-
1
-
-
3242884054
-
Fine-scale phylogenetic architecture of a complex bacterial community
-
Acinas SG, Klepac-Ceraj V, Hunt DE, Pharino C, Ceraj I, Distel DL, Polz MF (2004a) Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430:551-554
-
(2004)
Nature
, vol.430
, pp. 551-554
-
-
Acinas, S.G.1
Klepac-Ceraj, V.2
Hunt, D.E.3
Pharino, C.4
Ceraj, I.5
Distel, D.L.6
Polz, M.F.7
-
2
-
-
1942443733
-
Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons
-
Acinas SG, Marcelino LA, Klepac-Ceraj V, Polz MF (2004b) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186:2629-2635
-
(2004)
J Bacteriol
, vol.186
, pp. 2629-2635
-
-
Acinas, S.G.1
Marcelino, L.A.2
Klepac-Ceraj, V.3
Polz, M.F.4
-
3
-
-
9744231340
-
Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, reck and rpoB gene sequencing
-
Adekambi T, Drancourt M (2004) Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, reck and rpoB gene sequencing. Int J Syst Evol Microbiol 54:2095-2105
-
(2004)
Int J Syst Evol Microbiol
, vol.54
, pp. 2095-2105
-
-
Adekambi, T.1
Drancourt, M.2
-
4
-
-
0036842986
-
Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia
-
Akman L, Yamashita A, Watanabe H, Oshima K, Shiba T, Hattori M, Aksoy S (2002) Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat Genet 32:402-407
-
(2002)
Nat Genet
, vol.32
, pp. 402-407
-
-
Akman, L.1
Yamashita, A.2
Watanabe, H.3
Oshima, K.4
Shiba, T.5
Hattori, M.6
Aksoy, S.7
-
5
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
-
(1997)
Nucleic Acids Res
, vol.25
, 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
-
6
-
-
0028946084
-
Phylogenetic identification and in situ detection of individual microbial cells without cultivation
-
Amann RI, Ludwig W, Schleifer KH (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
-
7
-
-
2942555655
-
Molecular typing and phylogenetic analysis of enteroinvasive Escherichia coli using the fliC gene sequence
-
Amhaz JM, Andrade A, Bando SY, Tanaka TL, Moreira-Filho CA, Martinez MB (2004) Molecular typing and phylogenetic analysis of enteroinvasive Escherichia coli using the fliC gene sequence. FEMS Microbiol Lett 235:259-264
-
(2004)
FEMS Microbiol Lett
, vol.235
, pp. 259-264
-
-
Amhaz, J.M.1
Andrade, A.2
Bando, S.Y.3
Tanaka, T.L.4
Moreira-Filho, C.A.5
Martinez, M.B.6
-
8
-
-
0034681511
-
Evidence for a high frequency of simultaneous double-nucleotide substitutions
-
Averof M, Rokas A, Wolfe KH, Sharp PM (2000) Evidence for a high frequency of simultaneous double-nucleotide substitutions. Science 287:1283-1286
-
(2000)
Science
, vol.287
, pp. 1283-1286
-
-
Averof, M.1
Rokas, A.2
Wolfe, K.H.3
Sharp, P.M.4
-
9
-
-
0242384034
-
Review and re-analysis of domain-specific 16S primers
-
Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55:541-555
-
(2003)
J Microbiol Methods
, vol.55
, pp. 541-555
-
-
Baker, G.C.1
Smith, J.J.2
Cowan, D.A.3
-
10
-
-
0034637111
-
The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
-
Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289:905-920
-
(2000)
Science
, vol.289
, pp. 905-920
-
-
Ban, N.1
Nissen, P.2
Hansen, J.3
Moore, P.B.4
Steitz, T.A.5
-
11
-
-
0027361334
-
Evaluation of a technique for identification of Shiga-like toxin-producing Escherichia coli by using polymerase chain reaction and digoxigenin-labeled probes
-
Begum D, Strockbine NA, Sowers EG, Jackson MP (1993) Evaluation of a technique for identification of Shiga-like toxin-producing Escherichia coli by using polymerase chain reaction and digoxigenin-labeled probes. J Clin Microbiol 31:3153-3156
-
(1993)
J Clin Microbiol
, vol.31
, pp. 3153-3156
-
-
Begum, D.1
Strockbine, N.A.2
Sowers, E.G.3
Jackson, M.P.4
-
13
-
-
2142814314
-
Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): A single residue dictates differences in novobiocin potency against topoisomerase IV and DNA gyrase
-
Bellon S, Parsons JD, Wei Y, Hayakawa K, Swenson LL, Charifson PS, Lippke JA, Aldape R, Gross CH (2004) Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potency against topoisomerase IV and DNA gyrase. Antimicrob Agents Chemother 48:1856-1864
-
(2004)
Antimicrob Agents Chemother
, vol.48
, pp. 1856-1864
-
-
Bellon, S.1
Parsons, J.D.2
Wei, Y.3
Hayakawa, K.4
Swenson, L.L.5
Charifson, P.S.6
Lippke, J.A.7
Aldape, R.8
Gross, C.H.9
-
14
-
-
0038222576
-
Discordant phylogenies within the rrn loci of Rhizobia
-
van Berkum P, Terefework Z, Paulin L, Suomalainen S, Lindstrom K, Eardly BD (2003) Discordant phylogenies within the rrn loci of Rhizobia. J Bacteriol 185:2988-2998
-
(2003)
J Bacteriol
, vol.185
, pp. 2988-2998
-
-
Van Berkum, P.1
Terefework, Z.2
Paulin, L.3
Suomalainen, S.4
Lindstrom, K.5
Eardly, B.D.6
-
15
-
-
0033948149
-
Phylogenetic depth of the bacterial genera Aquifex and Thermotoga inferred from analysis of ribosomal protein, elongation factor, and RNA polymerase subunit sequences
-
Bocchetta M, Gribaldo S, Sanangelantoni A, Cammarano P (2000) Phylogenetic depth of the bacterial genera Aquifex and Thermotoga inferred from analysis of ribosomal protein, elongation factor, and RNA polymerase subunit sequences. J Mol Evol 50:366-380
-
(2000)
J Mol Evol
, vol.50
, pp. 366-380
-
-
Bocchetta, M.1
Gribaldo, S.2
Sanangelantoni, A.3
Cammarano, P.4
-
16
-
-
0035201828
-
Phylogenetic inferences from molecular sequences: Review and critique
-
Brocchieri L (2001) Phylogenetic inferences from molecular sequences: review and critique. Theor Popul Biol 59:27-40
-
(2001)
Theor Popul Biol
, vol.59
, pp. 27-40
-
-
Brocchieri, L.1
-
17
-
-
0034942865
-
Universal trees based on large combined protein sequence data sets
-
Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ (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
-
18
-
-
0033860303
-
Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences
-
Chang BS, Campbell DL (2000) Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences. Mol Biol Evol 17:1220-1231
-
(2000)
Mol Biol Evol
, vol.17
, pp. 1220-1231
-
-
Chang, B.S.1
Campbell, D.L.2
-
19
-
-
0030024243
-
Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level
-
Cilia V, Lafay B, Christen R (1996) Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level. Mol Biol Evol 13:451-461
-
(1996)
Mol Biol Evol
, vol.13
, pp. 451-461
-
-
Cilia, V.1
Lafay, B.2
Christen, R.3
-
20
-
-
0029027263
-
Intraspecific variation in smallsubunit rRNA sequences in GenBank: Why single sequences may not adequately represent prokaryotic taxa
-
Clayton RA, Sutton G, Hinkle PS Jr, Bult C, Fields C (1995) Intraspecific variation in smallsubunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int J Syst Bacteriol 45:595-599
-
(1995)
Int J Syst Bacteriol
, vol.45
, pp. 595-599
-
-
Clayton, R.A.1
Sutton, G.2
Hinkle Jr., P.S.3
Bult, C.4
Fields, C.5
-
21
-
-
0036407157
-
What are bacterial species?
-
Cohan FM (2002) What are bacterial species? Annu Rev Microbiol 56:457-487
-
(2002)
Annu Rev Microbiol
, vol.56
, pp. 457-487
-
-
Cohan, F.M.1
-
22
-
-
23944436830
-
Concepts of bacterial biodiversity for the age of genomics
-
Fraser CM, Read T, Nelson KE ed, Humana, Totowa
-
Cohan FM (2004) Concepts of bacterial biodiversity for the age of genomics. In: Fraser CM, Read T, Nelson KE (ed) Microbial genomes. Humana, Totowa, pp 175-194
-
(2004)
Microbial Genomes
, pp. 175-194
-
-
Cohan, F.M.1
-
23
-
-
0037251969
-
The ribosomal database project (RDP-II): Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
-
Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM (2003) The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442-443
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 442-443
-
-
Cole, J.R.1
Chai, B.2
Marsh, T.L.3
Farris, R.J.4
Wang, Q.5
Kulam, S.A.6
Chandra, S.7
McGarrell, D.M.8
Schmidt, T.M.9
Garrity, G.M.10
Tiedje, J.M.11
-
24
-
-
2942566096
-
Prokaryotic diversity and its limits: Microbial community structure in nature and implications for microbial ecology
-
Curtis TP, Sloan WT (2004) Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr Opin Microbiol 7:221-226
-
(2004)
Curr Opin Microbiol
, vol.7
, pp. 221-226
-
-
Curtis, T.P.1
Sloan, W.T.2
-
26
-
-
0036061865
-
A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history
-
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
-
(2002)
Genome Res
, vol.12
, pp. 1080-1090
-
-
Daubin, V.1
Gouy, M.2
Perriere, G.3
-
27
-
-
0042027842
-
Phylogenetics and the cohesion of bacterial genomes
-
Daubin V, Moran NA, Ochman H (2003) Phylogenetics and the cohesion of bacterial genomes. Science 301:829-832
-
(2003)
Science
, vol.301
, pp. 829-832
-
-
Daubin, V.1
Moran, N.A.2
Ochman, H.3
-
28
-
-
0035527414
-
Environmental diversity of bacteria and archaea
-
DeLong EF, Pace NR (2001) Environmental diversity of bacteria and archaea. Syst Biol 50:470-478
-
(2001)
Syst Biol
, vol.50
, pp. 470-478
-
-
DeLong, E.F.1
Pace, N.R.2
-
29
-
-
0029561021
-
The reck gene of Borrelia burgdorferi
-
Dew-Jager K, Yu WQ, Huang WM (1995) The reck gene of Borrelia burgdorferi. Gene 167:137-140
-
(1995)
Gene
, vol.167
, pp. 137-140
-
-
Dew-Jager, K.1
Yu, W.Q.2
Huang, W.M.3
-
31
-
-
0031981808
-
Santa Rosalia revisited: Why are there so many species of bacteria?
-
Dykhuizen DE (1998) Santa Rosalia revisited: why are there so many species of bacteria? Antonie Van Leeuwenhoek 73:25-33
-
(1998)
Antonie van Leeuwenhoek
, vol.73
, pp. 25-33
-
-
Dykhuizen, D.E.1
-
32
-
-
0024444791
-
Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA
-
Edwards U, Rogall T, Blocker H, Emde M, Bottger EC (1989) Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17:7843-7853
-
(1989)
Nucleic Acids Res
, vol.17
, pp. 7843-7853
-
-
Edwards, U.1
Rogall, T.2
Blocker, H.3
Emde, M.4
Bottger, E.C.5
-
33
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively misleading
-
Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401-410
-
(1978)
Syst Zool
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
34
-
-
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
-
35
-
-
0031027068
-
Diversity and depth-specific distribution of SARI 1 cluster rRNA genes from marine planktonic bacteria
-
Field KG, Gordon D, Wright T, Rappe M, Urback E, Vergin K, Giovannoni SJ (1997) Diversity and depth-specific distribution of SARI 1 cluster rRNA genes from marine planktonic bacteria. Appl Environ Microbiol 63:63-70
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 63-70
-
-
Field, K.G.1
Gordon, D.2
Wright, T.3
Rappe, M.4
Urback, E.5
Vergin, K.6
Giovannoni, S.J.7
-
36
-
-
0033004743
-
Compositional bias may affect both DNA-based and proteinbased phylogenetic reconstructions
-
Foster PG, Hickey DA (1999) Compositional bias may affect both DNA-based and proteinbased phylogenetic reconstructions. J Mol Evol 48:284-290
-
(1999)
J Mol Evol
, vol.48
, pp. 284-290
-
-
Foster, P.G.1
Hickey, D.A.2
-
37
-
-
0038180478
-
Detection and identification of Mycobacterium species isolates by DNA microarray
-
Fukushima M, Kakinuma K, Hayashi H, Nagai H, Ito K, Kawaguchi R (2003) Detection and identification of Mycobacterium species isolates by DNA microarray. J Clin Microbiol 41:2605-2615
-
(2003)
J Clin Microbiol
, vol.41
, pp. 2605-2615
-
-
Fukushima, M.1
Kakinuma, K.2
Hayashi, H.3
Nagai, H.4
Ito, K.5
Kawaguchi, R.6
-
38
-
-
0041422250
-
The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes
-
Gil R, Silva FJ, Zientz E, Delmotte F, Gonzalez-Candelas F, Latorre A, Rausell C, Kamerbeek J, Gadau J, Holldobler B, van Ham RC, Gross R, Moya A (2003) The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. Proc Natl Acad Sci USA 100:9388-9393
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 9388-9393
-
-
Gil, R.1
Silva, F.J.2
Zientz, E.3
Delmotte, F.4
Gonzalez-Candelas, F.5
Latorre, A.6
Rausell, C.7
Kamerbeek, J.8
Gadau, J.9
Holldobler, B.10
Van Ham, R.C.11
Gross, R.12
Moya, A.13
-
39
-
-
9044222878
-
HSP60 gene sequences as universal targets for microbial species identification: Studies with coagulase-negative staphylococci
-
Goh SH, Potter S, Wood JO, Hemmingsen SM, Reynolds RP, Chow AW (1996) HSP60 gene sequences as universal targets for microbial species identification: studies with coagulase-negative staphylococci. J Clin Microbiol 34:818-823
-
(1996)
J Clin Microbiol
, vol.34
, pp. 818-823
-
-
Goh, S.H.1
Potter, S.2
Wood, J.O.3
Hemmingsen, S.M.4
Reynolds, R.P.5
Chow, A.W.6
-
40
-
-
0034870192
-
Quantifying biodiversity: Procedures and pitfalls in the measurement and comparison of species richness
-
Gotelli NJ, Colwell RK (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecol Lett 4:379-391
-
(2001)
Ecol Lett
, vol.4
, pp. 379-391
-
-
Gotelli, N.J.1
Colwell, R.K.2
-
41
-
-
0032956536
-
Discontinuous occurrence of the hsp70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein
-
Gribaldo S, Lumia V, Creti R, de Macario EC, Sanangelantoni A, Cammarano P (1999) Discontinuous occurrence of the hsp70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein. J Bacteriol 181:434-443
-
(1999)
J Bacteriol
, vol.181
, pp. 434-443
-
-
Gribaldo, S.1
Lumia, V.2
Creti, R.3
De Macario, E.C.4
Sanangelantoni, A.5
Cammarano, P.6
-
42
-
-
0019293443
-
Reproducivility and correlation study of three deoxiribonucleic acid hybridization procedures
-
Grimont P A D, Popoff MY, Frimond F, Coynault C, Lemelin M. (1980) Reproducivility and correlation study of three deoxiribonucleic acid hybridization procedures. Curr Microbiol 4:325-330
-
(1980)
Curr Microbiol
, vol.4
, pp. 325-330
-
-
Grimont, P.A.D.1
Popoff, M.Y.2
Frimond, F.3
Coynault, C.4
Lemelin, M.5
-
43
-
-
0031794743
-
Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes
-
Gupta RS (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
-
44
-
-
0028261409
-
Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective
-
Gutell RR, Larsen N, Woese CR (1994) Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 58:10-26
-
(1994)
Microbiol Rev
, vol.58
, pp. 10-26
-
-
Gutell, R.R.1
Larsen, N.2
Woese, C.R.3
-
45
-
-
0036600570
-
The accuracy of ribosomal RNA comparative structure models
-
Gutell RR, Lee JC, Cannone JJ (2002) The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol 12:301-310
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 301-310
-
-
Gutell, R.R.1
Lee, J.C.2
Cannone, J.J.3
-
46
-
-
0036306089
-
Use of 16S ribosomal DNA for delineation of marine bacterioplankton species
-
Hagstrom A, Pommier T, Rohwer F, Simu K, Stolte W, Svensson D, Zweifel UL (2002) Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. Appl Environ Microbiol 68:3628-3633
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 3628-3633
-
-
Hagstrom, A.1
Pommier, T.2
Rohwer, F.3
Simu, K.4
Stolte, W.5
Svensson, D.6
Zweifel, U.L.7
-
47
-
-
0028215621
-
Codon usage patterns suggest independent evolution of two catabolic operons on toluene-degradative plasmid TOL pWWO of Pseudomonas putida
-
Harayama S (1994) Codon usage patterns suggest independent evolution of two catabolic operons on toluene-degradative plasmid TOL pWWO of Pseudomonas putida. J Mol Evol 38:328-335
-
(1994)
J Mol Evol
, vol.38
, pp. 328-335
-
-
Harayama, S.1
-
48
-
-
0027232202
-
Comparison of the nucleotide sequences of the meta-cleavage pathway genes of TOL plasmid pWWO from Pseudomonas putida with other metacleavage genes suggests that both single and multiple nucleotide substitutions contribute to enzyme evolution
-
Harayama S, Rekik M (1993) Comparison of the nucleotide sequences of the meta-cleavage pathway genes of TOL plasmid pWWO from Pseudomonas putida with other metacleavage genes suggests that both single and multiple nucleotide substitutions contribute to enzyme evolution. Mol Gen Genet 239:81-89
-
(1993)
Mol Gen Genet
, vol.239
, pp. 81-89
-
-
Harayama, S.1
Rekik, M.2
-
49
-
-
0141502460
-
Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium) species by using phenotypes, DNA-DNA hybridization and sequences of gyrB, and proposal of Streptomyces luteireticuli (ex Katoh and Arai 1957) corrig., sp. nov., nom. rev
-
Hatano K, Nishii T, Kasai H (2003) Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium) species by using phenotypes, DNA-DNA hybridization and sequences of gyrB, and proposal of Streptomyces luteireticuli (ex Katoh and Arai 1957) corrig., sp. nov., nom. rev. Int J Syst Evol Microbiol 53:1519-1529
-
(2003)
Int J Syst Evol Microbiol
, vol.53
, pp. 1519-1529
-
-
Hatano, K.1
Nishii, T.2
Kasai, H.3
-
50
-
-
4444360858
-
Cpndb: A chaperonin sequence database
-
Hill JE, Penny SL, Crowell KG, Goh SH, Hemmingsen SM (2004) cpnDB: a chaperonin sequence database. Genome Res 14:1669-1675
-
(2004)
Genome Res
, vol.14
, pp. 1669-1675
-
-
Hill, J.E.1
Penny, S.L.2
Crowell, K.G.3
Goh, S.H.4
Hemmingsen, S.M.5
-
51
-
-
0022516669
-
Evolutionary change in 5S rRNA secondary structure and a phylogenic tree of 352 5S rRNA species
-
Hori H, Osawa S (1986) Evolutionary change in 5S rRNA secondary structure and a phylogenic tree of 352 5S rRNA species. Biosystems 19:163-172
-
(1986)
Biosystems
, vol.19
, pp. 163-172
-
-
Hori, H.1
Osawa, S.2
-
52
-
-
0037217221
-
Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases
-
Hugenholtz P, Huber T (2003) Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int J Syst Evol Microbiol 53:289-293
-
(2003)
Int J Syst Evol Microbiol
, vol.53
, pp. 289-293
-
-
Hugenholtz, P.1
Huber, T.2
-
55
-
-
0019824131
-
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system
-
Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol 151:389-409
-
(1981)
J Mol Biol
, vol.151
, pp. 389-409
-
-
Ikemura, T.1
-
56
-
-
0024358140
-
Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes
-
Iwabe N, Kuma K, Hasegawa M, Osawa S, Miyata T (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
-
57
-
-
0033616714
-
Horizontal gene transfer among genomes: The complexity hypothesis
-
Jain R, Rivera MC, Lake JA (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96:3801-3806
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 3801-3806
-
-
Jain, R.1
Rivera, M.C.2
Lake, J.A.3
-
58
-
-
0034807791
-
New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences
-
Jian W, Zhu L, Dong X (2001) New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences. Int J Syst Evol Microbiol 51:1633-1638
-
(2001)
Int J Syst Evol Microbiol
, vol.51
, pp. 1633-1638
-
-
Jian, W.1
Zhu, L.2
Dong, X.3
-
59
-
-
0025061094
-
Limitations of the evolutionary parsimony method of phylogenetic analysis
-
Jin L, Nei M (1990a) Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol Biol Evol 7:82-102
-
(1990)
Mol Biol Evol
, vol.7
, pp. 82-102
-
-
Jin, L.1
Nei, M.2
-
61
-
-
0015905932
-
Use of nucleic-acid homologies in the taxonomy of anaerobic bacteria
-
Johnson JL (1973) Use of nucleic-acid homologies in the taxonomy of anaerobic bacteria. Int J Syst Bacterid 23:308-315
-
(1973)
Int J Syst Bacterid
, vol.23
, pp. 308-315
-
-
Johnson, J.L.1
-
62
-
-
0000732090
-
Evolution of protein molecules
-
Munro HN ed, Academic, New York
-
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic, New York, pp 21-132
-
(1969)
Mammalian Protein Metabolism
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
63
-
-
0025259313
-
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
-
Karlin S, Altschul SF (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci USA 87:2264-2268
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 2264-2268
-
-
Karlin, S.1
Altschul, S.F.2
-
64
-
-
0028970713
-
Bacterial classifications derived from reck protein sequence comparisons
-
Karlin S, Weinstock GM, Brendel V (1995) Bacterial classifications derived from reck protein sequence comparisons. J Bacteriol 177:6881-6893
-
(1995)
J Bacteriol
, vol.177
, pp. 6881-6893
-
-
Karlin, S.1
Weinstock, G.M.2
Brendel, V.3
-
65
-
-
1842332701
-
Compositional biases of bacterial genomes and evolutionary implications
-
Karlin S, Mrazek J, Campbell AM (1997) Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179:3899-3913
-
(1997)
J Bacteriol
, vol.179
, pp. 3899-3913
-
-
Karlin, S.1
Mrazek, J.2
Campbell, A.M.3
-
66
-
-
0002911514
-
Construction of the gyrB database for the identification and classification of bacteria
-
Kasai H, Watanabe K, Gasteiger E, Bairoch A, Isono K, Yamamoto S, Harayama S (1998) Construction of the gyrB database for the identification and classification of bacteria. Genome Inform Ser Workshop Genome Inform 9:13-21
-
(1998)
Genome Inform Ser Workshop Genome Inform
, vol.9
, pp. 13-21
-
-
Kasai, H.1
Watanabe, K.2
Gasteiger, E.3
Bairoch, A.4
Isono, K.5
Yamamoto, S.6
Harayama, S.7
-
67
-
-
0033986599
-
Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences
-
Kasai H, Ezaki T, Harayama S (2000) Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences. J Clin Microbiol 38:301-308
-
(2000)
J Clin Microbiol
, vol.38
, pp. 301-308
-
-
Kasai, H.1
Ezaki, T.2
Harayama, S.3
-
68
-
-
0025027077
-
New topoisomerase essential for chromosome segregation in E. coli
-
Kato J, Nishimura Y, Imamura R, Niki H, Hiraga S, Suzuki H (1990) New topoisomerase essential for chromosome segregation in E. coli. Cell 63:393-404
-
(1990)
Cell
, vol.63
, pp. 393-404
-
-
Kato, J.1
Nishimura, Y.2
Imamura, R.3
Niki, H.4
Hiraga, S.5
Suzuki, H.6
-
69
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120
-
(1980)
J Mol Evol
, vol.16
, pp. 111-120
-
-
Kimura, M.1
-
70
-
-
3242731518
-
Methods of studying soil microbial diversity
-
Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H, Trevors JT (2004) Methods of studying soil microbial diversity. J Microbiol Methods 58:169-188
-
(2004)
J Microbiol Methods
, vol.58
, pp. 169-188
-
-
Kirk, J.L.1
Beaudette, L.A.2
Hart, M.3
Moutoglis, P.4
Klironomos, J.N.5
Lee, H.6
Trevors, J.T.7
-
71
-
-
0036139211
-
MEGA2: Molecular evolutionary genetics analysis software
-
Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245
-
(2001)
Bioinformatics
, vol.17
, pp. 1244-1245
-
-
Kumar, S.1
Tamura, K.2
Jakobsen, I.B.3
Nei, M.4
-
73
-
-
0037216028
-
Phylogenetic study of Staphylococcus and Macrococcus species based on partial hsp60 gene sequences
-
Kwok AY, Chow AW (2003) Phylogenetic study of Staphylococcus and Macrococcus species based on partial hsp60 gene sequences. Int J Syst Evol Microbiol 53:87-92
-
(2003)
Int J Syst Evol Microbiol
, vol.53
, pp. 87-92
-
-
Kwok, A.Y.1
Chow, A.W.2
-
74
-
-
1142297445
-
Gyrb as a phylogenetic discriminator for members of the Bacillus anthracis-cereus-thuringiensis group
-
La Due MT, Satomi M, Agata N, Venkateswaran K (2004) gyrB as a phylogenetic discriminator for members of the Bacillus anthracis-cereus- thuringiensis group. J Microbiol Methods 56:383-394
-
(2004)
J Microbiol Methods
, vol.56
, pp. 383-394
-
-
La Due, M.T.1
Satomi, M.2
Agata, N.3
Venkateswaran, K.4
-
75
-
-
0037166285
-
An open conformation of the Thermus thertnophilus gyrase B ATP-binding domain
-
Lamour V, Hoermann L, Jeltsch JM, Oudet P, Moras D (2002) An open conformation of the Thermus thertnophilus gyrase B ATP-binding domain. J Biol Chem 277:18947-18953
-
(2002)
J Biol Chem
, vol.277
, pp. 18947-18953
-
-
Lamour, V.1
Hoermann, L.2
Jeltsch, J.M.3
Oudet, P.4
Moras, D.5
-
76
-
-
0008048504
-
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses
-
Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82:6955-6959
-
(1985)
Proc Natl Acad Sci USA
, vol.82
, pp. 6955-6959
-
-
Lane, D.J.1
Pace, B.2
Olsen, G.J.3
Stahl, D.A.4
Sogin, M.L.5
Pace, N.R.6
-
77
-
-
0035800661
-
Evolution of tuf genes: Ancient duplication, differential loss and gene conversion
-
Lathe WC 3rd, Bork P (2001) Evolution of tuf genes: ancient duplication, differential loss and gene conversion. FEBS Lett 502:113-116
-
(2001)
FEBS Lett
, vol.502
, pp. 113-116
-
-
Lathe III, W.C.1
Bork, P.2
-
78
-
-
1342271382
-
From gene trees to organismal phylogeny in prokaryotes: The case of the y-Proteobacteria
-
Lerat E, Daubin V, Moran NA. (2003) From gene trees to organismal phylogeny in prokaryotes: the case of the y-Proteobacteria. PLoS Biol 1:E19
-
(2003)
PLoS Biol
, vol.1
-
-
Lerat, E.1
Daubin, V.2
Moran, N.A.3
-
79
-
-
0036308535
-
Genetic diversity of the outer surface protein C gene of southern Borrelia isolates and its possible epidemiological, clinical, and pathogenetic implications
-
Lin T, Oliver JH Jr, Gao L (2002) Genetic diversity of the outer surface protein C gene of southern Borrelia isolates and its possible epidemiological, clinical, and pathogenetic implications. J Clin Microbiol 40:2572-2583
-
(2002)
J Clin Microbiol
, vol.40
, pp. 2572-2583
-
-
Lin, T.1
Oliver Jr., J.H.2
Gao, L.3
-
80
-
-
0027359258
-
Evolution of the reck gene and the molecular phylogeny of bacteria
-
Lloyd AT, Sharp PM (1993) Evolution of the reck gene and the molecular phylogeny of bacteria. J Mol Evol 37:399-407
-
(1993)
J Mol Evol
, vol.37
, pp. 399-407
-
-
Lloyd, A.T.1
Sharp, P.M.2
-
81
-
-
0035875112
-
Survey and summary: The applications of universal DNA base analogues
-
Loakes D (2001) Survey and summary: the applications of universal DNA base analogues. Nucleic Acids Res 29:2437-2447
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2437-2447
-
-
Loakes, D.1
-
82
-
-
0027998116
-
Bacterial phylogeny based on 16S and 23S rRNA sequence analysis
-
Ludwig W, Schleifer KH (1994) Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiol Rev 15:155-173
-
(1994)
FEMS Microbiol Rev
, vol.15
, pp. 155-173
-
-
Ludwig, W.1
Schleifer, K.H.2
-
83
-
-
0027818659
-
Phylogenetic relationships of Bacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase beta-subunit genes
-
Ludwig W, Neumaier J, Klugbauer N, Brockmann E, Roller C, Jilg S, Reetz K, Schachtner I, Ludvigsen A, Bachleitner M, et al (1993) Phylogenetic relationships of Bacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase beta-subunit genes. Antonie Van Leeuwenhoek 64:285-305
-
(1993)
Antonie van Leeuwenhoek
, vol.64
, pp. 285-305
-
-
Ludwig, W.1
Neumaier, J.2
Klugbauer, N.3
Brockmann, E.4
Roller, C.5
Jilg, S.6
Reetz, K.7
Schachtner, I.8
Ludvigsen, A.9
Bachleitner, M.10
-
84
-
-
4644290878
-
Estimating bacterial diversity from clone libraries with flat rank abundance distributions
-
Lunn M, Sloan WT, Curtis TP (2004) Estimating bacterial diversity from clone libraries with flat rank abundance distributions. Environ Microbiol 6:1081-1085
-
(2004)
Environ Microbiol
, vol.6
, pp. 1081-1085
-
-
Lunn, M.1
Sloan, W.T.2
Curtis, T.P.3
-
85
-
-
13144252236
-
Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms
-
Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG (1998) Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 95:3140-3145
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 3140-3145
-
-
Maiden, M.C.1
Bygraves, J.A.2
Feil, E.3
Morelli, G.4
Russell, J.E.5
Urwin, R.6
Zhang, Q.7
Zhou, J.8
Zurth, K.9
Caugant, D.A.10
Feavers, I.M.11
Achtman, M.12
Spratt, B.G.13
-
86
-
-
0026629643
-
Phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas as determined by 16S ribosomal DNA sequencing: Lack of congruence with results of DNA-DNA hybridizations
-
Martinez-Murcia AJ, Benlloch S, Collins MD (1992) Phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas as determined by 16S ribosomal DNA sequencing: lack of congruence with results of DNA-DNA hybridizations. Int J Syst Bacteriol 42:412-421
-
(1992)
Int J Syst Bacteriol
, vol.42
, pp. 412-421
-
-
Martinez-Murcia, A.J.1
Benlloch, S.2
Collins, M.D.3
-
87
-
-
3242876311
-
BLAST: At the core of a powerful and diverse set of sequence analysis tools
-
McGinnis S, Madden TL (2004) BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 32:W20-W25
-
(2004)
Nucleic Acids Res
, vol.32
-
-
McGinnis, S.1
Madden, T.L.2
-
88
-
-
0024241467
-
The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions
-
Medlin L, Elwood HJ, Stickel S, Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71:491-499
-
(1988)
Gene
, vol.71
, pp. 491-499
-
-
Medlin, L.1
Elwood, H.J.2
Stickel, S.3
Sogin, M.L.4
-
89
-
-
0036731845
-
Molecular evolution of aromatic polyketides and comparative sequence analysis of polyketide ketosynthase and 16S ribosomal DNA genes from various Streptomyces species
-
Metsa-Ketela M, Halo L, Munukka E, Hakala J, Mantsala P, Ylihonko K (2002) Molecular evolution of aromatic polyketides and comparative sequence analysis of polyketide ketosynthase and 16S ribosomal DNA genes from various Streptomyces species. Appl Environ Microbiol 68:4472-4479
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 4472-4479
-
-
Metsa-Ketela, M.1
Halo, L.2
Munukka, E.3
Hakala, J.4
Mantsala, P.5
Ylihonko, K.6
-
90
-
-
2942665966
-
Phylogenetic analysis of gastric and enterohepatic Helicobacter species based on partial HSP60 gene sequences
-
Mikkonen TP, Karenlampi RI, Hanninen ML (2004) Phylogenetic analysis of gastric and enterohepatic Helicobacter species based on partial HSP60 gene sequences. Int J Syst Evol Microbiol 54:753-758
-
(2004)
Int J Syst Evol Microbiol
, vol.54
, pp. 753-758
-
-
Mikkonen, T.P.1
Karenlampi, R.I.2
Hanninen, M.L.3
-
91
-
-
0030669211
-
Rpob sequence analysis as a novel basis for bacterial identification
-
Mollet C, Drancourt M, Raoult D (1997) rpoB sequence analysis as a novel basis for bacterial identification. Mol Microbiol 26:1005-1011
-
(1997)
Mol Microbiol
, vol.26
, pp. 1005-1011
-
-
Mollet, C.1
Drancourt, M.2
Raoult, D.3
-
92
-
-
0029866448
-
Accelerated evolution and Muller's rachet in endosymbiotic bacteria
-
Moran NA (1996) Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc Natl Acad Sci USA 93:2873-2378
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 2873-2378
-
-
Moran, N.A.1
-
93
-
-
0029798105
-
Analysis of the beta' subunit of DNA-dependent RNA polymerase does not support the hypothesis inferred from 16S rRNA analysis that Oenococcus oeni (formerly Leuconostoc oenos) is a tachytelic (fast-evolving) bacterium
-
Morse R, Collins MD, O'Hanlon K, Wallbanks S, Richardson PT (1996) Analysis of the beta' subunit of DNA-dependent RNA polymerase does not support the hypothesis inferred from 16S rRNA analysis that Oenococcus oeni (formerly Leuconostoc oenos) is a tachytelic (fast-evolving) bacterium. Int J Syst Bacteriol 46:1004-1009
-
(1996)
Int J Syst Bacteriol
, vol.46
, pp. 1004-1009
-
-
Morse, R.1
Collins, M.D.2
O'Hanlon, K.3
Wallbanks, S.4
Richardson, P.T.5
-
95
-
-
4544298806
-
Genome-wide molecular clock and horizontal gene transfer in bacterial evolution
-
Novichkov PS, Omelchenko MV, Gelfand MS, Mironov AA, Wolf YI, Koonin EV (2004) Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol 186:6575-6585
-
(2004)
J Bacteriol
, vol.186
, pp. 6575-6585
-
-
Novichkov, P.S.1
Omelchenko, M.V.2
Gelfand, M.S.3
Mironov, A.A.4
Wolf, Y.I.5
Koonin, E.V.6
-
97
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
Ochman H, Lawrence JG, Groisman EA (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
-
98
-
-
3843071047
-
Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species
-
Picard FJ, Ke D, Boudreau DK, Boissinot M, Huletsky A, Richard D, Ouellette M, Roy PH, Bergeron MG (2004) Use of tuf sequences for genus-specific PCR detection and phylogenetic analysis of 28 streptococcal species. J Clin Microbiol 42:3686-3695
-
(2004)
J Clin Microbiol
, vol.42
, pp. 3686-3695
-
-
Picard, F.J.1
Ke, D.2
Boudreau, D.K.3
Boissinot, M.4
Huletsky, A.5
Richard, D.6
Ouellette, M.7
Roy, P.H.8
Bergeron, M.G.9
-
99
-
-
9644268091
-
Development of PCR primers specific for the amplification and direct sequencing of gyrB genes from microbacteria, order Actinomycetales
-
Richert K, Brambilla E, Stackebrandt E (2005) Development of PCR primers specific for the amplification and direct sequencing of gyrB genes from microbacteria, order Actinomycetales. J Microbiol Methods 60:115-123
-
(2005)
J Microbiol Methods
, vol.60
, pp. 115-123
-
-
Richert, K.1
Brambilla, E.2
Stackebrandt, E.3
-
100
-
-
0026684272
-
Evidence that eukaryotes and eocyte prokaryotes are immediate relatives
-
Rivera MC, Lake JA (1992) Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257:74-76
-
(1992)
Science
, vol.257
, pp. 74-76
-
-
Rivera, M.C.1
Lake, J.A.2
-
101
-
-
0028949206
-
The mechanisms of DNA topoisomerases
-
Roca, J (1995) The mechanisms of DNA topoisomerases. Trends Biochem Sci 20:156-160
-
(1995)
Trends Biochem Sci
, vol.20
, pp. 156-160
-
-
Roca, J.1
-
102
-
-
2942528667
-
The path of the DNA along the dimer interface of topoisomerase II
-
Roca J (2004) The path of the DNA along the dimer interface of topoisomerase II. J Biol Chem 279:25783-25788
-
(2004)
J Biol Chem
, vol.279
, pp. 25783-25788
-
-
Roca, J.1
-
103
-
-
8744310123
-
Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization
-
Rocha EP (2004) Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res 14:2279-2286
-
(2004)
Genome Res
, vol.14
, pp. 2279-2286
-
-
Rocha, E.P.1
-
104
-
-
1242284655
-
An analysis of determinants of amino acids substitution rates in bacterial proteins
-
Rocha EP, Danchin A (2004) An analysis of determinants of amino acids substitution rates in bacterial proteins. Mol Biol Evol 21:108-116
-
(2004)
Mol Biol Evol
, vol.21
, pp. 108-116
-
-
Rocha, E.P.1
Danchin, A.2
-
105
-
-
0032052770
-
Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences
-
Rose TM, Schultz ER, Henikoff JG, Pietrokovski S, McCallum CM, Henikoff S (1998) Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res 26:1628-1635
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 1628-1635
-
-
Rose, T.M.1
Schultz, E.R.2
Henikoff, J.G.3
Pietrokovski, S.4
McCallum, C.M.5
Henikoff, S.6
-
106
-
-
0043122986
-
CODEHOP (consensus-degenerate hybrid oligonucleotide primer) PCR primer design
-
Rose TM, Henikoff JG, Henikoff S (2003) CODEHOP (consensus-degenerate hybrid oligonucleotide primer) PCR primer design. Nucleic Acids Res 31:3763-3766
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3763-3766
-
-
Rose, T.M.1
Henikoff, J.G.2
Henikoff, S.3
-
108
-
-
0028238297
-
Use of deoyinosinecontaining primers vs degenerate primers for polymerase chain reaction based on ambiguous sequence information
-
Rossolini GM, Cresti S, Ingianni A, Cattani P, Riccio ML, Satta G (1994) Use of deoyinosinecontaining primers vs degenerate primers for polymerase chain reaction based on ambiguous sequence information. Mol Cell Probes 8:91-98
-
(1994)
Mol Cell Probes
, vol.8
, pp. 91-98
-
-
Rossolini, G.M.1
Cresti, S.2
Ingianni, A.3
Cattani, P.4
Riccio, M.L.5
Satta, G.6
-
109
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
-
(1987)
Mol Biol Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
110
-
-
3042826875
-
Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins
-
Santos SR, Ochman H (2004) Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol 6:754-759
-
(2004)
Environ Microbiol
, vol.6
, pp. 754-759
-
-
Santos, S.R.1
Ochman, H.2
-
112
-
-
0034268836
-
Structure of functionally activated small ribosomal subunit at 3.3 A resolution
-
Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A (2000) Structure of functionally activated small ribosomal subunit at 3.3 A resolution. Cell 102:615-623
-
(2000)
Cell
, vol.102
, pp. 615-623
-
-
Schluenzen, F.1
Tocilj, A.2
Zarivach, R.3
Harms, J.4
Gluehmann, M.5
Janell, D.6
Bashan, A.7
Bartels, H.8
Agmon, I.9
Franceschi, F.10
Yonath, A.11
-
113
-
-
0037417067
-
Resistance genes of aminocoumarin producers: Two type II topoisomerase genes confer resistance against coumermycin Al and clorobiocin
-
Schmutz E, Muhlenweg A, Li SM, Heide L (2003) Resistance genes of aminocoumarin producers: two type II topoisomerase genes confer resistance against coumermycin Al and clorobiocin. Antimicrob Agents Chemother 47:869-877
-
(2003)
Antimicrob Agents Chemother
, vol.47
, pp. 869-877
-
-
Schmutz, E.1
Muhlenweg, A.2
Li, S.M.3
Heide, L.4
-
114
-
-
0034618559
-
Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS
-
Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H (2000) Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407:81-86
-
(2000)
Nature
, vol.407
, pp. 81-86
-
-
Shigenobu, S.1
Watanabe, H.2
Hattori, M.3
Sakaki, Y.4
Ishikawa, H.5
-
115
-
-
1542614592
-
Empirical models for substitution in ribosomal RNA
-
Smith AD, Lui TW, Tillier ER (2003) Empirical models for substitution in ribosomal RNA. Mol Biol Evol 21:419-427
-
(2003)
Mol Biol Evol
, vol.21
, pp. 419-427
-
-
Smith, A.D.1
Lui, T.W.2
Tillier, E.R.3
-
116
-
-
0027305615
-
Evidence from Aeromonas for genetic crossing-over in ribosomal sequences
-
Sneath PH (1993) Evidence from Aeromonas for genetic crossing-over in ribosomal sequences. Int J Syst Bacteriol 43:626-629
-
(1993)
Int J Syst Bacteriol
, vol.43
, pp. 626-629
-
-
Sneath, P.H.1
-
117
-
-
0030860220
-
Compilation of 5S rRNA and 5S rRNA gene sequences
-
Specht T, Szymanski M, Barciszewska MZ, Barciszewski J, Erdmann VA (1997) Compilation of 5S rRNA and 5S rRNA gene sequences. Nucleic Acids Res 25:96-97
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 96-97
-
-
Specht, T.1
Szymanski, M.2
Barciszewska, M.Z.3
Barciszewski, J.4
Erdmann, V.A.5
-
118
-
-
0024724926
-
DNA hybridization in animal taxonomy: A critique from first principles
-
Springer M, Krajewski C (1989) DNA hybridization in animal taxonomy: a critique from first principles. Q Rev Biol 64:291-318
-
(1989)
Q Rev Biol
, vol.64
, pp. 291-318
-
-
Springer, M.1
Krajewski, C.2
-
119
-
-
0028028182
-
Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology
-
Stackebrandt E and Gobel BM (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
Gobel, B.M.2
-
120
-
-
0035989633
-
Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology
-
Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kampfer P, Maiden MC, Nesme X, Rossello-Mora R, Swings J, Truper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043-1047
-
(2002)
Int J Syst Evol Microbiol
, vol.52
, pp. 1043-1047
-
-
Stackebrandt, E.1
Frederiksen, W.2
Garrity, G.M.3
Grimont, P.A.4
Kampfer, P.5
Maiden, M.C.6
Nesme, X.7
Rossello-Mora, R.8
Swings, J.9
Truper, H.G.10
Vauterin, L.11
Ward, A.C.12
Whitman, W.B.13
-
121
-
-
0034048695
-
Identification of the novobiocin biosynthetic gene cluster of Streptomyces spheroides NCIB 11891
-
Steffensky M, Muhlenweg A, Wang ZX, Li SM, Heide L (2000) Identification of the novobiocin biosynthetic gene cluster of Streptomyces spheroides NCIB 11891. Antimicrob Agents Chemother 44:1214-1222
-
(2000)
Antimicrob Agents Chemother
, vol.44
, pp. 1214-1222
-
-
Steffensky, M.1
Muhlenweg, A.2
Wang, Z.X.3
Li, S.M.4
Heide, L.5
-
122
-
-
0344430318
-
The variable part of the dnaK gene as an alternative marker for phylogenetic studies of rhizobia and related alpha Proteobacteria
-
Stepkowski T, Czaplinska M, Miedzinska K, Moulin L (2003) The variable part of the dnaK gene as an alternative marker for phylogenetic studies of rhizobia and related alpha Proteobacteria. Syst Appl Microbiol 26:483-494
-
(2003)
Syst Appl Microbiol
, vol.26
, pp. 483-494
-
-
Stepkowski, T.1
Czaplinska, M.2
Miedzinska, K.3
Moulin, L.4
-
123
-
-
0024039558
-
Cloning and characterization of a DNA gyrase B gene from Streptomyces sphaeroides that confers resistance to novobiocin
-
Thiara AS, Cundliffe E (1988) Cloning and characterization of a DNA gyrase B gene from Streptomyces sphaeroides that confers resistance to novobiocin. EMBO J 7:2255-2259
-
(1988)
EMBO J
, vol.7
, pp. 2255-2259
-
-
Thiara, A.S.1
Cundliffe, E.2
-
124
-
-
2942661513
-
Use of recA as an alternative phylogenetic marker in the family Vibrionaceae
-
Thompson CC, Thompson FL, Vandemeulebroecke K, Hoste B, Dawyndt P, Swings J (2004) Use of recA as an alternative phylogenetic marker in the family Vibrionaceae. Int J Syst Evol Microbiol 54:919-924
-
(2004)
Int J Syst Evol Microbiol
, vol.54
, pp. 919-924
-
-
Thompson, C.C.1
Thompson, F.L.2
Vandemeulebroecke, K.3
Hoste, B.4
Dawyndt, P.5
Swings, J.6
-
125
-
-
0031574072
-
The Clustal X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
-
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882
-
(1997)
Nucleic Acids Res
, vol.24
, pp. 4876-4882
-
-
Thompson, J.D.1
Gibson, T.J.2
Plewniak, F.3
Jeanmougin, F.4
Higgins, D.G.5
-
126
-
-
0036566806
-
Heteroduplexes in mixed-template amplifications: Formation, consequence and elimination by 'reconditioning PCR'
-
Thompson JR, Marcelino LA, Polz MF (2002) Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res 30:2083-2088
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 2083-2088
-
-
Thompson, J.R.1
Marcelino, L.A.2
Polz, M.F.3
-
128
-
-
0025256110
-
Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria
-
Torsvik V, Salte K, Sorheim R, Goksoyr J (1990b) Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl Environ Microbiol 56:776-781
-
(1990)
Appl Environ Microbiol
, vol.56
, pp. 776-781
-
-
Torsvik, V.1
Salte, K.2
Sorheim, R.3
Goksoyr, J.4
-
129
-
-
0037052493
-
Prokaryotic diversity - Magnitude, dynamics, and controlling factors
-
Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversity - magnitude, dynamics, and controlling factors. Science 296:1064-1066
-
(2002)
Science
, vol.296
, pp. 1064-1066
-
-
Torsvik, V.1
Ovreas, L.2
Thingstad, T.F.3
-
130
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37-43
-
(2004)
Nature
, vol.428
, pp. 37-43
-
-
Tyson, G.W.1
Chapman, J.2
Hugenholtz, P.3
Allen, E.E.4
Ram, R.J.5
Richardson, P.M.6
Solovyev, V.V.7
Rubin, E.M.8
Rokhsar, D.S.9
Banfield, J.F.10
-
131
-
-
0029789623
-
A quantitative map of nucleotide substitution rates in bacterial rRNA
-
Van de Peer Y, Chapelle S, De Wachter R (1996) A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acids Res 24:3381-3391
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 3381-3391
-
-
Van De Peer, Y.1
Chapelle, S.2
De Wachter, R.3
-
132
-
-
0029942146
-
Polyphasic taxonomy, a consensus approach to bacterial systematics
-
Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J. (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60:407-438
-
(1996)
Microbiol Rev
, vol.60
, pp. 407-438
-
-
Vandamme, P.1
Pot, B.2
Gillis, M.3
De Vos, P.4
Kersters, K.5
Swings, J.6
-
134
-
-
0027309533
-
Rates and patterns of base change in the small subunit ribosomal RNA gene
-
Vawter L, Brown WM (1993) Rates and patterns of base change in the small subunit ribosomal RNA gene. Genetics 134:597-608
-
(1993)
Genetics
, vol.134
, pp. 597-608
-
-
Vawter, L.1
Brown, W.M.2
-
135
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74
-
(2004)
Science
, vol.304
, pp. 66-74
-
-
Venter, J.C.1
Remington, K.2
Heidelberg, J.F.3
Halpern, A.L.4
Rusch, D.5
Eisen, J.A.6
Wu, D.7
Paulsen, I.8
Nelson, K.E.9
Nelson, W.10
Fouts, D.E.11
Levy, S.12
Knap, A.H.13
Lomas, M.W.14
Nealson, K.15
White, O.16
Peterson, J.17
Hoffman, J.18
Parsons, R.19
Baden-Tillson, H.20
Pfannkoch, C.21
Rogers, Y.H.22
Smith, H.O.23
more..
-
136
-
-
0028343191
-
Evolutionary relationships among bacterial groups as inferred from GroEL (Chaperonin) sequence comparisons
-
Viale AM, Arakaki AK, Soncini FC, Ferreyra RG (1994) Evolutionary relationships among bacterial groups as inferred from GroEL (Chaperonin) sequence comparisons. Int J Syst Bacteriol 44:527-533
-
(1994)
Int J Syst Bacteriol
, vol.44
, pp. 527-533
-
-
Viale, A.M.1
Arakaki, A.K.2
Soncini, F.C.3
Ferreyra, R.G.4
-
137
-
-
0037406933
-
Species-wide variation in the Escherichia coli flagellin (H-antigen) gene
-
Wang L, Rothemund D, Curd H, Reeves PR (2003) Species-wide variation in the Escherichia coli flagellin (H-antigen) gene. I Bacteriol 185:2936-2943
-
(2003)
I Bacteriol
, vol.185
, pp. 2936-2943
-
-
Wang, L.1
Rothemund, D.2
Curd, H.3
Reeves, P.R.4
-
138
-
-
0033743319
-
Identification of the coumermycin A (l) biosynthetic gene cluster of Streptomyces rishiriensis DSM 40489
-
Wang ZX, Li SM, Heide L (2000) Identification of the coumermycin A (l) biosynthetic gene cluster of Streptomyces rishiriensis DSM 40489. Antimicrob Agents Chemother 44:3040-3048
-
(2000)
Antimicrob Agents Chemother
, vol.44
, pp. 3040-3048
-
-
Wang, Z.X.1
Li, S.M.2
Heide, L.3
-
139
-
-
0033014982
-
An outbreak of nonflocculating catabolic populations caused the breakdown of a phenol-digesting activated-sludge process
-
Watanabe K, Teramoto M, Harayama S (1999) An outbreak of nonflocculating catabolic populations caused the breakdown of a phenol-digesting activated-sludge process. Appl Environ Microbiol 65:2813-2819
-
(1999)
Appl Environ Microbiol
, vol.65
, pp. 2813-2819
-
-
Watanabe, K.1
Teramoto, M.2
Harayama, S.3
-
140
-
-
0035795219
-
Design and evaluation of PCR primers to amplify 16S ribosomal DNA fragments used for community fingerprinting
-
Watanabe K, Kodama Y, Harayama S (2001a) Design and evaluation of PCR primers to amplify 16S ribosomal DNA fragments used for community fingerprinting. J Microbiol Methods 44:253-262
-
(2001)
J Microbiol Methods
, vol.44
, pp. 253-262
-
-
Watanabe, K.1
Kodama, Y.2
Harayama, S.3
-
141
-
-
0035167764
-
ICB database: The gyrB database for identification and classification of bacteria
-
Watanabe K, Nelson J, Harayama S, Kasai H (2001b) ICB database: the gyrB database for identification and classification of bacteria. Nucleic Acids Res 29:344-345
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 344-345
-
-
Watanabe, K.1
Nelson, J.2
Harayama, S.3
Kasai, H.4
-
142
-
-
0000770675
-
Report of the ad hoc committee on reconcilation of approaches to bacterial systematics
-
Wayne LG, Brenner DJ, Colwell RR, Grimont P A D, Kandler O, Krichevsky MI, Moore LH, Moore W E C, Murray R G E, Stachebrandt E, Starr MP, Truper HG (1987) Report of the ad hoc committee on reconcilation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463-464
-
(1987)
Int J Syst Bacteriol
, vol.37
, pp. 463-464
-
-
Wayne, L.G.1
Brenner, D.J.2
Colwell, R.R.3
Grimont, P.A.D.4
Kandler, O.5
Krichevsky, M.I.6
Moore, L.H.7
Moore, W.E.C.8
Murray, R.G.E.9
Stachebrandt, E.10
Starr, M.P.11
Truper, H.G.12
-
143
-
-
0029098588
-
Structure and mechanism of DNA topoisomerases
-
Wigley DB (1995) Structure and mechanism of DNA topoisomerases. Annu Rev Biophys Biomol Struct 24:185-208
-
(1995)
Annu Rev Biophys Biomol Struct
, vol.24
, pp. 185-208
-
-
Wigley, D.B.1
-
144
-
-
0026428621
-
Crystal structure of an N-terminal fragment of the DNA gyrase B protein
-
Wigley DB, Davies GJ, Dodson EJ, Maxwell A, Dodson G (1991) Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 351:624-629
-
(1991)
Nature
, vol.351
, pp. 624-629
-
-
Wigley, D.B.1
Davies, G.J.2
Dodson, E.J.3
Maxwell, A.4
Dodson, G.5
-
145
-
-
0034699518
-
Structure of the 30 S ribosomal subunit
-
Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, Vonhein C, Hartsch T, Ramakrishnan V (2000) Structure of the 30 S ribosomal subunit. Nature 407:327-339
-
(2000)
Nature
, vol.407
, pp. 327-339
-
-
Wimberly, B.T.1
Brodersen, D.E.2
Clemons Jr., W.M.3
Morgan-Warren, R.J.4
Carter, A.P.5
Vonhein, C.6
Hartsch, T.7
Ramakrishnan, V.8
-
146
-
-
0025300402
-
Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
-
Woese CR, Kandler O, Wheelis ML (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
-
147
-
-
0035945246
-
Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA
-
Wuyts J, Van de Peer Y, De Wachter R (2001) Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Res 29:5017-5028
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 5017-5028
-
-
Wuyts, J.1
Van De Peer, Y.2
De Wachter, R.3
-
148
-
-
0028948030
-
PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains
-
Yamamoto S, Harayama S (1995) PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61:1104-1109
-
(1995)
Appl Environ Microbiol
, vol.61
, pp. 1104-1109
-
-
Yamamoto, S.1
Harayama, S.2
-
149
-
-
0029863154
-
Phylogenetic analysis of Acinetobacter strains based on the nucleotide sequences of gyrB genes and on the amino acid sequences of their products
-
Yamamoto S, Harayama S (1996) Phylogenetic analysis of Acinetobacter strains based on the nucleotide sequences of gyrB genes and on the amino acid sequences of their products. Int J Syst Bacterid 46:506-511
-
(1996)
Int J Syst Bacterid
, vol.46
, pp. 506-511
-
-
Yamamoto, S.1
Harayama, S.2
-
150
-
-
0031827993
-
Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes
-
Yamamoto S, Harayama S (1998) Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int J Syst Bacterid 48:813-819
-
(1998)
Int J Syst Bacterid
, vol.48
, pp. 813-819
-
-
Yamamoto, S.1
Harayama, S.2
-
151
-
-
0032931780
-
Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: Comparison with the grouping by DNA-DNA hybridization
-
Yamamoto S, Bouvet PJ, Harayama S (1999) Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization. Int J Syst Bacteriol 49:87-95
-
(1999)
Int J Syst Bacteriol
, vol.49
, pp. 87-95
-
-
Yamamoto, S.1
Bouvet, P.J.2
Harayama, S.3
-
152
-
-
0037978013
-
Phylogenetic analysis of members of the genus Aeromonas based on gyrB gene sequences
-
Yanez MA, Catalan V, Apraiz D, Figueras MJ, Martinez-Murcia AJ (2003) Phylogenetic analysis of members of the genus Aeromonas based on gyrB gene sequences. Int J Syst Evol Microbiol 53:875-883
-
(2003)
Int J Syst Evol Microbiol
, vol.53
, pp. 875-883
-
-
Yanez, M.A.1
Catalan, V.2
Apraiz, D.3
Figueras, M.J.4
Martinez-Murcia, A.J.5
-
153
-
-
0345328128
-
Gene sequences useful for predicting relatedness of whole genomes in bacteria
-
Zeigler DR (2003) Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol 53:1893-1900
-
(2003)
Int J Syst Evol Microbiol
, vol.53
, pp. 1893-1900
-
-
Zeigler, D.R.1
|