Author Archives: Rory Johnson

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Postdoc Position: Bioinformatics of Long Non-Coding RNA in Cardiac Regeneration The “Genomics of Long Non-Coding RNAs in Disease” Laboratory at the University of Bern has an opportunity for a Bioinformatics Postdoc. Diseases of the heart are the single greatest cause ...

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How to count multi-mapping reads?

rna-seq

RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used (drop duplicated genes, distribute uniformly the reads, or estimate expression), but all ...

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Integrative deep models for alternative splicing

rna-seq

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 ...

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DART – novel RNA-seq de novo mapping algorithm

rna-seq

In recent years, the massively-parallel cDNA sequencing (RNA-Seq) technologies have become a powerful tool to provide high resolution measurement of expression and high sensitivity in detecting low abundance transcripts. However, RNA-seq data requires a huge amount of computational efforts. The ...

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Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites

rna-seq

Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. Tsinghua University researchers apply a soft-clustering method, RBPgroup, to various CLIP-seq datasets to group together RBPs that specifically bind the ...

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