-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schäffer 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
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
0030000545
-
Cloning, nucleotide sequence, and characterization of the genes encoding enzymes involved in the degradation of cumene to 2-hydroxy-6-oxo-7-methylocta-2, 4-dienoic acid in Pseudomonas fluorescens IP01
-
Aoki H, Kimura T, Habe H, Yamane H, Kodama T Omori T (1996) Cloning, nucleotide sequence, and characterization of the genes encoding enzymes involved in the degradation of cumene to 2-hydroxy-6-oxo-7-methylocta-2,4-dienoic acid in Pseudomonas fluorescens IP01. J Ferment Bioeng 81:187 196.
-
(1996)
J Ferment Bioeng
, vol.81
, pp. 187-196
-
-
Aoki, H.1
Kimura, T.2
Habe, H.3
Yamane, H.4
Kodama, T.5
Omori, T.6
-
3
-
-
0032444534
-
Two sets of biphenyl and PCB degradation genes on a linear plasmid in Rhodococcus erythropolis TA421
-
Arai H, Kosono S, Taguchi K, Maeda M, Song E, Fuji F, Chung SY Kudo T (1998) Two sets of biphenyl and PCB degradation genes on a linear plasmid in Rhodococcus erythropolis TA421. J Ferment Bioeng 86:595 599.
-
(1998)
J Ferment Bioeng
, vol.86
, pp. 595-599
-
-
Arai, H.1
Kosono, S.2
Taguchi, K.3
Maeda, M.4
Song, E.5
Fuji, F.6
Chung, S.Y.7
Kudo, T.8
-
4
-
-
15444365046
-
Subtle difference between benzene and toluene dioxygenases of Pseudomonas putida
-
Bagnéris C, Cammack R Mason JR (2005) Subtle difference between benzene and toluene dioxygenases of Pseudomonas putida. Appl Environ Microbiol 71:1570 1580.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 1570-1580
-
-
Bagnéris, C.1
Cammack, R.2
Mason, J.R.3
-
5
-
-
0037641131
-
Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR
-
Baldwin BR, Nakatsu CH Nies L (2003) Detection and enumeration of aromatic oxygenase genes by multiplex and real-time PCR. Appl Environ Microbiol 69:3350 3358.
-
(2003)
Appl Environ Microbiol
, vol.69
, pp. 3350-3358
-
-
Baldwin, B.R.1
Nakatsu, C.H.2
Nies, L.3
-
6
-
-
2942527326
-
Oligonucleotide microarrays in microbial diagnostics
-
Bodrossy L Sessitsch A (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol 7:245 254.
-
(2004)
Curr Opin Microbiol
, vol.7
, pp. 245-254
-
-
Bodrossy, L.1
Sessitsch, A.2
-
7
-
-
0038302040
-
Development and validation of a diagnostic microbial microarray for methanotrophs
-
Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A Sessitsch A (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5:566 582.
-
(2003)
Environ Microbiol
, vol.5
, pp. 566-582
-
-
Bodrossy, L.1
Stralis-Pavese, N.2
Murrell, J.C.3
Radajewski, S.4
Weilharter, A.5
Sessitsch, A.6
-
9
-
-
0141564886
-
Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities
-
Denef VJ, Park J, Rodrigues JLM, Tsoi TV, Hashsham SA Tiedje JM (2003) Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ Microbiol 5:933 943.
-
(2003)
Environ Microbiol
, vol.5
, pp. 933-943
-
-
Denef, V.J.1
Park, J.2
Rodrigues, J.L.M.3
Tsoi, T.V.4
Hashsham, S.A.5
Tiedje, J.M.6
-
10
-
-
0037391375
-
Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays
-
El Fantroussi S, Urakawa H, Bernhard AE, Kelly JJ, Noble PA, Smidt H, Yershov GM Stahl DA (2003) Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Appl Environ Microbiol 69:2377 2382.
-
(2003)
Appl Environ Microbiol
, vol.69
, pp. 2377-2382
-
-
El Fantroussi, S.1
Urakawa, H.2
Bernhard, A.E.3
Kelly, J.J.4
Noble, P.A.5
Smidt, H.6
Yershov, G.M.7
Stahl, D.A.8
-
11
-
-
0000122573
-
PHYLIP - Phylogeny Inference Package (Version 3.2)
-
Felsenstein J (1989) PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5:164 166.
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
12
-
-
4444337310
-
Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1
-
Furusawa Y, Nagarajan V, Tanokura M, Masai E, Fukuda M Senda T (2004) Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1. J Mol Biol 342:1041 1052.
-
(2004)
J Mol Biol
, vol.342
, pp. 1041-1052
-
-
Furusawa, Y.1
Nagarajan, V.2
Tanokura, M.3
Masai, E.4
Fukuda, M.5
Senda, T.6
-
13
-
-
0034029015
-
Aromatic hydrocarbon dioxygenases in environmental biotechnology
-
Gibson DT Parales RE (2000) Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr Opin Biotechnol 11:236 243.
-
(2000)
Curr Opin Biotechnol
, vol.11
, pp. 236-243
-
-
Gibson, D.T.1
Parales, R.E.2
-
14
-
-
25144487554
-
Use of microarrays with different probe sizes for monitoring gene expression
-
He Z, Wu L, Fields MW Zhou J (2005a) Use of microarrays with different probe sizes for monitoring gene expression. Appl Environ Microbiol 71:5154 5162.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 5154-5162
-
-
He, Z.1
Wu, L.2
Fields, M.W.3
Zhou, J.4
-
15
-
-
22144441403
-
Empirical establishment of oligonucleotide probe design criteria
-
He Z, Wu L, Li X, Fields MW Zhou J (2005b) Empirical establishment of oligonucleotide probe design criteria. Appl Environ Microbiol 71:3753 3760.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 3753-3760
-
-
He, Z.1
Wu, L.2
Li, X.3
Fields, M.W.4
Zhou, J.5
-
16
-
-
0036794831
-
Flow cytometry analysis of changes in the DNA content of the polychlorinated biphenyl degrader Comamonas testosteroni TK102: Effect of metabolites on cell-cell separation
-
Hiraoka Y, Yamada T, Tone K, Futaesaku Y Kimbara K (2002) Flow cytometry analysis of changes in the DNA content of the polychlorinated biphenyl degrader Comamonas testosteroni TK102: effect of metabolites on cell-cell separation. Appl Environ Microbiol 68:5104 5112.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 5104-5112
-
-
Hiraoka, Y.1
Yamada, T.2
Tone, K.3
Futaesaku, Y.4
Kimbara, K.5
-
17
-
-
0023442379
-
Nucleotide sequencing and characterization of the genes encoding benzene oxidation enzymes of Pseudomonas putida
-
Irie S, Doi S, Yorifuji T, Takagi M Yano K (1987) Nucleotide sequencing and characterization of the genes encoding benzene oxidation enzymes of Pseudomonas putida. J Bacteriol 169:5174 5179.
-
(1987)
J Bacteriol
, vol.169
, pp. 5174-5179
-
-
Irie, S.1
Doi, S.2
Yorifuji, T.3
Takagi, M.4
Yano, K.5
-
18
-
-
34547450068
-
Development of a 60-mer oligonucleotide microarray on the basis of benzene monooxygenase gene diversity
-
Iwai S, Kurisu F, Urakawa H, Yagi O Furumai H (2007) Development of a 60-mer oligonucleotide microarray on the basis of benzene monooxygenase gene diversity. Appl Microbiol Biotechnol 75:929 939.
-
(2007)
Appl Microbiol Biotechnol
, vol.75
, pp. 929-939
-
-
Iwai, S.1
Kurisu, F.2
Urakawa, H.3
Yagi, O.4
Furumai, H.5
-
19
-
-
0029150754
-
Nucleotide sequence analysis of genes encoding a toluene/benzene-2- monooxygenase from Pseudomonas sp. strain JS150
-
Johnson GR Olsen RH (1995) Nucleotide sequence analysis of genes encoding a toluene/benzene-2-monooxygenase from Pseudomonas sp. strain JS150. Appl Environ Microbiol 61:3336 3346.
-
(1995)
Appl Environ Microbiol
, vol.61
, pp. 3336-3346
-
-
Johnson, G.R.1
Olsen, R.H.2
-
20
-
-
0030475427
-
Gene organization and low regiospecificity in aromatic-ring hydroxylation of a benzene monooxygenase of Pseudomonas aeruginosa JI104
-
Kitayama A, Suzuki E, Kawakami Y Nagamune T (1996) Gene organization and low regiospecificity in aromatic-ring hydroxylation of a benzene monooxygenase of Pseudomonas aeruginosa JI104. J Ferment Bioeng 82:421 425.
-
(1996)
J Ferment Bioeng
, vol.82
, pp. 421-425
-
-
Kitayama, A.1
Suzuki, E.2
Kawakami, Y.3
Nagamune, T.4
-
21
-
-
0035210154
-
Optimization of an oligonucleotide microchip for microbial identification studies: A non-equilibrium dissociation approach
-
Liu WT, Mirzabekov AD Stahl DA (2001) Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ Microbiol 3:619 629.
-
(2001)
Environ Microbiol
, vol.3
, pp. 619-629
-
-
Liu, W.T.1
Mirzabekov, A.D.2
Stahl, D.A.3
-
22
-
-
0036795787
-
Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment
-
Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer KH Wagner M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68:5064 5081.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 5064-5081
-
-
Loy, A.1
Lehner, A.2
Lee, N.3
Adamczyk, J.4
Meier, H.5
Ernst, J.6
Schleifer, K.H.7
Wagner, M.8
-
25
-
-
19644372183
-
Isolation and characterization of benzene-tolerant Rhodococcus opacus strains
-
Na KS, Kuroda A, Takiguchi N, Ikeda T, Ohtake H Kato J (2005) Isolation and characterization of benzene-tolerant Rhodococcus opacus strains. J Biosci Bioeng 99:378 382.
-
(2005)
J Biosci Bioeng
, vol.99
, pp. 378-382
-
-
Na, K.S.1
Kuroda, A.2
Takiguchi, N.3
Ikeda, T.4
Ohtake, H.5
Kato, J.6
-
26
-
-
33745132697
-
Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation
-
Ní Chadhain SM, Norman RS, Pesce KV, Kukor JJ Zylstra GJ (2006) Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation. Appl Environ Microbiol 72:4078 4087.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 4078-4087
-
-
Ní Chadhain, S.M.1
Norman, R.S.2
Pesce, K.V.3
Kukor, J.J.4
Zylstra, G.J.5
-
27
-
-
0034051818
-
Substrate specificity of naphthalene dioxygenase: Effect of specific amino acids at the active site of the enzyme
-
Parales RE, Lee K, Resnick SM, Jiang H, Lessner DJ Gibson DT (2000) Substrate specificity of naphthalene dioxygenase: effect of specific amino acids at the active site of the enzyme. J Bacteriol 182:1641 1649.
-
(2000)
J Bacteriol
, vol.182
, pp. 1641-1649
-
-
Parales, R.E.1
Lee, K.2
Resnick, S.M.3
Jiang, H.4
Lessner, D.J.5
Gibson, D.T.6
-
29
-
-
3242773890
-
Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays
-
Rhee SK, Liu XD, Wu LY, Chong SC, Wan XF Zhou J (2004) Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl Environ Microbiol 70:4303 4317.
-
(2004)
Appl Environ Microbiol
, vol.70
, pp. 4303-4317
-
-
Rhee, S.K.1
Liu, X.D.2
Wu, L.Y.3
Chong, S.C.4
Wan, X.F.5
Zhou, J.6
-
30
-
-
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
-
31
-
-
15444362001
-
Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness
-
Schloss PD Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501 1506.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 1501-1506
-
-
Schloss, P.D.1
Handelsman, J.2
-
32
-
-
0036285535
-
Alteration of regiospecificity in biphenyl dioxygenase by active-site engineering
-
Suenaga H, Watanabe T, Sato M, Ngadiman Furukawa K (2002) Alteration of regiospecificity in biphenyl dioxygenase by active-site engineering. J Bacteriol 184:3682 3688.
-
(2002)
J Bacteriol
, vol.184
, pp. 3682-3688
-
-
Suenaga, H.1
Watanabe, T.2
Sato, M.3
Ngadiman4
Furukawa, K.5
-
33
-
-
0029859713
-
Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes
-
Sugimoto N, Nakano S, Yoneyama M Honda K (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res 24:4501 4505.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 4501-4505
-
-
Sugimoto, N.1
Nakano, S.2
Yoneyama, M.3
Honda, K.4
-
34
-
-
0027203859
-
The Pseudomonas putida ML2 plasmid-encoded genes for benzene dioxygenase are unusual in codon usage and low in G+C content
-
Tan HM, Tang HY, Joannou CL, Abdelwahab NH Mason JR (1993) The Pseudomonas putida ML2 plasmid-encoded genes for benzene dioxygenase are unusual in codon usage and low in G+C content. Gene 130:33 39.
-
(1993)
Gene
, vol.130
, pp. 33-39
-
-
Tan, H.M.1
Tang, H.Y.2
Joannou, C.L.3
Abdelwahab, N.H.4
Mason, J.R.5
-
35
-
-
0037195374
-
Detection of known and novel genes encoding aromatic ring-hydroxylating dioxygenases in soils and in aromatic hydrocarbon-degrading bacteria
-
Taylor PM, Medd JM, Schoenborn L, Hodgson B Janssen PH (2002) Detection of known and novel genes encoding aromatic ring-hydroxylating dioxygenases in soils and in aromatic hydrocarbon-degrading bacteria. FEMS Microbiol Lett 216:61 66.
-
(2002)
FEMS Microbiol Lett
, vol.216
, pp. 61-66
-
-
Taylor, P.M.1
Medd, J.M.2
Schoenborn, L.3
Hodgson, B.4
Janssen, P.H.5
-
36
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673 4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
37
-
-
27644563784
-
Protein engineering of toluene-o-xylene monooxygenase from Pseudomonas stutzeri OX1 for enhanced chlorinated ethene degradation and o-xylene oxidation
-
Vardar G Wood TK (2005) Protein engineering of toluene-o-xylene monooxygenase from Pseudomonas stutzeri OX1 for enhanced chlorinated ethene degradation and o-xylene oxidation. Appl Microbiol Biotechnol 68:510 517.
-
(2005)
Appl Microbiol Biotechnol
, vol.68
, pp. 510-517
-
-
Vardar, G.1
Wood, T.K.2
-
38
-
-
34248179977
-
Unravelling microbial communities with DNA-microarrays: Challenges and future directions
-
Wagner M, Smidt H, Loy A Zhou J (2007) Unravelling microbial communities with DNA-microarrays: challenges and future directions. Microb Ecol 53:498 506.
-
(2007)
Microb Ecol
, vol.53
, pp. 498-506
-
-
Wagner, M.1
Smidt, H.2
Loy, A.3
Zhou, J.4
-
39
-
-
84944178665
-
Hierarchical grouping to optimize an objective function
-
Ward JH (1963) Hierarchical grouping to optimize an objective function. J Am Stat Assoc 58:236 244.
-
(1963)
J Am Stat Assoc
, vol.58
, pp. 236-244
-
-
Ward, J.H.1
-
40
-
-
33646573004
-
Assessment of toluene/biphenyl dioxygenase gene diversity in benzene-polluted soils: Links between benzene biodegradation and genes similar to those encoding isopropylbenzene dioxygenases
-
Witzig R, Junca H, Hecht HJ Pieper DH (2006) Assessment of toluene/biphenyl dioxygenase gene diversity in benzene-polluted soils: links between benzene biodegradation and genes similar to those encoding isopropylbenzene dioxygenases. Appl Environ Microbiol 72:3504 3514.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 3504-3514
-
-
Witzig, R.1
Junca, H.2
Hecht, H.J.3
Pieper, D.H.4
-
41
-
-
0037772204
-
Microarrays for bacterial detection and microbial community analysis
-
Zhou J (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6:288 294.
-
(2003)
Curr Opin Microbiol
, vol.6
, pp. 288-294
-
-
Zhou, J.1
|