-
1
-
-
77950349491
-
Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome
-
Albrecht M., Sharma C.M., Reinhardt R., Vogel J., Rudel T. 2010. Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. Nucleic Acids Res 38: 868-877.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 868-877
-
-
Albrecht, M.1
Sharma, C.M.2
Reinhardt, R.3
Vogel, J.4
Rudel, T.5
-
2
-
-
85011941303
-
Computational prediction of sRNAs and their targets in bacteria
-
Backofen R., Hess W.R. 2010. Computational prediction of sRNAs and their targets in bacteria. RNA Biol 7: 33-42.
-
(2010)
RNA Biol
, vol.7
, pp. 33-42
-
-
Backofen, R.1
Hess, W.R.2
-
3
-
-
70349693543
-
Trainable grammars for speech recognition
-
doi: 10.1121/1.2017061
-
Baker J.K. 1979. Trainable grammars for speech recognition. J Acoust Soc Am 65: S132. doi: 10.1121/1.2017061.
-
(1979)
J Acoust Soc Am
, vol.65
-
-
Baker, J.K.1
-
4
-
-
34147132825
-
Identifying bacterial genes and endosymbiont DNA with Glimmer
-
DOI 10.1093/bioinformatics/btm009
-
Delcher A.L., Bratke K.A., Powers E.C., Salzberg S.L. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679. (Pubitemid 46554717)
-
(2007)
Bioinformatics
, vol.23
, Issue.6
, pp. 673-679
-
-
Delcher, A.L.1
Bratke, K.A.2
Powers, E.C.3
Salzberg, S.L.4
-
5
-
-
58149191274
-
Rfam: Updates to the RNA families database
-
Gardner P.P., Daub J., Tate J.G., Nawrocki E.P., Kolbe D.L., Lindgreen S., Wilkinson A.C., Finn R.D., Griffiths-Jones S., Eddy S.R., et al. 2008. Rfam: Updates to the RNA families database. Nucleic Acids Res 37: D136-D140.
-
(2008)
Nucleic Acids Res
, vol.37
-
-
Gardner, P.P.1
Daub, J.2
Tate, J.G.3
Nawrocki, E.P.4
Kolbe, D.L.5
Lindgreen, S.6
Wilkinson, A.C.7
Finn, R.D.8
Griffiths-Jones, S.9
Eddy, S.R.10
-
6
-
-
84873054511
-
RNAZ 2.0: Improved noncoding RNA detection
-
Gruber A.R., Findeiss S., Washietl S., Hofacker I.L., Stadler P.F. 2010. RNAZ 2.0: Improved noncoding RNA detection. Pac Symp Biocomput 15: 69-79.
-
(2010)
Pac Symp Biocomput
, vol.15
, pp. 69-79
-
-
Gruber, A.R.1
Findeiss, S.2
Washietl, S.3
Hofacker, I.L.4
Stadler, P.F.5
-
7
-
-
58149177178
-
SRNAMap: Genomic maps for small noncoding RNAs, their regulators, and their targets in microbial genomes
-
Huang H.Y., Chang H.Y., Chou C.H., Tseng C.P., Ho S.Y., Yang C.D., Ju Y.W., Huang H.D. 2009. sRNAMap: Genomic maps for small noncoding RNAs, their regulators, and their targets in microbial genomes. Nucleic Acids Res 37: D150-D154.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Huang, H.Y.1
Chang, H.Y.2
Chou, C.H.3
Tseng, C.P.4
Ho, S.Y.5
Yang, C.D.6
Ju, Y.W.7
Huang, H.D.8
-
8
-
-
34447499141
-
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
-
doi: 10.1186/gb-2007-8-2-r22
-
Kingsford C.L., Ayanbule K., Salzberg S.L. 2007. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol 8: R22. doi: 10.1186/gb-2007-8-2- r22.
-
(2007)
Genome Biol
, vol.8
-
-
Kingsford, C.L.1
Ayanbule, K.2
Salzberg, S.L.3
-
9
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
DOI 10.1093/bioinformatics/btm404
-
Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948. (Pubitemid 350162903)
-
(2007)
Bioinformatics
, vol.23
, Issue.21
, 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
Lopez, R.10
Thompson, J.D.11
Gibson, T.J.12
Higgins, D.G.13
-
10
-
-
75249105828
-
A broadening world of bacterial small RNAs
-
Liu J.M., Camilli A. 2010. A broadening world of bacterial small RNAs. Curr Opin Microbiol 13: 18-23.
-
(2010)
Curr Opin Microbiol
, vol.13
, pp. 18-23
-
-
Liu, J.M.1
Camilli, A.2
-
11
-
-
64549149245
-
Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing
-
doi: 10.1093/nar/gkp080
-
Liu J.M., Livny J., Lawrence M.S., Kimball M.D., Waldor M.K., Camilli A. 2009. Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res 37: e46. doi: 10.1093/nar/gkp080.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Liu, J.M.1
Livny, J.2
Lawrence, M.S.3
Kimball, M.D.4
Waldor, M.K.5
Camilli, A.6
-
12
-
-
34247173351
-
Identification of small RNAs in diverse bacterial species
-
DOI 10.1016/j.mib.2007.03.005, PII S1369527407000227, Cell Regulation (RNA Special Issue)
-
Livny J., Waldor M.K. 2007. Identification of small RNAs in diverse bacterial species. Curr Opin Microbiol 10: 96-101. (Pubitemid 46590045)
-
(2007)
Current Opinion in Microbiology
, vol.10
, Issue.2
, pp. 96-101
-
-
Livny, J.1
Waldor, M.K.2
-
13
-
-
33746533172
-
Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatics tool sRNAPredict2
-
Livny J., Brencic A., Lory S., Waldor M.K. 2006. Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatics tool sRNAPredict2. Nucleic Acids Res 34: 3484-3493.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3484-3493
-
-
Livny, J.1
Brencic, A.2
Lory, S.3
Waldor, M.K.4
-
14
-
-
52449093583
-
High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs
-
doi: 10.1371/journal.pone.0003197
-
Livny J., Teonadi H., Livny M., Waldor M.K. 2008. High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS ONE 3: e3197. doi: 10.1371/journal.pone.0003197.
-
(2008)
PLoS ONE
, vol.3
-
-
Livny, J.1
Teonadi, H.2
Livny, M.3
Waldor, M.K.4
-
15
-
-
0035890840
-
RNAMotif, an RNA secondary structure definition and search algorithm
-
Macke T., Ecker D., Gutell R., Gautheret D., Case D.A., Sampath R. 2001. RNAMotif - a new RNA secondary structure definition and discovery algorithm. Nucleic Acids Res 29: 4724-4735. (Pubitemid 33095034)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.22
, pp. 4724-4735
-
-
Macke, T.J.1
Ecker, D.J.2
Gutell, R.R.3
Gautheret, D.4
Case, D.A.5
Sampath, R.6
-
16
-
-
66449091512
-
Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles
-
Marchais A., Naville M., Bohn C., Bouloc P., Gautheret D. 2009. Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles. Genome Res 19: 1084-1092.
-
(2009)
Genome Res
, vol.19
, pp. 1084-1092
-
-
Marchais, A.1
Naville, M.2
Bohn, C.3
Bouloc, P.4
Gautheret, D.5
-
18
-
-
0034764307
-
SSAHA: A fast search method for large DNA databases
-
DOI 10.1101/gr.194201
-
Ning Z., Cox A.J., Mullikin J.C. 2001. SSAHA: A fast search method for large DNA databases. Genome Res 11: 1725-1729. (Pubitemid 33040499)
-
(2001)
Genome Research
, vol.11
, Issue.10
, pp. 1725-1729
-
-
Ning, Z.1
Cox, A.J.2
Mullikin, J.C.3
-
19
-
-
13444306641
-
NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
-
DOI 10.1093/nar/gki025
-
Pruitt K.D., Tatusova T., Maglott D.R. 2005. NCBI Reference Sequence (RefSeq): A curated nonredundant sequence database of genomics, transcripts, and proteins. Nucleic Acids Res 33: D501-D504. (Pubitemid 40207924)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.DATABASE ISS.
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
20
-
-
0003157183
-
Noncoding RNA gene detection using comparative sequence analysis
-
doi: 10.1186/1471-2105-2-8
-
Rivas E., Eddy S.R. 2001. Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2: 8. doi: 10.1186/1471-2105-2-8.
-
(2001)
BMC Bioinformatics
, vol.2
, pp. 8
-
-
Rivas, E.1
Eddy, S.R.2
-
21
-
-
70349736084
-
Experimental approaches for the discovery and characterization of regulatory small RNAs
-
Sharma C.M., Vogel J. 2009. Experimental approaches for the discovery and characterization of regulatory small RNAs. Curr Opin Microbiol 12: 536-546.
-
(2009)
Curr Opin Microbiol
, vol.12
, pp. 536-546
-
-
Sharma, C.M.1
Vogel, J.2
-
22
-
-
77949425194
-
The primary transcriptome of the major human pathogen Helicobacter pylori
-
Sharma C.M., Hoffmann S., Darfeuille F., Reignier J., Findeiss S., Sittka A., Chabas S., Reiche K., Hackermuller J., Reinhardt R., et al. 2010. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464: 250-255.
-
(2010)
Nature
, vol.464
, pp. 250-255
-
-
Sharma, C.M.1
Hoffmann, S.2
Darfeuille, F.3
Reignier, J.4
Findeiss, S.5
Sittka, A.6
Chabas, S.7
Reiche, K.8
Hackermuller, J.9
Reinhardt, R.10
-
23
-
-
50849105413
-
Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq
-
doi: 10.1371/journal.pgen.1000163
-
Sittka A., Lucchini S., Papenfort K., Charma C.M., Rolle K., Binnewies T.T., Hinton J.C.D., Vogel J. 2008. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 4: e1000163. doi: 10.1371/journal.pgen.1000163.
-
(2008)
PLoS Genet
, vol.4
-
-
Sittka, A.1
Lucchini, S.2
Papenfort, K.3
Charma, C.M.4
Rolle, K.5
Binnewies, T.T.6
Hinton, J.C.D.7
Vogel, J.8
-
24
-
-
67649268395
-
The Listeria transcriptional landscape from saprophytism to virulence
-
Toledo-Arana A., Dussurget O., Nikitas G., Sesto N., Guet-Revillet H., Balestrino D., Loh E., Gripenland J., Tiensuu T., Vaitkevicius K., et al. 2009. The Listeria transcriptional landscape from saprophytism to virulence. Nature 459: 950-956.
-
(2009)
Nature
, vol.459
, pp. 950-956
-
-
Toledo-Arana, A.1
Dussurget, O.2
Nikitas, G.3
Sesto, N.4
Guet-Revillet, H.5
Balestrino, D.6
Loh, E.7
Gripenland, J.8
Tiensuu, T.9
Vaitkevicius, K.10
-
26
-
-
0034906974
-
Xenorhabdus nematophilus as a model for host-bacterium interactions: rpoS is necessary for mutualism with nematodes
-
DOI 10.1128/JB.183.16.4687-4693.2001
-
Vivas E.I., Goodrich-Blair H. 2001. Xenorhabdus nematophila as a model for host-bacterium interactions: RpoS is necessary for mutualism with nematodes. J Bacteriol 183: 4687-4693. (Pubitemid 32708952)
-
(2001)
Journal of Bacteriology
, vol.183
, Issue.16
, pp. 4687-4693
-
-
Vivas, E.I.1
Goodrich-Blair, H.2
-
27
-
-
4143149651
-
Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics
-
DOI 10.1016/j.jmb.2004.07.018, PII S0022283604008289
-
Washietl S., Hofacker I.L. 2004. Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol 342: 19-30. (Pubitemid 39094502)
-
(2004)
Journal of Molecular Biology
, vol.342
, Issue.1
, pp. 19-30
-
-
Washietl, S.1
Hofacker, I.L.2
-
29
-
-
60149089144
-
Regulatory RNAs in bacteria
-
Waters L.S., Storz G. 2009. Regulatory RNAs in bacteria. Cell 136: 615-628.
-
(2009)
Cell
, vol.136
, pp. 615-628
-
-
Waters, L.S.1
Storz, G.2
-
30
-
-
62649160909
-
Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing
-
Yoder-Himes D.R., Chain P.S.G., Zhu Y., Wurtzel O., Rubin E.M., Tiedje J.M., Sorek R. 2009. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc Natl Acad Sci 106: 3976-3981.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 3976-3981
-
-
Yoder-Himes, D.R.1
Chain, P.S.G.2
Zhu, Y.3
Wurtzel, O.4
Rubin, E.M.5
Tiedje, J.M.6
Sorek, R.7
|