-
1
-
-
0023103008
-
Were the original eubacteria thermophiles?
-
Achenbach-Richter, L., Gupta, R., Stetter, K. O. & Woese, C. R. (1987). Were the original eubacteria thermophiles? Syst Appl Microbiol 9, 34-39.
-
(1987)
Syst Appl Microbiol
, vol.9
, pp. 34-39
-
-
Achenbach-Richter, L.1
Gupta, R.2
Stetter, K.O.3
Woese, C.R.4
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402. (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
3
-
-
0034942865
-
Universal trees based on large combined protein sequence data sets
-
Brown, J. R., Douady, C. J., Italia, M. J., Marshall, W. E. & Stanhope, M. J. (2001). Universal trees based on large combined protein sequence data sets. Nat Genet 28, 281-285.
-
(2001)
Nat Genet
, vol.28
, pp. 281-285
-
-
Brown, J.R.1
Douady, C.J.2
Italia, M.J.3
Marshall, W.E.4
Stanhope, M.J.5
-
4
-
-
0033988719
-
Phylogeny of sulfate-reducing bacteria
-
Castro, H. F., Williams, N. H. & Ogram, A. (2000). Phylogeny of sulfate-reducing bacteria. FEMS Microbiol Ecol 31, 1-9.
-
(2000)
FEMS Microbiol Ecol
, vol.31
, pp. 1-9
-
-
Castro, H.F.1
Williams, N.H.2
Ogram, A.3
-
5
-
-
33644700003
-
Toward automatic reconstruction of a highly resolved tree of life
-
DOI 10.1126/science.1123061
-
Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B. & Bork, P. (2006). Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287. (Pubitemid 43334717)
-
(2006)
Science
, vol.311
, Issue.5765
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
Doerks, T.2
Von Mering, C.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
-
6
-
-
2642588849
-
A genomic perspective on the relationship between the Aquificales and the epsilon-Proteobacteria
-
DOI 10.1078/0723-2020-00272
-
Coenye, T. & Vandamme, P. (2004). A genomic perspective on the relationship between the Aquificales and the epsilon-Proteobacteria. Syst Appl Microbiol 27, 313-322. (Pubitemid 38724492)
-
(2004)
Systematic and Applied Microbiology
, vol.27
, Issue.3
, pp. 313-322
-
-
Coenye, T.1
Vandamme, P.2
-
7
-
-
0032169271
-
Conservation of gene order: A fingerprint of proteins that physically interact
-
DOI 10.1016/S0968-0004(98)01274-2, PII S0968000498012742
-
Dandekar, T., Snel, B., Huynen, M. & Bork, P. (1998). Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 23, 324-328. (Pubitemid 28461862)
-
(1998)
Trends in Biochemical Sciences
, vol.23
, Issue.9
, pp. 324-328
-
-
Dandekar, T.1
Snel, B.2
Huynen, M.3
Bork, P.4
-
8
-
-
0036061865
-
A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history
-
DOI 10.1101/gr.187002
-
Daubin, V., Gouy, M. & Perriere, G. (2002). A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 12, 1080-1090. (Pubitemid 34785201)
-
(2002)
Genome Research
, vol.12
, Issue.7
, pp. 1080-1090
-
-
Daubin, V.1
Gouy, M.2
Perriere, G.3
-
9
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
Delsuc, F., Brinkmann, H. & Philippe, H. (2005). Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6, 361-375.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
10
-
-
0031756681
-
Coprothermobacter platensis sp. nov., a new anaerobic proteolytic thermophilic bacterium isolated from an anaerobic mesophilic sludge
-
Etchebehere, C., Pavan, M. E., Zorzópulos, J., Soubes, M. & Muxí, L. (1998). Coprothermobacter platensis sp. nov., a new anaerobic proteolytic thermophilic bacterium isolated from an anaerobic mesophilic sludge. Int J Syst Bacteriol 48, 1297-1304. (Pubitemid 28523342)
-
(1998)
International Journal of Systematic Bacteriology
, vol.48
, Issue.4
, pp. 1297-1304
-
-
Etchebehere, C.1
Pavan, M.E.2
Zorzopulos, J.3
Soubes, M.4
Muxi, L.5
-
11
-
-
2542452389
-
Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales
-
Griffiths, E. & Gupta, R. S. (2004). Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquificales. Int Microbiol 7, 41-52. (Pubitemid 38901144)
-
(2004)
International Microbiology
, vol.7
, Issue.1
, pp. 41-52
-
-
Griffiths, E.1
Gupta, R.S.2
-
12
-
-
34547910719
-
Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae
-
DOI 10.1099/mic.0.2007/009118-0
-
Griffiths, E. & Gupta, R. S. (2007). Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae. Microbiology 153, 2648-2654. (Pubitemid 47262054)
-
(2007)
Microbiology
, vol.153
, Issue.8
, pp. 2648-2654
-
-
Griffiths, E.1
Gupta, R.S.2
-
13
-
-
0031794743
-
Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria and eukaryotes
-
Gupta, R. S. (1998). Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria and eukaryotes. Microbiol Mol Biol Rev 62, 1435-1491.
-
(1998)
Microbiol Mol Biol Rev
, vol.62
, pp. 1435-1491
-
-
Gupta, R.S.1
-
14
-
-
0042861279
-
Evolutionary relationships among photosynthetic bacteria
-
Gupta, R. S. (2003). Evolutionary relationships among photosynthetic bacteria. Photosynth Res 76, 173-183.
-
(2003)
Photosynth Res
, vol.76
, pp. 173-183
-
-
Gupta, R.S.1
-
15
-
-
0036597701
-
Critical issues in bacterial phylogenies
-
Gupta, R. S. & Griffiths, E. (2002). Critical issues in bacterial phylogenies. Theor Popul Biol 61, 423-434.
-
(2002)
Theor Popul Biol
, vol.61
, pp. 423-434
-
-
Gupta, R.S.1
Griffiths, E.2
-
16
-
-
0027954493
-
Characterization of a new thermophilic sulfate-reducing bacterium Thermodesulfovibrio yellowstonii, gen. nov. and sp. nov.: Its phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain
-
Henry, E. A., Devereux, R., Maki, J. S., Gilmour, C. C., Woese, C. R., Mandelco, L., Schauder, R., Remsen, C. C. & Mitchell, R. (1994). Characterization of a new thermophilic sulfate-reducing bacterium Thermodesulfovibrio yellowstonii, gen. nov. and sp. nov.: its phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain. Arch Microbiol 161, 62-69.
-
(1994)
Arch Microbiol
, vol.161
, pp. 62-69
-
-
Henry, E.A.1
Devereux, R.2
Maki, J.S.3
Gilmour, C.C.4
Woese, C.R.5
Mandelco, L.6
Schauder, R.7
Remsen, C.C.8
Mitchell, R.9
-
17
-
-
0031662188
-
Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity
-
Hugenholtz, P., Goebel, B. M. & Pace, N. R. (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180, 4765-4774. (Pubitemid 28429361)
-
(1998)
Journal of Bacteriology
, vol.180
, Issue.18
, pp. 4765-4774
-
-
Hugenholtz, P.1
Goebel, B.M.2
Pace, N.R.3
-
18
-
-
2942576138
-
Evolution of bacterial RNA polymerase: Implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer
-
Iyer, L. M., Koonin, E. V. & Aravind, L. (2004). Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 335, 73-88.
-
(2004)
Gene
, vol.335
, pp. 73-88
-
-
Iyer, L.M.1
Koonin, E.V.2
Aravind, L.3
-
19
-
-
0033616714
-
Horizontal gene transfer among genomes: The complexity hypothesis
-
DOI 10.1073/pnas.96.7.3801
-
Jain, R., Rivera, M. C. & Lake, J. A. (1999). Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A 96, 3801-3806. (Pubitemid 29168991)
-
(1999)
Proceedings of the National Academy of Sciences of the United States of America
, vol.96
, Issue.7
, pp. 3801-3806
-
-
Jain, R.1
Rivera, M.C.2
Lake, J.A.3
-
20
-
-
0036499057
-
SHOT: A web server for the construction of genome phylogenies
-
DOI 10.1016/S0168-9525(01)02597-5, PII S0168952501025975
-
Korbel, J. O., Snel, B., Huynen, M. A. & Bork, P. (2002). SHOT: a web server for the construction of genome phylogenies. Trends Genet 18, 158-162. (Pubitemid 34164642)
-
(2002)
Trends in Genetics
, vol.18
, Issue.3
, pp. 158-162
-
-
Korbel, J.O.1
Snel, B.2
Huynen, M.A.3
Bork, P.4
-
21
-
-
0034992826
-
The closest BLAST hit is often not the nearest neighbor
-
Koski, L. B. & Golding, G. B. (2001). The closest BLAST hit is often not the nearest neighbor. J Mol Evol 52, 540-542.
-
(2001)
J Mol Evol
, vol.52
, pp. 540-542
-
-
Koski, L.B.1
Golding, G.B.2
-
22
-
-
0035824060
-
Gene arrangements and phylogeny in the class Proteobacteria
-
Kunisawa, T. (2001). Gene arrangements and phylogeny in the class Proteobacteria. J Theor Biol 213, 9-19.
-
(2001)
J Theor Biol
, vol.213
, pp. 9-19
-
-
Kunisawa, T.1
-
23
-
-
0037763690
-
Gene arrangements and branching orders of Gram-positive bacteria
-
Kunisawa, T. (2003). Gene arrangements and branching orders of Gram-positive bacteria. J Theor Biol 222, 495-503.
-
(2003)
J Theor Biol
, vol.222
, pp. 495-503
-
-
Kunisawa, T.1
-
24
-
-
33644907541
-
Dichotomy of major bacterial phyla inferred from gene arrangement comparisons
-
Kunisawa, T. (2006). Dichotomy of major bacterial phyla inferred from gene arrangement comparisons. J Theor Biol 239, 367-375.
-
(2006)
J Theor Biol
, vol.239
, pp. 367-375
-
-
Kunisawa, T.1
-
25
-
-
0030854739
-
TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe, T. M. & Eddy, S. R. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25, 955-964.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
26
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson, W. R. & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85, 2444-2448.
-
(1988)
Proc Natl Acad Sci U S a
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
27
-
-
0021828111
-
Dictyoglomus thermophilumn gen. nov., sp. nov., a chemoorganotrophic, anaerobic, thermophilic bacterium
-
Saiki, T., Kobayashi, Y., Kawagoe, K. & Beppu, T. (1985). Dictyoglomus thermophilum gen. nov., sp. nov., a chemoorganotrophic, anaerobic, thermophilic bacterium. Int J Syst Bacteriol 35, 253-259. (Pubitemid 15025685)
-
(1985)
International Journal of Systematic Bacteriology
, vol.35
, Issue.3
, pp. 253-259
-
-
Saiki, T.1
Kobayashi, Y.2
Kawagoe, K.3
Beppu, T.4
-
28
-
-
0026680446
-
Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome
-
Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B. F. & Cedergren, R. (1992). Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proc Natl Acad Sci U S A 89, 6575-6579.
-
(1992)
Proc Natl Acad Sci U S a
, vol.89
, pp. 6575-6579
-
-
Sankoff, D.1
Leduc, G.2
Antoine, N.3
Paquin, B.4
Lang, B.F.5
Cedergren, R.6
-
29
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov, R. L., Koonin, E. V. & Lipman, D. J. (1997). A genomic perspective on protein families. Science 278, 631-637.
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
30
-
-
0035162592
-
The COG database: New developments in phylogenetic classification of proteins from complete genomes
-
Tatusov, R. L., Natale, D. A., Garkavtsev, I. V., Tatusova, T. A., Shankavaram, U. T., Rao, B. S., Kiryutin, B., Galperin, M. Y., Fedorova, N. D. & Koonin, E. V. (2001). The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29, 22-28.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
Tatusova, T.A.4
Shankavaram, U.T.5
Rao, B.S.6
Kiryutin, B.7
Galperin, M.Y.8
Fedorova, N.D.9
Koonin, E.V.10
-
31
-
-
2942668180
-
Evaluation of the phylogenetic position of the planctomycete 'Rhodopirellula baltica' SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees
-
Teeling, H., Lombardot, T., Bauer, M., Ludwig, W. & Glöckner, F. O. (2004). Evaluation of the phylogenetic position of the planctomycete 'Rhodopirellula baltica' SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees. Int J Syst Evol Microbiol 54, 791-801.
-
(2004)
Int J Syst Evol Microbiol
, vol.54
, pp. 791-801
-
-
Teeling, H.1
Lombardot, T.2
Bauer, M.3
Ludwig, W.4
Glöckner, F.O.5
-
32
-
-
0028079873
-
Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria
-
Teske, A., Alm, E., Regan, J. M., Toze, S., Rittmann, B. E. & Stahl, D. A. (1994). Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria. J Bacteriol 176, 6623-6630. (Pubitemid 24338076)
-
(1994)
Journal of Bacteriology
, vol.176
, Issue.21
, pp. 6623-6630
-
-
Teske, A.1
Alm, E.2
Regan, J.M.3
Toze, S.4
Rittmann, B.E.5
Stahl, D.A.6
-
33
-
-
33744927902
-
The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance
-
Wagner, M. & Horn, M. (2006). The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol 17, 241-249.
-
(2006)
Curr Opin Biotechnol
, vol.17
, pp. 241-249
-
-
Wagner, M.1
Horn, M.2
-
34
-
-
63849207489
-
Three genomes from the phylum Acidobacteria provide insight into their lifestyles in soils
-
Ward, N. L., Challacombe, J. F., Janssen, P. H., Henrissat, B., Coutinho, P. M., Wu, M., Xie, G., Haft, D. H., Sait, M. & other authors (2009). Three genomes from the phylum Acidobacteria provide insight into their lifestyles in soils. Appl Environ Microbiol 75, 2046-2056.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 2046-2056
-
-
Ward, N.L.1
Challacombe, J.F.2
Janssen, P.H.3
Henrissat, B.4
Coutinho, P.M.5
Wu, M.6
Xie, G.7
Haft, D.H.8
Sait, M.9
-
35
-
-
0348044549
-
Genome trees constructed using five different approaches suggest new major bacterial clades
-
Wolf, Y. I., Rogozin, I. B., Grishin, N. V., Tatusov, R. L. & Koonin, E. V. (2001). Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 1, 8.
-
(2001)
BMC Evol Biol
, vol.1
, pp. 8
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Grishin, N.V.3
Tatusov, R.L.4
Koonin, E.V.5
-
36
-
-
55649110049
-
A simple, fast, and accurate method of phylogenomic inference
-
Wu, M. & Eisen, J. A. (2008). A simple, fast, and accurate method of phylogenomic inference. Genome Biol 9, R151.
-
(2008)
Genome Biol
, vol.9
-
-
Wu, M.1
Eisen, J.A.2
|