-
1
-
-
51649108915
-
Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator
-
Agari, Y., Kashihara, A., Yokoyama, S., Kuramitsu, S. & Shinkai, A. (2008). Global gene expression mediated by Thermus thermophilus SdrP, a CRP/FNR family transcriptional regulator. Mol Microbiol 70, 60-75.
-
(2008)
Mol Microbiol
, vol.70
, pp. 60-75
-
-
Agari, Y.1
Kashihara, A.2
Yokoyama, S.3
Kuramitsu, S.4
Shinkai, A.5
-
2
-
-
0035980053
-
DNA Chain Length Dependence of Formation and Dynamics of hMutSα.hMutLα.Heteroduplex Complexes
-
DOI 10.1074/jbc.M105076200
-
Blackwell, L. J., Wang, S. & Modrich, P. (2001). DNA chain length dependence of formation and dynamics of hMutSα.hMutLα.heteroduplex complexes. J Biol Chem 276, 33233-33240. (Pubitemid 37384777)
-
(2001)
Journal of Biological Chemistry
, vol.276
, Issue.35
, pp. 33233-33240
-
-
Blackwell, L.J.1
Wang, S.2
Modrich, P.3
-
3
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
DOI 10.1093/bioinformatics/19.2.185
-
Bolstad, B. M., Irizarry, R. A., Astrand, M. & Speed, T. P. (2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193. (Pubitemid 36181903)
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
4
-
-
3543012707
-
Crystallography and NMR system: A new software suite for macromolecular structure determination
-
DOI 10.1107/S0907444998003254
-
Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M. & other authors (1998). Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54, 905-921. (Pubitemid 28443603)
-
(1998)
Acta Crystallographica Section D: Biological Crystallography
, vol.54
, Issue.5
, pp. 905-921
-
-
Brunger, A.T.1
Adams, P.D.2
Clore, G.M.3
Delano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.-S.7
Kuszewski, J.8
Nilges, M.9
Pannu, N.S.10
Read, R.J.11
Rice, L.M.12
Simonson, T.13
Warren, G.L.14
-
5
-
-
10744226888
-
Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs
-
DOI 10.1016/S0092-8674(04)00127-8
-
Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J. & other authors (2004). Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499-509. (Pubitemid 38264428)
-
(2004)
Cell
, vol.116
, Issue.4
, pp. 499-509
-
-
Cawley, S.1
Bekiranov, S.2
Ng, H.H.3
Kapranov, P.4
Sekinger, E.A.5
Kampa, D.6
Piccolboni, A.7
Sementchenko, V.8
Cheng, J.9
Williams, A.J.10
Wheeler, R.11
Wong, B.12
Drenkow, J.13
Yamanaka, M.14
Patel, S.15
Brubaker, S.16
Tammana, H.17
Helt, G.18
Struhl, K.19
Gingeras, T.R.20
more..
-
6
-
-
0028103275
-
The CCP4 suite: Programs for protein crystallography
-
Collaborative Computational Project, Number 4
-
Collaborative Computational Project, Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50, 760-763.
-
(1994)
Acta Crystallogr D Biol Crystallogr
, vol.50
, pp. 760-763
-
-
-
8
-
-
35948977727
-
Crystal structure of a blue laccase from Lentinus tigrinus: Evidences for intermediates in the molecular oxygen reductive splitting by multicopper oxidases
-
DOI 10.1186/1472-6807-7-60
-
Ferraroni, M., Myasoedova, N. M., Schmatchenko, V., Leontievsky, A. A., Golovleva, L. A., Scozzafava, A. & Briganti, F. (2007). Crystal structure of a blue laccase from Lentinus tigrinus: evidences for intermediates in the molecular oxygen reductive splitting by multicopper oxidases. BMC Struct Biol 7, 60. (Pubitemid 350077018)
-
(2007)
BMC Structural Biology
, vol.7
, pp. 60
-
-
Ferraroni, M.1
Myasoedova, N.M.2
Schmatchenko, V.3
Leontievsky, A.A.4
Golovleva, L.A.5
Scozzafava, A.6
Briganti, F.7
-
9
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y. & other authors (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5, R80.
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
Ellis, B.7
Gautier, L.8
Ge, Y.9
-
10
-
-
0043123208
-
ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins
-
DOI 10.1093/nar/gkg556
-
Gouet, P., Robert, X. & Courcelle, E. (2003). ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 31, 3320-3323. (Pubitemid 37442149)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3320-3323
-
-
Gouet, P.1
Robert, X.2
Courcelle, E.3
-
11
-
-
0035850879
-
Disruption of Thermus thermophilus genes by homologous recombination using a thermostable kanamycin-resistant marker
-
DOI 10.1016/S0014-5793(01)02926-X, PII S001457930102926X
-
Hashimoto, Y., Yano, T., Kuramitsu, S. & Kagamiyama, H. (2001). Disruption of Thermus thermophilus genes by homologous recombination using a thermostable kanamycin-resistant marker. FEBS Lett 506, 231-234. (Pubitemid 32964819)
-
(2001)
FEBS Letters
, vol.506
, Issue.3
, pp. 231-234
-
-
Hashimoto, Y.1
Yano, T.2
Kuramitsu, S.3
Kagamiyama, H.4
-
12
-
-
0031865006
-
Touring protein fold space with Dali/FSSP
-
DOI 10.1093/nar/26.1.316
-
Holm, L. & Sander, C. (1998). Touring protein fold space with Dali/FSSP. Nucleic Acids Res 26, 316-319. (Pubitemid 28291549)
-
(1998)
Nucleic Acids Research
, vol.26
, Issue.1
, pp. 316-319
-
-
Holm, L.1
Sander, C.2
-
13
-
-
0032730861
-
Directed evolution of thermostable kanamycin-resistance gene: A convenient selection marker for Thermus thermophilus
-
Hoseki, J., Yano, T., Koyama, Y., Kuramitsu, S. & Kagamiyama, H. (1999). Directed evolution of thermostable kanamycin-resistance gene: a convenient selection marker for Thermus thermophilus. J Biochem 126, 951-956.
-
(1999)
J Biochem
, vol.126
, pp. 951-956
-
-
Hoseki, J.1
Yano, T.2
Koyama, Y.3
Kuramitsu, S.4
Kagamiyama, H.5
-
14
-
-
0035985581
-
How oxygen damages microbes: Oxygen tolerance and obligate anaerobiosis
-
Imlay, J. A. (2002). How oxygen damages microbes: oxygen tolerance and obligate anaerobiosis. Adv Microb Physiol 46, 111-153.
-
(2002)
Adv Microb Physiol
, vol.46
, pp. 111-153
-
-
Imlay, J.A.1
-
15
-
-
70349435274
-
DNA recognition and wrapping by Escherichia coli RcnR
-
Iwig, J. S. & Chivers, P. T. (2009). DNA recognition and wrapping by Escherichia coli RcnR. J Mol Biol 393, 514-526.
-
(2009)
J Mol Biol
, vol.393
, pp. 514-526
-
-
Iwig, J.S.1
Chivers, P.T.2
-
16
-
-
33748666848
-
Nickel homeostasis in Escherichia coli - The rcnR-rcnA efflux pathway and its linkage to NikR function
-
Iwig, J. S., Rowe, J. L. & Chivers, P. T. (2006). Nickel homeostasis in Escherichia coli - the rcnR-rcnA efflux pathway and its linkage to NikR function. Mol Microbiol 62, 252-262.
-
(2006)
Mol Microbiol
, vol.62
, pp. 252-262
-
-
Iwig, J.S.1
Rowe, J.L.2
Chivers, P.T.3
-
17
-
-
45249113233
-
Ni(II) and Co(II) sensing by Escherichia coli RcnR
-
DOI 10.1021/ja710067d
-
Iwig, J. S., Leitch, S., Herbst, R. W., Maroney, M. J. & Chivers, P. T. (2008). Ni(II) and Co(II) sensing by Escherichia coli RcnR. J Am Chem Soc 130, 7592-7606. (Pubitemid 351842123)
-
(2008)
Journal of the American Chemical Society
, vol.130
, Issue.24
, pp. 7592-7606
-
-
Iwig, J.S.1
Leitch, S.2
Herbst, R.W.3
Maroney, M.J.4
Chivers, P.T.5
-
18
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
19
-
-
40349106220
-
Insights into different dependence of dNTP triphosphohydrolase on metal ion species from intracellular ion concentrations in Thermus thermophilus
-
Kondo, N., Nishikubo, T., Wakamatsu, T., Ishikawa, H., Nakagawa, N., Kuramitsu, S. & Masui, R. (2008). Insights into different dependence of dNTP triphosphohydrolase on metal ion species from intracellular ion concentrations in Thermus thermophilus. Extremophiles 12, 217-223.
-
(2008)
Extremophiles
, vol.12
, pp. 217-223
-
-
Kondo, N.1
Nishikubo, T.2
Wakamatsu, T.3
Ishikawa, H.4
Nakagawa, N.5
Kuramitsu, S.6
Masui, R.7
-
20
-
-
34548232365
-
Inference of Macromolecular Assemblies from Crystalline State
-
DOI 10.1016/j.jmb.2007.05.022, PII S0022283607006420
-
Krissinel, E. & Henrick, K. (2007). Inference of macromolecular assemblies from crystalline state. J Mol Biol 372, 774-797. (Pubitemid 47321791)
-
(2007)
Journal of Molecular Biology
, vol.372
, Issue.3
, pp. 774-797
-
-
Krissinel, E.1
Henrick, K.2
-
21
-
-
0025366034
-
Pre-steady-state kinetics of Escherichia coli aspartate aminotransferase catalyzed reactions and thermodynamic aspects of its substrate specificity
-
DOI 10.1021/bi00475a010
-
Kuramitsu, S., Hiromi, K., Hayashi, H., Morino, Y. & Kagamiyama, H. (1990). Pre-steady-state kinetics of Escherichia coli aspartate aminotransferase catalyzed reactions and thermodynamic aspects of its substrate specificity. Biochemistry 29, 5469-5476. (Pubitemid 20202271)
-
(1990)
Biochemistry
, vol.29
, Issue.23
, pp. 5469-5476
-
-
Kuramitsu, S.1
Hiromi, K.2
Hayashi, H.3
Morino, Y.4
Kagamiyama, H.5
-
22
-
-
36448991500
-
CLUSTAL W and CLUSTAL X version 2.0
-
Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A. & other authors (2007). CLUSTAL W and CLUSTAL X version 2.0. Bioinformatics 23, 2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
-
23
-
-
0000243829
-
PROCHECK: A program to check the stereochemical quality of protein structures
-
Laskowski, R. A., McArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26, 283-291.
-
(1993)
J Appl Cryst
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
McArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
24
-
-
0022273106
-
15N heteronuclear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type
-
15N heteronuclear NMR studies of Escherichia coli thioredoxin in samples isotopically labeled by residue type. Biochemistry 24, 7263-7268.
-
(1985)
Biochemistry
, vol.24
, pp. 7263-7268
-
-
LeMaster, D.M.1
Richards, F.M.2
-
25
-
-
33845736364
-
CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator
-
DOI 10.1038/nchembio844, PII NCHEMBIO844
-
Liu, T., Ramesh, A., Ma, Z., Ward, S. K., Zhang, L., George, G. N., Talaat, A. M., Sacchettini, J. C. & Giedroc, D. P. (2007). CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator. Nat Chem Biol 3, 60-68. (Pubitemid 46005700)
-
(2007)
Nature Chemical Biology
, vol.3
, Issue.1
, pp. 60-68
-
-
Liu, T.1
Ramesh, A.2
Ma, Z.3
Ward, S.K.4
Zhang, L.5
George, G.N.6
Talaat, A.M.7
Sacchettini, J.C.8
Giedroc, D.P.9
-
26
-
-
0037441653
-
Structure validation by Cα geometry: φ,ψ and Cβ deviation
-
Lovell, S. C., Davis, I. W., Arendall, W. B., III, de Bakker, P. I., Word, J. M., Prisant, M. G., Richardson, J. S. & Richardson, D. C. (2003). Structure validation by Cα geometry: φ,ψ and Cβ deviation. Proteins 50, 437-450.
-
(2003)
Proteins
, vol.50
, pp. 437-450
-
-
Lovell, S.C.1
Davis, I.W.2
Arendall III, W.B.3
De Bakker, P.I.4
Word, J.M.5
Prisant, M.G.6
Richardson, J.S.7
Richardson, D.C.8
-
27
-
-
65249102750
-
Molecular insights into the metal selectivity of the copper(I)-sensing repressor CsoR from Bacillus subtilis
-
Ma, Z., Cowart, D. M., Scott, R. A. & Giedroc, D. P. (2009a). Molecular insights into the metal selectivity of the copper(I)-sensing repressor CsoR from Bacillus subtilis. Biochemistry 48, 3325-3334.
-
(2009)
Biochemistry
, vol.48
, pp. 3325-3334
-
-
Ma, Z.1
Cowart, D.M.2
Scott, R.A.3
Giedroc, D.P.4
-
28
-
-
70350637580
-
Coordination chemistry of bacterial metal transport and sensing
-
Ma, Z., Jacobsen, F. E. & Giedroc, D. P. (2009b). Coordination chemistry of bacterial metal transport and sensing. Chem Rev 109, 4644-4681.
-
(2009)
Chem Rev
, vol.109
, pp. 4644-4681
-
-
Ma, Z.1
Jacobsen, F.E.2
Giedroc, D.P.3
-
29
-
-
0015955554
-
Description of Thermus thermophilus (Yoshida and Oshima) com. nov., a non-sporulating thermophilic bacterium from a Japanese thermal spa
-
Oshima, T. & Imahori, K. (1974). Description of Thermus thermophilus (Yoshida and Oshima) com. nov., a non-sporulating thermophilic bacterium from a Japanese thermal spa. Int J Syst Bacteriol 24, 102-112.
-
(1974)
Int J Syst Bacteriol
, vol.24
, pp. 102-112
-
-
Oshima, T.1
Imahori, K.2
-
30
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
DOI 10.1016/S0076-6879(97)76066-X
-
Otwinowski, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276, 307-326. (Pubitemid 27085611)
-
(1997)
Methods in Enzymology
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
31
-
-
0035788112
-
ARP/wARP and molecular replacement
-
Perrakis, A., Harkiolaki, M., Wilson, K. S. & Lamzin, V. S. (2001). ARP/wARP and molecular replacement. Acta Crystallogr D Biol Crystallogr 57, 1445-1450.
-
(2001)
Acta Crystallogr D Biol Crystallogr
, vol.57
, pp. 1445-1450
-
-
Perrakis, A.1
Harkiolaki, M.2
Wilson, K.S.3
Lamzin, V.S.4
-
32
-
-
0017681196
-
DNA sequencing with chain-terminating inhibitors
-
Sanger, F., Nicklen, S. & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74, 5463-5467.
-
(1977)
Proc Natl Acad Sci U S A
, vol.74
, pp. 5463-5467
-
-
Sanger, F.1
Nicklen, S.2
Coulson, A.R.3
-
34
-
-
37449020787
-
CsoR regulates the copper efflux operon copZA in Bacillus subtilis
-
Smaldone, G. T. & Helmann, J. D. (2007). CsoR regulates the copper efflux operon copZA in Bacillus subtilis. Microbiology 153, 4123-4128.
-
(2007)
Microbiology
, vol.153
, pp. 4123-4128
-
-
Smaldone, G.T.1
Helmann, J.D.2
-
35
-
-
0042424602
-
Statistical significance for genomewide studies
-
Storey, J. D. & Tibshirani, R. (2003). Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100, 9440-9445.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
-
37
-
-
0033985228
-
Iron and oxidative stress in bacteria
-
Touati, D. (2000). Iron and oxidative stress in bacteria. Arch Biochem Biophys 373, 1-6.
-
(2000)
Arch Biochem Biophys
, vol.373
, pp. 1-6
-
-
Touati, D.1
-
38
-
-
14244270520
-
Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus
-
DOI 10.1107/S0907444902011770
-
Vassylyeva, M. N., Lee, J., Sekine, S. I., Laptenko, O., Kuramitsu, S., Shibata, T., Inoue, Y., Borukhov, S., Vassylyev, D. G. & Yokoyama, S. (2002). Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus. Acta Crystallogr D Biol Crystallogr 58, 1497-1500. (Pubitemid 35028853)
-
(2002)
Acta Crystallographica Section D: Biological Crystallography
, vol.58
, Issue.9
, pp. 1497-1500
-
-
Vassylyeva, M.N.1
Lee, J.2
Sekine, S.-I.3
Laptenko, O.4
Kuramitsu, S.5
Shibata, T.6
Inoue, Y.7
Borukhov, S.8
Vassylyev, D.G.9
Yokoyama, S.10
-
39
-
-
0033762813
-
Structural genomics projects in Japan
-
Yokoyama, S., Hirota, H., Kigawa, T., Yabuki, T., Shirouzu, M., Terada, T., Ito, Y., Matsuo, Y., Kuroda, Y. & other authors (2000). Structural genomics projects in Japan. Nat Struct Biol 7 (Suppl.), 943-945.
-
(2000)
Nat Struct Biol
, vol.7
, Issue.SUPPL.
, pp. 943-945
-
-
Yokoyama, S.1
Hirota, H.2
Kigawa, T.3
Yabuki, T.4
Shirouzu, M.5
Terada, T.6
Ito, Y.7
Matsuo, Y.8
Kuroda, Y.9
|