Optimizing Splicing Junction Detection in Next Generation Sequencing Data on a Virtual-GRID Infrastructure [PDF]
, 2012 The new protocol for sequencing the messenger RNA in a cell, named RNA-seq produce millions of short sequence fragments. Next Generation Sequencing technology allows more accurate analysis but increase needs in term of computational resources. This paper
Abate, Francesco +5 more
core
Using nucleolytic toxins as restriction enzymes enables new RNA applications [PDF]
Over the past five decades, DNA restriction enzymes have revolutionized biotechnology. While these enzymes are widely used in DNA research and DNA engineering, the emerging field of RNA and mRNA therapeutics requires sequence-specific RNA ...
Combes, Francis +11 more
core +1 more source
Sequence-specific binding of single-stranded RNA: is there a code for recognition? [PDF]
, 2006 A code predicting the RNA sequence that will be bound by a certain protein based on its amino acid sequence or its structure would provide a useful tool for the design of RNA binders with desired sequence-specificity.
Albertini +91 more
core +2 more sources
FEBS Letters, EarlyView.The S1025 peptide is the major antidote to the YrzI toxin, which we renamed here as SpyT (Small Peptide YrzI Toxin) and SpyA (Small Peptide YrzI Antitoxin) (1). Degradation of the toxin–antitoxin spyTA mRNA, either by a translation‐dependent cleavage by the endoribonuclease Rae1 (2) or by direct attack by 3′‐exoribonucleases (3), also contributes to ...
Laetitia Gilet +4 more
wiley +1 more source
3D RNA and functional interactions from evolutionary couplings [PDF]
arXiv, 2015 Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and structure of RNAs and RNA-protein complexes.
arxiv
Identifying RNA contacts from SHAPE-MaP by partial correlation analysis [PDF]
, 2014 In a recent paper Siegfried et al. published a new sequence-based structural RNA assay that utilizes mutational profiling to detect base pairing (MaP).
Doudna, Jennifer +2 more
core +3 more sources
The power of microRNA regulation—insights into immunity and metabolism
FEBS Letters, EarlyView.MicroRNAs are emerging as crucial regulators at the intersection of metabolism and immunity. This review examines how miRNAs coordinate glucose and lipid metabolism while simultaneously modulating T‐cell development and immune responses. Moreover, it highlights how cutting‐edge artificial intelligence applications can identify miRNA biomarkers ...
Stefania Oliveto +2 more
wiley +1 more source
Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15
BMC Bioinformatics, 2017 Background Proteins recognize many different aspects of RNA ranging from single stranded regions to discrete secondary or tertiary structures. High-throughput sequencing (HTS) of in vitro selected populations offers a large scale method to study RNA ...
Shermin Pei +2 more
doaj +1 more source
RNA secondary structures having a compatible sequence of certain nucleotide ratios [PDF]
arXiv, 2016 Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc- and stack-length restrictions.
arxiv
The Reverse Transcription Signature of N-\u3csub\u3e1\u3c/sub\u3e-Methyladenosine in RNA-Seq is Sequence Dependent [PDF]
, 2015 The combination of Reverse Transcription (RT) and high-throughput sequencing has emerged as a powerful combination to detect modified nucleotides in RNA via analysis of either abortive RT-products or of the incorporation of mismatched dNTPs into cDNA ...
Alfonzo, Juan +14 more
core +1 more source