Advances in next-generation DNA sequencing technologies are now enabling detailed characterization of sequence variations in cancer genomes. With whole genome sequencing...
Read More »Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates
A key component in many RNA-Seq based studies is contrasting multiple replicates from different experimental conditions. In this setup, replicates play a key role as they allow to capture underlying biological variability inherent to the compared conditions, as well as ...
Read More »Analysis and prediction of exon skipping events from RNA-Seq with sequence information using rotation forest
In bioinformatics, exon skipping (ES) event prediction is an essential part of alternative splicing (AS) event analysis. Although many methods have been developed to predict ES events, a solution has yet to be found. In this study, given the limitations ...
Read More »FreePSI – an alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome
Alternative splicing plays an important role in many cellular processes of eukaryotic organisms. The exon-inclusion ratio, also known as percent spliced in, is often regarded as one of the most effective measures of alternative splicing events. The existing methods for ...
Read More »confFuse – high-confidence fusion gene detection
Fusion genes play an important role in the tumorigenesis of many cancers. Next-generation sequencing (NGS) technologies have been successfully applied in fusion gene detection for the last several years, and a number of NGS-based tools have been developed for identifying ...
Read More »Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly
It is generally thought that most canonical or non-canonical splicing events involving U2- and U12 spliceosomes occur within nuclear pre-mRNAs. However, the question of whether at least some U12-type splicing occurs in the cytoplasm is still unclear. In recent years ...
Read More »Exon-junction arrays – a viable alternative to RNA-seq for detection of alternative splicing events?
RNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used for the analysis of gene expression, but show poor validation rate with regard to splicing events. Commercial arrays that include probes within exon ...
Read More »Integrative deep models for alternative splicing
Advancements in sequencing technologies have highlighted the role of alternative splicing (AS) in increasing transcriptome complexity. This role of AS, combined with the relation of aberrant splicing to malignant states, motivated two streams of research, experimental and computational. The first ...
Read More »Personal genome approach to RNA-Seq read alignment enables the discovery of splicing variations
RNA-seq is a powerful and popular technology for studying posttranscriptional regulation of gene expression, such as alternative splicing. The first step in analyzing RNA-seq data is to map the sequenced reads back to the genome. However, commonly used RNA-seq aligners ...
Read More »GFusion – an Effective Algorithm to Identify Fusion Genes from Cancer RNA-Seq Data
Fusion gene derived from genomic rearrangement plays a key role in cancer initiation. The discovery of novel gene fusions may be of significant importance in cancer diagnosis and treatment. Meanwhile, next generation sequencing technology provide a sensitive and efficient way ...
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