[HTML][HTML] Comprehensive analysis of alternative splicing across tumors from 8,705 patients
Our comprehensive analysis of alternative splicing across 32 The Cancer Genome Atlas
cancer types from 8,705 patients detects alternative splicing events and tumor variants by
reanalyzing RNA and whole-exome sequencing data. Tumors have up to 30% more …
cancer types from 8,705 patients detects alternative splicing events and tumor variants by
reanalyzing RNA and whole-exome sequencing data. Tumors have up to 30% more …
[HTML][HTML] Multiple reference genomes and transcriptomes for Arabidopsis thaliana
Genetic differences between Arabidopsis thaliana accessions underlie the plant's extensive
phenotypic variation, and until now these have been interpreted largely in the context of the
annotated reference accession Col-0. Here we report the sequencing, assembly and …
phenotypic variation, and until now these have been interpreted largely in the context of the
annotated reference accession Col-0. Here we report the sequencing, assembly and …
[HTML][HTML] Systematic evaluation of spliced alignment programs for RNA-seq data
High-throughput RNA sequencing is an increasingly accessible method for studying gene
structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the
alignment of partial transcript reads to a reference genome sequence. To assess the …
structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the
alignment of partial transcript reads to a reference genome sequence. To assess the …
[HTML][HTML] Genomic basis for RNA alterations in cancer
Transcript alterations often result from somatic changes in cancer genomes 1. Various forms
of RNA alterations have been described in cancer, including overexpression 2, altered
splicing 3 and gene fusions 4; however, it is difficult to attribute these to underlying genomic …
of RNA alterations have been described in cancer, including overexpression 2, altered
splicing 3 and gene fusions 4; however, it is difficult to attribute these to underlying genomic …
DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation
Epigenome modulation potentially provides a mechanism for organisms to adapt, within and
between generations. However, neither the extent to which this occurs, nor the mechanisms
involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis …
between generations. However, neither the extent to which this occurs, nor the mechanisms
involved are known. Here we investigate DNA methylation variation in Swedish Arabidopsis …
Nonsense-mediated decay of alternative precursor mRNA splicing variants is a major determinant of the Arabidopsis steady state transcriptome
G Drechsel, A Kahles, AK Kesarwani, E Stauffer… - The Plant …, 2013 - Am Soc Plant Biol
The nonsense-mediated decay (NMD) surveillance pathway can recognize erroneous
transcripts and physiological mRNAs, such as precursor mRNA alternative splicing (AS)
variants. Currently, information on the global extent of coupled AS and NMD remains scarce …
transcripts and physiological mRNAs, such as precursor mRNA alternative splicing (AS)
variants. Currently, information on the global extent of coupled AS and NMD remains scarce …
SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data
Motivation: Understanding the occurrence and regulation of alternative splicing (AS) is a key
task towards explaining the regulatory processes that shape the complex transcriptomes of
higher eukaryotes. With the advent of high-throughput sequencing of RNA (RNA-Seq), the …
task towards explaining the regulatory processes that shape the complex transcriptomes of
higher eukaryotes. With the advent of high-throughput sequencing of RNA (RNA-Seq), the …
Polypyrimidine tract binding protein homologs from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes
C Rühl, E Stauffer, A Kahles, G Wagner… - The Plant …, 2012 - Am Soc Plant Biol
Alternative splicing (AS) generates transcript variants by variable exon/intron definition and
massively expands transcriptome diversity. Changes in AS patterns have been found to be
linked to manifold biological processes, yet fundamental aspects, such as the regulation of …
massively expands transcriptome diversity. Changes in AS patterns have been found to be
linked to manifold biological processes, yet fundamental aspects, such as the regulation of …
[HTML][HTML] A pan-cancer transcriptome analysis reveals pervasive regulation through alternative promoters
Most human protein-coding genes are regulated by multiple, distinct promoters, suggesting
that the choice of promoter is as important as its level of transcriptional activity. However,
while a global change in transcription is recognized as a defining feature of cancer, the …
that the choice of promoter is as important as its level of transcriptional activity. However,
while a global change in transcription is recognized as a defining feature of cancer, the …
RNA‐Seq read alignments with PALMapper
Next‐generation sequencing technologies have revolutionized genome and transcriptome
sequencing. RNA‐Seq experiments are able to generate huge amounts of transcriptome
sequence reads at a fraction of the cost of Sanger sequencing. Reads produced by these …
sequencing. RNA‐Seq experiments are able to generate huge amounts of transcriptome
sequence reads at a fraction of the cost of Sanger sequencing. Reads produced by these …