Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines [PDF]
, 2017 Neuroblastoma cell lines are an important and cost-effective model used to study oncogenic drivers of the disease. While many of these cell lines have been previously characterized with SNP, methylation, and/or mRNA expression microarrays, there has not ...
Adams, Rebecca N. +9 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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Recent advances in RNA sequence analysis [PDF]
F1000 Biology Reports, 2010 The latest high-throughput DNA sequencing technology can now be applied on a large scale to capture the complete set of mRNA transcripts in a cell, using a technique called RNA-seq. Although RNA-seq is only 2 years old, it has rapidly swept through the field of genomics, and it is now being used to analyze the transcriptomes of organisms ranging from ...
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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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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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Organization and transient expression of the gene for human U11 snRNA [PDF]
, 1991 The nucleotide sequence of U11 small nuclear RNA, a minor U RNA from HeLa cells, was determined. Computer analysis of the sequence (135 residues) predicts two strong hairpin loops which are separated by seventeen nucleotides containing an Sm binding site
Suter-Crazzolara, C., Keller, W.
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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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Structural Alignment of RNAs Using Profile-csHMMs and Its Application to RNA Homology Search: Overview and New Results [PDF]
, 2008 Systematic research on noncoding RNAs (ncRNAs) has revealed that many ncRNAs are actively involved in various biological networks. Therefore, in order to fully understand the mechanisms of these networks, it is crucial to understand the roles of ncRNAs ...
Vaidyanathan, P. P., Yoon, Byung-Jun
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RNA sequence analysis data of Peronospora destructor maintained on onions
Data in Brief, 2019 Peronospora destructor (Berk.) is an important biotrophic oomycete that causes downy mildew on onion (Allium Cepa L.) worldwide, especially in humid and temperate regions.
Kazuki Fujiwara +4 more
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Expanding the repertoire of human tandem repeat RNA-binding proteins.
PLoS ONE, 2023 Protein regions consisting of arrays of tandem repeats are known to bind other molecular partners, including nucleic acid molecules. Although the interactions between repeat proteins and DNA are already widely explored, studies characterising tandem ...
Agustín Ormazábal +6 more
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