Evolutionary conservation of RNA sequence and structure
Wiley Interdisciplinary Reviews - RNA, 2021 An RNA structure prediction from a single‐sequence RNA folding program is not evidence for an RNA whose structure is important for function. Random sequences have plausible and complex predicted structures not easily distinguishable from those of ...
Elena Rivas
semanticscholar +1 more source
A Robust and Precise ConvNet for Small Non-Coding RNA Classification (RPC-snRC)
IEEE Access, 2021 Small non-coding RNAs (ncRNAs) are attracting increasing attention as they are now considered potentially valuable resources in the development of new drugs intended to cure several human diseases.
Muhammad Nabeel Asim +5 more
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Noncoding RNA gene detection using comparative sequence analysis
BMC Bioinformatics, 2001 Background Noncoding RNA genes produce transcripts that exert their function without ever producing proteins. Noncoding RNA gene sequences do not have strong statistical signals, unlike protein coding genes.
Eddy Sean R, Rivas Elena
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Small RNA sequencing profiles of mir-181 and mir-221, the most relevant microRNAs in acute myeloid leukemia [PDF]
The Korean Journal of Internal Medicine, 2019 Background/Aims To evaluate and select microRNAs relevant to acute myeloid leukemia (AML) pathogenesis, we analyzed differential microRNA expression by quantitative small RNA next-generation sequencing using duplicate marrow samples from individual AML ...
Yun-Gyoo Lee +5 more
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RNA cytosine methylation analysis by bisulfite sequencing [PDF]
Nucleic Acids Research, 2008 Covalent modifications of nucleic acids play an important role in regulating their functions. Among these modifications, (cytosine-5) DNA methylation is best known for its role in the epigenetic regulation of gene expression. Post-transcriptional RNA modification is a characteristic feature of noncoding RNAs, and has been described for rRNAs, tRNAs and
Schaefer, Matthias +3 more
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Quantifying the relationship between sequence and three-dimensional structure conservation in RNA
BMC Bioinformatics, 2010 Background In recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing ...
Capriotti Emidio, Marti-Renom Marc A
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ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV [PDF]
PeerJ, 2018 In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication.
Ryan J. Andrews +2 more
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A Beginner’s Guide to Analysis of RNA Sequencing Data [PDF]
American Journal of Respiratory Cell and Molecular Biology, 2018 Abstract Since the first publications coining the term RNA-seq (RNA sequencing) appeared in 2008, the number of publications containing RNA-seq data has grown exponentially, hitting an all-time high of 2,808 publications in 2016 (PubMed).
Clarissa M, Koch +6 more
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Representation learning applications in biological sequence analysis
bioRxiv, 2021 Remarkable advances in high-throughput sequencing have resulted in rapid data accumulation, and analyzing biological (DNA/RNA/protein) sequences to discover new insights in biology has become more critical and challenging.
Hitoshi Iuchi +8 more
semanticscholar +1 more source
Tracking Cryptosporidium parvum by Sequence Analysis of Small Double-Stranded RNA
Emerging Infectious Diseases, 2001 We sequenced a 173-nucleotide fragment of the small double-stranded viruslike RNA of Cryptosporidium parvum isolates from 23 calves and 38 humans. Sequence diversity was detected at 17 sites.
Lihua Xiao +3 more
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