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Open AccessPredicting the impact of rare variants on RNA splicing in CAGI6
Variants which disrupt splicing are a frequent cause of rare disease that have been under-ascertained clinically. Accurate and efficient methods to predict a variant’s impact on splicing are needed to interpre...
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Article
Open AccessExpanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems
CRISPR-Cas12a is a promising genome editing system for targeting AT-rich genomic regions. Comprehensive genome engineering requires simultaneous targeting of multiple genes at defined locations. Here, to expan...
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Article
Open AccessYanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis
Ultra-fast pseudo-alignment approaches are the tool of choice in transcript-level RNA sequencing (RNA-seq) analyses. Unfortunately, these methods couple the tasks of pseudo-alignment and transcript quantificat...
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Article
Open AccessTranscriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana
Regulation of pre-mRNA splicing diversifies protein products and affects many biological processes. Arabidopsis thaliana Serine/Arginine-rich 45 (SR45), regulates pre-mRNA splicing by interacting with other regul...
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Open AccessErratum to: Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm
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Open AccessEvaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm
Clustering protein sequences according to inferred homology is a fundamental step in the analysis of many large data sets. Since the publication of the Markov Clustering (MCL) algorithm in 2002, it has been th...
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Article
Open AccessInsights from GWAS: emerging landscape of mechanisms underlying complex trait disease
There are now over 2000 loci in the human genome where genome wide association studies (GWAS) have found one or more SNPs to be associated with altered risk of a complex trait disease. At each of these loci, t...
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Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
A new algorithm speeds up the quantification of transcripts from RNA-seq data by doing away with read map**.
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Article
Open AccessEvolutionary dynamics of U12-type spliceosomal introns
Many multicellular eukaryotes have two types of spliceosomes for the removal of introns from messenger RNA precursors. The major (U2) spliceosome processes the vast majority of introns, referred to as U2-type ...
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Article
Open AccessThe draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
In the early 1990s an outbreak of papaya ringspot virus (PRSV) in the papaya groves in the Puna district of Hawaii caused severe damage to an important crop. Since then, the planting of two transgenic cultivar...
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Open AccessFeatures generated for computational splice-site prediction correspond to functional elements
Accurate selection of splice sites during the splicing of precursors to messenger RNA requires both relatively well-characterized signals at the splice sites and auxiliary signals in the adjacent exons and int...
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Open AccessA computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana
Algorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been ...
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Article
Open AccessComprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
Recently, genomic sequencing efforts were finished for Oryza sativa (cultivated rice) and Arabidopsis thaliana (Arabidopsis). Additionally, these two plant species have extensive cDNA and expressed sequence tag (...
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Sequence similarity
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Article
Are snRNPs involved in splicing?
Discrete, stable small RNA molecules are found in the nuclei of cells1 from a wide variety of eukaryotic organisms2. Many of these small nuclear RNA (snRNA) species, which range in size from about 90 to 220 nucle...
