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1
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22144446758
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Databases and software for the comparisons of prokaryotic genomes
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Field D., Feil E., and Wilson G. Databases and software for the comparisons of prokaryotic genomes. Microbiology 151 (2005) 2125-2132
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(2005)
Microbiology
, vol.151
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Field, D.1
Feil, E.2
Wilson, G.3
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2
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33745067721
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Ten years of bacterial genome sequencing: 10 comparative-genomics-based discoveries
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A rich overview of the outcomes of comparative genomic studies over the past years.
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Binnewies T.T., Motro Y., Hallin P.F., Lund O., David Dunn D., La T., Hampson D.J., Bellgard M., Wassenaar T.M., and Ussery D.W. Ten years of bacterial genome sequencing: 10 comparative-genomics-based discoveries. Funct Integr Genomics 6 (2006) 165-185. A rich overview of the outcomes of comparative genomic studies over the past years.
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(2006)
Funct Integr Genomics
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, pp. 165-185
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Binnewies, T.T.1
Motro, Y.2
Hallin, P.F.3
Lund, O.4
David Dunn, D.5
La, T.6
Hampson, D.J.7
Bellgard, M.8
Wassenaar, T.M.9
Ussery, D.W.10
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3
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25644458211
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The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
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This database represents a new chapter in the way in which we annotate genomes. Annotations in the SEED database are the result of expert curations of single 'subsystems' (a pathway or particular function) across all available genomes.
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Overbeek R., Begley T., Butler R.M., Choudhuri J.V., Chuang H.Y., Cohoon M., de Crecy-Lagard V., Diaz N., Disz T., Edwards R., et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33 (2005) 5691-5702. This database represents a new chapter in the way in which we annotate genomes. Annotations in the SEED database are the result of expert curations of single 'subsystems' (a pathway or particular function) across all available genomes.
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(2005)
Nucleic Acids Res
, vol.33
, pp. 5691-5702
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Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
Cohoon, M.6
de Crecy-Lagard, V.7
Diaz, N.8
Disz, T.9
Edwards, R.10
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4
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24644462173
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Accurate multiplex polony sequencing of an evolved bacterial genome
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Proof of principle of one of the ultra-high-throughput sequencing technologies applied to the sequencing of a strain of E. coli, which was shown to diverge from its last sequenced ancestor by a mere 200 generations.
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Shendure J., Porreca G.J., Reppas N.B., Lin X., McCutcheon J.P., Rosenbaum A.M., Wang M.D., Zhang K., Mitra R.D., and Church G.M. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309 (2005) 1728-1732. Proof of principle of one of the ultra-high-throughput sequencing technologies applied to the sequencing of a strain of E. coli, which was shown to diverge from its last sequenced ancestor by a mere 200 generations.
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(2005)
Science
, vol.309
, pp. 1728-1732
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Shendure, J.1
Porreca, G.J.2
Reppas, N.B.3
Lin, X.4
McCutcheon, J.P.5
Rosenbaum, A.M.6
Wang, M.D.7
Zhang, K.8
Mitra, R.D.9
Church, G.M.10
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27944482204
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Pyrosequencing: nucleotide sequencing technology with bacterial genotyping applications
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Clarke S.C. Pyrosequencing: nucleotide sequencing technology with bacterial genotyping applications. Expert Rev Mol Diagn 5 (2005) 947-953
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(2005)
Expert Rev Mol Diagn
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Clarke, S.C.1
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6
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33745595097
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Using pyrosequencing to shed light on deep mine microbial ecology under extreme hydrogeologic conditions
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The first application of pyrosequencing technology for the characterization of the metagenomes of two microbial communities.
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Edwards R.A., Rodriguez-Brito B., Wegley L., Haynes M., Breitbart M., Peterson D.M., Saar M.O., Alexander S., Alexander Jr. E.C., and Rohwer F. Using pyrosequencing to shed light on deep mine microbial ecology under extreme hydrogeologic conditions. BMC Genomics 7 (2006) 57. The first application of pyrosequencing technology for the characterization of the metagenomes of two microbial communities.
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(2006)
BMC Genomics
, vol.7
, pp. 57
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Edwards, R.A.1
Rodriguez-Brito, B.2
Wegley, L.3
Haynes, M.4
Breitbart, M.5
Peterson, D.M.6
Saar, M.O.7
Alexander, S.8
Alexander Jr., E.C.9
Rohwer, F.10
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7
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28644447550
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Ecological perspectives on our complete genome collection
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Martiny J.B.H., and Field D. Ecological perspectives on our complete genome collection. Ecol Lett 8 (2005) 1334-1345
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(2005)
Ecol Lett
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, pp. 1334-1345
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Martiny, J.B.H.1
Field, D.2
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8
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11144354360
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Environmental genome shotgun sequencing of the Sargasso Sea
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Landmark study that opened the doors to the investigation of natural microbial communities using shotgun sequencing. It includes attempted reconstructions of genomes from dominant species.
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Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., Wu D.Y., Paulsen I., Nelson K.E., Nelson W., et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 (2004) 66-74. Landmark study that opened the doors to the investigation of natural microbial communities using shotgun sequencing. It includes attempted reconstructions of genomes from dominant species.
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(2004)
Science
, vol.304
, pp. 66-74
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Venter, J.C.1
Remington, K.2
Heidelberg, J.F.3
Halpern, A.L.4
Rusch, D.5
Eisen, J.A.6
Wu, D.Y.7
Paulsen, I.8
Nelson, K.E.9
Nelson, W.10
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9
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33646547584
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Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances
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Xu J. Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol 15 (2006) 1713-1731
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(2006)
Mol Ecol
, vol.15
, pp. 1713-1731
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Xu, J.1
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10
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30944449613
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A molecular revolution in the study of intestinal microflora
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Furrie E. A molecular revolution in the study of intestinal microflora. Gut 55 (2006) 141-143
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(2006)
Gut
, vol.55
, pp. 141-143
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Furrie, E.1
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11
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33744804299
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Metagenomic analysis of the human distal gut microbiome
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14 microorganisms whose collective genome (or 'microbiome') contains at least 100 times as many genes as our own genome. Metagenomic characterization of the gut community, as well as comparison to our bacterial genome collection, shows that humans are a 'super-organism' made up of eukaryotic and bacterial metabolic potential that is enriched for the production of amino acids, xenobiotics, methanogenesis, vitamins and other metabolites.
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14 microorganisms whose collective genome (or 'microbiome') contains at least 100 times as many genes as our own genome. Metagenomic characterization of the gut community, as well as comparison to our bacterial genome collection, shows that humans are a 'super-organism' made up of eukaryotic and bacterial metabolic potential that is enriched for the production of amino acids, xenobiotics, methanogenesis, vitamins and other metabolites.
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(2006)
Science
, vol.312
, pp. 1355-1359
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Gill, S.R.1
Pop, M.2
Deboy, R.T.3
Eckburg, P.B.4
Turnbaugh, P.J.5
Samuel, B.S.6
Gordon, J.I.7
Relman, D.A.8
Fraser-Liggett, C.M.9
Nelson, K.E.10
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12
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25444524604
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Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial 'pan-genome'
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In a comparison of seven S. agalactiae genomes it was found that each new strain contributed on average 33 new genes, thus firmly establishing the concept of the pan-genome.
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Tettelin H., Masignani V., Cieslewicz M.J., Donati C., Medini D., Ward N.L., Angiuoli S.V., Crabtree J., Jones A.L., Durkin A.S., et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial 'pan-genome'. Proc Natl Acad Sci USA 102 (2005) 13950-13955. In a comparison of seven S. agalactiae genomes it was found that each new strain contributed on average 33 new genes, thus firmly establishing the concept of the pan-genome.
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(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 13950-13955
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Tettelin, H.1
Masignani, V.2
Cieslewicz, M.J.3
Donati, C.4
Medini, D.5
Ward, N.L.6
Angiuoli, S.V.7
Crabtree, J.8
Jones, A.L.9
Durkin, A.S.10
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13
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33645827531
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Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach
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Good illustration of the power of comparative genomics to detect genes under selection. By analyzing seven E. coli genomes, it was also confirmed that the pan-genome of this species is vast - on average each new isolate contributes 441 new genes.
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Chen S.L., Hung C.S., Xu J., Reigstad C.S., Magrini V., Sabo A., Blasiar D., Bieri T., Meyer R.R., Ozersky P., et al. Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci USA 103 (2006) 5977-5982. Good illustration of the power of comparative genomics to detect genes under selection. By analyzing seven E. coli genomes, it was also confirmed that the pan-genome of this species is vast - on average each new isolate contributes 441 new genes.
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(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 5977-5982
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Chen, S.L.1
Hung, C.S.2
Xu, J.3
Reigstad, C.S.4
Magrini, V.5
Sabo, A.6
Blasiar, D.7
Bieri, T.8
Meyer, R.R.9
Ozersky, P.10
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14
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27444438599
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The microbial pan-genome
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Useful review of the pan-genome concept and the mathematical models for calculating the extent of the pan-genome for different species on the basis of the availability of multiple genomes.
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Medini D., Donati C., Tettelin H., Masignani V., and Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev 15 (2005) 589-594. Useful review of the pan-genome concept and the mathematical models for calculating the extent of the pan-genome for different species on the basis of the availability of multiple genomes.
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(2005)
Curr Opin Genet Dev
, vol.15
, pp. 589-594
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Medini, D.1
Donati, C.2
Tettelin, H.3
Masignani, V.4
Rappuoli, R.5
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15
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17644391346
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A glimpse into the expanded genome content of Vibrio cholerae through identification of genes present in environmental strains
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Purdy A., Rohwer F., Edwards R., Azam F., and Bartlett D.H. A glimpse into the expanded genome content of Vibrio cholerae through identification of genes present in environmental strains. J Bacteriol 187 (2005) 2992-3001
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(2005)
J Bacteriol
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, pp. 2992-3001
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Purdy, A.1
Rohwer, F.2
Edwards, R.3
Azam, F.4
Bartlett, D.H.5
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16
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33744482546
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Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor
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Velicer G.J., Raddatz G., Keller H., Deiss S., Lanz C., Dinkelacker I., and Schuster S.C. Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor. Proc Natl Acad Sci USA 103 (2006) 8107-8112
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(2006)
Proc Natl Acad Sci USA
, vol.103
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Velicer, G.J.1
Raddatz, G.2
Keller, H.3
Deiss, S.4
Lanz, C.5
Dinkelacker, I.6
Schuster, S.C.7
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17
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33744488606
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Evolution of an obligate social cheater to a superior cooperator
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Fiegna F., Yu Y.T., Kadam S.V., and Velicer G.J. Evolution of an obligate social cheater to a superior cooperator. Nature 441 (2006) 310-314
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(2006)
Nature
, vol.441
, pp. 310-314
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Fiegna, F.1
Yu, Y.T.2
Kadam, S.V.3
Velicer, G.J.4
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18
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22744439617
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Island size and bacterial diversity in an archipelago of engineering machines
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van der Gast C.J., Lilley A.K., Ager D., and Thompson I.P. Island size and bacterial diversity in an archipelago of engineering machines. Environ Microbiol 7 (2005) 1220-1226
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(2005)
Environ Microbiol
, vol.7
, pp. 1220-1226
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van der Gast, C.J.1
Lilley, A.K.2
Ager, D.3
Thompson, I.P.4
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19
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22544432221
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Larger islands house more bacterial taxa
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Bell T., Ager D., Song J.I., Newman J.A., Thompson I.P., Lilley A.K., and van der Gast C.J. Larger islands house more bacterial taxa. Science 308 (2005) 1884
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(2005)
Science
, vol.308
, pp. 1884
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Bell, T.1
Ager, D.2
Song, J.I.3
Newman, J.A.4
Thompson, I.P.5
Lilley, A.K.6
van der Gast, C.J.7
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20
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33644643005
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Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs
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This paper describes the use of clusters of orthologous genes to detect and correct unannotated genes in complete genomes.
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Powell B.C., and Hutchison III C.A. Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs. BMC Bioinformatics 7 (2006) 31. This paper describes the use of clusters of orthologous genes to detect and correct unannotated genes in complete genomes.
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(2006)
BMC Bioinformatics
, vol.7
, pp. 31
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Powell, B.C.1
Hutchison III, C.A.2
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21
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0346494857
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A database for in-depth analysis of prokaryotic gene fusion events
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Suhre K., Claverie J.M., and Fusion D.B. A database for in-depth analysis of prokaryotic gene fusion events. Nucleic Acids Res 32 (2004) D273-D276
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(2004)
Nucleic Acids Res
, vol.32
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Suhre, K.1
Claverie, J.M.2
Fusion, D.B.3
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22
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32044474423
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Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host
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Toh H., Weiss B.L., Perkin S.A., Yamashita A., Oshima K., Hattori M., and Aksoy S. Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. Genome Res 16 (2006) 149-156
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(2006)
Genome Res
, vol.16
, pp. 149-156
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Toh, H.1
Weiss, B.L.2
Perkin, S.A.3
Yamashita, A.4
Oshima, K.5
Hattori, M.6
Aksoy, S.7
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23
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Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains
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Pichon C., and Felden B. Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc Natl Acad Sci USA 102 (2005) 14249-14254
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(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 14249-14254
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Pichon, C.1
Felden, B.2
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24
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22144491675
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Orphans as taxonomically restricted and ecologically important genes
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Wilson G.A., Bertrand N., Patel Y., Hughes J.B., Feil E.J., and Field D. Orphans as taxonomically restricted and ecologically important genes. Microbiology 151 (2005) 2499-2501
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(2005)
Microbiology
, vol.151
, pp. 2499-2501
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Wilson, G.A.1
Bertrand, N.2
Patel, Y.3
Hughes, J.B.4
Feil, E.J.5
Field, D.6
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25
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11144310562
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Estimation of the number of authentic orphan genes in bacterial genomes
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311-313
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Fukuchi S., and Nishikawa K. Estimation of the number of authentic orphan genes in bacterial genomes. DNA Res 11 (2004) 219-231 311-313
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(2004)
DNA Res
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Fukuchi, S.1
Nishikawa, K.2
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27
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Genome update: annotation quality in sequenced microbial genomes
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Ussery D.W., and Hallin P.F. Genome update: annotation quality in sequenced microbial genomes. Microbiology 150 (2004) 2015-2017
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(2004)
Microbiology
, vol.150
, pp. 2015-2017
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Ussery, D.W.1
Hallin, P.F.2
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28
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33748092050
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Genome reviews: standardising content and representation of information about complete genomes
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Sterk P., Kersey P.J., and Apweiler R. Genome reviews: standardising content and representation of information about complete genomes. OMICS 10 (2006) 114-118
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(2006)
OMICS
, vol.10
, pp. 114-118
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Sterk, P.1
Kersey, P.J.2
Apweiler, R.3
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29
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13844266109
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Genome properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
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A database of 'assertions' about genomes derived from automated analysis of pathways and a variety of other traits. Curated information from the literature is also included.
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Haft D.H., Selengut J.D., Brinkac L.M., Zafar N., and White O. Genome properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics 21 (2005) 293-306. A database of 'assertions' about genomes derived from automated analysis of pathways and a variety of other traits. Curated information from the literature is also included.
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(2005)
Bioinformatics
, vol.21
, pp. 293-306
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Haft, D.H.1
Selengut, J.D.2
Brinkac, L.M.3
Zafar, N.4
White, O.5
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30
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33644873697
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The integrated microbial genomes (IMG) system
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The Joint Genome Institute's IMG system (http://img.jgi.doe.gov/) is a major effort to provide an integrative environment that facilitates the genomic analysis of isolate organisms on a comparative level. Data can be organized by, for example, phylogeny, phenotypic or ecotypic properties.
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Markowitz V.M., Korzeniewski F., Palaniappan K., Szeto E., Werner G., Padki A., Zhao X., Dubchak I., Hugenholtz P., Anderson I., et al. The integrated microbial genomes (IMG) system. Nucleic Acids Res 34 (2006) D344-D348. The Joint Genome Institute's IMG system (http://img.jgi.doe.gov/) is a major effort to provide an integrative environment that facilitates the genomic analysis of isolate organisms on a comparative level. Data can be organized by, for example, phylogeny, phenotypic or ecotypic properties.
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(2006)
Nucleic Acids Res
, vol.34
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Markowitz, V.M.1
Korzeniewski, F.2
Palaniappan, K.3
Szeto, E.4
Werner, G.5
Padki, A.6
Zhao, X.7
Dubchak, I.8
Hugenholtz, P.9
Anderson, I.10
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31
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33748705169
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American Society for Microbiology, Washington, DC. Call for the systematic annotation of hypothetical and orphan genes using empirical methods.
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Roberts R.J., Karp P., Kasif S., Linn S., and Buckley M.R. An Experimental Approach to Genome Annotation. Critical Issues Colloquia Report (2005), American Society for Microbiology, Washington, DC. Call for the systematic annotation of hypothetical and orphan genes using empirical methods.
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(2005)
An Experimental Approach to Genome Annotation. Critical Issues Colloquia Report
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Roberts, R.J.1
Karp, P.2
Kasif, S.3
Linn, S.4
Buckley, M.R.5
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32
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13844316454
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Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations
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Excellent demonstration of the use of transcriptomic approaches to the validation of genomic annotation.
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Kolker E., Picone A.F., Galperin M.Y., Romine M.F., Higdon R., Makarova K.S., Kolker N., Anderson G.A., Qiu X., Auberry K.J., et al. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci USA 102 (2005) 2099-2104. Excellent demonstration of the use of transcriptomic approaches to the validation of genomic annotation.
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(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 2099-2104
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Kolker, E.1
Picone, A.F.2
Galperin, M.Y.3
Romine, M.F.4
Higdon, R.5
Makarova, K.S.6
Kolker, N.7
Anderson, G.A.8
Qiu, X.9
Auberry, K.J.10
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33
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33748066310
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Evidence standards in experimental and inferential INSDC Third Party Annotation data
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Cochrane G., Bates K., Apweiler R., Tateno Y., Mashima J., Kosuge T., Mizrachi I.K., Schafer S., and Fetchko M. Evidence standards in experimental and inferential INSDC Third Party Annotation data. OMICS 10 (2006) 105-113
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(2006)
OMICS
, vol.10
, pp. 105-113
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Cochrane, G.1
Bates, K.2
Apweiler, R.3
Tateno, Y.4
Mashima, J.5
Kosuge, T.6
Mizrachi, I.K.7
Schafer, S.8
Fetchko, M.9
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34
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31644444476
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MaGe: a microbial genome annotation system supported by synteny results
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Vallenet D., Labarre L., Rouy Z., Barbe V., Bocs S., Cruveiller S., Lajus A., Pascal G., Scarpelli C., and Medigue C. MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res 34 (2006) 53-65
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(2006)
Nucleic Acids Res
, vol.34
, pp. 53-65
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Vallenet, D.1
Labarre, L.2
Rouy, Z.3
Barbe, V.4
Bocs, S.5
Cruveiller, S.6
Lajus, A.7
Pascal, G.8
Scarpelli, C.9
Medigue, C.10
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35
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27144524216
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Automatic detection of subsystem/pathway variants in genome analysis
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Ye Y., Osterman A., Overbeek R., and Godzik A. Automatic detection of subsystem/pathway variants in genome analysis. Bioinformatics 21 (2005) i478-i486
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(2005)
Bioinformatics
, vol.21
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Ye, Y.1
Osterman, A.2
Overbeek, R.3
Godzik, A.4
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36
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33744784298
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An application of statistics to comparative metagenomic
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Statistical method for testing the significance of metabolic differences between two datasets for protein-function assignments.
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Rodriguez-Brito B., Rohwer F., and Edwards R.A. An application of statistics to comparative metagenomic. BMC Bioinformatics 7 (2006) 162. Statistical method for testing the significance of metabolic differences between two datasets for protein-function assignments.
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(2006)
BMC Bioinformatics
, vol.7
, pp. 162
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Rodriguez-Brito, B.1
Rohwer, F.2
Edwards, R.A.3
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37
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33644520519
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The genomes on line database (GOLD) v. 2: a monitor of genome projects worldwide
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This updated version of GOLD contains a wide range of searchable, viewable and downloadable descriptive information about genomes curated from the literature.
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Liolios K., Tavernarakis N., Hugenholtz P., and Kyrpides N.C. The genomes on line database (GOLD) v. 2: a monitor of genome projects worldwide. Nucleic Acids Res 34 (2006) D332-D334. This updated version of GOLD contains a wide range of searchable, viewable and downloadable descriptive information about genomes curated from the literature.
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(2006)
Nucleic Acids Res
, vol.34
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Liolios, K.1
Tavernarakis, N.2
Hugenholtz, P.3
Kyrpides, N.C.4
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38
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33745085561
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Sequencing genomes from single cells by polymerase cloning
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Demonstration that genome sequencing can be accomplished from single cells without the need for cultivation.
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Zhang K., Martiny A., Reppas N.B., Barry K.W., Malek J., Chisholm S.W., and Church G.M. Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24 (2006) 680-686. Demonstration that genome sequencing can be accomplished from single cells without the need for cultivation.
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(2006)
Nat Biotechnol
, vol.24
, pp. 680-686
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Zhang, K.1
Martiny, A.2
Reppas, N.B.3
Barry, K.W.4
Malek, J.5
Chisholm, S.W.6
Church, G.M.7
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39
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17644373764
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Cataloguing our current genome collection
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Field D., and Hughes J. Cataloguing our current genome collection. Microbiology 151 (2005) 1016-1019
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Cataloguing our Current Genome Collection II
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Field D., Morrison N., Selengut J.D., and Sterk P. Cataloguing our Current Genome Collection II. OMICS 10 (2006) 100-104
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OMICS
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Field, D.1
Morrison, N.2
Selengut, J.D.3
Sterk, P.4
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41
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CBS genome atlas database: a dynamic storage for bioinformatic results and sequence data
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Content continues to accumulate in this genomic database from the authors of the 'Genome Update' monthly column in Microbiology.
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Hallin P.F., and Ussery D.W. CBS genome atlas database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics 20 (2004) 3682-3686. Content continues to accumulate in this genomic database from the authors of the 'Genome Update' monthly column in Microbiology.
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Bioinformatics
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Hallin, P.F.1
Ussery, D.W.2
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Global analysis of predicted proteomes: functional adaptation of physical properties
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Knight C.G., Kassen R., Hebestreit H., and Rainey P.B. Global analysis of predicted proteomes: functional adaptation of physical properties. Proc Natl Acad Sci USA 101 (2004) 8390-8395
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Knight, C.G.1
Kassen, R.2
Hebestreit, H.3
Rainey, P.B.4
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Genome update: DNA repeats in bacterial genomes
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Ussery D.W., Binnewies T.T., Gouveia-Oliveira R., Jarmer H., and Hallin P.F. Genome update: DNA repeats in bacterial genomes. Microbiology 150 (2004) 3519-3521
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Microbiology
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Binnewies, T.T.2
Gouveia-Oliveira, R.3
Jarmer, H.4
Hallin, P.F.5
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44
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Genome update: distribution of two-component transduction systems in 250 bacterial genomes
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Kiil K., Ferchaud J.B., David C., Binnewies T.T., Wu H., Sicheritz-Ponten T., Willenbrock H., and Ussery D.W. Genome update: distribution of two-component transduction systems in 250 bacterial genomes. Microbiology 151 (2005) 3447-3452
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Microbiology
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Kiil, K.1
Ferchaud, J.B.2
David, C.3
Binnewies, T.T.4
Wu, H.5
Sicheritz-Ponten, T.6
Willenbrock, H.7
Ussery, D.W.8
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Inference and analysis of the relative stability of bacterial chromosomes
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Study of the loss of synteny in bacterial chromosomes.
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Rocha E.P. Inference and analysis of the relative stability of bacterial chromosomes. Mol Biol Evo 23 (2006) 513-522. Study of the loss of synteny in bacterial chromosomes.
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Mol Biol Evo
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Rocha, E.P.1
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Towards a genome-based taxonomy for prokaryotes
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Comparisons of shared gene content show that taxonomic classifications of these genomes might need to be revised in light of whole proteome information.
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Konstantinidis K.T., and Tiedje J.M. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187 (2005) 6258-6264. Comparisons of shared gene content show that taxonomic classifications of these genomes might need to be revised in light of whole proteome information.
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J Bacteriol
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Konstantinidis, K.T.1
Tiedje, J.M.2
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47
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Toward automatic reconstruction of a highly resolved tree of life
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Genomes are an excellent source of phylogenetic markers. This study uses 31 orthologous loci, pruned for any cases of horizontal gene transfer from 191 genomes, to build the tree of life across all three domains.
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Ciccarelli F.D., Doerks T., von Mering C., Creevey C.J., Snel B., and Bork P. Toward automatic reconstruction of a highly resolved tree of life. Science 311 (2006) 1283-1287. Genomes are an excellent source of phylogenetic markers. This study uses 31 orthologous loci, pruned for any cases of horizontal gene transfer from 191 genomes, to build the tree of life across all three domains.
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Science
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Ciccarelli, F.D.1
Doerks, T.2
von Mering, C.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
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48
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Genomic insights that advance the species definition for prokaryotes
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The concept of a species is notoriously difficult to apply to bacteria. This study compared the gene content of 70 closely related and fully sequenced bacterial genomes. The results suggest that species boundaries do appear to exist, but are more conservative than current species definitions, and are better drawn on the basis of both ecology on shared gene content (evolutionary distance).
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Konstantinidis K.T., and Tiedje J.M. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102 (2005) 2567-2572. The concept of a species is notoriously difficult to apply to bacteria. This study compared the gene content of 70 closely related and fully sequenced bacterial genomes. The results suggest that species boundaries do appear to exist, but are more conservative than current species definitions, and are better drawn on the basis of both ecology on shared gene content (evolutionary distance).
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(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 2567-2572
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Konstantinidis, K.T.1
Tiedje, J.M.2
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Engineered bacteriophage-defence systems in bioprocessing
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Sturino J.M., and Klaenhammer T.R. Engineered bacteriophage-defence systems in bioprocessing. Nat Rev Microbiol 4 (2006) 395-404
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Nat Rev Microbiol
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Sturino, J.M.1
Klaenhammer, T.R.2
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50
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How genomics has affected the concept of microbiology
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An excellent overview of how the comparison of microbial genomes with the genomes from fungi and viruses (such as the mimivirus, which has a genome size more than double than that of the smallest bacteria and contains tRNA genes) is changing our concept of what it means to be a bacterium.
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Ward N., and Fraser C.M. How genomics has affected the concept of microbiology. Curr Opin Microbiol 8 (2005) 564-571. An excellent overview of how the comparison of microbial genomes with the genomes from fungi and viruses (such as the mimivirus, which has a genome size more than double than that of the smallest bacteria and contains tRNA genes) is changing our concept of what it means to be a bacterium.
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(2005)
Curr Opin Microbiol
, vol.8
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Ward, N.1
Fraser, C.M.2
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