-
1
-
-
0028946084
-
Phylogenetic identification and in situ detection of individual microbial cells without cultivation
-
Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
-
(1995)
Microbiol. Rev.
, vol.59
, pp. 143-169
-
-
Amann, R.I.1
Ludwig, W.2
Schleifer, K.H.3
-
2
-
-
0032456296
-
Molecular phylogenetic analysis of a bacterial community in Sulfur River, Parker Cave, Kentucky
-
Angert, E. R., D. E. Northup, A.-L. Reysenbach, A. S. Peek, B. M. Goebel, and N. R. Pace. 1998. Molecular phylogenetic analysis of a bacterial community in Sulfur River, Parker Cave, Kentucky. Am. Mineralogist 83:1583-1592.
-
(1998)
Am. Mineralogist
, vol.83
, pp. 1583-1592
-
-
Angert, E.R.1
Northup, D.E.2
Reysenbach, A.-L.3
Peek, A.S.4
Goebel, B.M.5
Pace, N.R.6
-
3
-
-
0034602344
-
A kingdom-level phylogeny of eukaryotes based on combined protein data
-
Baldauf, S. L., A. J. Roger, I. Wenk-Siefert, and W. F. Doolittle. 2000. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977.
-
(2000)
Science
, vol.290
, pp. 972-977
-
-
Baldauf, S.L.1
Roger, A.J.2
Wenk-Siefert, I.3
Doolittle, W.F.4
-
4
-
-
0029832927
-
Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences
-
Barns, S. M., C. F. Delwiche, J. D. Palmer, and N. R. Pace. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93:9188-9193.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 9188-9193
-
-
Barns, S.M.1
Delwiche, C.F.2
Palmer, J.D.3
Pace, N.R.4
-
5
-
-
20444491634
-
A review of long-branch attraction
-
Bergsten, J. 2005. A review of long-branch attraction. Cladistics 21:163-193.
-
(2005)
Cladistics
, vol.21
, pp. 163-193
-
-
Bergsten, J.1
-
6
-
-
0036793770
-
Microbial composition of near-boiling silica-depositing thermal springs throughout Yellowstone National Park
-
Blank, C. E., S. L. Cady, and N. R. Pace. 2002. Microbial composition of near-boiling silica-depositing thermal springs throughout Yellowstone National Park. Appl. Environ. Microbiol. 68:5123-5135.
-
(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 5123-5135
-
-
Blank, C.E.1
Cady, S.L.2
Pace, N.R.3
-
7
-
-
0034942865
-
Universal trees based on large combined protein sequence data sets
-
Brown, J. R., C. J. Douady, M. J. Italia, W. E. Marshall, and M. J. Stanhope. 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
-
8
-
-
2942571539
-
The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
-
Cannone, J. J., S. Subramanian, M. N. Schnare, J. R. Collett, L. M. D'Souza, Y. Du, B. Feng, N. Lin, L. V. Madabusi, K. M. Muller, N. Pande, Z. Shang, N. Yu, and R. R. Gutell. 2002. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinform. 3:2.
-
(2002)
BMC Bioinform.
, vol.3
, pp. 2
-
-
Cannone, J.J.1
Subramanian, S.2
Schnare, M.N.3
Collett, J.R.4
D'Souza, L.M.5
Du, Y.6
Feng, B.7
Lin, N.8
Madabusi, L.V.9
Muller, K.M.10
Pande, N.11
Shang, Z.12
Yu, N.13
Gutell, R.R.14
-
9
-
-
33644700003
-
Toward automatic reconstruction of a highly resolved tree of life
-
Ciccarelli, F. D., T. Doerks, C. von Mering, C. J. Creevey, B. Snel, and P. Bork. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287.
-
(2006)
Science
, vol.311
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
Doerks, T.2
Von Mering, C.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
-
10
-
-
58149200948
-
The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis
-
Cole, J. R., Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, T. Marsh, G. M. Garrity, and J. M. Tiedje. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-D145.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
Fish, J.4
Chai, B.5
Farris, R.J.6
Kulam-Syed-Mohideen, A.S.7
McGarrell, D.M.8
Marsh, T.9
Garrity, G.M.10
Tiedje, J.M.11
-
11
-
-
0035068917
-
A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data
-
Dalevi, D., P. Hugenholtz, and L. L. Blackall. 2001. A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data. Int. J. Syst. Evol. Microbiol. 51:385-391.
-
(2001)
Int. J. Syst. Evol. Microbiol.
, vol.51
, pp. 385-391
-
-
Dalevi, D.1
Hugenholtz, P.2
Blackall, L.L.3
-
13
-
-
0036061865
-
A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history
-
DOI 10.1101/gr.187002
-
Daubin, V., M. Gouy, and G. Perriere. 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
-
14
-
-
0037062470
-
Novel kingdom-level eukaryotic diversity in anoxic environments
-
Dawson, S. C., and N. R. Pace. 2002. Novel kingdom-level eukaryotic diversity in anoxic environments. Proc. Natl. Acad. Sci. USA 99:8324-8329.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 8324-8329
-
-
Dawson, S.C.1
Pace, N.R.2
-
15
-
-
19144362371
-
Microbial community genomics in the ocean
-
DeLong, E. F. 2005. Microbial community genomics in the ocean. Nat. Rev. Microbiol. 3:459-469.
-
(2005)
Nat. Rev. Microbiol.
, vol.3
, pp. 459-469
-
-
DeLong, E.F.1
-
16
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis, T. Z., P. Hugenholtz, N. Larsen, M. Rojas, E. L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G. L. Andersen. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:5069-5072.
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
Huber, T.7
Dalevi, D.8
Hu, P.9
Andersen, G.L.10
-
17
-
-
0032189023
-
Microbial diversity in a hydrocarbon- and chlorinated-solvent- contaminated aquifer undergoing intrinsic bioremediation
-
Dojka, M. A., P. Hugenholtz, S. K. Haack, and N. R. Pace. 1998. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64:3869-3877.
-
(1998)
Appl. Environ. Microbiol.
, vol.64
, pp. 3869-3877
-
-
Dojka, M.A.1
Hugenholtz, P.2
Haack, S.K.3
Pace, N.R.4
-
18
-
-
0000461280
-
Confidence limits on phylogenies: An approach using the bootstrap
-
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
19
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
-
(1981)
J. Mol. Evol.
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
20
-
-
71449098276
-
Natural history of the archaeal domain
-
R. A. Garrett and H.-P. Klenk (ed.), Blackwell, Malden, MA
-
Forterre, P., S. Gribaldo, and C. Brochier-Armanet. 2007. Natural history of the archaeal domain, p. 17-28. In R. A. Garrett and H.-P. Klenk (ed.), Archaea: evolution, physiology, and molecular biology. Blackwell, Malden, MA.
-
(2007)
Archaea: Evolution, Physiology, and Molecular Biology
, pp. 17-28
-
-
Forterre, P.1
Gribaldo, S.2
Brochier-Armanet, C.3
-
21
-
-
65549085150
-
The ultramicrobacterium "Elusimicrobium minutum" gen. nov., sp. nov., the first cultivated representative of the termite group 1 phylum
-
Geissinger, O., D. P. Herlemann, E. Morschel, U. G. Maier, and A. Brune. 2009. The ultramicrobacterium "Elusimicrobium minutum" gen. nov., sp. nov., the first cultivated representative of the termite group 1 phylum. Appl. Environ. Microbiol. 75:2831-2840.
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, pp. 2831-2840
-
-
Geissinger, O.1
Herlemann, D.P.2
Morschel, E.3
Maier, U.G.4
Brune, A.5
-
22
-
-
0024722874
-
+-ATPase: Implications for the origin of eukaryotes
-
+-ATPase: implications for the origin of eukaryotes. Proc. Natl. Acad. Sci. USA 86:6661-6665.
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.86
, pp. 6661-6665
-
-
Gogarten, J.P.1
Kibak, H.2
Dittrich, P.3
Taiz, L.4
Bowman, E.J.5
Bowman, B.J.6
Manolson, M.F.7
Poole, R.J.8
Date, T.9
Oshima, T.10
-
24
-
-
2342531664
-
New perspective on uncultured bacterial phylogenetic division OP11
-
Harris, J. K., S. T. Kelley, and N. R. Pace. 2004. New perspective on uncultured bacterial phylogenetic division OP11. Appl. Environ. Microbiol. 70:845-849.
-
(2004)
Appl. Environ. Microbiol.
, vol.70
, pp. 845-849
-
-
Harris, J.K.1
Kelley, S.T.2
Pace, N.R.3
-
25
-
-
65549153499
-
Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1)
-
Herlemann, D. P., O. Geissinger, W. Ikeda-Ohtsubo, V. Kunin, H. Sun, A. Lapidus, P. Hugenholtz, and A. Brune. 2009. Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1). Appl. Environ. Microbiol. 75:2841-2849.
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, pp. 2841-2849
-
-
Herlemann, D.P.1
Geissinger, O.2
Ikeda-Ohtsubo, W.3
Kunin, V.4
Sun, H.5
Lapidus, A.6
Hugenholtz, P.7
Brune, A.8
-
26
-
-
36549020646
-
Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: Insights into the pneumococcal supragenome
-
Hiller, N. L., B. Janto, J. S. Hogg, R. Boissy, S. Yu, E. Powell, R. Keefe, N. E. Ehrlich, K. Shen, J. Hayes, K. Barbadora, W. Klimke, D. Dernovoy, T. Tatusova, J. Parkhill, S. D. Bentley, J. C. Post, G. D. Ehrlich, and F. Z. Hu. 2007. Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J. Bacteriol. 189:8186-8195.
-
(2007)
J. Bacteriol.
, vol.189
, pp. 8186-8195
-
-
Hiller, N.L.1
Janto, B.2
Hogg, J.S.3
Boissy, R.4
Yu, S.5
Powell, E.6
Keefe, R.7
Ehrlich, N.E.8
Shen, K.9
Hayes, J.10
Barbadora, K.11
Klimke, W.12
Dernovoy, D.13
Tatusova, T.14
Parkhill, J.15
Bentley, S.D.16
Post, J.C.17
Ehrlich, G.D.18
Hu, F.Z.19
-
27
-
-
12044253190
-
An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis
-
Hillis, D. M. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
-
(1993)
Syst. Biol.
, vol.42
, pp. 182-192
-
-
Hillis, D.M.1
-
28
-
-
0028362880
-
Application and accuracy of molecular phylogenies
-
Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham. 1994. Application and accuracy of molecular phylogenies. Science 264:671-677.
-
(1994)
Science
, vol.264
, pp. 671-677
-
-
Hillis, D.M.1
Huelsenbeck, J.P.2
Cunningham, C.W.3
-
29
-
-
0003671904
-
-
2nd ed. Sinauer Associates, Inc., Sunderland, MA
-
Hillis, D. M., C. Moritz, and B. K. Mable. 1996. Molecular systematics, 2nd ed. Sinauer Associates, Inc., Sunderland, MA.
-
(1996)
Molecular Systematics
-
-
Hillis, D.M.1
Moritz, C.2
Mable, B.K.3
-
30
-
-
0037379673
-
Phylogeny estimation: Traditional and Bayesian approaches
-
Holder, M., and P. O. Lewis. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4:275-284.
-
(2003)
Nat. Rev. Genet.
, vol.4
, pp. 275-284
-
-
Holder, M.1
Lewis, P.O.2
-
31
-
-
0018369831
-
Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species
-
Hori, H., and S. Osawa. 1979. Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species. Proc. Natl. Acad. Sci. USA 76:381-385.
-
(1979)
Proc. Natl. Acad. Sci. USA
, vol.76
, pp. 381-385
-
-
Hori, H.1
Osawa, S.2
-
32
-
-
0036181778
-
Exploring prokaryotic diversity in the genomic era
-
0003
-
Hugenholtz, P. 2002. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3:reviews0003.1-0003.8. (Pubitemid 34162808)
-
(2002)
Genome Biology
, vol.3
, Issue.2
-
-
Hugenholtz, P.1
-
33
-
-
0031912606
-
Novel division level bacterial diversity in a Yellowstone hot spring
-
Hugenholtz, P., C. Pitulle, K. L. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180:366-376. (Pubitemid 28100302)
-
(1998)
Journal of Bacteriology
, vol.180
, Issue.2
, pp. 366-376
-
-
Hugenholtz, P.1
Pitulle, C.2
Hershberger, K.L.3
Pace, N.R.4
-
34
-
-
0035163571
-
Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives
-
Hugenholtz, P., G. W. Tyson, R. I. Webb, A. M. Wagner, and L. L. Blackall. 2001. Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives. Appl. Environ. Microbiol. 67:411-419.
-
(2001)
Appl. Environ. Microbiol.
, vol.67
, pp. 411-419
-
-
Hugenholtz, P.1
Tyson, G.W.2
Webb, R.I.3
Wagner, A.M.4
Blackall, L.L.5
-
35
-
-
0024358140
-
Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes
-
Iwabe, N., K. Kuma, M. Hasegawa, S. Osawa, and T. Miyata. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. USA 86:9355-9359.
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.86
, pp. 9355-9359
-
-
Iwabe, N.1
Kuma, K.2
Hasegawa, M.3
Osawa, S.4
Miyata, T.5
-
36
-
-
27444442657
-
The tree of eukaryotes
-
Keeling, P. J., G. Burger, D. G. Durnford, B. F. Lang, R. W. Lee, R. E. Pearlman, A. J. Roger, and M. W. Gray. 2005. The tree of eukaryotes. Trends Ecol. Evol. 20:670-676.
-
(2005)
Trends Ecol. Evol.
, vol.20
, pp. 670-676
-
-
Keeling, P.J.1
Burger, G.2
Durnford, D.G.3
Lang, B.F.4
Lee, R.W.5
Pearlman, R.E.6
Roger, A.J.7
Gray, M.W.8
-
37
-
-
0033977617
-
Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi
-
Keeling, P. J., M. A. Luker, and J. D. Palmer. 2000. Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi. Mol. Biol. Evol. 17:23-31.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 23-31
-
-
Keeling, P.J.1
Luker, M.A.2
Palmer, J.D.3
-
38
-
-
39149110563
-
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans
-
King, N., M. J. Westbrook, S. L. Young, A. Kuo, M. Abedin, J. Chapman, S. Fairclough, U. Hellsten, Y. Isogai, I. Letunic, M. Marr, D. Pincus, N. Putnam, A. Rokas, K. J. Wright, R. Zuzow, W. Dirks, M. Good, D. Goodstein, D. Lemons, W. Li, J. B. Lyons, A. Morris, S. Nichols, D. J. Richter, A. Salamov, J. G. Sequencing, P. Bork, W. A. Lim, G. Manning, W. T. Miller, W. McGinnis, H. Shapiro, R. Tjian, I. V. Grigoriev, and D. Rokhsar. 2008. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451:783-788.
-
(2008)
Nature
, vol.451
, pp. 783-788
-
-
King, N.1
Westbrook, M.J.2
Young, S.L.3
Kuo, A.4
Abedin, M.5
Chapman, J.6
Fairclough, S.7
Hellsten, U.8
Isogai, Y.9
Letunic, I.10
Marr, M.11
Pincus, D.12
Putnam, N.13
Rokas, A.14
Wright, K.J.15
Zuzow, R.16
Dirks, W.17
Good, M.18
Goodstein, D.19
Lemons, D.20
Li, W.21
Lyons, J.B.22
Morris, A.23
Nichols, S.24
Richter, D.J.25
Salamov, A.26
Sequencing, J.G.27
Bork, P.28
Lim, W.A.29
Manning, G.30
Miller, W.T.31
McGinnis, W.32
Shapiro, H.33
Tjian, R.34
Grigoriev, I.V.35
Rokhsar, D.36
more..
-
39
-
-
0035173421
-
rrndb: The Ribosomal RNA operon copy number database
-
Klappenbach, J. A., P. R. Saxman, J. R. Cole, and T. M. Schmidt. 2001. rrndb: the Ribosomal RNA operon copy number database. Nucleic Acids Res. 29:181-184.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 181-184
-
-
Klappenbach, J.A.1
Saxman, P.R.2
Cole, J.R.3
Schmidt, T.M.4
-
40
-
-
0032955637
-
RNA polymerase of Aquifex pyrophilus: Implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria
-
Klenk, H. P., T. D. Meier, P. Durovic, V. Schwass, F. Lottspeich, P. P. Dennis, and W. Zillig. 1999. RNA polymerase of Aquifex pyrophilus: implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria. J. Mol. Evol. 48:528-541.
-
(1999)
J. Mol. Evol.
, vol.48
, pp. 528-541
-
-
Klenk, H.P.1
Meier, T.D.2
Durovic, P.3
Schwass, V.4
Lottspeich, F.5
Dennis, P.P.6
Zillig, W.7
-
41
-
-
0026613365
-
The early evolution of eukaryotes: A geological perspective
-
Knoll, A. H. 1992. The early evolution of eukaryotes: a geological perspective. Science 256:622-627.
-
(1992)
Science
, vol.256
, pp. 622-627
-
-
Knoll, A.H.1
-
42
-
-
25644435673
-
Isolation of an autotrophic ammonia-oxidizing marine archaeon
-
DOI 10.1038/nature03911, PII N03911
-
Konneke, M., A. E. Bernhard, J. R. de la Torre, C. B. Walker, J. B. Waterbury, and D. A. Stahl. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543-546. (Pubitemid 41613550)
-
(2005)
Nature
, vol.437
, Issue.7058
, pp. 543-546
-
-
Konneke, M.1
Bernhard, A.E.2
De La Torre, J.R.3
Walker, C.B.4
Waterbury, J.B.5
Stahl, D.A.6
-
43
-
-
34250665888
-
RNAmmer: Consistent and rapid annotation of ribosomal RNA genes
-
DOI 10.1093/nar/gkm160
-
Lagesen, K., P. Hallin, E. A. Rodland, H. H. Staerfeldt, T. Rognes, and D. W. Ussery. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100-3108. (Pubitemid 47073647)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.9
, pp. 3100-3108
-
-
Lagesen, K.1
Hallin, P.2
Rodland, E.A.3
Staerfeldt, H.-H.4
Rognes, T.5
Ussery, D.W.6
-
44
-
-
0037108325
-
The closest unicellular relatives of animals
-
Lang, B. F., C. O'Kelly, T. Nerad, M. W. Gray, and G. Burger. 2002. The closest unicellular relatives of animals. Curr. Biol. 12:1773-1778.
-
(2002)
Curr. Biol.
, vol.12
, pp. 1773-1778
-
-
Lang, B.F.1
O'Kelly, C.2
Nerad, T.3
Gray, M.W.4
Burger, G.5
-
45
-
-
64549128536
-
DNA replication and cell cycle
-
R. Caviccioli (ed.), ASM Press, Washington, DC
-
Lao-Sirieix, S.-H., V. L. Marsh, and S. D. Bell. 2007. DNA replication and cell cycle, p. 93-109. In R. Caviccioli (ed.), Archaea: molecular and cellular biology. ASM Press, Washington, DC.
-
(2007)
Archaea: Molecular and Cellular Biology
, pp. 93-109
-
-
Lao-Sirieix, S.-H.1
Marsh, V.L.2
Bell, S.D.3
-
46
-
-
34548846699
-
Evolution of the core and pangenome of Streptococcus: Positive selection, recombination, and genome composition
-
Lefebvre, T., and M. J. Stanhope. 2007. Evolution of the core and pangenome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol. 8:R71.
-
(2007)
Genome Biol.
, vol.8
-
-
Lefebvre, T.1
Stanhope, M.J.2
-
47
-
-
33646584137
-
Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat
-
Ley, R. E., J. K. Harris, J. Wilcox, J. R. Spear, S. R. Miller, B. M. Bebout, J. A. Maresca, D. A. Bryant, M. L. Sogin, and N. R. Pace. 2006. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl. Environ. Microbiol. 72:3685-3695.
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 3685-3695
-
-
Ley, R.E.1
Harris, J.K.2
Wilcox, J.3
Spear, J.R.4
Miller, S.R.5
Bebout, B.M.6
Maresca, J.A.7
Bryant, D.A.8
Sogin, M.L.9
Pace, N.R.10
-
48
-
-
0030031972
-
Phylogenetic diversity of the intestinal bacterial community in the termite Reticulitermes speratus
-
Ohkuma, M., and T. Kudo. 1996. Phylogenetic diversity of the intestinal bacterial community in the termite Reticulitermes speratus. Appl. Environ. Microbiol. 62:461-468.
-
(1996)
Appl. Environ. Microbiol.
, vol.62
, pp. 461-468
-
-
Ohkuma, M.1
Kudo, T.2
-
49
-
-
0022462668
-
Microbial ecology and evolution: A ribosomal RNA approach
-
Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace, and D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40:337-365.
-
(1986)
Annu. Rev. Microbiol.
, vol.40
, pp. 337-365
-
-
Olsen, G.J.1
Lane, D.J.2
Giovannoni, S.J.3
Pace, N.R.4
Stahl, D.A.5
-
50
-
-
0030982247
-
A molecular view of microbial diversity and the biosphere
-
Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-740.
-
(1997)
Science
, vol.276
, pp. 734-740
-
-
Pace, N.R.1
-
51
-
-
0034019771
-
Phylogeny of eukaryotes based on ribosomal RNA: Long-branch attraction and models of sequence evolution
-
Philippe, H., and A. Germot. 2000. Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution. Mol. Biol. Evol. 17:830-834.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 830-834
-
-
Philippe, H.1
Germot, A.2
-
52
-
-
37549027613
-
SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
-
Pruesse, E., C. Quast, K. Knittel, B. M. Fuchs, W. Ludwig, J. Peplies, and F. O. Glockner. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35:7188-7196.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
Quast, C.2
Knittel, K.3
Fuchs, B.M.4
Ludwig, W.5
Peplies, J.6
Glockner, F.O.7
-
53
-
-
68149093715
-
Search for a 'Tree of Life' in the thicket of the phylogenetic forest
-
Puigbo, P., Y. I. Wolf, and E. V. Koonin. 2009. Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J. Biol. 8:59.
-
(2009)
J. Biol.
, vol.8
, pp. 59
-
-
Puigbo, P.1
Wolf, Y.I.2
Koonin, E.V.3
-
55
-
-
53849104729
-
The pangenome structure of Escherichia coli: Comparative genomic analysis of E. coli commensal and pathogenic isolates
-
Rasko, D. A., M. J. Rosovitz, G. S. Myers, E. F. Mongodin, W. F. Fricke, P. Gajer, J. Crabtree, M. Sebaihia, N. R. Thomson, R. Chaudhuri, I. R. Henderson, V. Sperandio, and J. Ravel. 2008. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J. Bacteriol. 190:6881-6893.
-
(2008)
J. Bacteriol.
, vol.190
, pp. 6881-6893
-
-
Rasko, D.A.1
Rosovitz, M.J.2
Myers, G.S.3
Mongodin, E.F.4
Fricke, W.F.5
Gajer, P.6
Crabtree, J.7
Sebaihia, M.8
Thomson, N.R.9
Chaudhuri, R.10
Henderson, I.R.11
Sperandio, V.12
Ravel, J.13
-
57
-
-
27844500146
-
Phylogenetic diversity and ecology of environmental archaea
-
Robertson, C. E., J. K. Harris, J. R. Spear, and N. R. Pace. 2005. Phylogenetic diversity and ecology of environmental archaea. Curr. Opin. Microbiol. 8:638-642.
-
(2005)
Curr. Opin. Microbiol.
, vol.8
, pp. 638-642
-
-
Robertson, C.E.1
Harris, J.K.2
Spear, J.R.3
Pace, N.R.4
-
60
-
-
12544255323
-
The real 'kingdoms' of eukaryotes
-
Simpson, A. G., and A. J. Roger. 2004. The real 'kingdoms' of eukaryotes. Curr. Biol. 14:R693-R696.
-
(2004)
Curr. Biol.
, vol.14
-
-
Simpson, A.G.1
Roger, A.J.2
-
61
-
-
0024962760
-
Phylogenetic meaning of the kingdom concept: An unusual ribosomal RNA from Giardia lamblia
-
Sogin, M. L., J. H. Gunderson, H. J. Elwood, R. A. Alonso, and D. A. Peattie. 1989. Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia. Science 243:75-77.
-
(1989)
Science
, vol.243
, pp. 75-77
-
-
Sogin, M.L.1
Gunderson, J.H.2
Elwood, H.J.3
Alonso, R.A.4
Peattie, D.A.5
-
62
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored "rare biosphere."
-
Sogin, M. L., H. G. Morrison, J. A. Huber, D. M. Welch, S. M. Huse, P. R. Neal, J. M. Arrieta, and J. H. Herndl. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere." Proc. Natl. Acad. Sci. USA 103:12115-12120.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
Welch, D.M.4
Huse, S.M.5
Neal, P.R.6
Arrieta, J.M.7
Herndl, J.H.8
-
63
-
-
0028028182
-
Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology
-
Stackebrandt, E., and B. M. Goebel. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-849.
-
(1994)
Int. J. Syst. Bacteriol.
, vol.44
, pp. 846-849
-
-
Stackebrandt, E.1
Goebel, B.M.2
-
64
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
DOI 10.1093/bioinformatics/btl446
-
Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690. (Pubitemid 44642609)
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2688-2690
-
-
Stamatakis, A.1
-
66
-
-
0037252616
-
The EMBL Nucleotide Sequence Database: Major new developments
-
Stoesser, G., W. Baker, A. van den Broek, M. Garcia-Pastor, C. Kanz, T. Kulikova, R. Leinonen, Q. Lin, V. Lombard, R. Lopez, R. Mancuso, F. Nardone, P. Stoehr, M. A. Tuli, K. Tzouvara, and R. Vaughan. 2003. The EMBL Nucleotide Sequence Database: major new developments. Nucleic Acids Res. 31:17-22.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 17-22
-
-
Stoesser, G.1
Baker, W.2
Van Den Broek, A.3
Garcia-Pastor, M.4
Kanz, C.5
Kulikova, T.6
Leinonen, R.7
Lin, Q.8
Lombard, V.9
Lopez, R.10
Mancuso, R.11
Nardone, F.12
Stoehr, P.13
Tuli, M.A.14
Tzouvara, K.15
Vaughan, R.16
-
67
-
-
34447313685
-
Transcription: Mechanism and regulation
-
R. Caviccioli (ed.), ASM Press, Washington, DC
-
Thomm, M. 2007. Transcription: mechanism and regulation, p. 139-157. In R. Caviccioli (ed.), Archaea: molecular and cellular biology. ASM Press, Washington, DC.
-
(2007)
Archaea: Molecular and Cellular Biology
, pp. 139-157
-
-
Thomm, M.1
-
68
-
-
14544287770
-
Genotypic diversity within a natural coastal bacterioplankton population
-
Thompson, J. R., S. Pacocha, C. Pharino, V. Klepac-Ceraj, D. E. Hunt, J. Benoit, R. Sarma-Rupavtarm, D. L. Distel, and M. F. Polz. 2005. Genotypic diversity within a natural coastal bacterioplankton population. Science 307:1311-1313.
-
(2005)
Science
, vol.307
, pp. 1311-1313
-
-
Thompson, J.R.1
Pacocha, S.2
Pharino, C.3
Klepac-Ceraj, V.4
Hunt, D.E.5
Benoit, J.6
Sarma-Rupavtarm, R.7
Distel, D.L.8
Polz, M.F.9
-
69
-
-
20244376755
-
Comparative metagenomics of microbial communities
-
Tringe, S. G., C. von Mering, A. Kobayashi, A. A. Salamov, K. Chen, H. W. Chang, M. Podar, J. M. Short, E. J. Mathur, J. C. Detter, P. Bork, P. Hugenholtz, and E. M. Rubin. 2005. Comparative metagenomics of microbial communities. Science 308:554-557.
-
(2005)
Science
, vol.308
, pp. 554-557
-
-
Tringe, S.G.1
Von Mering, C.2
Kobayashi, A.3
Salamov, A.A.4
Chen, K.5
Chang, H.W.6
Podar, M.7
Short, J.M.8
Mathur, E.J.9
Detter, J.C.10
Bork, P.11
Hugenholtz, P.12
Rubin, E.M.13
-
70
-
-
0027241482
-
Monophyletic origins of the metazoa: An evolutionary link with fungi
-
Wainright, P. O., G. Hinkle, M. L. Sogin, and S. K. Stickel. 1993. Monophyletic origins of the metazoa: an evolutionary link with fungi. Science 260:340-342. (Pubitemid 23160139)
-
(1993)
Science
, vol.260
, Issue.5106
, pp. 340-342
-
-
Wainright, P.O.1
Hinkle, G.2
Sogin, M.L.3
Stickel, S.K.4
-
71
-
-
0023184331
-
Bacterial evolution
-
Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
-
(1987)
Microbiol. Rev.
, vol.51
, pp. 221-271
-
-
Woese, C.R.1
-
72
-
-
0034682457
-
Interpreting the universal phylogenetic tree
-
Woese, C. R. 2000. Interpreting the universal phylogenetic tree. Proc. Natl. Acad. Sci. USA 97:8392-8396.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 8392-8396
-
-
Woese, C.R.1
-
73
-
-
0001271789
-
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
-
Woese, C. R., and G. E. Fox. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA 74:5088-5090.
-
(1977)
Proc. Natl. Acad. Sci. USA
, vol.74
, pp. 5088-5090
-
-
Woese, C.R.1
Fox, G.E.2
-
74
-
-
0025300402
-
Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
-
Woese, C. R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:4576-4579.
-
(1990)
Proc. Natl. Acad. Sci. USA
, vol.87
, pp. 4576-4579
-
-
Woese, C.R.1
Kandler, O.2
Wheelis, M.L.3
-
75
-
-
0036719929
-
Genome trees and the tree of life
-
Wolf, Y. I., I. B. Rogozin, N. V. Grishin, and E. V. Koonin. 2002. Genome trees and the tree of life. Trends Genet. 18:472-479.
-
(2002)
Trends Genet.
, vol.18
, pp. 472-479
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Grishin, N.V.3
Koonin, E.V.4
-
76
-
-
39749201627
-
Broadly sampled multigene trees of eukaryotes
-
Yoon, H. S., J. Grant, Y. I. Tekle, M. Wu, B. C. Chaon, J. C. Cole, J. M. Logsdon, Jr., D. J. Patterson, D. Bhattacharya, and L. A. Katz. 2008. Broadly sampled multigene trees of eukaryotes. BMC Evol. Biol. 8:14.
-
(2008)
BMC Evol. Biol.
, vol.8
, pp. 14
-
-
Yoon, H.S.1
Grant, J.2
Tekle, Y.I.3
Wu, M.4
Chaon, B.C.5
Cole, J.C.6
Logsdon Jr., J.M.7
Patterson, D.J.8
Bhattacharya, D.9
Katz, L.A.10
-
77
-
-
0013776758
-
Molecules as documents of evolutionary history
-
Zuckerkandl, E., and L. Pauling. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8:357-366.
-
(1965)
J. Theor. Biol.
, vol.8
, pp. 357-366
-
-
Zuckerkandl, E.1
Pauling, L.2
-
78
-
-
0036699481
-
Increased taxon sampling greatly reduces phylogenetic error
-
Zwickl, D. J., and D. M. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51:588-598.
-
(2002)
Syst. Biol.
, vol.51
, pp. 588-598
-
-
Zwickl, D.J.1
Hillis, D.M.2
|