-
1
-
-
18744382506
-
ProtTest: Selection of best-fit models of protein evolution
-
Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105.
-
(2005)
Bioinformatics
, vol.21
, pp. 2104-2105
-
-
Abascal, F.1
Zardoya, R.2
Posada, D.3
-
2
-
-
34250886391
-
Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis
-
Aivaliotis M, et al. 2007. Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis. J Proteome Res. 6:2195-2204.
-
(2007)
J Proteome Res.
, vol.6
, pp. 2195-2204
-
-
Aivaliotis, M.1
-
3
-
-
10644271631
-
Archaeal genetics - The third way
-
Allers T, Mevarech M. 2005. Archaeal genetics-the third way. Nat Rev Genet. 6:58-73.
-
(2005)
Nat Rev Genet.
, vol.6
, pp. 58-73
-
-
Allers, T.1
Mevarech, M.2
-
4
-
-
77955931732
-
Evolution in regulatory regions rapidly compensates the cost of nonoptimal codon usage
-
Amorós-Moya D, Bedhomme S, Hermann M, Bravo I. 2010. Evolution in regulatory regions rapidly compensates the cost of nonoptimal codon usage. Mol Biol Evol. 27:2141-2151.
-
(2010)
Mol Biol Evol.
, vol.27
, pp. 2141-2151
-
-
Amorós-Moya, D.1
Bedhomme, S.2
Hermann, M.3
Bravo, I.4
-
5
-
-
84862186261
-
Ancient origin of the divergent forms of leucyl-tRNA synthetases in Halobacteriales
-
Andam C, Harlow T, Papke RT, Gogarten JP. 2012. Ancient origin of the divergent forms of leucyl-tRNA synthetases in Halobacteriales. BMC Evol Biol. 12:85.
-
(2012)
BMC Evol Biol.
, vol.12
, pp. 85
-
-
Andam, C.1
Harlow, T.2
Papke, R.T.3
Gogarten, J.P.4
-
6
-
-
79957438170
-
Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes
-
Anderson I, et al. 2011. Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes. PLoS One 6:e20237.
-
(2011)
PLoS One
, vol.6
-
-
Anderson, I.1
-
7
-
-
79957464372
-
Complete genome sequence of Halorhabdus utahensis type strain (AX-2T)
-
Anderson IJ, et al. 2009. Complete genome sequence of Halorhabdus utahensis type strain (AX-2T). Stand Genomic Sci. 1:218-225.
-
(2009)
Stand Genomic Sci.
, vol.1
, pp. 218-225
-
-
Anderson, I.J.1
-
8
-
-
84859173462
-
Complete genome sequence of Halopiger xanaduensis type strain (SH-6T)
-
Anderson IJ, et al. 2012. Complete genome sequence of Halopiger xanaduensis type strain (SH-6T). Stand Genomic Sci. 6:31-42.
-
(2012)
Stand Genomic Sci.
, vol.6
, pp. 31-42
-
-
Anderson, I.J.1
-
9
-
-
0033301308
-
Fluorescence in situ hybridization analysis of the prokaryotic community inhabiting crystallizer ponds
-
Antón J, Llobet-Brossa E, Rodréguez-Valera F, Amann R. 1999. Fluorescence in situ hybridization analysis of the prokaryotic community inhabiting crystallizer ponds. Environ Microbiol. 1:517-523.
-
(1999)
Environ Microbiol.
, vol.1
, pp. 517-523
-
-
Antón, J.1
Llobet-Brossa, E.2
Rodréguez-Valera, F.3
Amann, R.4
-
11
-
-
84555188616
-
BEAGLE: An application programming interface and high-performance computing library for statistical phylogenetics
-
Ayres DL, et al. 2011. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst Biol. 61:170-173.
-
(2011)
Syst Biol.
, vol.61
, pp. 170-173
-
-
Ayres, D.L.1
-
12
-
-
40549120596
-
The RAST server: Rapid annotations using subsystems technology
-
Aziz R, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75.
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.1
-
13
-
-
8744235102
-
Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea
-
Baliga NS, et al. 2004. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 14: 2221-2234.
-
(2004)
Genome Res.
, vol.14
, pp. 2221-2234
-
-
Baliga, N.S.1
-
14
-
-
38049079313
-
Dihydroxyacetone metabolism in Salinibacter ruber and in Haloquadratum walsbyi
-
Bardavid RE, Oren A. 2008. Dihydroxyacetone metabolism in Salinibacter ruber and in Haloquadratum walsbyi. Extremophiles 12:125-131.
-
(2008)
Extremophiles
, vol.12
, pp. 125-131
-
-
Bardavid, R.E.1
Oren, A.2
-
15
-
-
0002844544
-
Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
-
Baum BR. 1992. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41:3-10.
-
(1992)
Taxon
, vol.41
, pp. 3-10
-
-
Baum, B.R.1
-
17
-
-
33747334086
-
The genome of the square archaeon Haloquadratum walsbyi: Life at the limits of water activity
-
Bolhuis H, et al. 2006. The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics 7:169.
-
(2006)
BMC Genomics
, vol.7
, pp. 169
-
-
Bolhuis, H.1
-
18
-
-
2942545812
-
Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes
-
Boucher Y, Douady C, Sharma A, Kamekura M, Doolittle W. 2004. Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. J Bacteriol. 186:3980-3990.
-
(2004)
J Bacteriol.
, vol.186
, pp. 3980-3990
-
-
Boucher, Y.1
Douady, C.2
Sharma, A.3
Kamekura, M.4
Doolittle, W.5
-
19
-
-
0242276676
-
Lateral gene transfer and the origins of prokaryotic groups
-
Boucher Y, et al. 2003. Lateral gene transfer and the origins of prokaryotic groups. Annu Rev Genet. 37:283-328.
-
(2003)
Annu Rev Genet.
, vol.37
, pp. 283-328
-
-
Boucher, Y.1
-
20
-
-
84862672984
-
Spatial and seasonal prokaryotic community dynamics in ponds of increasing salinity of Sfax solar saltern in Tunisia
-
Boujelben I, et al. 2012. Spatial and seasonal prokaryotic community dynamics in ponds of increasing salinity of Sfax solar saltern in Tunisia. Antonie Leeuwenhoek. 101:845-857.
-
(2012)
Antonie Leeuwenhoek.
, vol.101
, pp. 845-857
-
-
Boujelben, I.1
-
21
-
-
0000367652
-
The limits of amino acid sequence data in angiosperm phylogenetic reconstruction
-
Bremer K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803.
-
(1988)
Evolution
, vol.42
, pp. 795-803
-
-
Bremer, K.1
-
22
-
-
0034565944
-
The evolutionary history of ribosomal protein RpS14: Horizontal gene transfer at the heart of the ribosome
-
Brochier C, Philippe H, Moreira D. 2000. The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet. 16:529-533.
-
(2000)
Trends Genet.
, vol.16
, pp. 529-533
-
-
Brochier, C.1
Philippe, H.2
Moreira, D.3
-
23
-
-
0001925593
-
A note on the metric properties of trees
-
Buneman P. 1974. A note on the metric properties of trees. J Comb Theory A. 17:48-50.
-
(1974)
J Comb Theory A.
, vol.17
, pp. 48-50
-
-
Buneman, P.1
-
24
-
-
33847214237
-
Haloquadratum walsbyi gen. nov., sp. nov., the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain
-
Burns DG, et al. 2007. Haloquadratum walsbyi gen. nov., sp. nov., the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain. Int J Syst Evol Microbiol. 57:387-392.
-
(2007)
Int J Syst Evol Microbiol.
, vol.57
, pp. 387-392
-
-
Burns, D.G.1
-
25
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho C, et al. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 421
-
-
Camacho, C.1
-
26
-
-
84887212360
-
Are protein domains modules of lateral genetic transfer?
-
Chan C, Darling A, Beiko R, RaganM. 2009. Are protein domains modules of lateral genetic transfer? PLoS One 4:e4524.
-
(2009)
PLoS One
, vol.4
-
-
Chan, C.1
Darling, A.2
Beiko, R.3
Ragan, M.4
-
27
-
-
41149089793
-
SeqinR 1.0-2: A contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis
-
Bastolla U, Porto M, Roman H, Vendruscolo M, editors. New York: Springer-Verlag.
-
Charif D, Lobry J. 2007. SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. In: Bastolla U, Porto M, Roman H, Vendruscolo M, editors. Structural approaches to sequence evolution: molecules, networks, populations. New York: Springer-Verlag. p. 207-232.
-
(2007)
Structural Approaches to Sequence Evolution: Molecules, Networks, Populations
, pp. 207-232
-
-
Charif, D.1
Lobry, J.2
-
28
-
-
0026574926
-
Transformation of members of the genus Haloarcula with shuttle vectors based on Halobacterium halobium and Haloferax volcanii plasmid replicons
-
Cline SW, Doolittle WF. 1992. Transformation of members of the genus Haloarcula with shuttle vectors based on Halobacterium halobium and Haloferax volcanii plasmid replicons. J Bacteriol. 174: 1076-1080.
-
(1992)
J Bacteriol.
, vol.174
, pp. 1076-1080
-
-
Cline, S.W.1
Doolittle, W.F.2
-
29
-
-
65649092976
-
Biopython: Freely available Python tools for computational molecular biology and bioinformatics
-
Cock P, et al. 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422-1423.
-
(2009)
Bioinformatics
, vol.25
, pp. 1422-1423
-
-
Cock, P.1
-
30
-
-
79952840493
-
The complexity hypothesis revisited: Connectivity rather than function constitutes a barrier to horizontal gene transfer
-
Cohen O, Gophna U, Pupko T. 2011. The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Mol Biol Evol. 28:1481-1489.
-
(2011)
Mol Biol Evol.
, vol.28
, pp. 1481-1489
-
-
Cohen, O.1
Gophna, U.2
Pupko, T.3
-
31
-
-
78751561457
-
Quantifying nonvertical inheritance in the evolution of Legionella pneumophila
-
CoscolláM, Comas I, González-Candelas F. 2011. Quantifying nonvertical inheritance in the evolution of Legionella pneumophila. Mol Biol Evol. 28:985-1001.
-
(2011)
Mol Biol Evol.
, vol.28
, pp. 985-1001
-
-
Coscollá, M.1
Comas, I.2
González-Candelas, F.3
-
32
-
-
34547299728
-
Genomic plasticity in prokaryotes: The case of the square haloarchaeon
-
Cuadros-Orellana S, et al. 2007. Genomic plasticity in prokaryotes: the case of the square haloarchaeon. ISME J. 1:235-245.
-
(2007)
ISME J.
, vol.1
, pp. 235-245
-
-
Cuadros-Orellana, S.1
-
33
-
-
80053224495
-
Phylogenomic networks
-
Dagan T. 2011. Phylogenomic networks. Trends Microbiol. 19:483-491.
-
(2011)
Trends Microbiol.
, vol.19
, pp. 483-491
-
-
Dagan, T.1
-
36
-
-
77954143123
-
Impact of recombination on bacterial evolution
-
Didelot X, Maiden MCJ. 2010. Impact of recombination on bacterial evolution. Trends Microbiol. 18:315-322.
-
(2010)
Trends Microbiol.
, vol.18
, pp. 315-322
-
-
Didelot, X.1
Maiden, M.C.J.2
-
37
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
Doolittle WF. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2128.
-
(1999)
Science
, vol.284
, pp. 2124-2128
-
-
Doolittle, W.F.1
-
38
-
-
66049089612
-
On the origin of prokaryotic species
-
Doolittle WF, Zhaxybayeva O. 2009. On the origin of prokaryotic species. Genome 19:744-756.
-
(2009)
Genome
, vol.19
, pp. 744-756
-
-
Doolittle, W.F.1
Zhaxybayeva, O.2
-
39
-
-
38649110663
-
BEAST: Bayesian evolutionary analysis by sampling trees
-
Drummond A, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214.
-
(2007)
BMC Evol Biol.
, vol.7
, pp. 214
-
-
Drummond, A.1
Rambaut, A.2
-
41
-
-
79959307357
-
Haloquadratum walsbyi: Limited diversity in a global pond
-
Dyall-Smith ML, et al. 2011. Haloquadratum walsbyi: limited diversity in a global pond. PLoS One 6:e20968.
-
(2011)
PLoS One
, vol.6
-
-
Dyall-Smith, M.L.1
-
42
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar R. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.1
-
43
-
-
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.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
44
-
-
35048898799
-
Genetic exchange across a species boundary in the archaeal genus Ferroplasma
-
Eppley J, Tyson G, Getz W, Banfield J. 2007. Genetic exchange across a species boundary in the archaeal genus Ferroplasma. Genetics 177: 407-416.
-
(2007)
Genetics
, vol.177
, pp. 407-416
-
-
Eppley, J.1
Tyson, G.2
Getz, W.3
Banfield, J.4
-
45
-
-
25844454133
-
Living with two extremes: Conclusions from the genome sequence of Natronomonas pharaonis
-
Falb M, et al. 2005. Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis. Genome Res. 15: 1336-1343.
-
(2005)
Genome Res.
, vol.15
, pp. 1336-1343
-
-
Falb, M.1
-
46
-
-
40449102414
-
Metabolism of halophilic archaea
-
Falb M, et al. 2008. Metabolism of halophilic archaea. Extremophiles 12: 177-196.
-
(2008)
Extremophiles
, vol.12
, pp. 177-196
-
-
Falb, M.1
-
47
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively mislead
-
Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively mislead. Syst Zool. 27:401-410.
-
(1978)
Syst Zool.
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
48
-
-
3242701529
-
Modeling compositional heterogeneity
-
Foster PG. 2004. Modeling compositional heterogeneity. Syst Biol. 53: 485-495.
-
(2004)
Syst Biol.
, vol.53
, pp. 485-495
-
-
Foster, P.G.1
-
49
-
-
38649114368
-
Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia
-
Fournier G, Gogarten J. 2008. Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia. J Bacteriol. 190:1124-1127.
-
(2008)
J Bacteriol.
, vol.190
, pp. 1124-1127
-
-
Fournier, G.1
Gogarten, J.2
-
50
-
-
33846625056
-
Recombination and the nature of bacterial speciation
-
Fraser C, Hanage W, Spratt B. 2007. Recombination and the nature of bacterial speciation. Science 315:476-480.
-
(2007)
Science
, vol.315
, pp. 476-480
-
-
Fraser, C.1
Hanage, W.2
Spratt, B.3
-
51
-
-
23944499633
-
Horizontal gene transfer, genome innovation, and evolution
-
Gogarten J, Townsend J. 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.1
Townsend, J.2
-
52
-
-
0036405356
-
INTEINS: Structure, function, and evolution
-
Gogarten JP, Senejani AG, Zhaxybayeva O, Olendzenski L, Hilario E. 2002. INTEINS: structure, function, and evolution. Annu Rev Microbiol. 56: 263-287.
-
(2002)
Annu Rev Microbiol.
, vol.56
, pp. 263-287
-
-
Gogarten, J.P.1
Senejani, A.G.2
Zhaxybayeva, O.3
Olendzenski, L.4
Hilario, E.5
-
53
-
-
45749124657
-
TNT, a free program for phylogenetic analysis
-
Goloboff PA, Farris JS, Nixon KC. 2008. TNT, a free program for phylogenetic analysis. Cladistics 24:774-786.
-
(2008)
Cladistics
, vol.24
, pp. 774-786
-
-
Goloboff, P.A.1
Farris, J.S.2
Nixon, K.C.3
-
54
-
-
0000664456
-
Class III. Halobacteria class. nov
-
Boone DR, Castenholz RW, editors. 2nd ed. New York: Springer-Verlag
-
Grant W, Kamekura M, McGenity T, Ventosa A. 2001. Class III. Halobacteria class. nov. In: Boone DR, Castenholz RW, editors. Bergey's manual of systematic bacteriology volume 1: the archaea and the deeply branching and phototrophic bacteria. 2nd ed. New York: Springer-Verlag. p. 169.
-
(2001)
Bergey's Manual of Systematic Bacteriology Volume 1: The Archaea and the Deeply Branching and Phototrophic Bacteria
, pp. 169
-
-
Grant, W.1
Kamekura, M.2
McGenity, T.3
Ventosa, A.4
-
55
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52: 696-704.
-
(2003)
Syst Biol.
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
56
-
-
77956519355
-
GenoPlotR: Comparative gene and genome visualization in R
-
Guy L, Kultima JR, Andersson SGE. 2010. genoPlotR: comparative gene and genome visualization in R. Bioinformatics 26:2334-2335.
-
(2010)
Bioinformatics
, vol.26
, pp. 2334-2335
-
-
Guy, L.1
Kultima, J.R.2
Andersson, S.G.E.3
-
58
-
-
77954362415
-
The complete genome sequence of Haloferax volcanii DS2, a model archaeon
-
Hartman AL, et al. 2010. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One 5:e9605.
-
(2010)
PLoS One
, vol.5
-
-
Hartman, A.L.1
-
59
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa M, Kishino H, Yano Ta. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22: 160-174.
-
(1985)
J Mol Evol.
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, Ta.3
-
60
-
-
0022387142
-
Resistance to [beta]-lactam antibiotics by re-modelling the active site of an E. coli penicillin-binding protein
-
Hedge PJ, Spratt BG. 1985. Resistance to [beta]-lactam antibiotics by re-modelling the active site of an E. coli penicillin-binding protein. Nature 318:478-480.
-
(1985)
Nature
, vol.318
, pp. 478-480
-
-
Hedge, P.J.1
Spratt, B.G.2
-
61
-
-
0027738868
-
Horizontal transfer of ATPase genes - The tree of life becomes a net of life
-
Hilario E, Gogarten J. 1993. Horizontal transfer of ATPase genes-the tree of life becomes a net of life. BioSystems 31:111-119.
-
(1993)
BioSystems
, vol.31
, pp. 111-119
-
-
Hilario, E.1
Gogarten, J.2
-
62
-
-
0030305457
-
R: A language for data analysis and graphics
-
Ihaka R, Gentleman R. 1996. R: a language for data analysis and graphics. J Comput Graph Stat. 5:299-314.
-
(1996)
J Comput Graph Stat.
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
-
63
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh K,Misawa K, Kuma KI, Miyata T. 2002.MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059-3066.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 3059-3066
-
-
Katoh Kmisawa, K.1
Kuma, K.I.2
Miyata, T.3
-
64
-
-
78751692201
-
A methylaspartate cycle in haloarchaea
-
Khomyakova M, Bükmez Ö, Thomas LK, Erb TJ, Berg IA. 2011. A methylaspartate cycle in haloarchaea. Science 331:334-337.
-
(2011)
Science
, vol.331
, pp. 334-337
-
-
Khomyakova, M.1
Bükmez, O.2
Thomas, L.K.3
Erb, T.J.4
Berg, I.A.5
-
65
-
-
79959849261
-
Comparison of phylogenetic trees and search for a central trend in the "forest of life"
-
Koonin E, Puigbo P, Wolf Y. 2011. Comparison of phylogenetic trees and search for a central trend in the "forest of life." J Comput Biol. 18: 917-924.
-
(2011)
J Comput Biol.
, vol.18
, pp. 917-924
-
-
Koonin, E.1
Puigbo, P.2
Wolf, Y.3
-
66
-
-
15844406550
-
HyPhy: Hypothesis testing using phylogenies
-
Kosakovsky Pond S, Frost S,Muse S. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676-679.
-
(2005)
Bioinformatics
, vol.21
, pp. 676-679
-
-
Kosakovsky Pond, S.1
Frost Smuse, S.2
-
67
-
-
0035448522
-
When does a clone deserve a name? A perspective on bacterial species based on population genetics
-
Lan R, Reeves P. 2001. When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol. 9: 419-424.
-
(2001)
Trends Microbiol.
, vol.9
, pp. 419-424
-
-
Lan, R.1
Reeves, P.2
-
68
-
-
34248159030
-
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
-
Lartillot N, Brinkmann H, Philippe H. 2007. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol. 7(Suppl 1):S4.
-
(2007)
BMC Evol Biol.
, vol.7
, Issue.SUPPL. 1
-
-
Lartillot, N.1
Brinkmann, H.2
Philippe, H.3
-
69
-
-
2442691520
-
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
-
Lartillot N, Philippe H. 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol. 21:1095-1109.
-
(2004)
Mol Biol Evol.
, vol.21
, pp. 1095-1109
-
-
Lartillot, N.1
Philippe, H.2
-
70
-
-
77955410887
-
The myth of bacterial species and speciation
-
Lawrence J, Retchless A. 2010. The myth of bacterial species and speciation. Biol Philos. 25:569-588.
-
(2010)
Biol Philos.
, vol.25
, pp. 569-588
-
-
Lawrence, J.1
Retchless, A.2
-
71
-
-
0032482924
-
Molecular archaeology of the Escherichia coli genome
-
Lawrence JG, Ochman H. 1998. Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A. 95:9413-9417.
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, pp. 9413-9417
-
-
Lawrence, J.G.1
Ochman, H.2
-
72
-
-
45849154166
-
An improved general amino acid replacement matrix
-
Le SQ, Gascuel O. 2008. An improved general amino acid replacement matrix. Mol Biol Evol. 25:1307-1320.
-
(2008)
Mol Biol Evol.
, vol.25
, pp. 1307-1320
-
-
Le, S.Q.1
Gascuel, O.2
-
73
-
-
33748299286
-
Environmental genomics of "haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species
-
Legault B, et al. 2006. Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics 7:171.
-
(2006)
BMC Genomics
, vol.7
, pp. 171
-
-
Legault, B.1
-
74
-
-
80052624718
-
Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator
-
Lin Y, Rajan V, Moret B. 2011. Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator. J Comput Biol. 18:1131-1139.
-
(2011)
J Comput Biol.
, vol.18
, pp. 1131-1139
-
-
Lin, Y.1
Rajan, V.2
Moret, B.3
-
75
-
-
27144538817
-
Evolution: The biochemical architecture of an ancient adaptive landscape
-
Lunzer M, Miller SP, Felsheim R, Dean AM. 2005. Evolution: the biochemical architecture of an ancient adaptive landscape. Science 310: 499-501.
-
(2005)
Science
, vol.310
, pp. 499-501
-
-
Lunzer, M.1
Miller, S.P.2
Felsheim, R.3
Dean, A.M.4
-
76
-
-
84864245183
-
Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux
-
Lynch EA, et al. 2012. Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux. PLoS One 7:e41389.
-
(2012)
PLoS One
, vol.7
-
-
Lynch, E.A.1
-
77
-
-
0345306751
-
The origins of genome complexity
-
Lynch M, Conery J. 2003. The origins of genome complexity. Science 302: 1401-1404.
-
(2003)
Science
, vol.302
, pp. 1401-1404
-
-
Lynch, M.1
Conery, J.2
-
78
-
-
0032766490
-
Comparative genomics of the Archaea (Euryarchaeota): Evolution of conserved protein families, the stable core, and the variable shell
-
Makarova KS, et al. 1999. Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res. 9:608-628.
-
(1999)
Genome Res.
, vol.9
, pp. 608-628
-
-
Makarova, K.S.1
-
79
-
-
78149420666
-
Complete genome sequence of Halogeometricum borinquense type strain (PR3T)
-
Malfatti S, et al. 2009. Complete genome sequence of Halogeometricum borinquense type strain (PR3T). Stand Genomic Sci. 1: 150-159.
-
(2009)
Stand Genomic Sci.
, vol.1
, pp. 150-159
-
-
Malfatti, S.1
-
80
-
-
84861878662
-
Quartet decomposition server: A platform for analyzing phylogenetic trees
-
Mao F, et al. 2012. Quartet decomposition server: a platform for analyzing phylogenetic trees. BMC Bioinformatics 13:123.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 123
-
-
Mao, F.1
-
81
-
-
0033082247
-
Mosaic bacterial chromosomes: A challenge en route to a tree of genomes
-
MartinW. 1999. Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. Bioessays 21:99-104.
-
(1999)
Bioessays
, vol.21
, pp. 99-104
-
-
Martin, W.1
-
82
-
-
4944262629
-
Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes
-
Medrano-Soto A, Moreno-Hagelsieb G, Vinuesa P, Christen J, Collado- Vides J. 2004. Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes.Mol Biol Evol. 21:1884-1894.
-
(2004)
Mol Biol Evol.
, vol.21
, pp. 1884-1894
-
-
Medrano-Soto, A.1
Moreno-Hagelsieb, G.2
Vinuesa, P.3
Christen, J.4
Collado- Vides, J.5
-
83
-
-
78049410030
-
Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene
-
Minegishi H, et al. 2010. Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene. Int J Syst Evol Microbiol. 60: 2398-2408.
-
(2010)
Int J Syst Evol Microbiol.
, vol.60
, pp. 2398-2408
-
-
Minegishi, H.1
-
84
-
-
34547588704
-
KAAS: An automatic genome annotation and pathway reconstruction server
-
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35:W182-W185.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Moriya, Y.1
Itoh, M.2
Okuda, S.3
Yoshizawa, A.C.4
Kanehisa, M.5
-
85
-
-
77950466524
-
AQUA: Automated quality improvement for multiple sequence alignments
-
Müller J, Creevey CJ, Thompson JD, Arendt D, Bork P. 2010. AQUA: automated quality improvement for multiple sequence alignments. Bioinformatics 26:263-265.
-
(2010)
Bioinformatics
, vol.26
, pp. 263-265
-
-
Müller, J.1
Creevey, C.J.2
Thompson, J.D.3
Arendt, D.4
Bork, P.5
-
86
-
-
0026602645
-
Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui
-
Mylvaganam S, Dennis PP. 1992. Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130:399-410.
-
(1992)
Genetics
, vol.130
, pp. 399-410
-
-
Mylvaganam, S.1
Dennis, P.P.2
-
87
-
-
84864615070
-
Low species barriers in halophilic archaea and the formation of recombinant hybrids
-
Naor A, Lapierre P, Mevarech M, Papke RT, Gophna U. 2012. Low species barriers in halophilic archaea and the formation of recombinant hybrids. Curr Biol. 22:1444-1448.
-
(2012)
Curr Biol.
, vol.22
, pp. 1444-1448
-
-
Naor, A.1
Lapierre, P.2
Mevarech, M.3
Papke, R.T.4
Gophna, U.5
-
88
-
-
84355162254
-
De novometagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities
-
Narasingarao P, et al. 2012. De novometagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J. 6:81-93.
-
(2012)
ISME J.
, vol.6
, pp. 81-93
-
-
Narasingarao, P.1
-
89
-
-
0033609333
-
Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima
-
Nelson KE, et al. 1999. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323-329.
-
(1999)
Nature
, vol.399
, pp. 323-329
-
-
Nelson, K.E.1
-
90
-
-
33845974881
-
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography
-
Normand P, et al. 2007. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res. 17:7-15.
-
(2007)
Genome Res.
, vol.17
, pp. 7-15
-
-
Normand, P.1
-
91
-
-
0015722319
-
Slightly deleterious mutant substitutions in evolution
-
Ohta T. 1973. Slightly deleterious mutant substitutions in evolution. Nature 246:96-98.
-
(1973)
Nature
, vol.246
, pp. 96-98
-
-
Ohta, T.1
-
92
-
-
0027020232
-
The nearly neutral theory of molecular evolution
-
Ohta T. 1992. The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst. 23:263-286.
-
(1992)
Annu Rev Ecol Syst.
, vol.23
, pp. 263-286
-
-
Ohta, T.1
-
93
-
-
0642312313
-
Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ
-
Omelchenko M, Makarova K,Wolf Y, Rogozin I, Koonin E. 2003. Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ. Genome Biol. 4:R55.
-
(2003)
Genome Biol.
, vol.4
-
-
Omelchenko, M.1
Makarova Kwolf, Y.2
Rogozin, I.3
Koonin, E.4
-
94
-
-
42949104034
-
Microbial life at high salt concentrations: Phylogenetic and metabolic diversity
-
Oren A. 2008. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Syst. 4:2.
-
(2008)
Saline Syst.
, vol.4
, pp. 2
-
-
Oren, A.1
-
95
-
-
35348887800
-
Searching for species in haloarchaea
-
Papke R, et al. 2007. Searching for species in haloarchaea. Proc Natl Acad Sci U S A. 104:14092-14097.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 14092-14097
-
-
Papke, R.1
-
96
-
-
83055169245
-
A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales
-
Papke R, et al. 2011. A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales. Int J Syst Evol Microbiol. 61:2984-2995.
-
(2011)
Int J Syst Evol Microbiol.
, vol.61
, pp. 2984-2995
-
-
Papke, R.1
-
98
-
-
0035177259
-
Similarity of phylogenetic trees as indicator of protein-protein interaction
-
Pazos F, Valencia A. 2001. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 14:609-614.
-
(2001)
Protein Eng.
, vol.14
, pp. 609-614
-
-
Pazos, F.1
Valencia, A.2
-
99
-
-
71049152453
-
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer
-
Pearson T, et al. 2009. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol. 7:78.
-
(2009)
BMC Biol.
, vol.7
, pp. 78
-
-
Pearson, T.1
-
100
-
-
34247481878
-
IPython: A system for interactive scientific computing
-
Pérez F, Granger BE. 2007. IPython: a system for interactive scientific computing. Comput Sci Eng. 9:21-29.
-
(2007)
Comput Sci Eng.
, vol.9
, pp. 21-29
-
-
Pérez, F.1
Granger, B.E.2
-
101
-
-
0036084146
-
InBase: The intein database
-
Perler FB. 2002. InBase: the intein database. Nucleic Acids Res. 30: 383-384.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 383-384
-
-
Perler, F.B.1
-
102
-
-
40449120475
-
Evolution in the laboratory: The genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1
-
Pfeiffer F, et al. 2008. Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1. Genomics 91:335-346.
-
(2008)
Genomics
, vol.91
, pp. 335-346
-
-
Pfeiffer, F.1
-
103
-
-
79953315166
-
Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes
-
Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T. 2011. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res. 21:599-609.
-
(2011)
Genome Res.
, vol.21
, pp. 599-609
-
-
Popa, O.1
Hazkani-Covo, E.2
Landan, G.3
Martin, W.4
Dagan, T.5
-
104
-
-
34247324752
-
BranchClust: A phylogenetic algorithm for selecting gene families
-
Poptsova M, Gogarten JP. 2007. BranchClust: a phylogenetic algorithm for selecting gene families. BMC Bioinformatics 8:120.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 120
-
-
Poptsova, M.1
Gogarten, J.P.2
-
105
-
-
0031773680
-
MODELTEST: Testing the model of DNA substitution
-
Posada D, Crandall KA. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
-
(1998)
Bioinformatics
, vol.14
, pp. 817-818
-
-
Posada, D.1
Crandall, K.A.2
-
106
-
-
77949718257
-
FastTree 2-approximately maximum-likelihood trees for large alignments
-
Price MN, Dehal PS, Arkin AP. 2010. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490.
-
(2010)
PLoS One
, vol.5
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
107
-
-
2642518198
-
Isolation of haloarchaea that grow at low salinities
-
Purdy K, et al. 2004. Isolation of haloarchaea that grow at low salinities. Environ Microbiol. 6:591-595.
-
(2004)
Environ Microbiol.
, vol.6
, pp. 591-595
-
-
Purdy, K.1
-
108
-
-
0026822436
-
Phylogenetic inference based on matrix representation of trees
-
Ragan M. 1992. Phylogenetic inference based on matrix representation of trees. Mol Phylogenet Evol. 1:53-58.
-
(1992)
Mol Phylogenet Evol.
, vol.1
, pp. 53-58
-
-
Ragan, M.1
-
109
-
-
5344230543
-
-
last accessed January 16, 2011
-
Rambaut A, Drummond A. 2007. Tracer v1.4.1. Available from: http://beast.bio.ed.ac.uk/Tracer, last accessed January 16, 2011.
-
(2007)
Tracer v1.4.1
-
-
Rambaut, A.1
Drummond, A.2
-
110
-
-
0034201441
-
EMBOSS: The European molecular biology open software suite
-
Rice P, Longden L, Bleasby A. 2000. EMBOSS: the European molecular biology open software suite. Trends Genet. 16:276-277.
-
(2000)
Trends Genet.
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, L.2
Bleasby, A.3
-
111
-
-
0027278850
-
The effect of DNA sequence divergence on sexual isolation in bacillus
-
Roberts M, Cohan F. 1993. The effect of DNA sequence divergence on sexual isolation in bacillus. Genetics 134:401-408.
-
(1993)
Genetics
, vol.134
, pp. 401-408
-
-
Roberts, M.1
Cohan, F.2
-
112
-
-
77956537114
-
Complete genome sequence of Halalkalicoccus jeotgali B3(T), an extremely halophilic archaeon
-
Roh SW, et al. 2010. Complete genome sequence of Halalkalicoccus jeotgali B3(T), an extremely halophilic archaeon. J Bacteriol. 192: 4528-4529.
-
(2010)
J Bacteriol.
, vol.192
, pp. 4528-4529
-
-
Roh, S.W.1
-
113
-
-
0024447751
-
The mechanism of DNA transfer in the mating system of an archaebacterium
-
Rosenshine I, Tchelet R, Mevarech M. 1989. The mechanism of DNA transfer in the mating system of an archaebacterium. Science 245: 1387-1389.
-
(1989)
Science
, vol.245
, pp. 1387-1389
-
-
Rosenshine, I.1
Tchelet, R.2
Mevarech, M.3
-
114
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
-
(1987)
Mol Biol Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
115
-
-
0032523049
-
Panmictic structure of Helicobacter pylori demonstrated by the comparative study of six genetic markers
-
Salaün L, et al. 1998. Panmictic structure of Helicobacter pylori demonstrated by the comparative study of six genetic markers. FEMS Microbiol Lett. 161:231-239.
-
(1998)
FEMS Microbiol Lett.
, vol.161
, pp. 231-239
-
-
Salaün, L.1
-
116
-
-
78149419515
-
Complete genome sequence of Haloterrigena turkmenica type strain (4kT)
-
Saunders E, et al. 2010. Complete genome sequence of Haloterrigena turkmenica type strain (4kT). Stand Genomic Sci. 2:107-116.
-
(2010)
Stand Genomic Sci.
, vol.2
, pp. 107-116
-
-
Saunders, E.1
-
117
-
-
84860504598
-
A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T
-
Siddaramappa S, et al. 2012. A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T. BMC Genomics 13:165.
-
(2012)
BMC Genomics
, vol.13
, pp. 165
-
-
Siddaramappa, S.1
-
118
-
-
0023865255
-
Hybrid penicillin-binding proteins in penicillin-resistant strains of Neisseria gonorrhoeae
-
Spratt BG. 1988. Hybrid penicillin-binding proteins in penicillin-resistant strains of Neisseria gonorrhoeae. Nature 332:173-176.
-
(1988)
Nature
, vol.332
, pp. 173-176
-
-
Spratt, B.G.1
-
119
-
-
18644368714
-
The BioPerl toolkit: Perl modules for the life sciences
-
Stajich J, et al. 2002. The BioPerl toolkit: Perl modules for the life sciences. Genome Res. 12:1611-1618.
-
(2002)
Genome Res.
, vol.12
, pp. 1611-1618
-
-
Stajich, J.1
-
120
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
121
-
-
77954202497
-
DendroPy: A Python library for phylogenetic computing
-
Sukumaran J, Holder MT. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26:1569-1571.
-
(2010)
Bioinformatics
, vol.26
, pp. 1569-1571
-
-
Sukumaran, J.1
Holder, M.T.2
-
123
-
-
0035824873
-
Towards a reliable objective function for multiple sequence alignments
-
Thompson JD, Plewniak F, Ripp R, Thierry JC, Poch O. 2001. Towards a reliable objective function for multiple sequence alignments. J Mol Biol. 314:937-951.
-
(2001)
J Mol Biol.
, vol.314
, pp. 937-951
-
-
Thompson, J.D.1
Plewniak, F.2
Ripp, R.3
Thierry, J.C.4
Poch, O.5
-
124
-
-
0038391401
-
RASCAL: Rapid scanning and correction of multiple sequence alignments
-
Thompson JD, Thierry JC, Poch O. 2003. RASCAL: rapid scanning and correction of multiple sequence alignments. Bioinformatics 19: 1155-1161.
-
(2003)
Bioinformatics
, vol.19
, pp. 1155-1161
-
-
Thompson, J.D.1
Thierry, J.C.2
Poch, O.3
-
125
-
-
14544287770
-
Genotypic diversity within a natural coastal bacterioplankton population
-
Thompson JR, et al. 2005. Genotypic diversity within a natural coastal bacterioplankton population. Science 307:1311-1313.
-
(2005)
Science
, vol.307
, pp. 1311-1313
-
-
Thompson, J.R.1
-
126
-
-
77952891383
-
Complete genome sequence of Halomicrobium mukohataei type strain (arg-2T)
-
Tindall BJ, et al. 2009. Complete genome sequence of Halomicrobium mukohataei type strain (arg-2T). Stand Genomic Sci. 1:270-277.
-
(2009)
Stand Genomic Sci.
, vol.1
, pp. 270-277
-
-
Tindall, B.J.1
-
127
-
-
79851505378
-
Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes
-
Treangen TJ, Rocha EPC. 2011. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet. 7: e1001284.
-
(2011)
PLoS Genet.
, vol.7
-
-
Treangen, T.J.1
Rocha, E.P.C.2
-
128
-
-
79959482487
-
Association between translation efficiency and horizontal gene transfer within microbial communities
-
Tuller T, et al. 2011. Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Res. 39:4743-4755.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 4743-4755
-
-
Tuller, T.1
-
129
-
-
0042638450
-
Halosimplex carlsbadense gen. nov., sp. nov., a unique halophilic archaeon, with three 16S rRNA genes, that grows only in defined medium with glycerol and acetate or pyruvate
-
Vreeland R, et al. 2002. Halosimplex carlsbadense gen. nov., sp. nov., a unique halophilic archaeon, with three 16S rRNA genes, that grows only in defined medium with glycerol and acetate or pyruvate. Extremophiles 6:445-452.
-
(2002)
Extremophiles
, vol.6
, pp. 445-452
-
-
Vreeland, R.1
-
130
-
-
0030924545
-
Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria
-
Vulić M, Dionisio F, Taddei F, Radman M. 1997. Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc Natl Acad Sci U S A. 94:9763-9767.
-
(1997)
Proc Natl Acad Sci U S A
, vol.94
, pp. 9763-9767
-
-
Vulić, M.1
Dionisio, F.2
Taddei, F.3
Radman, M.4
-
131
-
-
8444238946
-
Evolution of the RNA polymerase B' subunit gene (rpoB') in Halobacteriales: A complementary molecular marker to the SSU rRNA gene
-
Walsh DA, Bapteste E, Kamekura M, Doolittle WF. 2004. Evolution of the RNA polymerase B' subunit gene (rpoB') in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol Biol Evol. 21: 2340-2351.
-
(2004)
Mol Biol Evol.
, vol.21
, pp. 2340-2351
-
-
Walsh, D.A.1
Bapteste, E.2
Kamekura, M.3
Doolittle, W.F.4
-
132
-
-
21044435697
-
Perspective: Sign epistasis and genetic constraint on evolutionary trajectories
-
Weinreich D,Watson R, Chao L. 2005. Perspective: sign epistasis and genetic constraint on evolutionary trajectories. Evolution 59:1165-1174.
-
(2005)
Evolution
, vol.59
, pp. 1165-1174
-
-
Weinreich, D.1
Watson, R.2
Chao, L.3
-
133
-
-
33645666942
-
Darwinian evolution can follow only very few mutational paths to fitter proteins
-
Weinreich DM, Delaney NF, DePristo MA, Hartl DL. 2006. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312:111-114.
-
(2006)
Science
, vol.312
, pp. 111-114
-
-
Weinreich, D.M.1
Delaney, N.F.2
Depristo, M.A.3
Hartl, D.L.4
-
134
-
-
0037168538
-
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli
-
Welch RA, et al. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci U S A. 99:17020-17024.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 17020-17024
-
-
Welch, R.A.1
-
135
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 18:691-699.
-
(2001)
Mol Biol Evol.
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
136
-
-
33847062460
-
Of clades and clans: Terms for phylogenetic relationships in unrooted trees
-
Wilkinson M, McInerney JO, Hirt RP, Foster PG, Embley TM. 2007. Of clades and clans: terms for phylogenetic relationships in unrooted trees. Trends Ecol Evol. 22:114-115.
-
(2007)
Trends Ecol Evol.
, vol.22
, pp. 114-115
-
-
Wilkinson, M.1
McInerney, J.O.2
Hirt, R.P.3
Foster, P.G.4
Embley, T.M.5
-
137
-
-
80052097306
-
A rooted net of life
-
Williams D, et al. 2011. A rooted net of life. Biol Direct. 6:45.
-
(2011)
Biol Direct.
, vol.6
, pp. 45
-
-
Williams, D.1
-
139
-
-
1542723403
-
CbiZ, an amidohydrolase enzyme required for salvaging the coenzyme B12 precursor cobinamide in archaea
-
Woodson JD, Escalante-Semerena JC. 2004. CbiZ, an amidohydrolase enzyme required for salvaging the coenzyme B12 precursor cobinamide in archaea. Proc Natl Acad Sci U S A. 101:3591-3596.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 3591-3596
-
-
Woodson, J.D.1
Escalante-Semerena, J.C.2
-
140
-
-
0037215529
-
The cobY gene of the archaeon Halobacterium sp. strain NRC-1 is required for de novo cobamide synthesis
-
Woodson JD, Peck RF, KrebsMP, Escalante-Semerena JC. 2003. The cobY gene of the archaeon Halobacterium sp. strain NRC-1 is required for de novo cobamide synthesis. J Bacteriol. 185:311-316.
-
(2003)
J Bacteriol.
, vol.185
, pp. 311-316
-
-
Woodson, J.D.1
Peck, R.F.2
Krebs, M.P.3
Escalante-Semerena, J.C.4
-
141
-
-
0025318864
-
The "effective number of codons" used in a gene
-
Wright F. 1990. The "effective number of codons" used in a gene. Gene 87:23-29.
-
(1990)
Gene
, vol.87
, pp. 23-29
-
-
Wright, F.1
-
142
-
-
0000907353
-
The roles of mutation, inbreeding, crossbreeding, and selection in evolution
-
Ithaca, NY
-
Wright S. 1932. The roles of mutation, inbreeding, crossbreeding, and selection in evolution. Proceedings of the VI International Congress of Genetics; Ithaca, NY.
-
(1932)
Proceedings of the VI International Congress of Genetics
-
-
Wright, S.1
-
143
-
-
80555156624
-
Parallel evolution of transcriptome architecture during genome reorganization
-
Yoon SH, et al. 2011. Parallel evolution of transcriptome architecture during genome reorganization. Genome Res. 21:1892-1904.
-
(2011)
Genome Res.
, vol.21
, pp. 1892-1904
-
-
Yoon, S.H.1
-
144
-
-
65549102123
-
Detection and quantitative assessment of horizontal gene transfer
-
Zhaxybayeva O. 2009. Detection and quantitative assessment of horizontal gene transfer. Methods Mol Biol. 532:195-213.
-
(2009)
Methods Mol Biol.
, vol.532
, pp. 195-213
-
-
Zhaxybayeva, O.1
-
146
-
-
77149147828
-
Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus
-
Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP. 2009. Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus. Genome Biol Evol. 2009:325-339.
-
(2009)
Genome Biol Evol.
, vol.2009
, pp. 325-339
-
-
Zhaxybayeva, O.1
Doolittle, W.F.2
Papke, R.T.3
Gogarten, J.P.4
-
147
-
-
33748277982
-
Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
-
Zhaxybayeva O, Gogarten J, Charlebois R, Doolittle W, Papke R. 2006. Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res. 16: 1099-1108.
-
(2006)
Genome Res.
, vol.16
, pp. 1099-1108
-
-
Zhaxybayeva, O.1
Gogarten, J.2
Charlebois, R.3
Doolittle, W.4
Papke, R.5
-
148
-
-
9144255640
-
An improved probability mapping approach to assess genome mosaicism
-
Zhaxybayeva O, Gogarten JP. 2003. An improved probability mapping approach to assess genome mosaicism. BMC Genomics 4:37.
-
(2003)
BMC Genomics
, vol.4
, pp. 37
-
-
Zhaxybayeva, O.1
Gogarten, J.P.2
-
149
-
-
65249126970
-
On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales
-
Zhaxybayeva O, et al. 2009. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci U S A. 106:5865-5870.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 5865-5870
-
-
Zhaxybayeva, O.1
|