
Spiers, A.J.2
Crossman, L.C.3
Ager, D.4
Ciric, L.5
Dow, J.M.6
-
71
-
-
0036152835
-
Mobile elements as a combination of functional modules
-
Toussaint, A., and Merlin, C. (2002) Mobile elements as a combination of functional modules. Plasmid 47: 26-35.
-
(2002)
Plasmid
, vol.47
, pp. 26-35
-
-
Toussaint, A.1
Merlin, C.2
-
72
-
-
0023504678
-
Genetic analysis of a transposon carrying toluene degrading genes on a TOL plasmid pWW0
-
Tsuda, M., and Iino, T. (1987) Genetic analysis of a transposon carrying toluene degrading genes on a TOL plasmid pWW0. Mol Gen Genet 210: 270-276.
-
(1987)
Mol Gen Genet
, vol.210
, pp. 270-276
-
-
Tsuda, M.1
Iino, T.2
-
73
-
-
0036850918
-
Two dnaB genes are associated with the origin of replication of pQBR55, an exogenously isolated plasmid from the rhizosphere of sugar beet
-
Turner, S.L., Lilley, A.K., and Bailey, M.J. (2002) Two dnaB genes are associated with the origin of replication of pQBR55, an exogenously isolated plasmid from the rhizosphere of sugar beet. FEMS Microbiol Ecol 42: 209-215.
-
(2002)
FEMS Microbiol Ecol
, vol.42
, pp. 209-215
-
-
Turner, S.L.1
Lilley, A.K.2
Bailey, M.J.3
-
74
-
-
34248189594
-
The environmental plasmid pQBR103 alters the single-cell Raman spectral profile of Pseudomonas fluorescens SBW25
-
Ude, S., Bailey, M.J., Huang, W.E., and Spiers, A.J. (2007) The environmental plasmid pQBR103 alters the single-cell Raman spectral profile of Pseudomonas fluorescens SBW25. Microb Ecol 53: 494-497.
-
(2007)
Microb Ecol
, vol.53
, pp. 494-497
-
-
Ude, S.1
Bailey, M.J.2
Huang, W.E.3
Spiers, A.J.4
-
75
-
-
0030945359
-
Description of a novel plasmid replicative origin from a genetically distinct family of conjugative plasmids associated with phytosphere microflora
-
Viegas, C.A., Lilley, A.K., Bruce, K., and Bailey, M.J. (1997) Description of a novel plasmid replicative origin from a genetically distinct family of conjugative plasmids associated with phytosphere microflora. FEMS Microbiol Lett 149: 121-127.
-
(1997)
FEMS Microbiol Lett
, vol.149
, pp. 121-127
-
-
Viegas, C.A.1
Lilley, A.K.2
Bruce, K.3
Bailey, M.J.4
-
76
-
-
0036937356
-
Global features of the Pseudomonas putida KT2440 genome sequence
-
Weinel, C., Nelson, K.E., and Tümmler, B. (2002) Global features of the Pseudomonas putida KT2440 genome sequence. Environ Microbiol 4: 809-818.
-
(2002)
Environ Microbiol
, vol.4
, pp. 809-818
-
-
Weinel, C.1
Nelson, K.E.2
Tümmler, B.3
-
78
-
-
75149160441
-
Have we underestimated the importance of humans in the biogeography of free-living terrestrial microorganisms?
-
Wilkinson, D.M. (2010) Have we underestimated the importance of humans in the biogeography of free-living terrestrial microorganisms? J Biogeogr 37: 393-397.
-
(2010)
J Biogeogr
, vol.37
, pp. 393-397
-
-
Wilkinson, D.M.1
-
79
-
-
78651267246
-
Pseudomonas genome database: Improved comparative analysis and population genomics capability for Pseudomonas genomes
-
Winsor, G.L., Lam, D.K.W., Fleming, L., Lo, R., Whiteside, M.D., Yu, N.Y., etal. (2011) Pseudomonas genome database: Improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res 39: D596-D600.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D596-D600
-
-
Winsor, G.L.1
Lam, D.K.W.2
Fleming, L.3
Lo, R.4
Whiteside, M.D.5
Yu, N.Y.6
-
80
-
-
65349092727
-
Environment can alter selection in host-parasite interactions
-
Wolinska, J., and King, K.C. (2009) Environment can alter selection in host-parasite interactions. Trends Parasitol 25: 236-244.
-
(2009)
Trends Parasitol
, vol.25
, pp. 236-244
-
-
Wolinska, J.1
King, K.C.2
-
81
-
-
84880262794
-
Complete sequence of pOZ176, a 500-kilobase IncP-2 plasmid encoding IMP-9-mediated carbapenem resistance, from outbreak isolate pseudomonas aeruginosa 96
-
Xiong, J., Alexander, D.C., Ma, J.H., Deraspe, M., Low, D.E., Jamieson, F.B., and Roy, P.H. (2013) Complete sequence of pOZ176, a 500-kilobase IncP-2 plasmid encoding IMP-9-mediated carbapenem resistance, from outbreak isolate pseudomonas aeruginosa 96. Antimicrob Agents Chemother 57: 3775-3782.
-
(2013)
Antimicrob Agents Chemother
, vol.57
, pp. 3775-3782
-
-
Xiong, J.1
Alexander, D.C.2
Ma, J.H.3
Deraspe, M.4
Low, D.E.5
Jamieson, F.B.6
Roy, P.H.7
-
82
-
-
0034800374
-
InterProScan - an integration platform for the signature-recognition methods in InterPro
-
Zdobnov, E.M., and Apweiler, R. (2001) InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.
-
(2001)
Bioinformatics
, vol.17
, pp. 847-848
-
-
Zdobnov, E.M.1
Apweiler, R.2
-
83
-
-
34648851349
-
Construction and validation of a neutrally-marked strain of Pseudomonas fluorescens SBW25
-
Zhang, X.-X., and Rainey, P.B. (2007) Construction and validation of a neutrally-marked strain of Pseudomonas fluorescens SBW25. J Microbiol Methods 71: 78-81.
-
(2007)
J Microbiol Methods
, vol.71
, pp. 78-81
-
-
Zhang, X.-X.1
Rainey, P.B.2
-
84
-
-
10644253782
-
The indigenous Pseudomonas plasmid pQBR103 encodes plant-inducible genes, including three putative helicases
-
Zhang, X.-X., Lilley, A.K., Bailey, M.J., and Rainey, P.B. (2004) The indigenous Pseudomonas plasmid pQBR103 encodes plant-inducible genes, including three putative helicases. FEMS Microbiol Ecol 51: 9-17.
-
(2004)
FEMS Microbiol Ecol
, vol.51
, pp. 9-17
-
-
Zhang, X.-X.1
Lilley, A.K.2
Bailey, M.J.3
Rainey, P.B.4
|