-
1
-
-
84857134358
-
Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target
-
Robinson, A., Causer, R.J. & Dixon, N.E. Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target. Curr. Drug Targets 13, 352-372 (2012).
-
(2012)
Curr. Drug Targets
, vol.13
, pp. 352-372
-
-
Robinson, A.1
Causer, R.J.2
Dixon, N.E.3
-
3
-
-
0031692027
-
DNA repair in Mycobacterium tuberculosis. What have we learnt from the genome sequence?
-
Mizrahi, V. & Andersen, S.J. DNA repair in Mycobacterium tuberculosis. What have we learnt from the genome sequence? Mol. Microbiol. 29, 1331-1339 (1998).
-
(1998)
Mol. Microbiol.
, vol.29
, pp. 1331-1339
-
-
Mizrahi, V.1
Andersen, S.J.2
-
4
-
-
4644335120
-
Lack of mismatch correction facilitates genome evolution in mycobacteria
-
Springer, B. et al. Lack of mismatch correction facilitates genome evolution in mycobacteria. Mol. Microbiol. 53, 1601-1609 (2004).
-
(2004)
Mol. Microbiol.
, vol.53
, pp. 1601-1609
-
-
Springer, B.1
-
5
-
-
79955460244
-
Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection
-
Ford, C.B. et al. Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat. Genet. 43, 482-486 (2011).
-
(2011)
Nat. Genet.
, vol.43
, pp. 482-486
-
-
Ford, C.B.1
-
6
-
-
84884992001
-
Genomic analysis identifes targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis
-
Farhat, M.R. et al. Genomic analysis identifes targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat. Genet. 45, 1183-1189 (2013).
-
(2013)
Nat. Genet.
, vol.45
, pp. 1183-1189
-
-
Farhat, M.R.1
-
7
-
-
0035931926
-
Massive gene decay in the leprosy bacillus
-
Cole, S.T. et al. Massive gene decay in the leprosy bacillus. Nature 409, 1007-1011 (2001).
-
(2001)
Nature
, vol.409
, pp. 1007-1011
-
-
Cole, S.T.1
-
8
-
-
79959431646
-
DNA replicases from a bacterial perspective
-
McHenry, C.S. DNA replicases from a bacterial perspective. Annu. Rev. Biochem. 80, 403-436 (2011).
-
(2011)
Annu. Rev. Biochem.
, vol.80
, pp. 403-436
-
-
McHenry, C.S.1
-
10
-
-
51249093024
-
Insights into the replisome from the structure of a ternary complex of the DNA polymerase III α-subunit
-
Wing, R.A., Bailey, S. & Steitz, T.A. Insights into the replisome from the structure of a ternary complex of the DNA polymerase III α-subunit. J. Mol. Biol. 382, 859-869 (2008).
-
(2008)
J. Mol. Biol.
, vol.382
, pp. 859-869
-
-
Wing, R.A.1
Bailey, S.2
Steitz, T.A.3
-
11
-
-
84877613987
-
A structural role for the PHP domain in E. Coli DNA polymerase III
-
Barros, T. et al. A structural role for the PHP domain in E. coli DNA polymerase III. BMC Struct. Biol. 13, 8 (2013).
-
(2013)
BMC Struct. Biol.
, vol.13
, pp. 8
-
-
Barros, T.1
-
12
-
-
0035940515
-
Comprehensive identifcation of conditionally essential genes in mycobacteria
-
Sassetti, C.M., Boyd, D.H. & Rubin, E.J. Comprehensive identifcation of conditionally essential genes in mycobacteria. Proc. Natl. Acad. Sci. USA 98, 12712-12717 (2001).
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 12712-12717
-
-
Sassetti, C.M.1
Boyd, D.H.2
Rubin, E.J.3
-
13
-
-
77749301852
-
Synergistic effects of UdgB and Ung in mutation prevention and protection against commonly encountered DNA damaging agents in Mycobacterium smegmatis
-
Malshetty, V.S., Jain, R., Srinath, T., Kurthkoti, K. & Varshney, U. Synergistic effects of UdgB and Ung in mutation prevention and protection against commonly encountered DNA damaging agents in Mycobacterium smegmatis. Microbiology 156, 940-949 (2010).
-
(2010)
Microbiology
, vol.156
, pp. 940-949
-
-
Malshetty, V.S.1
Jain, R.2
Srinath, T.3
Kurthkoti, K.4
Varshney, U.5
-
14
-
-
84867339877
-
Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing
-
Lee, H., Popodi, E., Tang, H. & Foster, P.L. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc. Natl. Acad. Sci. USA 109, E2774-E2783 (2012).
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. E2774-E2783
-
-
Lee, H.1
Popodi, E.2
Tang, H.3
Foster, P.L.4
-
15
-
-
9244225098
-
Mutants in the Exo i motif of Escherichia coli dnaQ: Defective proofreading and inviability due to error catastrophe
-
Fijalkowska, I.J. & Schaaper, R.M. Mutants in the Exo I motif of Escherichia coli dnaQ: defective proofreading and inviability due to error catastrophe. Proc. Natl. Acad. Sci. USA 93, 2856-2861 (1996).
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 2856-2861
-
-
Fijalkowska, I.J.1
Schaaper, R.M.2
-
16
-
-
33646397599
-
Evolution of mutation rates in bacteria
-
Denamur, E. & Matic, I. Evolution of mutation rates in bacteria. Mol. Microbiol. 60, 820-827 (2006).
-
(2006)
Mol. Microbiol.
, vol.60
, pp. 820-827
-
-
Denamur, E.1
Matic, I.2
-
17
-
-
0035949599
-
A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems
-
Dalrymple, B.P., Kongsuwan, K., Wijffels, G., Dixon, N.E. & Jennings, P.A. A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems. Proc. Natl. Acad. Sci. USA 98, 11627-11632 (2001).
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 11627-11632
-
-
Dalrymple, B.P.1
Kongsuwan, K.2
Wijffels, G.3
Dixon, N.E.4
Jennings, P.A.5
-
18
-
-
0035175673
-
TIGRFAMs: A protein family resource for the functional identifcation of proteins
-
Haft, D.H. et al. TIGRFAMs: a protein family resource for the functional identifcation of proteins. Nucleic Acids Res. 29, 41-43 (2001).
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 41-43
-
-
Haft, D.H.1
-
19
-
-
84896734255
-
Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes
-
Timinskas, K., Balvociute, M., Timinskas, A. & Venclovas, C. Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes. Nucleic Acids Res. 42, 1393-1413 (2014).
-
(2014)
Nucleic Acids Res.
, Issue.42
, pp. 1393-1413
-
-
Timinskas, K.1
Balvociute, M.2
Timinskas, A.3
Venclovas, C.4
-
20
-
-
84880648722
-
Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases
-
Jordheim, L.P., Durantel, D., Zoulim, F. & Dumontet, C. Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases. Nat. Rev. Drug Discov. 12, 447-464 (2013).
-
(2013)
Nat. Rev. Drug Discov.
, vol.12
, pp. 447-464
-
-
Jordheim, L.P.1
Durantel, D.2
Zoulim, F.3
Dumontet, C.4
-
21
-
-
40949138190
-
Structure-activity relationship for adenosine kinase from Mycobacterium tuberculosis
-
Long, M.C. et al. Structure-activity relationship for adenosine kinase from Mycobacterium tuberculosis. Biochem. Pharmacol. 75, 1588-1600 (2008).
-
(2008)
Biochem. Pharmacol.
, vol.75
, pp. 1588-1600
-
-
Long, M.C.1
-
22
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
23
-
-
77956295988
-
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
-
24
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo, M.A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
-
(2011)
Nat. Genet.
, vol.43
, pp. 491-498
-
-
Depristo, M.A.1
-
25
-
-
84879682699
-
Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis
-
Ford, C.B. et al. Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat. Genet. 45, 784-790 (2013).
-
(2013)
Nat. Genet.
, vol.45
, pp. 784-790
-
-
Ford, C.B.1
-
26
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
27
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh, K., Misawa, K., Kuma, K.-I. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059-3066 (2002).
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.-I.3
Miyata, T.4
-
28
-
-
84890037468
-
Infernal 1.1: 100-fold faster RNA homology searches
-
Nawrocki, E.P. & Eddy, S.R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29, 2933-2935 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 2933-2935
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
29
-
-
77949718257
-
FastTree 2-approximately maximum-likelihood trees for large alignments
-
Price, M.N., Dehal, P.S. & Arkin, A.P. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
-
(2010)
PLoS ONE
, vol.5
, pp. e9490
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
30
-
-
84899553363
-
RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312-1313 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
31
-
-
79960004119
-
Interactive Tree of Life v2: Online annotation and display of phylogenetic trees made easy
-
Letunic, I. & Bork, P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 39, W475-W478 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W475-W478
-
-
Letunic, I.1
Bork, P.2
-
32
-
-
84895895475
-
Evolution and transmission of drug-resistant tuberculosis in a Russian population
-
Casali, N. et al. Evolution and transmission of drug-resistant tuberculosis in a Russian population. Nat. Genet. 46, 279-286 (2014).
-
(2014)
Nat. Genet.
, vol.46
, pp. 279-286
-
-
Casali, N.1
-
33
-
-
84885009252
-
Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifes genes and intergenic regions associated with drug resistance
-
Zhang, H. et al. Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifes genes and intergenic regions associated with drug resistance. Nat. Genet. 45, 1255-1260 (2013).
-
(2013)
Nat. Genet.
, vol.45
, pp. 1255-1260
-
-
Zhang, H.1
-
34
-
-
84884995578
-
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans
-
Comas, I. et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat. Genet. 45, 1176-1182 (2013).
-
(2013)
Nat. Genet.
, vol.45
, pp. 1176-1182
-
-
Comas, I.1
-
35
-
-
0031985277
-
Rapid, low-technology MIC determination with clinical Mycobacterium tuberculosis isolates by using the microplate Alamar Blue assay
-
Franzblau, S.G. et al. Rapid, low-technology MIC determination with clinical Mycobacterium tuberculosis isolates by using the microplate Alamar Blue assay. J. Clin. Microbiol. 36, 362-366 (1998).
-
(1998)
J. Clin. Microbiol.
, vol.36
, pp. 362-366
-
-
Franzblau, S.G.1
-
36
-
-
14844294424
-
Protein production by auto-induction in high-density shaking cultures
-
Studier, F.W. Protein production by auto-induction in high-density shaking cultures. Protein Expr. Purif. 41, 207-234 (2005).
-
(2005)
Protein Expr. Purif.
, vol.41
, pp. 207-234
-
-
Studier, F.W.1
-
37
-
-
84877587406
-
Architecture of the Pol III-clamp-exonuclease complex reveals key roles of the exonuclease subunit in processive DNA synthesis and repair
-
Toste Rêgo, A., Holding, A.N., Kent, H. & Lamers, M.H. Architecture of the Pol III-clamp-exonuclease complex reveals key roles of the exonuclease subunit in processive DNA synthesis and repair. EMBO J. 32, 1334-1343 (2013).
-
(2013)
EMBO J.
, vol.32
, pp. 1334-1343
-
-
Toste Rêgo, A.1
Holding, A.N.2
Kent, H.3
Lamers, M.H.4
-
38
-
-
48849113878
-
Comparative protein structure modeling using MODELLER
-
Chapter 2, Unit 2.9
-
Eswar, N. et al. Comparative protein structure modeling using MODELLER. Curr. Protoc. Protein Sci. Chapter 2, Unit 2.9 (2007).
-
(2007)
Curr. Protoc. Protein Sci
-
-
Eswar, N.1
-
39
-
-
33748146034
-
The structure of T. Aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases
-
Bailey, S., Wing, R.A. & Steitz, T.A. The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases. Cell 126, 893-904 (2006).
-
(2006)
Cell
, vol.126
, pp. 893-904
-
-
Bailey, S.1
Wing, R.A.2
Steitz, T.A.3
-
40
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin, M.A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
-
41
-
-
0043123208
-
ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of
-
Gouet, P. ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of. Nucleic Acids Res. 31, 3320-3323 (2003).
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3320-3323
-
-
Gouet, P.1
|