-
1
-
-
84877896488
-
Programmed heterogeneity: Epigenetic mechanisms in bacteria
-
Casadesús, J. and Low, D. (2013) Programmed heterogeneity: epigenetic mechanisms in bacteria. J. Biol. Chem., 288, 13929-13935.
-
(2013)
J. Biol. Chem.
, vol.288
, pp. 13929-13935
-
-
Casadesús, J.1
Low, D.2
-
2
-
-
84874194072
-
DNA methylation: Roles in mammalian development
-
Smith, Z. and Meissner, A. (2013) DNA methylation: roles in mammalian development. Nat. Rev. Genet., 14, 204-220.
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 204-220
-
-
Smith, Z.1
Meissner, A.2
-
3
-
-
0242266619
-
The mechanism by which DNA adenine methylase and PapI activate the pap epigenetic switch
-
Hernday, A., Braaten, B. and Low, D. (2003) The mechanism by which DNA adenine methylase and PapI activate the pap epigenetic switch. Mol. Cell, 12, 947-957.
-
(2003)
Mol. Cell
, vol.12
, pp. 947-957
-
-
Hernday, A.1
Braaten, B.2
Low, D.3
-
4
-
-
0026793461
-
Evidence for global regulatory control of pilus expression in Escherichia coli by Lrp and DNA methylation: Model building based on analysis of pap
-
van der Woude, M., Braaten, B. and Low, D. (1992) Evidence for global regulatory control of pilus expression in Escherichia coli by Lrp and DNA methylation: model building based on analysis of pap. Mol. Microbiol., 6, 2429-2435.
-
(1992)
Mol. Microbiol.
, vol.6
, pp. 2429-2435
-
-
Van Der Woude, M.1
Braaten, B.2
Low, D.3
-
5
-
-
0030550360
-
Phase-variable outer membrane proteins in Escherichia coli
-
Owen, P., Meehan, M., de Loughry-Doherty, H and Henderson, I. (1996) Phase-variable outer membrane proteins in Escherichia coli. FEMS Immunol. Med. Microbiol., 16, 63-76.
-
(1996)
FEMS Immunol. Med. Microbiol.
, vol.16
, pp. 63-76
-
-
Owen, P.1
Meehan, M.2
De Loughry-Doherty, H.3
Henderson, I.4
-
7
-
-
33749246561
-
Epigenetic gene regulation in the bacterial world
-
Casadesús, J. and Low, D. (2006) Epigenetic gene regulation in the bacterial world. Microbiol. Mol. Biol. Rev., 70, 830-856.
-
(2006)
Microbiol. Mol. Biol. Rev.
, vol.70
, pp. 830-856
-
-
Casadesús, J.1
Low, D.2
-
8
-
-
34548569008
-
Haemophilus influenzae phasevarions have evolved from type III DNA restriction systems into epigenetic regulators of gene expression
-
Fox, K., Dowideit, S., Erwin, A., Srikhanta, Y., Smith, A. and Jennings, M. (2007) Haemophilus influenzae phasevarions have evolved from type III DNA restriction systems into epigenetic regulators of gene expression. Nucleic Acids Res., 35, 5242-5252.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 5242-5252
-
-
Fox, K.1
Dowideit, S.2
Erwin, A.3
Srikhanta, Y.4
Smith, A.5
Jennings, M.6
-
9
-
-
17344370012
-
The phasevarion: A genetic system controlling coordinated, random switching of expression of multiple genes
-
Srikhanta, Y., Maguire, T., Stacey, K., Grimmond, S. and Jennings, M. (2005) The phasevarion: a genetic system controlling coordinated, random switching of expression of multiple genes. Proc. Natl Acad. Sci. U. S. A., 102, 5547-5551.
-
(2005)
Proc. Natl Acad. Sci. U. S. A.
, vol.102
, pp. 5547-5551
-
-
Srikhanta, Y.1
Maguire, T.2
Stacey, K.3
Grimmond, S.4
Jennings, M.5
-
10
-
-
66349122956
-
Phasevarions mediate random switching of gene expression in pathogenic Neisseria
-
Srikhanta, Y., Dowideit, S., Edwards, J., Falsetta, M., Wu, H., Harrison, O., Fox, K., Seib, K., Maguire, T., Wang, A. et al. (2009) Phasevarions mediate random switching of gene expression in pathogenic Neisseria. PLoS Pathog., 5, e1000400
-
(2009)
PLoS Pathog.
, vol.5
, pp. e1000400
-
-
Srikhanta, Y.1
Dowideit, S.2
Edwards, J.3
Falsetta, M.4
Wu, H.5
Harrison, O.6
Fox, K.7
Seib, K.8
Maguire, T.9
Wang, A.10
-
11
-
-
82655180443
-
Phasevarion mediated epigenetic gene regulation in Helicobacter pylori
-
Srikhanta, Y., Gorrell, R., Steen, J., Gawthorne, J., Kwok, T., Grimmond, S., Roy, R. and Jennings, M. (2011) Phasevarion mediated epigenetic gene regulation in Helicobacter pylori. PloS One, 6, e27569.
-
(2011)
PloS One
, vol.6
, pp. e27569
-
-
Srikhanta, Y.1
Gorrell, R.2
Steen, J.3
Gawthorne, J.4
Kwok, T.5
Grimmond, S.6
Roy, R.7
Jennings, M.8
-
12
-
-
84919773076
-
ModM DNA methyltransferase methylome analysis reveals a potential role for Moraxella catarrhalis phasevarions in otitis media
-
Blakeway, L., Power, P., Jen, F., Worboys, S., Boitano, M., Clark, T., Korlach, J., Bakaletz, L., Jennings, M., Peak, I. et al. (2014) ModM DNA methyltransferase methylome analysis reveals a potential role for Moraxella catarrhalis phasevarions in otitis media. FASEB J., pii, fj.14-256578.
-
(2014)
FASEB J.
-
-
Blakeway, L.1
Power, P.2
Jen, F.3
Worboys, S.4
Boitano, M.5
Clark, T.6
Korlach, J.7
Bakaletz, L.8
Jennings, M.9
Peak, I.10
-
13
-
-
76949108806
-
The phasevarion: Phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes
-
Srikhanta, Y., Fox, K. and Jennings, M. (2010) The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes. Nat. Rev. Microbiol., 8, 196-206.
-
(2010)
Nat. Rev. Microbiol.
, vol.8
, pp. 196-206
-
-
Srikhanta, Y.1
Fox, K.2
Jennings, M.3
-
14
-
-
66449121652
-
Finding the fifth base: Genome-wide sequencing of cytosine methylation
-
Lister, R. and Ecker, J. (2009) Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res., 19, 959-966.
-
(2009)
Genome Res.
, vol.19
, pp. 959-966
-
-
Lister, R.1
Ecker, J.2
-
15
-
-
77952967431
-
Direct detection of DNA methylation during single-molecule, real-time sequencing
-
Flusberg, B., Webster, D., Lee, J., Travers, K., Olivares, E., Clark, T., Korlach, J. and Turner, S. (2010) Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods, 7, 461-465.
-
(2010)
Nat. Methods
, vol.7
, pp. 461-465
-
-
Flusberg, B.1
Webster, D.2
Lee, J.3
Travers, K.4
Olivares, E.5
Clark, T.6
Korlach, J.7
Turner, S.8
-
16
-
-
84856453032
-
Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine
-
Song, C., Clark, T., Lu, X., Kislyuk, A., Dai, Q., Turner, S., He, C. and Korlach, J. (2012) Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine. Nat. Methods, 9, 75-77.
-
(2012)
Nat. Methods
, vol.9
, pp. 75-77
-
-
Song, C.1
Clark, T.2
Lu, X.3
Kislyuk, A.4
Dai, Q.5
Turner, S.6
He, C.7
Korlach, J.8
-
17
-
-
84870880581
-
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing
-
Fang, G., Munera, D., Friedman, D., Mandlik, A., Chao, M., Banerjee, O., Feng, Z., Losic, B., Mahajan, M., Jabado, O. et al. (2012) Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat. Biotechnol., 30, 1232-1239.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 1232-1239
-
-
Fang, G.1
Munera, D.2
Friedman, D.3
Mandlik, A.4
Chao, M.5
Banerjee, O.6
Feng, Z.7
Losic, B.8
Mahajan, M.9
Jabado, O.10
-
18
-
-
84895786974
-
The complex methylome of the human gastric pathogen Helicobacter pylori
-
Krebes, J., Morgan, R., Bunk, B., Sproer, C., Luong, K., Parusel, R., Anton, B., Konig, C., Josenhans, C., Overmann, J. et al. (2014) The complex methylome of the human gastric pathogen Helicobacter pylori. Nucleic Acids Res., 42, 2415-2432.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 2415-2432
-
-
Krebes, J.1
Morgan, R.2
Bunk, B.3
Sproer, C.4
Luong, K.5
Parusel, R.6
Anton, B.7
Konig, C.8
Josenhans, C.9
Overmann, J.10
-
19
-
-
84873507965
-
Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution
-
Maria, L., Luong, K., Verónica, L., Delgado, J., Fang, G., Spittle, K., Clark, T., Schadt, E., Turner, S., Korlach, J. et al. (2013) Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PLoS Genet., 9, e1003191.
-
(2013)
PLoS Genet.
, vol.9
, pp. e1003191
-
-
Maria, L.1
Luong, K.2
Verónica, L.3
Delgado, J.4
Fang, G.5
Spittle, K.6
Clark, T.7
Schadt, E.8
Turner, S.9
Korlach, J.10
-
20
-
-
84871222928
-
The methylomes of six bacteria
-
Murray, I., Clark, T., Morgan, R., Boitano, M., Anton, B., Luong, K., Fomenkov, A., Turner, S., Korlach, J. and Roberts, R. (2012) The methylomes of six bacteria. Nucleic Acids Res., 40, 11450-11462.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 11450-11462
-
-
Murray, I.1
Clark, T.2
Morgan, R.3
Boitano, M.4
Anton, B.5
Luong, K.6
Fomenkov, A.7
Turner, S.8
Korlach, J.9
Roberts, R.10
-
21
-
-
84861802222
-
Direct detection and sequencing of damaged DNA bases
-
Clark, T., Spittle, K., Turner, S. and Korlach, J. (2011) Direct detection and sequencing of damaged DNA bases. Genome Integr., 2, 10.
-
(2011)
Genome Integr.
, vol.2
, pp. 10
-
-
Clark, T.1
Spittle, K.2
Turner, S.3
Korlach, J.4
-
22
-
-
84870939871
-
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases
-
Schadt, E., Banerjee, O., Fang, G., Feng, Z., Wong, W., Zhang, X., Kislyuk, A., Clark, T., Luong, K., Alona, K. et al. (2013) Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Res., 23, 129-141.
-
(2013)
Genome Res.
, vol.23
, pp. 129-141
-
-
Schadt, E.1
Banerjee, O.2
Fang, G.3
Feng, Z.4
Wong, W.5
Zhang, X.6
Kislyuk, A.7
Clark, T.8
Luong, K.9
Alona, K.10
-
23
-
-
51449100343
-
Genetic requirement for pneumococcal ear infection
-
Chen, H., Ma, Y., Yang, J., Christopher, O., Lee, S., Mazurkiewicz, J., Haataja, S., Yan, J., Gao, G. and Zhang, J. (2008) Genetic requirement for pneumococcal ear infection. PloS One, 3, e2950
-
(2008)
PloS One
, vol.3
, pp. e2950
-
-
Chen, H.1
Ma, Y.2
Yang, J.3
Christopher, O.4
Lee, S.5
Mazurkiewicz, J.6
Haataja, S.7
Yan, J.8
Gao, G.9
Zhang, J.10
-
24
-
-
84864014649
-
Complete genome sequence of Streptococcus pneumoniae strain ST556, a multidrug-resistant isolate from an otitis media patient
-
Li, G., Hu, F., Yang, X., Cui, Y., Yang, J., Qu, F., Gao, G. and Zhang, J. (2012) Complete genome sequence of Streptococcus pneumoniae strain ST556, a multidrug-resistant isolate from an otitis media patient. J. Bacteriol., 194, 3294-3295.
-
(2012)
J. Bacteriol.
, vol.194
, pp. 3294-3295
-
-
Li, G.1
Hu, F.2
Yang, X.3
Cui, Y.4
Yang, J.5
Qu, F.6
Gao, G.7
Zhang, J.8
-
25
-
-
70349611730
-
Tn-seq: High-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
-
Van Opijnen, T., Bodi, K. and Camilli, A. (2009) Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat. Methods, 6, 767-772.
-
(2009)
Nat. Methods
, vol.6
, pp. 767-772
-
-
Van Opijnen, T.1
Bodi, K.2
Camilli, A.3
-
26
-
-
84857877933
-
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing
-
Clark, T., Murray, I., Morgan, R., Kislyuk, A., Spittle, K., Boitano, M., Fomenkov, A., Roberts, R. and Korlach, J. (2012) Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Res., 40, e29.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e29
-
-
Clark, T.1
Murray, I.2
Morgan, R.3
Kislyuk, A.4
Spittle, K.5
Boitano, M.6
Fomenkov, A.7
Roberts, R.8
Korlach, J.9
-
27
-
-
77956125365
-
A flexible and efficient template format for circular consensus sequencing and SNP detection
-
Travers, K., Chin, C., Rank, D., Eid, J. and Turner, S. (2010) A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res., 38, e159.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. e159
-
-
Travers, K.1
Chin, C.2
Rank, D.3
Eid, J.4
Turner, S.5
-
28
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B. et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science, 323, 133-138.
-
(2009)
Science
, vol.323
, pp. 133-138
-
-
Eid, J.1
Fehr, A.2
Gray, J.3
Luong, K.4
Lyle, J.5
Otto, G.6
Peluso, P.7
Rank, D.8
Baybayan, P.9
Bettman, B.10
-
29
-
-
84875981516
-
Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic
-
Feng, Z., Fang, G., Korlach, J., Clark, T., Luong, K., Zhang, X., Wong, W. and Schadt, E. (2013) Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic. PLoS Comput. Biol., 9, e1002935.
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1002935
-
-
Feng, Z.1
Fang, G.2
Korlach, J.3
Clark, T.4
Luong, K.5
Zhang, X.6
Wong, W.7
Schadt, E.8
-
30
-
-
33744957535
-
Streptococcus pneumoniae recruits complement factor H through the amino terminus of CbpA
-
Lu, L., Ma, Y. and Zhang, J. (2006) Streptococcus pneumoniae recruits complement factor H through the amino terminus of CbpA. J. Biol. Chem., 281, 15464-15474.
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 15464-15474
-
-
Lu, L.1
Ma, Y.2
Zhang, J.3
-
31
-
-
20044369888
-
Profiling the humoral immune response to infection by using proteome microarrays: High-throughput vaccine and diagnostic antigen discovery
-
Davies, D., Liang, X., Hernandez, J., Randall, A., Hirst, S., Mu, Y., Romero, K., Nguyen, T., Mina, K., Crotty, S. et al. (2005) Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Proc. Natl Acad. Sci. U. S. A., 102, 547-552.
-
(2005)
Proc. Natl Acad. Sci. U. S. A.
, vol.102
, pp. 547-552
-
-
Davies, D.1
Liang, X.2
Hernandez, J.3
Randall, A.4
Hirst, S.5
Mu, Y.6
Romero, K.7
Nguyen, T.8
Mina, K.9
Crotty, S.10
-
32
-
-
33947109822
-
RR06 activates transcription of spr1996 and cbpA in Streptococcus pneumoniae
-
Ma, Z. and Zhang, J. (2007) RR06 activates transcription of spr1996 and cbpA in Streptococcus pneumoniae. J. Bacteriol., 189, 2497-2509.
-
(2007)
J. Bacteriol.
, vol.189
, pp. 2497-2509
-
-
Ma, Z.1
Zhang, J.2
-
33
-
-
84866266717
-
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): Application and theory
-
Chaisson, M. and Tesler, G. (2012) Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics, 13, 238.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 238
-
-
Chaisson, M.1
Tesler, G.2
-
34
-
-
66349110658
-
Efficient exact motif discovery
-
Marschall, T. and Rahmann, S. (2009) Efficient exact motif discovery. Bioinformatics, 25, i356-i364.
-
(2009)
Bioinformatics
, vol.25
, pp. i356-i364
-
-
Marschall, T.1
Rahmann, S.2
-
35
-
-
75549086595
-
REBASE - A database for DNA restriction and modification: Enzymes, genes and genomes
-
Roberts, R., Vincze, T., Posfai, J. and Macelis, D. (2010) REBASE - a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res., 38, D234-D236.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. D234-D236
-
-
Roberts, R.1
Vincze, T.2
Posfai, J.3
Macelis, D.4
-
36
-
-
84971500108
-
Genetics of streptococcus pneumoniae
-
Fischetti, V. A., Novick, R. P., Ferretti, J. J., Portnoy, D. A. and Rood, J. I. eds, American Society for Microbiology Press, Washington, DC
-
Yother, J. (2006) Genetics of streptococcus pneumoniae. In: Fischetti, V. A., Novick, R. P., Ferretti, J. J., Portnoy, D. A. and Rood, J. I. (eds). Gram-Positive Pathogens, American Society for Microbiology Press, Washington, DC, pp. 275-288.
-
(2006)
Gram-positive Pathogens
, pp. 275-288
-
-
Yother, J.1
-
37
-
-
84877896488
-
Programmed heterogeneity: Epigenetic mechanisms in bacteria
-
Casadesús, J. and Low, D. (2013) Programmed heterogeneity: epigenetic mechanisms in bacteria. J. Biol. Chem., 288, 13929-13935.
-
(2013)
J. Biol. Chem.
, vol.288
, pp. 13929-13935
-
-
Casadesús, J.1
Low, D.2
-
38
-
-
0026338873
-
Restriction and modification systems
-
Wilson, G. and Murray, N. (1991) Restriction and modification systems. Annu. Rev. Genet., 25, 585-627.
-
(1991)
Annu. Rev. Genet.
, vol.25
, pp. 585-627
-
-
Wilson, G.1
Murray, N.2
-
39
-
-
84875192951
-
Detection and quantification of methylation in DNA using solid-state nanopores
-
Shim, J., Humphreys, G., Venkatesan, B., Munz, J., Zou, X., Sathe, C., Schulten, K., Kosari, F., Nardulli, A., Vasmatzis, G. et al. (2013) Detection and quantification of methylation in DNA using solid-state nanopores. Sci. Rep., 3, 1389.
-
(2013)
Sci. Rep.
, vol.3
, pp. 1389
-
-
Shim, J.1
Humphreys, G.2
Venkatesan, B.3
Munz, J.4
Zou, X.5
Sathe, C.6
Schulten, K.7
Kosari, F.8
Nardulli, A.9
Vasmatzis, G.10
-
40
-
-
84888118119
-
Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA
-
Laszlo, A., Derrington, I., Brinkerhoff, H., Langford, K., Nova, I., Samson, J., Bartlett, J., Pavlenok, M. and Gundlach, J. (2013) Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA. Proc. Natl Acad. Sci. U. S. A., 110, 18904-18909.
-
(2013)
Proc. Natl Acad. Sci. U. S. A.
, vol.110
, pp. 18904-18909
-
-
Laszlo, A.1
Derrington, I.2
Brinkerhoff, H.3
Langford, K.4
Nova, I.5
Samson, J.6
Bartlett, J.7
Pavlenok, M.8
Gundlach, J.9
-
41
-
-
84888101866
-
Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands
-
Schreiber, J., Wescoe, Z., Robin, A., Vivian, J., Baatar, B., Karplus, K. and Akeson, M. (2013) Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands. Proc. Natl Acad. Sci. U. S. A., 110, 18910-18915.
-
(2013)
Proc. Natl Acad. Sci. U. S. A.
, vol.110
, pp. 18910-18915
-
-
Schreiber, J.1
Wescoe, Z.2
Robin, A.3
Vivian, J.4
Baatar, B.5
Karplus, K.6
Akeson, M.7
|