-
2
-
-
0032401911
-
Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination
-
Washio, T., Sasayama, J. and Tomita, M. (1998) Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination. Nucleic Acids Res., 26, 5456-5463. (Pubitemid 28542748)
-
(1998)
Nucleic Acids Research
, vol.26
, Issue.23
, pp. 5456-5463
-
-
Washio, T.1
Sasayama, J.2
Tomita, M.3
-
3
-
-
73249130761
-
Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants
-
Langridge, G.C., Phan, M.D., Turner, D.J., Perkins, T.T., Parts, L., Haase, J., Charles, I., Maskell, D.J., Peters, S.E., Dougan, G. et al. (2009) Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res., 19, 2308-2316.
-
(2009)
Genome Res.
, vol.19
, pp. 2308-2316
-
-
Langridge, G.C.1
Phan, M.D.2
Turner, D.J.3
Perkins, T.T.4
Parts, L.5
Haase, J.6
Charles, I.7
Maskell, D.J.8
Peters, S.E.9
Dougan, G.10
-
4
-
-
0027457186
-
Identification of a putative Bacillus subtilis rho gene
-
Quirk, P.G., Dunkley, E.A., Lee, P. and Krulwich, T.A. (1993) Identification of a putative Bacillus subtilis rho gene. J. Bacteriol., 175, 647-654. (Pubitemid 23046925)
-
(1993)
Journal of Bacteriology
, vol.175
, Issue.3
, pp. 647-654
-
-
Quirk, P.G.1
Dunkley Jr., E.A.2
Lee, P.3
Krulwich, T.A.4
-
5
-
-
0025663103
-
Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures
-
d'Aubenton Carafa, Y., Brody, E. and Thermes, C. (1990) Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J. Mol. Biol., 216, 835-858.
-
(1990)
J. Mol. Biol.
, vol.216
, pp. 835-858
-
-
D'Aubenton Carafa, Y.1
Brody, E.2
Thermes, C.3
-
6
-
-
2642621561
-
Compilation of DNA sequences of Escherichia coli K12: Description of the interactive databases ECD and ECDC (version 1997)
-
DOI 10.1093/nar/26.1.46
-
Kroger, M. and Wahl, R. (1998) Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC. Nucleic Acids Res., 26, 46-49. (Pubitemid 28291511)
-
(1998)
Nucleic Acids Research
, vol.26
, Issue.1
, pp. 46-49
-
-
Kroger, M.1
Wahl, R.2
-
7
-
-
55449129670
-
Prediction of transcriptional terminators in Bacillus subtilis and related species
-
de Hoon, M.J., Makita, Y., Nakai, K. and Miyano, S. (2005) Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput. Biol., 1, e25.
-
(2005)
PLoS Comput. Biol.
, vol.1
-
-
De Hoon, M.J.1
Makita, Y.2
Nakai, K.3
Miyano, S.4
-
8
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N.N., Kunin, V., Goodwin, L., Wu, M., Tindall, B.J. et al. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462, 1056-1060.
-
(2009)
Nature
, vol.462
, pp. 1056-1060
-
-
Wu, D.1
Hugenholtz, P.2
Mavromatis, K.3
Pukall, R.4
Dalin, E.5
Ivanova, N.N.6
Kunin, V.7
Goodwin, L.8
Wu, M.9
Tindall, B.J.10
-
9
-
-
77954617345
-
Transcription attenuation in bacteria: Theme and variations
-
Naville, M. and Gautheret, D. (2010) Transcription attenuation in bacteria: theme and variations. Brief. Funct. Genomic Proteomic, 9, 178-189.
-
(2010)
Brief. Funct. Genomic Proteomic
, vol.9
, pp. 178-189
-
-
Naville, M.1
Gautheret, D.2
-
10
-
-
33746533172
-
Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNAencoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2
-
Livny, J., Brencic, A., Lory, S. and Waldor, M.K. (2006) Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNAencoding genes in 10 diverse pathogens using the bioinformatic 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
-
11
-
-
58849150431
-
The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair
-
Fineran, P.C., Blower, T.R., Foulds, I.J., Humphreys, D.P., Lilley, K.S. and Salmond, G.P. (2009) The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Proc. Natl Acad. Sci. USA, 106, 894-899.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 894-899
-
-
Fineran, P.C.1
Blower, T.R.2
Foulds, I.J.3
Humphreys, D.P.4
Lilley, K.S.5
Salmond, G.P.6
-
12
-
-
44849094549
-
Biocomputational prediction of small non-coding RNAs in Streptomyces
-
Panek, J., Bobek, J., Mikulk, K., Basler, M. and Vohradsky, J. (2008) Biocomputational prediction of small non-coding RNAs in Streptomyces. BMC Genomics, 9, 217.
-
(2008)
BMC Genomics
, vol.9
, pp. 217
-
-
Panek, J.1
Bobek, J.2
Mikulk, K.3
Basler, M.4
Vohradsky, J.5
-
13
-
-
77957788941
-
SRNAscanner: A computational tool for intergenic small RNA detection in bacterial genomes
-
Sridhar, J., Narmada, S.R., Sabarinathan, R., Ou, H.Y., Deng, Z., Sekar, K., Rafi, Z.A. and Rajakumar, K. (2010) sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes. PLoS ONE, 5, e11970.
-
(2010)
PLoS ONE
, vol.5
-
-
Sridhar, J.1
Narmada, S.R.2
Sabarinathan, R.3
Ou, H.Y.4
Deng, Z.5
Sekar, K.6
Rafi, Z.A.7
Rajakumar, K.8
-
14
-
-
0035444240
-
Prediction of rho-independent transcriptional terminators in Escherichia coli
-
Lesnik, E.A., Sampath, R., Levene, H.B., Henderson, T.J., McNeil, J.A. and Ecker, D.J. (2001) Prediction of rho-independent transcriptional terminators in Escherichia coli. Nucleic Acids Res., 29, 3583-3594. (Pubitemid 32898772)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.17
, pp. 3583-3594
-
-
Lesnik, E.A.1
Sampath, R.2
Levene, H.B.3
Henderson, T.J.4
McNeil, J.A.5
Ecker, D.J.6
-
15
-
-
32944456612
-
Intrinsic terminator prediction and its application in synechococcus sp. WH8102
-
DOI 10.1007/s11390-005-0465-7
-
Wan, X.-F. and Xu, D. (2005) Intrinsic terminator prediction and its application in Synechococcus sp. WH8102. J. Comput. Sci. Technol., 20, 465-482. (Pubitemid 43257721)
-
(2005)
Journal of Computer Science and Technology
, vol.20
, Issue.4
, pp. 465-482
-
-
Wan, X.-F.1
Xu, D.2
-
16
-
-
34447499141
-
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
-
Kingsford, C.L., Ayanbule, K. and Salzberg, S.L. (2007) Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol., 8, R22.
-
(2007)
Genome Biol.
, vol.8
-
-
Kingsford, C.L.1
Ayanbule, K.2
Salzberg, S.L.3
-
17
-
-
0028272315
-
RNA sequence analysis using covariance models
-
Eddy, S.R. and Durbin, R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res., 11, 2079-2088. (Pubitemid 24192908)
-
(1994)
Nucleic Acids Research
, vol.22
, Issue.11
, pp. 2079-2088
-
-
Eddy, S.R.1
Durbin, R.2
-
18
-
-
0036464509
-
Conserved economics of transcription termination in eubacteria
-
Unniraman, S., Prakash, R. and Nagaraja, V. (2002) Conserved economics of transcription termination in eubacteria. Nucleic Acids Res., 30, 675-684. (Pubitemid 34679632)
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.3
, pp. 675-684
-
-
Unniraman, S.1
Prakash, R.2
Nagaraja, V.3
-
19
-
-
0028593508
-
Stochastic context-free grammars for tRNA modeling
-
Sakakibara, Y., Brown, M., Hughey, R., Mian, I.S., Sjolander, K., Underwood, R.C. and Haussler, D. (1994) Stochastic context-free grammars for tRNA modeling. Nucleic Acids Res., 22, 5112-5120.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 5112-5120
-
-
Sakakibara, Y.1
Brown, M.2
Hughey, R.3
Mian, I.S.4
Sjolander, K.5
Underwood, R.C.6
Haussler, D.7
-
20
-
-
0028272315
-
RNA sequence analysis using covariance models
-
Eddy, S.R. and Durbin, R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res., 22, 2079-2088. (Pubitemid 24192908)
-
(1994)
Nucleic Acids Research
, vol.22
, Issue.11
, pp. 2079-2088
-
-
Eddy, S.R.1
Durbin, R.2
-
21
-
-
2942607685
-
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
-
Eddy, S.R. (2002) A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics, 3, 18.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 18
-
-
Eddy, S.R.1
-
22
-
-
13444287763
-
Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy
-
DOI 10.1093/bioinformatics/bth925
-
Weinberg, Z. and Ruzzo, W.L. (2004) Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy. Bioinformatics, 20(Suppl. 1), i334-i341. (Pubitemid 41296707)
-
(2004)
Bioinformatics
, vol.20
, Issue.SUPPL. 1
-
-
Weinberg, Z.1
Ruzzo, W.L.2
-
23
-
-
30344443658
-
Sequence-based heuristics for faster annotation of non-coding RNA families
-
DOI 10.1093/bioinformatics/bti743
-
Weinberg, Z. and Ruzzo, W.L. (2006) Sequence-based heuristics for faster annotation of non-coding RNA families. Bioinformatics, 22, 35-39. (Pubitemid 43057006)
-
(2006)
Bioinformatics
, vol.22
, Issue.1
, pp. 35-39
-
-
Weinberg, Z.1
Ruzzo, W.L.2
-
24
-
-
34047240607
-
Query-dependent banding (QDB) for faster RNA similarity searches
-
Nawrocki, E.P. and Eddy, S.R. (2007) Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput. Biol., 3, e56.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
25
-
-
65549118801
-
Local RNA structure alignment with incomplete sequence
-
Kolbe, D.L. and Eddy, S.R. (2009) Local RNA structure alignment with incomplete sequence. Bioinformatics, 25, 1236-1243.
-
(2009)
Bioinformatics
, vol.25
, pp. 1236-1243
-
-
Kolbe, D.L.1
Eddy, S.R.2
-
26
-
-
65549111754
-
Infernal 1.0: Inference of RNA alignments
-
Nawrocki, E.P., Kolbe, D.L. and Eddy, S.R. (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337.
-
(2009)
Bioinformatics
, vol.25
, pp. 1335-1337
-
-
Nawrocki, E.P.1
Kolbe, D.L.2
Eddy, S.R.3
-
27
-
-
78650791283
-
R2R-software to speed the depiction of aesthetic consensus RNA secondary structures
-
Weinberg, Z. and Breaker, R.R. (2011) R2R-software to speed the depiction of aesthetic consensus RNA secondary structures. BMC Bioinformatics, 12, 3.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 3
-
-
Weinberg, Z.1
Breaker, R.R.2
-
28
-
-
48449091195
-
WAR: Webserver for aligning structural RNAs
-
Torarinsson, E. and Lindgreen, S. (2008) WAR: webserver for aligning structural RNAs. Nucleic Acids Res., 36, W79-W84.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Torarinsson, E.1
Lindgreen, S.2
-
29
-
-
32544452741
-
CMfinder - A covariance model based RNA motif finding algorithm
-
DOI 10.1093/bioinformatics/btk008
-
Yao, Z., Weinberg, Z. and Ruzzo, W.L. (2006) CMfinder-a covariance model based RNA motif finding algorithm. Bioinformatics, 22, 445-452. (Pubitemid 43231419)
-
(2006)
Bioinformatics
, vol.22
, Issue.4
, pp. 445-452
-
-
Yao, Z.1
Weinberg, Z.2
Ruzzo, W.L.3
-
30
-
-
84871219030
-
-
Gesellschaft für Informatik (GI), Bonn, Germany
-
Otto, W., Will, S. and Backofen, R. (2008) In Proceedings of German Conference on Bioinformatics (GCB'2008), Vol. P-136. Lecture Notes in Informatics (LNI), Gesellschaft für Informatik (GI), Bonn, Germany, pp. 178-188.
-
(2008)
Proceedings of German Conference on Bioinformatics (GCB'2008), Vol. P-136. Lecture Notes in Informatics (LNI)
, pp. 178-188
-
-
Otto, W.1
Will, S.2
Backofen, R.3
-
31
-
-
13444309635
-
RALEE-RNA ALignment editor in Emacs
-
Griffiths-Jones, S. (2005) RALEE-RNA ALignment editor in Emacs. Bioinformatics, 21, 257-259.
-
(2005)
Bioinformatics
, vol.21
, pp. 257-259
-
-
Griffiths-Jones, S.1
-
32
-
-
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. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res., 37, D136-D140.
-
(2009)
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
-
33
-
-
33751018002
-
Rnall: An efficient algorithm for predicting RNA local secondary structural landscape in genomes
-
DOI 10.1142/S0219720006002363, PII S0219720006002363
-
Wan, X.F., Lin, G. and Xu, D. (2006) Rnall: an efficient algorithm for predicting RNA local secondary structural landscape in genomes. J. Bioinform. Comput. Biol., 4, 1015-1031. (Pubitemid 44742257)
-
(2006)
Journal of Bioinformatics and Computational Biology
, vol.4
, Issue.5
, pp. 1015-1031
-
-
Wan, X.-F.1
Lin, G.2
Xu, D.3
-
34
-
-
0033572893
-
No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
-
Workman, C. and Krogh, A. (1999) No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res., 27, 4816-4822. (Pubitemid 30006673)
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.24
, pp. 4816-4822
-
-
Workman, C.1
Krogh, A.2
-
35
-
-
75549091111
-
Improvements to services at the European Nucleotide Archive
-
Leinonen, R., Akhtar, R., Birney, E., Bonfield, J., Bower, L., Corbett, M., Cheng, Y., Demiralp, F., Faruque, N., Goodgame, N. et al. (2010) Improvements to services at the European Nucleotide Archive. Nucleic Acids Res., 38, D39-D45.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Leinonen, R.1
Akhtar, R.2
Birney, E.3
Bonfield, J.4
Bower, L.5
Corbett, M.6
Cheng, Y.7
Demiralp, F.8
Faruque, N.9
Goodgame, N.10
-
36
-
-
0035834664
-
Alternate paradigm for intrinsic transcription termination in eubacteria
-
Unniraman, S., Prakash, R. and Nagaraja, V. (2001) Alternate paradigm for intrinsic transcription termination in eubacteria. J. Biol. Chem., 276, 41850-41855.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 41850-41855
-
-
Unniraman, S.1
Prakash, R.2
Nagaraja, V.3
-
37
-
-
54349098430
-
Genome-wide analysis of the intrinsic terminators of transcription across the genus Mycobacterium
-
Mitra, A., Angamuthu, K. and Nagaraja, V. (2008) Genome-wide analysis of the intrinsic terminators of transcription across the genus Mycobacterium. Tuberculosis (Edinb), 88, 566-575.
-
(2008)
Tuberculosis (Edinb)
, vol.88
, pp. 566-575
-
-
Mitra, A.1
Angamuthu, K.2
Nagaraja, V.3
-
38
-
-
67649976624
-
Occurrence, divergence and evolution of intrinsic terminators across eubacteria
-
Mitra, A., Angamuthu, K., Jayashree, H.V. and Nagaraja, V. (2009) Occurrence, divergence and evolution of intrinsic terminators across eubacteria. Genomics, 94, 110-116.
-
(2009)
Genomics
, vol.94
, pp. 110-116
-
-
Mitra, A.1
Angamuthu, K.2
Jayashree, H.V.3
Nagaraja, V.4
-
39
-
-
48449095385
-
The Vienna RNA websuite
-
Gruber, A.R., Lorenz, R., Bernhart, S.H., Neubock, R. and Hofacker, I.L. (2008) The Vienna RNA websuite. Nucleic Acids Res., 36, W70-W74.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Gruber, A.R.1
Lorenz, R.2
Bernhart, S.H.3
Neubock, R.4
Hofacker, I.L.5
-
40
-
-
4444378880
-
Conserved regulatory motifs in bacteria: Riboswitches and beyond
-
DOI 10.1016/j.tig.2004.08.003, PII S0168952504002227
-
Abreu-Goodger, C., Ontiveros-Palacios, N., Ciria, R. and Merino, E. (2004) Conserved regulatory motifs in bacteria: riboswitches and beyond. Trends Genet., 20, 475-479. (Pubitemid 39201066)
-
(2004)
Trends in Genetics
, vol.20
, Issue.10
, pp. 475-479
-
-
Abreu-Goodger, C.1
Ontiveros-Palacios, N.2
Ciria, R.3
Merino, E.4
-
41
-
-
68249102779
-
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi
-
Perkins, T.T., Kingsley, R.A., Fookes, M.C., Gardner, P.P., James, K.D., Yu, L., Assefa, S.A., He, M., Croucher, N.J., Pickard, D.J. et al. (2009) A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet., 5, e1000569.
-
(2009)
PLoS Genet.
, vol.5
-
-
Perkins, T.T.1
Kingsley, R.A.2
Fookes, M.C.3
Gardner, P.P.4
James, K.D.5
Yu, L.6
Assefa, S.A.7
He, M.8
Croucher, N.J.9
Pickard, D.J.10
|