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Identification of cyanobacterial non-coding RNAs by comparative genome analysis
Ilka M Axmann, Philip Kensche, Jörg Vogel, Stefan Kohl, Hanspeter Herzel, Wolfgang R Hess
Genome Biol. 2005; 6(9): R73. Published online 2005 August 17. doi: 10.1186/gb-2005-6-9-r73
PMCID:
PMC1242208
Abstract Full Text PDF–1.2M Supplementary Material

Is Cited by the Following 32 Articles in this Archive:

An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains
Christophe Pichon, Laurence du Merle, Marie Elise Caliot, Patrick Trieu-Cuot, Chantal Le Bouguénec
Nucleic Acids Res. 2012 April; 40(7): 2846–2861. Published online 2011 December 1. doi: 10.1093/nar/gkr1141
PMCID:
PMC3326304
Abstract Full Text PDF–5.8M Supplementary Material
nocoRNAc: Characterization of non-coding RNAs in prokaryotes
Alexander Herbig, Kay Nieselt
BMC Bioinformatics. 2011; 12: 40. Published online 2011 January 31. doi: 10.1186/1471-2105-12-40
PMCID:
PMC3230914
Abstract Full Text PDF–3.3M Supplementary Material
Small RNAs in the Genus Clostridium
Yili Chen, Dinesh C. Indurthi, Shawn W. Jones, Eleftherios T. Papoutsakis
mBio. 2011 Jan-Feb; 2(1): e00340-10. Published online 2011 January 25. doi: 10.1128/mBio.00340-10
PMCID:
PMC3025663
Abstract Full Text PDF–1.8M Supplementary Material
A comparative genome-wide study of ncRNAs in trypanosomatids
Tirza Doniger, Rodolfo Katz, Chaim Wachtel, Shulamit Michaeli, Ron Unger
BMC Genomics. 2010; 11: 615. Published online 2010 November 4. doi: 10.1186/1471-2164-11-615
PMCID:
PMC3091756
Abstract Full Text PDF–2.0M Supplementary Material
sRNATarBase: A comprehensive database of bacterial sRNA targets verified by experiments
Yuan Cao, Jiayao Wu, Qian Liu, Yalin Zhao, Xiaomin Ying, Lei Cha, Ligui Wang, Wuju Li
RNA. 2010 November; 16(11): 2051–2057. doi: 10.1261/rna.2193110
PMCID:
PMC2957045
Abstract Full Text PDF–685K
Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus
Claudia Steglich, Debbie Lindell, Matthias Futschik, Trent Rector, Robert Steen, Sallie W Chisholm
Genome Biol. 2010; 11(5): R54. Published online 2010 May 19. doi: 10.1186/gb-2010-11-5-r54
PMCID:
PMC2897979
Abstract Full Text PDF–1.4M Supplementary Material
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
Zasha Weinberg, Joy X Wang, Jarrod Bogue, Jingying Yang, Keith Corbino, Ryan H Moy, Ronald R Breaker
Genome Biol. 2010; 11(3): R31. Published online 2010 March 15. doi: 10.1186/gb-2010-11-3-r31
PMCID:
PMC2864571
Abstract Full Text PDF–1.1M Supplementary Material
Evidence for a major role of antisense RNAs in cyanobacterial gene regulation
Jens Georg, Björn Voß, Ingeborg Scholz, Jan Mitschke, Annegret Wilde, Wolfgang R Hess
Mol Syst Biol. 2009; 5: 305. Published online 2009 September 15. doi: 10.1038/msb.2009.63
PMCID:
PMC2758717
Abstract Full Text PDF–3.1M Supplementary Material
Ecological Genomics of Marine Picocyanobacteria
D. J. Scanlan, M. Ostrowski, S. Mazard, A. Dufresne, L. Garczarek, W. R. Hess, A. F. Post, M. Hagemann, I. Paulsen, F. Partensky
Microbiol Mol Biol Rev. 2009 June; 73(2): 249–299. doi: 10.1128/MMBR.00035-08
PMCID:
PMC2698417
Abstract Full Text PDF–5.6M Supplementary Material
Biocomputational prediction of non-coding RNAs in model cyanobacteria
Björn Voß, Jens Georg, Verena Schön, Susanne Ude, Wolfgang R Hess
BMC Genomics. 2009; 10: 123. Published online 2009 March 23. doi: 10.1186/1471-2164-10-123
PMCID:
PMC2662882
Abstract Full Text PDF–969K
Whole-Genome Tiling Array Analysis of Mycobacterium leprae RNA Reveals High Expression of Pseudogenes and Noncoding Regions
Takeshi Akama, Koichi Suzuki, Kazunari Tanigawa, Akira Kawashima, Huhehasi Wu, Noboru Nakata, Yasunori Osana, Yasubumi Sakakibara, Norihisa Ishii
J Bacteriol. 2009 May; 191(10): 3321–3327. Published online 2009 March 13. doi: 10.1128/JB.00120-09
PMCID:
PMC2687151
Abstract Full Text PDF–872K Supplementary Material
Computational prediction of novel non-coding RNAs in Arabidopsis thaliana
Dandan Song, Yang Yang, Bin Yu, Binglian Zheng, Zhidong Deng, Bao-Liang Lu, Xuemei Chen, Tao Jiang
BMC Bioinformatics. 2009; 10(Suppl 1): S36. Published online 2009 January 30. doi: 10.1186/1471-2105-10-S1-S36
PMCID:
PMC2648795
Abstract Full Text PDF–415K
Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011
Claudio Valverde, Jonathan Livny, Jan-Philip Schlüter, Jan Reinkensmeier, Anke Becker, Gustavo Parisi
BMC Genomics. 2008; 9: 416. Published online 2008 September 16. doi: 10.1186/1471-2164-9-416
PMCID:
PMC2573895
Abstract Full Text PDF–1.7M Supplementary Material
High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs
Jonathan Livny, Hidayat Teonadi, Miron Livny, Matthew K. Waldor
PLoS ONE. 2008; 3(9): e3197. Published online 2008 September 12. doi: 10.1371/journal.pone.0003197
Correction in:
PLoS ONE. 2008; 3(11): 10.1371/annotation/a03e1870-1dd7-4c16-8c46-2268eeb2a50a.
PMCID:
PMC2527527
Abstract Full Text PDF–501K Supplementary Material Correction
The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus
Claudia Steglich, Matthias E. Futschik, Debbie Lindell, Bjoern Voss, Sallie W. Chisholm, Wolfgang R. Hess
PLoS Genet. 2008 August; 4(8): e1000173. Published online 2008 August 29. doi: 10.1371/journal.pgen.1000173
Correction in:
PLoS Genet. 2008 November; 4(11): 10.1371/annotation/411b74ae-c4ce-43c9-bdd2-60c2bf60e672.
PMCID:
PMC2518516
Abstract Full Text PDF–491K Supplementary Material Correction
Small RNAs Establish Delays and Temporal Thresholds in Gene Expression
Stefan Legewie, Dennis Dienst, Annegret Wilde, Hanspeter Herzel, Ilka M. Axmann
Biophys J. 2008 October 1; 95(7): 3232–3238. Published online 2008 July 3. doi: 10.1529/biophysj.108.133819
PMCID:
PMC2547459
Abstract Full Text PDF–305K Supplementary Material
Dinucleotide controlled null models for comparative RNA gene prediction
Tanja Gesell, Stefan Washietl
BMC Bioinformatics. 2008; 9: 248. Published online 2008 May 27. doi: 10.1186/1471-2105-9-248
PMCID:
PMC2453142
Abstract Full Text PDF–535K
Biocomputational prediction of small non-coding RNAs in Streptomyces
Josef Pánek, Jan Bobek, Karel Mikulík, Marek Basler, Jiří Vohradský
BMC Genomics. 2008; 9: 217. Published online 2008 May 13. doi: 10.1186/1471-2164-9-217
PMCID:
PMC2422843
Abstract Full Text PDF–1.1M Supplementary Material
Two Seemingly Homologous Noncoding RNAs Act Hierarchically to Activate glmS mRNA Translation
Johannes H Urban, Jörg Vogel
PLoS Biol. 2008 March; 6(3): e64. Published online 2008 March 18. doi: 10.1371/journal.pbio.0060064
PMCID:
PMC2267818
Abstract Full Text PDF–627K Supplementary Material
Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021
Vincent M Ulvé, Emeric W Sevin, Angélique Chéron, Frédérique Barloy-Hubler
BMC Genomics. 2007; 8: 467. Published online 2007 December 19. doi: 10.1186/1471-2164-8-467
PMCID:
PMC2245857
Abstract Full Text PDF–815K Supplementary Material
Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021
Vincent M Ulvé, Emeric W Sevin, Angélique Chéron, Frédérique Barloy-Hubler
BMC Genomics. 2007; 8: 467. Published online 2007 December 19. doi: 10.1186/1471-2164-8-467
PMCID:
PMC2245857
Abstract Full Text PDF–815K Supplementary Material
Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics
Coral del Val, Elena Rivas, Omar Torres-Quesada, Nicolás Toro, José I Jiménez-Zurdo
Mol Microbiol. 2007 December; 66(5): 1080–1091. Published online 2007 October 26. doi: 10.1111/j.1365-2958.2007.05978.x
PMCID:
PMC2780559
Abstract Full Text PDF–333K Supplementary Material
A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria
Björn Voß, Gregor Gierga, Ilka M Axmann, Wolfgang R Hess
BMC Genomics. 2007; 8: 375. Published online 2007 October 17. doi: 10.1186/1471-2164-8-375
PMCID:
PMC2190773
Abstract Full Text PDF–872K Supplementary Material
A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes
Zizhen Yao, Jeffrey Barrick, Zasha Weinberg, Shane Neph, Ronald Breaker, Martin Tompa, Walter L Ruzzo
PLoS Comput Biol. 2007 July; 3(7): e126. Published online 2007 July 6. doi: 10.1371/journal.pcbi.0030126
PMCID:
PMC1913097
Abstract Full Text PDF–1.2M Supplementary Material
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline
Zasha Weinberg, Jeffrey E. Barrick, Zizhen Yao, Adam Roth, Jane N. Kim, Jeremy Gore, Joy Xin Wang, Elaine R. Lee, Kirsten F. Block, Narasimhan Sudarsan, Shane Neph, Martin Tompa, Walter L. Ruzzo, Ronald R. Breaker
Nucleic Acids Res. 2007 July; 35(14): 4809–4819. Published online 2007 July. doi: 10.1093/nar/gkm487
PMCID:
PMC1950547
Abstract Full Text PDF–182K Supplementary Material
Translational control and target recognition by Escherichia coli small RNAs in vivo
Johannes H. Urban, Jörg Vogel
Nucleic Acids Res. 2007 February; 35(3): 1018–1037. Published online 2007 January 30. doi: 10.1093/nar/gkl1040
PMCID:
PMC1807950
Abstract Full Text PDF–2.6M
Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets
Pierre Mandin, Francis Repoila, Massimo Vergassola, Thomas Geissmann, Pascale Cossart
Nucleic Acids Res. 2007 February; 35(3): 962–974. Published online 2007 January 26. doi: 10.1093/nar/gkl1096
PMCID:
PMC1807966
Abstract Full Text PDF–970K Supplementary Material
Structural analysis of aligned RNAs
Björn Voß
Nucleic Acids Res. 2006 November; 34(19): 5471–5481. Published online 2006 October 4. doi: 10.1093/nar/gkl692
PMCID:
PMC1636479
Abstract Full Text PDF–1.4M Supplementary Material
Identification of small non-coding RNAs from mitochondria and chloroplasts
Birgit Lung, Anja Zemann, Monika J. Madej, Markus Schuelke, Sandra Techritz, Stephanie Ruf, Ralph Bock, Alexander Hüttenhofer
Nucleic Acids Res. 2006; 34(14): 3842–3852. Published online 2006 August 9. doi: 10.1093/nar/gkl448
PMCID:
PMC1557801
Abstract Full Text PDF–334K Supplementary Material
An internal antisense RNA regulates expression of the photosynthesis gene isiA
Ulf Dühring, Ilka M. Axmann, Wolfgang R. Hess, Annegret Wilde
Proc Natl Acad Sci U S A. 2006 May 2; 103(18): 7054–7058. Published online 2006 April 24. doi: 10.1073/pnas.0600927103
PMCID:
PMC1459017
Abstract Full Text PDF–608K
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