-
1
-
-
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. 215:403-410.
-
(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
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402. (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, 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
-
3
-
-
0029938306
-
Codon usage and base composition in Rickettsia prowazekii
-
DOI 10.1007/BF02352282
-
Andersson SG, Sharp PM. 1996. Codon usage and base composition in Rickettsia prowazekii. J Mol Evol. 42:525-536. (Pubitemid 26197142)
-
(1996)
Journal of Molecular Evolution
, vol.42
, Issue.5
, pp. 525-536
-
-
Andersson, S.G.E.1
Sharp, P.M.2
-
4
-
-
0034664813
-
SURVEY AND SUMMARY: Holliday junction resolvases and related nucleases: Identification of new families, phyletic distribution and evolutionary trajectories
-
Aravind L, Makarova KS, Koonin EV. 2000. SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res. 28:3417-3432.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 3417-3432
-
-
Aravind, L.1
Makarova, K.S.2
Koonin, E.V.3
-
5
-
-
0036083739
-
Transformation of dimethylsulphoniopropionate to dimethyl sulphide during summer in the North Sea with an examination of key processes via a modelling approach
-
DOI 10.1016/S0967-0645(02)00072-3, PII S0967064502000723
-
Archer SD, Gilbert FJ, Nightingale PD, Zubkov MV, Taylor AH, Smith GC, Burkill PH. 2002. Transformation of dimethylsulphoniopropionate to dimethyl sulphide during summer in the North Sea with an examination of key processes via a modelling approach. Deep Sea Research II. 49:3067-3101. (Pubitemid 34657349)
-
(2002)
Deep-Sea Research Part II: Topical Studies in Oceanography
, vol.49
, Issue.15
, pp. 3067-3101
-
-
Archer, S.D.1
Gilbert, F.J.2
Nightingale, P.D.3
Zubkov, M.V.4
Taylor, A.H.5
Smith, G.C.6
Burkill, P.H.7
-
6
-
-
71549167300
-
Computational analysis of tRNA identity
-
Ardell DH. 2010. Computational analysis of tRNA identity. FEBS Lett. 584:325-333.
-
(2010)
FEBS Lett.
, vol.584
, pp. 325-333
-
-
Ardell, D.H.1
-
7
-
-
52149099649
-
Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae)
-
Belfiore NM, Liu L, Moritz C. 2008. Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae). Syst Biol. 57:294-310.
-
(2008)
Syst Biol.
, vol.57
, pp. 294-310
-
-
Belfiore, N.M.1
Liu, L.2
Moritz, C.3
-
8
-
-
23144452801
-
GeneMark: Web software for gene finding in prokaryotes, eukaryotes and viruses
-
DOI 10.1093/nar/gki487
-
Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 33:W451-W454. (Pubitemid 44529960)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISS.
-
-
Besemer, J.1
Borodovsky, M.2
-
9
-
-
63849269776
-
Prokaryotic genomes and diversity in the surface ocean: Interrogating the global ocean sampling metagenome
-
Biers EJ, Sun S, Howard EC. 2009. Prokaryotic genomes and diversity in the surface ocean: interrogating the global ocean sampling metagenome. Appl Environ Microbiol. 75:2221-2229.
-
(2009)
Appl Environ Microbiol.
, vol.75
, pp. 2221-2229
-
-
Biers, E.J.1
Sun, S.2
Howard, E.C.3
-
10
-
-
47249122561
-
A site-and time-heterogeneous model of amino acid replacement
-
Blanquart S, Lartillot N. 2008. A site-and time-heterogeneous model of amino acid replacement. Mol Biol Evol. 25:842-858.
-
(2008)
Mol Biol Evol.
, vol.25
, pp. 842-858
-
-
Blanquart, S.1
Lartillot, N.2
-
11
-
-
3042840997
-
Computational inference of scenarios for α-proteobacterial genome evolution
-
DOI 10.1073/pnas.0400975101
-
Boussau B, Karlberg EO, Frank AC, Legault BA, Andersson SG. 2004. Computational inference of scenarios for alpha-proteobacterial genome evolution. Proc Natl Acad Sci U S A. 101:9722-9727. (Pubitemid 38869303)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.26
, pp. 9722-9727
-
-
Boussau, B.1
Karlberg, E.O.2
Frank, A.C.3
Legault, B.-A.4
Andersson, S.G.E.5
-
12
-
-
80052846879
-
A phylometagenomic exploration of oceanic Alphaproteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade
-
Forthcoming
-
Brindefalk B, Ettema TJ, Viklund J, Thollesson M, Andersson SG. Forthcoming 2011. A phylometagenomic exploration of oceanic Alphaproteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade. PloS One.
-
(2011)
PloS One
-
-
Brindefalk, B.1
Ettema, T.J.2
Viklund, J.3
Thollesson, M.4
Andersson, S.G.5
-
13
-
-
0025919354
-
Biochemical basis for whole-cell uptake kinetics: Specific affinity, oligotrophic capacity, and the meaning of the Michaelis constant
-
Button DK. 1991. Biochemical basis for whole-cell uptake kinetics: specific affinity, oligotrophic capacity, and the meaning of the Michaelis constant. Appl Environ Microbiol. 57:2033-2038.
-
(1991)
Appl Environ Microbiol.
, vol.57
, pp. 2033-2038
-
-
Button, D.K.1
-
14
-
-
34848903282
-
Intracellular pathogens go extreme: genome evolution in the Rickettsiales
-
DOI 10.1016/j.tig.2007.08.002, PII S0168952507002673
-
Darby AC, Cho NH, Fuxelius HH, Westberg J, Andersson SG. 2007. Intracellular pathogens go extreme: genome evolution in the Rickettsiales. Trends Genet. 23:511-520. (Pubitemid 47503445)
-
(2007)
Trends in Genetics
, vol.23
, Issue.10
, pp. 511-520
-
-
Darby, A.C.1
Cho, N.-H.2
Fuxelius, H.-H.3
Westberg, J.4
Andersson, S.G.E.5
-
15
-
-
0033485517
-
Improved microbial gene identification with GLIMMER
-
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27:4636-4641.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 4636-4641
-
-
Delcher, A.L.1
Harmon, D.2
Kasif, S.3
White, O.4
Salzberg, S.L.5
-
16
-
-
31544483932
-
Community genomics among stratified microbial assemblages in the ocean's inferior
-
DOI 10.1126/science.1120250
-
DeLong EF, Preston CM, Mincer T, et al. (12 co-authors). 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311:496-503. (Pubitemid 43157723)
-
(2006)
Science
, vol.311
, Issue.5760
, pp. 496-503
-
-
DeLong, E.F.1
Preston, C.M.2
Mincer, T.3
Rich, V.4
Hallam, S.J.5
Frigaard, N.-U.6
Martinez, A.7
Sullivan, M.B.8
Edwards, R.9
Brito, B.R.10
Chisholm, S.W.11
Karl, D.M.12
-
17
-
-
28044436397
-
Accelerated evolution associated with genome reduction in a free-living prokaryote
-
Dufresne A, Garczarek L, Partensky F. 2005. Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol. 6:R14.
-
(2005)
Genome Biol.
, vol.6
-
-
Dufresne, A.1
Garczarek, L.2
Partensky, F.3
-
18
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30:1575-1584. (Pubitemid 34679732)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.7
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
19
-
-
4143093598
-
A genome phylogeny for mitochondria among α-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes
-
DOI 10.1093/molbev/msh160
-
Esser C, Ahmadinejad N, Wiegand C, et al. (15 co-authors). 2004. A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol. 21:1643-1660. (Pubitemid 39096881)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.9
, pp. 1643-1660
-
-
Esser, C.1
Ahmadinejad, N.2
Wiegand, C.3
Rotte, C.4
Sebastiani, F.5
Gelius-Dietrich, G.6
Henze, K.7
Kretschmann, E.8
Richly, E.9
Leister, D.10
Bryant, D.11
Steel, M.A.12
Lockhart, P.J.13
Penny, D.14
Martin, W.15
-
20
-
-
67649118279
-
The alpha-proteobacteria: The Darwin finches of the bacterial world
-
Ettema TJ, Andersson SG. 2009. The alpha-proteobacteria: the Darwin finches of the bacterial world. Biol Lett. 5:429-432.
-
(2009)
Biol Lett.
, vol.5
, pp. 429-432
-
-
Ettema, T.J.1
Andersson, S.G.2
-
21
-
-
27944438100
-
6-alkylguanine-DNA alkyltransferase
-
DOI 10.1021/bi051460d
-
Fang Q, Kanugula S, Pegg AE. 2005. Function of domains of human O6-alkylguanine-DNA alkyltransferase. Biochemistry 44:15396-15405. (Pubitemid 41681474)
-
(2005)
Biochemistry
, vol.44
, Issue.46
, pp. 15396-15405
-
-
Fang, Q.1
Kanugula, S.2
Pegg, A.E.3
-
22
-
-
38549146894
-
The Pfam protein families database
-
DOI 10.1093/nar/gkm960
-
Finn RD, Tate J, Mistry J, et al. (11 co-authors). 2008. The Pfam protein families database. Nucleic Acids Res. 36:D281-D288. (Pubitemid 351149737)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Finn, R.D.1
Tate, J.2
Mistry, J.3
Coggill, P.C.4
Sammut, S.J.5
Hotz, H.-R.6
Ceric, G.7
Forslund, K.8
Eddy, S.R.9
Sonnhammer, E.L.L.10
Bateman, A.11
-
23
-
-
3242701529
-
Modeling compositional heterogeneity
-
DOI 10.1080/10635150490445779
-
Foster PG. 2004. Modeling compositional heterogeneity. Syst Biol. 53:485-495. (Pubitemid 38958537)
-
(2004)
Systematic Biology
, vol.53
, Issue.3
, pp. 485-495
-
-
Foster, P.G.1
-
24
-
-
0033004743
-
Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions
-
Foster PG, Hickey DA. 1999. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J Mol Evol. 48:284-290. (Pubitemid 29116073)
-
(1999)
Journal of Molecular Evolution
, vol.48
, Issue.3
, pp. 284-290
-
-
Foster, P.G.1
Hickey, D.A.2
-
25
-
-
0030964031
-
The role of the mutT gene of Escherichia cell in maintaining replication fidelity
-
DOI 10.1016/S0168-6445(97)00045-4, PII S0168644597000454
-
Fowler RG, Schaaper RM. 1997. The role of the mutT gene of Escherichia coli in maintaining replication fidelity. FEMS Microbiol Rev. 21:43-54. (Pubitemid 27376758)
-
(1997)
FEMS Microbiology Reviews
, vol.21
, Issue.1
, pp. 43-54
-
-
Fowler, R.G.1
Schaaper, R.M.2
-
26
-
-
0037415388
-
Interactions among the Escherichia coli mutT, mutM, and mutY damage prevention pathways
-
DOI 10.1016/S1568-7864(02)00193-3, PII S1568786402001933
-
Fowler RG, White SJ, Koyama C, Moore SC, Dunn RL, Schaaper RM. 2003. Interactions among the Escherichia coli mutT, mutM, and mutY damage prevention pathways. DNA Repair (Amst). 2:159-173. (Pubitemid 36071503)
-
(2003)
DNA Repair
, vol.2
, Issue.2
, pp. 159-173
-
-
Fowler, R.G.1
White, S.J.2
Koyama, C.3
Moore, S.C.4
Dunn, R.L.5
Schaaper, R.M.6
-
27
-
-
0025344222
-
A sensitive genetic assay for the detection of cytosine deamination: Determination of rate constants and the activation energy
-
Frederico LA, Kunkel TA, Shaw BR. 1990. A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry 29:2532-2537. (Pubitemid 20100849)
-
(1990)
Biochemistry
, vol.29
, Issue.10
, pp. 2532-2537
-
-
Frederico, L.A.1
Kunkel, T.A.2
Ramsay Shaw, B.3
-
28
-
-
41649114407
-
Microbial community gene expression in ocean surface waters
-
DOI 10.1073/pnas.0708897105
-
Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong EF. 2008. Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A. 105:3805-3810. (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
-
29
-
-
36849019025
-
The genomic and metabolic diversity of Rickettsia
-
DOI 10.1016/j.resmic.2007.09.008, PII S0923250807001787, Microbial Genomics
-
Fuxelius HH, Darby A, Min CK, Cho NH, Andersson SG. 2007. The genomic and metabolic diversity of Rickettsia. Res Microbiol. 158:745-753. (Pubitemid 350235177)
-
(2007)
Research in Microbiology
, vol.158
, Issue.10
, pp. 745-753
-
-
Fuxelius, H.-H.1
Darby, A.2
Min, C.-K.3
Cho, N.-H.4
Andersson, S.G.E.5
-
30
-
-
43549090899
-
Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction
-
Fuxelius HH, Darby AC, Cho NH, Andersson SG. 2008. Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction. Genome Biol. 9:R42.
-
(2008)
Genome Biol.
, vol.9
-
-
Fuxelius, H.H.1
Darby, A.C.2
Cho, N.H.3
Andersson, S.G.4
-
31
-
-
46749116439
-
A rare SAR11 fosmid clone confirming genetic variability in the 'Candidatus Pelagibacter ubique' genome
-
DOI 10.1038/ismej.2008.49, PII ISMEJ200849
-
Gilbert JA, Muhling M, Joint I. 2008. A rare SAR11 fosmid clone confirming genetic variability in the 'Candidatus Pelagibacter ubique' genome. ISME J. 2:790-793. (Pubitemid 351951571)
-
(2008)
ISME Journal
, vol.2
, Issue.7
, pp. 790-793
-
-
Gilbert, J.A.1
Muhling, M.2
Joint, I.3
-
33
-
-
43849087058
-
The small genome of an abundant coastal ocean methylotroph
-
DOI 10.1111/j.1462-2920.2008.01598.x
-
Giovannoni SJ, Hayakawa DH, Tripp HJ, Stingl U, Givan SA, Cho JC, Oh HM, Kitner JB, Vergin KL, Rappe MS. 2008. The small genome of an abundant coastal ocean methylotroph. Environ Microbiol. 10:1771-1782. (Pubitemid 351793619)
-
(2008)
Environmental Microbiology
, vol.10
, Issue.7
, pp. 1771-1782
-
-
Giovannoni, S.J.1
Hayakawa, D.H.2
Tripp, H.J.3
Stingl, U.4
Givan, S.A.5
Cho, J.-C.6
Oh, H.-M.7
Kitner, J.B.8
Vergin, K.L.9
Rappe, M.S.10
-
34
-
-
23844446418
-
Genetics: Genome streamlining in a cosmopolitan oceanic bacterium
-
DOI 10.1126/science.1114057
-
Giovannoni SJ, Tripp HJ, Givan S, et al. (14 co-authors). 2005. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:1242-1245. (Pubitemid 41170917)
-
(2005)
Science
, vol.309
, Issue.5738
, pp. 1242-1245
-
-
Giovannoni, S.J.1
Tripp, H.J.2
Givan, S.3
Podar, M.4
Vergin, K.L.5
Baptista, D.6
Bibbs, L.7
Eads, J.8
Richardson, T.H.9
Noordewier, M.10
Rappe, M.S.11
Short, J.M.12
Carrington, J.C.13
Mathur, E.J.14
-
35
-
-
0034791722
-
The rise and fall of mutator bacteria
-
DOI 10.1016/S1369-5274(00)00254-X
-
Giraud A, Radman M, Matic I, Taddei F. 2001. The rise and fall of mutator bacteria. Curr Opin Microbiol. 4:582-585. (Pubitemid 32964108)
-
(2001)
Current Opinion in Microbiology
, vol.4
, Issue.5
, pp. 582-585
-
-
Giraud, A.1
Radman, M.2
Matic, I.3
Taddei, F.4
-
36
-
-
78049445172
-
Evidence that mutation is universally biased towards AT in bacteria
-
Hershberg R, Petrov DA. 2010. Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet. 6:e1001115.
-
(2010)
PLoS Genet.
, vol.6
-
-
Hershberg, R.1
Petrov, D.A.2
-
38
-
-
73949101830
-
Mutators and hypermutability in bacteria: The Escherichia coli paradigm
-
Jayaraman R. 2009. Mutators and hypermutability in bacteria: the Escherichia coli paradigm. J Genet. 88:379-391.
-
(2009)
J Genet.
, vol.88
, pp. 379-391
-
-
Jayaraman, R.1
-
39
-
-
68049142320
-
Multiple alignment of DNA sequences with MAFFT
-
Katoh K, Asimenos G, Toh H. 2009. Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol. 537:39-64.
-
(2009)
Methods Mol Biol.
, vol.537
, pp. 39-64
-
-
Katoh, K.1
Asimenos, G.2
Toh, H.3
-
40
-
-
37749041470
-
Patterns and implications of gene gain and loss in the evolution of Prochlorococcus
-
14 co-authors
-
Kettler GC, Martiny AC, Huang K, et al. (14 co-authors). 2007. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet. 3:e231.
-
(2007)
PLoS Genet.
, vol.3
-
-
Kettler, G.C.1
Martiny, A.C.2
Huang, K.3
-
41
-
-
33847302458
-
Inconsistency of phylogenetic estimates from concatenated data under coalescence
-
Kubatko LS, Degnan JH. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst Biol. 56:17-24.
-
(2007)
Syst Biol.
, vol.56
, pp. 17-24
-
-
Kubatko, L.S.1
Degnan, J.H.2
-
42
-
-
34248159030
-
Suppression of longbranch attraction artefacts in the animal phylogeny using a siteheterogeneous model
-
Lartillot N, Brinkmann H, Philippe H. 2007. Suppression of longbranch attraction artefacts in the animal phylogeny using a siteheterogeneous model. BMC Evol Biol. 1 (7 Suppl): S4.
-
(2007)
BMC Evol Biol.
, vol.1
, Issue.7 SUPPL.
-
-
Lartillot, N.1
Brinkmann, H.2
Philippe, H.3
-
43
-
-
2442691520
-
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
-
DOI 10.1093/molbev/msh112
-
Lartillot N, Philippe H. 2004. A Bayesian mixture model for acrosssite heterogeneities in the amino-acid replacement process. Mol Biol Evol. 21:1095-1109. (Pubitemid 38658218)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.6
, pp. 1095-1109
-
-
Lartillot, N.1
Philippe, H.2
-
44
-
-
45849154166
-
An improved general amino acid replacement matrix
-
DOI 10.1093/molbev/msn067
-
Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25:1307-1320. (Pubitemid 351882003)
-
(2008)
Molecular Biology and Evolution
, vol.25
, Issue.7
, pp. 1307-1320
-
-
Le, S.Q.1
Gascuel, O.2
-
45
-
-
0035038404
-
A time-series assessment of the nitrogen cycle at BATS
-
DOI 10.1016/S0967-0645(00)00168-5, PII S0967064500001685
-
Lipschultz F. 2001. A time-series assessment of the nitrogen cycle at BATS. Deep Sea Research II. 48:1897-1924. (Pubitemid 32434580)
-
(2001)
Deep-Sea Research Part II: Topical Studies in Oceanography
, vol.48
, Issue.8-9
, pp. 1897-1924
-
-
Lipschultz, F.1
-
46
-
-
65349159321
-
Evolution of mutation rates: Phylogenomic analysis of the photolyase/cryptochrome family
-
Lucas-Lledo JI, Lynch M. 2009. Evolution of mutation rates: phylogenomic analysis of the photolyase/cryptochrome family. Mol Biol Evol. 26:1143-1153.
-
(2009)
Mol Biol Evol.
, vol.26
, pp. 1143-1153
-
-
Lucas-Lledo, J.I.1
Lynch, M.2
-
47
-
-
34047093352
-
Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus
-
Martins-Pinheiro M, Marques RC, Menck CF. 2007. Genome analysis of DNA repair genes in the alpha proteobacterium Caulobacter crescentus. BMC Microbiol. 7:17.
-
(2007)
BMC Microbiol.
, vol.7
, pp. 17
-
-
Martins-Pinheiro, M.1
Marques, R.C.2
Menck, C.F.3
-
48
-
-
68249126127
-
Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont
-
McCutcheon JP, McDonald BR, Moran NA. 2009. Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont. PLoS Genet. 5:e1000565.
-
(2009)
PLoS Genet.
, vol.5
-
-
McCutcheon, J.P.1
McDonald, B.R.2
Moran, N.A.3
-
49
-
-
0026701365
-
The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7, 8-dihydro-8-oxoguanine)
-
Michaels ML, Miller JH. 1992. The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7, 8-dihydro-8-oxoguanine). J Bacteriol. 174:6321-6325.
-
(1992)
J Bacteriol.
, vol.174
, pp. 6321-6325
-
-
Michaels, M.L.1
Miller, J.H.2
-
51
-
-
0037180794
-
SAR11 clade dominates ocean surface bacterioplankton communities
-
DOI 10.1038/nature01240
-
Morris RM, Rappe MS, Connon SA, Vergin KL, Siebold WA, Carlson CA, Giovannoni SJ. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420:806-810. (Pubitemid 36019626)
-
(2002)
Nature
, vol.420
, Issue.6917
, pp. 806-810
-
-
Morris, R.M.1
Rappe, M.S.2
Connon, S.A.3
Vergin, K.L.4
Siebold, W.A.5
Carlson, C.A.6
Giovannoni, S.J.7
-
52
-
-
25144481245
-
Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda Atlantic Time-series Study site
-
Morris RM, Vergin KL, Cho J-C, Rappé MS, Carlson CA, Giovannoni SJ. 2005. Temporal and spatial response of bacterioplankton lineages to annual convective overturn at the Bermuda. Atlantic Time-series Study site. Limnol. Oceanogr 50:1687-1696. (Pubitemid 41356448)
-
(2005)
Limnology and Oceanography
, vol.50
, Issue.5
, pp. 1687-1696
-
-
Morris, R.M.1
Vergin, K.L.2
Cho, J.-C.3
Rappe, M.S.4
Carlson, C.A.5
Giovannoni, S.J.6
-
53
-
-
77955950911
-
Compositional heterogeneity and phylogenomic inference of metazoan relationships
-
Nesnidal MP, Helmkampf M, Bruchhaus I, Hausdorf B. 2010. Compositional heterogeneity and phylogenomic inference of metazoan relationships. Mol Biol Evol. 27:2095-2104.
-
(2010)
Mol Biol Evol.
, vol.27
, pp. 2095-2104
-
-
Nesnidal, M.P.1
Helmkampf, M.2
Bruchhaus, I.3
Hausdorf, B.4
-
54
-
-
24744468387
-
Bacterial genome size reduction by experimental evolution
-
DOI 10.1073/pnas.0503654102
-
Nilsson AI, Koskiniemi S, Eriksson S, Kugelberg E, Hinton JC, Andersson DI. 2005. Bacterial genome size reduction by experimental evolution. Proc Natl Acad Sci U S A. 102:12112-12116. (Pubitemid 41291137)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.34
, pp. 12112-12116
-
-
Nilsson, A.I.1
Koskiniemi, S.2
Eriksson, S.3
Kugelberg, E.4
Hinton, J.C.D.5
Andersson, D.I.6
-
55
-
-
0034685940
-
High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection
-
Oliver A, Canton R, Campo P, Baquero F, Blazquez J. 2000. High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. Science 288:1251-1254.
-
(2000)
Science
, vol.288
, pp. 1251-1254
-
-
Oliver, A.1
Canton, R.2
Campo, P.3
Baquero, F.4
Blazquez, J.5
-
56
-
-
77952757937
-
RecN is a cohesin-like protein that stimulates intermolecular DNA interactions in vitro
-
Reyes ED, Patidar PL, Uranga LA, Bortoletto AS, Lusetti SL. 2010. RecN is a cohesin-like protein that stimulates intermolecular DNA interactions in vitro. J Biol Chem. 285:16521-16529.
-
(2010)
J Biol Chem.
, vol.285
, pp. 16521-16529
-
-
Reyes, E.D.1
Patidar, P.L.2
Uranga, L.A.3
Bortoletto, A.S.4
Lusetti, S.L.5
-
57
-
-
55449115425
-
Comparative and evolutionary analysis of the bacterial homologous recombination systems
-
Rocha EP, Cornet E, Michel B. 2005. Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genet. 1:e15.
-
(2005)
PLoS Genet.
, vol.1
-
-
Rocha, E.P.1
Cornet, E.2
Michel, B.3
-
58
-
-
0036606915
-
Base composition bias might result from competition for metabolic resources
-
DOI 10.1016/S0168-9525(02)02690-2, PII S0168952502026902
-
Rocha EP, Danchin A. 2002. Base composition bias might result from competition for metabolic resources. Trends Genet. 18:291-294. (Pubitemid 34607118)
-
(2002)
Trends in Genetics
, vol.18
, Issue.6
, pp. 291-294
-
-
Rocha, E.P.C.1
Danchin, A.2
-
59
-
-
33947238287
-
The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific
-
40 co-authors
-
Rusch DB, Halpern AL, Sutton G, et al. (40 co-authors). 2007. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5:e77.
-
(2007)
PLoS Biol.
, vol.5
-
-
Rusch, D.B.1
Halpern, A.L.2
Sutton, G.3
-
60
-
-
37549059994
-
Mismatch repair proteins collaborate with methyltransferases in the repair of O (6)-methylguanine
-
Rye PT, Delaney JC, Netirojjanakul C, Sun DX, Liu JZ, Essigmann JM. 2008. Mismatch repair proteins collaborate with methyltransferases in the repair of O (6)-methylguanine. DNA Repair (Amst). 7:170-176.
-
(2008)
DNA Repair (Amst)
, vol.7
, pp. 170-176
-
-
Rye, P.T.1
Delaney, J.C.2
Netirojjanakul, C.3
Sun, D.X.4
Liu, J.Z.5
Essigmann, J.M.6
-
61
-
-
59149085483
-
RecFOR and RecOR as distinct RecA loading pathways
-
Sakai A, Cox MM. 2009. RecFOR and RecOR as distinct RecA loading pathways. J Biol Chem. 284:3264-3272.
-
(2009)
J Biol Chem.
, vol.284
, pp. 3264-3272
-
-
Sakai, A.1
Cox, M.M.2
-
62
-
-
18544367670
-
Enhanced repair of cyclobutane pyrimidine dimers and improved UV resistance in photolyase transgenic mice
-
DOI 10.1093/emboj/cdf456
-
Schul W, Jans J, Rijksen YM, et al. (11 co-authors). 2002. Enhanced repair of cyclobutane pyrimidine dimers and improved UV resistance in photolyase transgenic mice. EMBO J. 21:4719-4729. (Pubitemid 34984359)
-
(2002)
EMBO Journal
, vol.21
, Issue.17
, pp. 4719-4729
-
-
Schul, W.1
Jans, J.2
Rijksen, Y.M.A.3
Klemann, K.H.M.4
Eker, A.P.M.5
De Wit, J.6
Nikaido, O.7
Nakajima, S.8
Yasui, A.9
Hoeijmakers, J.H.J.10
Van Der Horst, G.T.J.11
-
63
-
-
58149505604
-
Discovering functional novelty in metagenomes: Examples from lightmediated processes
-
Singh AH, Doerks T, Letunic I, Raes J, Bork P. 2009. Discovering functional novelty in metagenomes: examples from lightmediated processes. J Bacteriol. 191:32-41.
-
(2009)
J Bacteriol.
, vol.191
, pp. 32-41
-
-
Singh, A.H.1
Doerks, T.2
Letunic, I.3
Raes, J.4
Bork, P.5
-
64
-
-
58049112263
-
Transport functions dominate the SAR11 metaproteome at lownutrient extremes in the Sargasso Sea
-
Sowell SM, Wilhelm LJ, Norbeck AD, Lipton MS, Nicora CD, Barofsky DF, Carlson CA, Smith RD, Giovanonni SJ. 2009. Transport functions dominate the SAR11 metaproteome at lownutrient extremes in the Sargasso Sea. ISME J. 3:93-105.
-
(2009)
ISME J.
, vol.3
, pp. 93-105
-
-
Sowell, S.M.1
Wilhelm, L.J.2
Norbeck, A.D.3
Lipton, M.S.4
Nicora, C.D.5
Barofsky, D.F.6
Carlson, C.A.7
Smith, R.D.8
Giovanonni, S.J.9
-
65
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
DOI 10.1093/bioinformatics/btl446
-
Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. (Pubitemid 44642609)
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2688-2690
-
-
Stamatakis, A.1
-
66
-
-
75149150388
-
TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
-
Stover BC, Muller KF. 2010. TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11:7.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 7
-
-
Stover, B.C.1
Muller, K.F.2
-
68
-
-
34547489084
-
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
-
DOI 10.1080/10635150701472164, PII 780704285
-
Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56:564-577. (Pubitemid 47171631)
-
(2007)
Systematic Biology
, vol.56
, Issue.4
, pp. 564-577
-
-
Talavera, G.1
Castresana, J.2
-
69
-
-
77953809752
-
Evolutionary microbial genomics: Insights into bacterial host adaptation
-
Toft C, Andersson SG. 2010. Evolutionary microbial genomics: insights into bacterial host adaptation. Nat Rev Genet. 11:465-475.
-
(2010)
Nat Rev Genet.
, vol.11
, pp. 465-475
-
-
Toft, C.1
Andersson, S.G.2
-
70
-
-
34548406920
-
High intraspecific recombination rate in a native population of Candidatus Pelagibacter ubique (SAR11)
-
DOI 10.1111/j.1462-2920.2007.01361.x
-
Vergin KL, Tripp HJ, Wilhelm LJ, Denver DR, Rappe MS, Giovannoni SJ. 2007. High intraspecific recombination rate in a native population of Candidatus Pelagibacter ubique (SAR11). Environ Microbiol. 9:2430-2440. (Pubitemid 47366655)
-
(2007)
Environmental Microbiology
, vol.9
, Issue.10
, pp. 2430-2440
-
-
Vergin, K.L.1
Tripp, H.J.2
Wilhelm, L.J.3
Denver, D.R.4
Rappe, M.S.5
Giovannoni, S.J.6
-
71
-
-
77954655737
-
No evidence for elemental-based streamlining of prokaryotic genomes
-
author reply: 320-1311
-
Vieira-Silva S, Touchon M, Rocha EP. 2010. No evidence for elemental-based streamlining of prokaryotic genomes. Trends Ecol Evol. 25:319-320; author reply: 320-1311.
-
(2010)
Trends Ecol Evol.
, vol.25
, pp. 319-320
-
-
Vieira-Silva, S.1
Touchon, M.2
Rocha, E.P.3
-
72
-
-
58549084151
-
A comparison of homologous recombination rates in bacteria and archaea
-
Vos M, Didelot X. 2009. A comparison of homologous recombination rates in bacteria and archaea. ISME J. 3:199-208.
-
(2009)
ISME J.
, vol.3
, pp. 199-208
-
-
Vos, M.1
Didelot, X.2
-
74
-
-
38849200974
-
Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data
-
Wilhelm LJ, Tripp HJ, Givan SA, Smith DP, Giovannoni SJ. 2007. Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data. Biol. Direct. 2:27.
-
(2007)
Biol. Direct.
, vol.2
, pp. 27
-
-
Wilhelm, L.J.1
Tripp, H.J.2
Givan, S.A.3
Smith, D.P.4
Giovannoni, S.J.5
-
75
-
-
34347390665
-
A robust species tree for the Alphaproteobacteria
-
DOI 10.1128/JB.00269-07
-
Williams KP, Sobral BW, Dickerman AW. 2007. A robust species tree for the alphaproteobacteria. J Bacteriol. 189:4578-4586. (Pubitemid 47025569)
-
(2007)
Journal of Bacteriology
, vol.189
, Issue.13
, pp. 4578-4586
-
-
Williams, K.P.1
Sobral, B.W.2
Dickerman, A.W.3
-
76
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
34 co-authors
-
Wu D, Hugenholtz P, Mavromatis K, et al. (34 co-authors). 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462:1056-1060.
-
(2009)
Nature
, vol.462
, pp. 1056-1060
-
-
Wu, D.1
Hugenholtz, P.2
Mavromatis, K.3
-
77
-
-
0034604416
-
Phosphate depletion in the Western North Atlantic Ocean
-
DOI 10.1126/science.289.5480.759
-
Wu J, Sunda W, Boyle EA, Karl DM. 2000. Phosphate depletion in the western North Atlantic Ocean. Science 289:759-762. (Pubitemid 30650192)
-
(2000)
Science
, vol.289
, Issue.5480
, pp. 759-762
-
-
Wu, J.1
Sunda, W.2
Boyle, E.A.3
Karl, D.M.4
-
78
-
-
0036080476
-
Rapid turnover of dissolved DMS and DMSP by defined bacterioplankton communities in the stratified euphotic zone of the North Sea
-
DOI 10.1016/S0967-0645(02)00069-3, PII S0967064502000693
-
Zubkov MV, Fuchs BM, Archer SD, Kiene RP, PH Burkill AR. 2002. Rapid turnover of dissolved DMS and DMSP by defined bacterioplankton communities in the stratified euphotic zone of the North Sea. Deep Sea Research II. 49:3017-3038. (Pubitemid 34657346)
-
(2002)
Deep-Sea Research Part II: Topical Studies in Oceanography
, vol.49
, Issue.15
, pp. 3017-3038
-
-
Zubkov, M.V.1
Fuchs, B.M.2
Archer, S.D.3
Kiene, R.P.4
Amann, R.5
Burkill, P.H.6
-
79
-
-
9244236007
-
The recombination genes addAB are not restricted to gram-positive bacteria: Genetic analysis of the recombination initiation enzymes RecF and AddAB in Rhizobium etli
-
DOI 10.1128/JB.186.23.7905-7913.2004
-
Zuniga-Castillo J, Romero D, Martinez-Salazar JM. 2004. The recombination genes addAB are not restricted to gram-positive bacteria: genetic analysis of the recombination initiation enzymes RecF and AddAB in Rhizobium etli. J Bacteriol. 186:7905-7913. (Pubitemid 39552501)
-
(2004)
Journal of Bacteriology
, vol.186
, Issue.23
, pp. 7905-7913
-
-
Zuniga-Castillo, J.1
Romero, D.2
Martinez-Salazar, J.M.3
|