Small RNA gene identification and mRNA target predictions in bacteria
暂无分享,去创建一个
[1] G. Storz,et al. Identification of novel small RNAs using comparative genomics and microarrays. , 2001, Genes & development.
[2] G. Storz,et al. Global analysis of small RNA and mRNA targets of Hfq , 2003, Molecular microbiology.
[3] P. Stadler,et al. Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome , 2005, Nature Biotechnology.
[4] D. Ecker,et al. RNAMotif, an RNA secondary structure definition and search algorithm. , 2001, Nucleic acids research.
[5] E. Rivas,et al. Identification of differentially expressed small non-coding RNAs in the legume endosymbiont Sinorhizobium meliloti by comparative genomics , 2007, Molecular microbiology.
[6] S. Eddy,et al. Noncoding RNA genes identified in AT-rich hyperthermophiles , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[7] I-Min A. Dubchak,et al. A computational approach to identify genes for functional RNAs in genomic sequences. , 2001, Nucleic acids research.
[8] G. Storz,et al. Target prediction for small, noncoding RNAs in bacteria , 2006, Nucleic acids research.
[9] B. Felden,et al. Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[10] S. Altuvia. Identification of bacterial small non-coding RNAs: experimental approaches. , 2007, Current opinion in microbiology.
[11] F. Vandenesch,et al. Staphylococcus aureus RNAIII and the endoribonuclease III coordinately regulate spa gene expression , 2005, The EMBO journal.
[12] Jörg Vogel,et al. Experimental approaches to identify non-coding RNAs , 2006, Nucleic acids research.
[13] PichonChristophe,et al. Small RNA gene identification and mRNA target predictions in bacteria , 2008 .
[14] P. Babitzke,et al. CsrB sRNA family: sequestration of RNA-binding regulatory proteins. , 2007, Current opinion in microbiology.
[15] Jonathan Livny,et al. Identification of small RNAs in diverse bacterial species. , 2007, Current opinion in microbiology.
[16] Elena Rivas,et al. Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs , 2000, Bioinform..
[17] Gisela Storz,et al. 20 Versatile Roles of Small RNA Regulators in Bacteria , 2006 .
[18] G. Storz,et al. Small RNAs in Escherichia coli. , 1999, Trends in microbiology.
[19] F. Vandenesch,et al. Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. , 2007, Genes & development.
[20] S. Eddy. Computational Genomics of Noncoding RNA Genes , 2002, Cell.
[21] Timothy R. Hughes,et al. Considerations in the identification of functional RNA structural elements in genomic alignments , 2007, BMC Bioinformatics.
[22] Sean R. Eddy,et al. Rfam: annotating non-coding RNAs in complete genomes , 2004, Nucleic Acids Res..
[23] M. Tomita,et al. Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model. , 2006, Gene.
[24] P. Schattner. Searching for RNA genes using base-composition statistics. , 2002, Nucleic acids research.
[25] Peter F. Stadler,et al. Thermodynamics of RNA-RNA Binding , 2006, German Conference on Bioinformatics.
[26] B. Berger,et al. MSARI: multiple sequence alignments for statistical detection of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[27] Dean Laslett,et al. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. , 2004, Nucleic acids research.
[28] Kaizhong Zhang,et al. RNA-RNA Interaction Prediction and Antisense RNA Target Search , 2006, J. Comput. Biol..
[29] Elena Rivas,et al. Noncoding RNA gene detection using comparative sequence analysis , 2001, BMC Bioinformatics.
[30] Peter F Stadler,et al. Fast and reliable prediction of noncoding RNAs , 2005, Proc. Natl. Acad. Sci. USA.
[31] J. Vogel,et al. RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. , 2003, Nucleic acids research.
[32] B. Felden,et al. Proteins that interact with bacterial small RNA regulators. , 2007, FEMS microbiology reviews.
[33] S. Bergström,et al. The Etiological Agent of Lyme Disease, Borrelia burgdorferi, Appears To Contain Only a Few Small RNA Molecules , 2004, Journal of bacteriology.
[34] S. Gottesman,et al. Effect of RyhB Small RNA on Global Iron Use in Escherichia coli , 2005, Journal of bacteriology.
[35] G. Storz,et al. MicC, a Second Small-RNA Regulator of Omp Protein Expression in Escherichia coli , 2004, Journal of bacteriology.
[36] M. Zuker. On finding all suboptimal foldings of an RNA molecule. , 1989, Science.
[37] J. Vogel,et al. Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA. , 2005, Genes & development.
[38] David H. Mathews,et al. Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change , 2006, BMC Bioinformatics.
[39] E. Kolker,et al. Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. , 2002, Nucleic acids research.
[40] S. Eddy,et al. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.
[41] Ilka M. Axmann,et al. Identification of cyanobacterial non-coding RNAs by comparative genome analysis , 2005, Genome Biology.
[42] Sangsoo Kim,et al. CONSORF: a consensus prediction system for prokaryotic coding sequences , 2007, Bioinform..
[43] R. Griffey,et al. A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. , 2002, Bio Systems.
[44] Daniel Gautheret,et al. The ERPIN server: an interface to profile-based RNA motif identification , 2004, Nucleic Acids Res..
[45] R. Giegerich,et al. Fast and effective prediction of microRNA/target duplexes. , 2004, RNA.
[46] Christophe Pichon,et al. Intergenic sequence inspector: searching and identifying bacterial RNAs , 2003, Bioinform..
[47] S. Eddy,et al. Computational identification of noncoding RNAs in E. coli by comparative genomics , 2001, Current Biology.
[48] P. Clote,et al. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. , 2005, RNA.
[49] Pascale Cossart,et al. Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets , 2007, Nucleic acids research.
[50] P. Bouloc,et al. Down-regulation of Porins by a Small RNA Bypasses the Essentiality of the Regulated Intramembrane Proteolysis Protease RseP in Escherichia coli* , 2006, Journal of Biological Chemistry.
[51] V. Bordeau,et al. A Small Bacterial RNA Regulates a Putative ABC Transporter* , 2005, Journal of Biological Chemistry.
[52] Ivo L. Hofacker,et al. The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures , 2007, Nucleic Acids Res..
[53] M. A. Rosenblad,et al. Prediction of signal recognition particle RNA genes. , 2002, Nucleic acids research.
[54] A. R. Merchant,et al. High guanine–cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes , 2001, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[55] J. Livny,et al. sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes , 2005, Nucleic acids research.
[56] H. Margalit,et al. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli , 2001, Current Biology.
[57] N. Majdalani,et al. Small RNA regulators and the bacterial response to stress. , 2006, Cold Spring Harbor symposia on quantitative biology.
[58] Jörg Vogel,et al. How to find small non-coding RNAs in bacteria , 2005, Biological chemistry.
[59] Diego di Bernardo,et al. ddbRNA: detection of conserved secondary structures in multiple alignments , 2003, Bioinform..
[60] J. Vogel,et al. Target identification of small noncoding RNAs in bacteria. , 2007, Current opinion in microbiology.
[61] C. Burks,et al. Identifying potential tRNA genes in genomic DNA sequences. , 1991, Journal of molecular biology.