Algorithmic approaches for identification of RNA editing sites.
Brief Funct Genomic Proteomic. 2006.
PMID: 16769677
Review.
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Algorithmic approaches for identification of RNA editing sites.
Brief Funct Genomic Proteomic. 2006 Mar;5(1):43-5. doi: 10.1093/bfgp/ell014. Epub 2006 Feb 22.
Brief Funct Genomic Proteomic. 2006.
PMID: 16769677
Review.
Recently a number of groups have introduced computational methods for the detection of A-to-I RNA editing sites. These approaches have resulted in finding thousands of editing sites within the genomic repeats, as well as a few novel genet …
Recently a number of groups have introduced computational methods for the detection of A-to-I RNA editing sites. These …
ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species.
Brief Bioinform. 2023 May 19;24(3):bbad170. doi: 10.1093/bib/bbad170.
Brief Bioinform. 2023.
PMID: 37150785
Free PMC article.
Therefore, accurate identification of A-to-I editing sites is crucial for understanding RNA-level (i.e. transcriptional) modifications and their potential roles in molecular functions. ...We anticipate that ATTIC can be utilized as a useful tool to acc …
Therefore, accurate identification of A-to-I editing sites is crucial for understanding RNA-level (i.e. transcri …
Accurate detection for a wide range of mutation and editing sites of microRNAs from small RNA high-throughput sequencing profiles.
Nucleic Acids Res. 2016 Aug 19;44(14):e123. doi: 10.1093/nar/gkw471. Epub 2016 May 26.
Nucleic Acids Res. 2016.
PMID: 27229138
Free PMC article.
From 70 sRNA HTS profiles with over 1.3 billion reads, MiRME has detected thousands of statistically significant M/E sites, including 3'-editing sites, 57 A-to-I editing sites (of which 32 are novel), as well as some putative non-canonical ed …
From 70 sRNA HTS profiles with over 1.3 billion reads, MiRME has detected thousands of statistically significant M/E sites, including …
Bivartect: accurate and memory-saving breakpoint detection by direct read comparison.
Bioinformatics. 2020 May 1;36(9):2725-2730. doi: 10.1093/bioinformatics/btaa059.
Bioinformatics. 2020.
PMID: 31985791
Free PMC article.
MOTIVATION: Genetic variant calling with high-throughput sequencing data has been recognized as a useful tool for better understanding of disease mechanism and detection of potential off-target sites in genome editing. Since most of the variant calling algorithms …
MOTIVATION: Genetic variant calling with high-throughput sequencing data has been recognized as a useful tool for better understanding of di …
Genome-wide profiling of the C. elegans dsRNAome.
RNA. 2015 May;21(5):786-800. doi: 10.1261/rna.048801.114. Epub 2015 Mar 24.
RNA. 2015.
PMID: 25805852
Free PMC article.
To identify dsRNAs expressed in Caenorhabditis elegans, we developed a bioinformatics pipeline that identifies dsRNA by detecting clustered RNA editing sites, which are strictly limited to long dsRNA substrates of Adenosine Deaminases that act on RNA ( …
To identify dsRNAs expressed in Caenorhabditis elegans, we developed a bioinformatics pipeline that identifies dsRNA by detecting clustered …
Systematic identification of edited microRNAs in the human brain.
Genome Res. 2012 Aug;22(8):1533-40. doi: 10.1101/gr.131573.111. Epub 2012 Apr 12.
Genome Res. 2012.
PMID: 22499667
Free PMC article.
Our algorithm successfully identified many of the known editing sites in mature miRNAs and revealed 17 novel human sites, 12 of which are in the recognition sites of the miRNAs. We confirmed most of the editing events using in vitro ADAR …
Our algorithm successfully identified many of the known editing sites in mature miRNAs and revealed 17 novel human s …
GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.
BMC Genomics. 2017 May 15;18(1):379. doi: 10.1186/s12864-017-3746-y.
BMC Genomics. 2017.
PMID: 28506212
Free PMC article.
In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candidate nuclease when programmed with a particular guide RNA, as well as the cleavage efficiency of these sites. Powerful new exper …
In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candida …
Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis.
Mob DNA. 2014 Jan 13;5(1):2. doi: 10.1186/1759-8753-5-2.
Mob DNA. 2014.
PMID: 24410776
Free PMC article.
They recognize DNA target sites largely by base pairing of sequences within the intron RNA and achieve high DNA target specificity by using the ribozyme active site to couple correct base pairing to RNA-catalyzed intron integration. ...Finally, spurred by new …
They recognize DNA target sites largely by base pairing of sequences within the intron RNA and achieve high DNA target specifi …
RNA-eXpress annotates novel transcript features in RNA-seq data.
Bioinformatics. 2013 Mar 15;29(6):810-2. doi: 10.1093/bioinformatics/btt034. Epub 2013 Feb 8.
Bioinformatics. 2013.
PMID: 23396121
Free PMC article.
Biologically relevant transcribed features also include large and small non-coding RNA, new transcription start sites, alternative promoters, RNA editing and processing of coding transcripts. ...The framework is designed to be easily accessible while a …
Biologically relevant transcribed features also include large and small non-coding RNA, new transcription start sites, alterna …
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