-
1
-
-
0023930214
-
Conway de Macario, E., and Daniels, L
-
Belay, N., Johnson, R., Rajagopal, B. S., Conway de Macario, E., and Daniels, L. (1988). Methanogenic bacteria from human dental plaque. Appl. Environ. Microbiol. 54, 600-603.
-
(1988)
Appl. Environ. Microbiol.
, vol.54
, pp. 600-603
-
-
Belay, N.1
Johnson, R.2
Rajagopal, B.S.3
-
2
-
-
83755194968
-
CRISPR loci reveal networks of gene exchange in archaea
-
Brodt, A., Lurie-Weinberger, M. N., and Gophna, U. (2012). CRISPR loci reveal networks of gene exchange in archaea. Biol. Direct 6, 65.
-
(2012)
Biol. Direct
, vol.6
, pp. 65
-
-
Brodt, A.1
Lurie-Weinberger, M.N.2
Gophna, U.3
-
3
-
-
0035988323
-
The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea
-
Deppenmeier, U., Johann, A., Hartsch, T., Merkl, R., Schmitz, R. A., Martinez-Arias, R., Henne, A., Wiezer, A., Baumer, S., Jacobi, C., Bruggemann, H., Lienard, T., Christmann, A., Bomeke, M., Steckel, S., Bhattacharyya, A., Lykidis, A., Overbeek, R., Klenk, H. P., Gunsalus, R. P., Fritz, H. J., and Gottschalk, G. (2002). The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J. Mol. Microbiol. Biotechnol. 4, 453-461.
-
(2002)
J. Mol. Microbiol. Biotechnol.
, vol.4
, pp. 453-461
-
-
Deppenmeier, U.1
Johann, A.2
Hartsch, T.3
Merkl, R.4
Schmitz, R.A.5
Martinez-Arias, R.6
Henne, A.7
Wiezer, A.8
Baumer, S.9
Jacobi, C.10
Bruggemann, H.11
Lienard, T.12
Christmann, A.13
Bomeke, M.14
Steckel, S.15
Bhattacharyya, A.16
Lykidis, A.17
Overbeek, R.18
Klenk, H.P.19
Gunsalus, R.P.20
Fritz, H.J.21
Gottschalk, G.22
more..
-
4
-
-
0037471694
-
How big is the iceberg of which organellar genes in nuclear genomes are but the tip
-
discussion 57-38
-
Doolittle, W. F., Boucher, Y., Nesbo, C. L., Douady, C. J., Andersson, J. O., and Roger, A. J. (2003). How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Philos. Trans. R. Soc. Lond. B Biol. Sci. 358, 39-57; discussion 57-38.
-
(2003)
Philos Trans. R. Soc. Lond. B Biol. Sci.
, vol.358
, pp. 39-57
-
-
Doolittle, W.F.1
Boucher, Y.2
Nesbo, C.L.3
Douady, C.J.4
Andersson, J.O.5
Roger, A.J.6
-
5
-
-
70349408423
-
High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol
-
doi:10.1371/journal.pone.0007063
-
Dridi, B., Henry, M., El Khechine, A., Raoult, D., and Drancourt, M. (2009). High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS ONE 4, e7063. doi:10.1371/journal.pone.0007063
-
(2009)
PLoS ONE
, vol.4
-
-
Dridi, B.1
Henry, M.2
El Khechine, A.3
Raoult, D.4
Drancourt, M.5
-
6
-
-
20544444045
-
Diversity of the human intestinal microbial flora
-
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill,S.R.,Nelson,K. E., and Relman, D. A. (2005). Diversity of the human intestinal microbial flora. Science 308, 1635-1638.
-
(2005)
Science
, vol.308
, pp. 1635-1638
-
-
Eckburg, P.B.1
Bik, E.M.2
Bernstein, C.N.3
Purdom, E.4
Dethlefsen, L.5
Sargent, M.6
Gill, S.R.7
Nelson, K.E.8
Relman, D.A.9
-
7
-
-
30744456055
-
The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation andATP synthesis
-
Fricke, W. F., Seedorf, H., Henne, A., Kruer, M., Liesegang, H., Hedderich, R., Gottschalk, G., and Thauer, R. K. (2006). The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. J. Bacteriol. 188, 642-658.
-
(2006)
J. Bacteriol.
, vol.188
, pp. 642-658
-
-
Fricke, W.F.1
Seedorf, H.2
Henne, A.3
Kruer, M.4
Liesegang, H.5
Hedderich, R.6
Gottschalk, G.7
Thauer, R.K.8
-
8
-
-
4944233611
-
Phy-loGenie: automated phylome generation and analysis
-
Frickey, T.,and Lupas,A.N. (2004). Phy-loGenie: automated phylome generation and analysis. Nucleic Acids Res. 32, 5231-5238.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 5231-5238
-
-
Frickey, T.1
Lupas, A.N.2
-
9
-
-
78649821044
-
Conflicts targeting epige-netic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems
-
Ishikawa,K.,Fukuda,E.,and Kobayashi, I. (2010). Conflicts targeting epige-netic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems. DNA Res. 17, 325-342.
-
(2010)
DNA Res
, vol.17
, pp. 325-342
-
-
Ishikawa, K.1
Fukuda, E.2
Kobayashi, I.3
-
10
-
-
46249085739
-
Evolution of mammals and their gut microbes
-
Ley, R. E., Hamady, M., Lozupone, C., Turnbaugh, P. J., Ramey, R. R., Bircher, J. S., Schlegel, M. L., Tucker, T. A., Schrenzel, M. D., Knight, R., and Gordon, J. I. (2008). Evolution of mammals and their gut microbes. Science 320, 1647-1651.
-
(2008)
Science
, vol.320
, pp. 1647-1651
-
-
Ley, R.E.1
Hamady, M.2
Lozupone, C.3
Turnbaugh, P.J.4
Ramey, R.R.5
Bircher, J.S.6
Schlegel, M.L.7
Tucker, T.A.8
Schrenzel, M.D.9
Knight, R.10
Gordon, J.I.11
-
11
-
-
67650699549
-
Gene order phy-logeny and the evolution of methanogens
-
doi:10.1371/journal.pone.0006069
-
Luo, H., Zhiyi, S., Arndt, W., Shi, J., Friedman, R., and Tang, J. (2009). Gene order phy-logeny and the evolution of methanogens. PLoS ONE 4, e6069. doi:10.1371/journal.pone.0006069
-
(2009)
PLoS ONE
, vol.4
-
-
Luo, H.1
Zhiyi, S.2
Arndt, W.3
Shi, J.4
Friedman, R.5
Tang, J.6
-
12
-
-
84855189641
-
Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen
-
Lurie-Weinberger, M. N., Peeri, M., and Gophna, U. (2011). Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen. Genomics 99, 52-58.
-
(2011)
Genomics
, vol.99
, pp. 52-58
-
-
Lurie-Weinberger, M.N.1
Peeri, M.2
Gophna, U.3
-
13
-
-
0021921541
-
Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen
-
Miller, T. L., and Wolin, M. J. (1985). Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen. Arch. Microbiol. 141, 116-122.
-
(1985)
Arch. Microbiol.
, vol.141
, pp. 116-122
-
-
Miller, T.L.1
Wolin, M.J.2
-
14
-
-
0033609333
-
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
-
Nelson, K. E., Clayton, R. A., Gill, S. R., Gwinn, M. L., Dodson, R. J., Haft, D. H., Hickey, E. K., Peterson, J. D., Nelson, W. C., Ketchum, K. A., Mcdonald, L., Utterback, T. R., Malek, J. A., Linher, K. D., Gar-rett, M. M., Stewart, A. M., Cotton, M. D., Pratt, M. S., Phillips, C. A., Richardson, D., Heidelberg, J., Sutton, G. G., Fleischmann, R. D., Eisen, J. A., White, O., Salzberg, S. L., Smith, H. O.,Venter, J. C., and Fraser, C. M. (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
Clayton, R.A.2
Gill, S.R.3
Gwinn, M.L.4
Dodson, R.J.5
Haft, D.H.6
Hickey, E.K.7
Peterson, J.D.8
Nelson, W.C.9
Ketchum, K.A.10
Mcdonald, L.11
Utterback, T.R.12
Malek, J.A.13
Linher, K.D.14
Gar-rett, M.M.15
Stewart, A.M.16
Cotton, M.D.17
Pratt, M.S.18
Phillips, C.A.19
Richardson, D.20
Heidelberg, J.21
Sutton, G.G.22
Fleischmann, R.D.23
Eisen, J.A.24
White, O.25
Salzberg, S.L.26
Smith, H.O.27
Venter, J.C.28
Fraser, C.M.29
more..
-
15
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
Ochman, H., Lawrence, J. G., and Groisman, E. A. (2000). Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299-304.
-
(2000)
Nature
, vol.405
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.A.3
-
16
-
-
0023375195
-
The neighbor-joining method: a new method for reconstructing phylo-genetic trees
-
Saitou, N., and Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylo-genetic trees. Mol. Biol. Evol. 4, 406-425.
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
17
-
-
34447296622
-
Genomic and metabolic adaptations of Methanobre-vibacter smithii to the human gut
-
Samuel, B. S., Hansen, E. E., Manchester, J. K., Coutinho, P. M., Hen-rissat, B., Fulton, R., Latreille, P., Kim, K., Wilson, R. K., and Gor-don,J. I. (2007). Genomic and metabolic adaptations of Methanobre-vibacter smithii to the human gut. Proc. Natl. Acad. Sci. U.S.A. 104, 10643-10648.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 10643-10648
-
-
Samuel, B.S.1
Hansen, E.E.2
Manchester, J.K.3
Coutinho, P.M.4
Hen-rissat, B.5
Fulton, R.6
Latreille, P.7
Kim, K.8
Wilson, R.K.9
Gordon, J.I.10
-
18
-
-
0023650543
-
The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications
-
Sharp, P. M., and Li, W. H. (1987). The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15, 1281-1295.
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
19
-
-
5044247756
-
INCA: synonymous codon usage analysis and clustering by means of self-organizing map
-
Supek, F., and Vlahovicek, K. (2004). INCA: synonymous codon usage analysis and clustering by means of self-organizing map. Bioinformatics 20, 2329-2330.
-
(2004)
Bioinformatics
, vol.20
, pp. 2329-2330
-
-
Supek, F.1
Vlahovicek, K.2
-
20
-
-
74949120671
-
Reconstructing ancestral gene content by coevolution
-
Tuller, T., Birin, H., Gophna, U., Kupiec, M., and Ruppin, E. (2010). Reconstructing ancestral gene content by coevolution. Genome Res. 20, 122-132.
-
(2010)
Genome Res
, vol.20
, pp. 122-132
-
-
Tuller, T.1
Birin, H.2
Gophna, U.3
Kupiec, M.4
Ruppin, E.5
-
21
-
-
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
|