Splicify – a proteogenomic pipeline to detect differentially expressed protein isoforms based on integrating RNA-Seq and Mass Spec data

August 1, 2017 Leave a comment 3,889 Views

Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, ...

Integration of mass spectrometry and RNA-Seq data to confirm human ab initio predicted genes and lncRNAs

October 28, 2014 Leave a comment 5,551 Views

Tandem mass spectrometry (MS/MS) has been used to improve genome annotation in various organisms. The classical approach is to construct comprehensive theoretical peptide database with six frame translation model from the whole open reading frame (ORF) of a genome, and ...

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Tag Archives: Tandem mass spectrometry

Splicify – a proteogenomic pipeline to detect differentially expressed protein isoforms based on integrating RNA-Seq and Mass Spec data

Integration of mass spectrometry and RNA-Seq data to confirm human ab initio predicted genes and lncRNAs

Circall – fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data

Single-cell analysis support the use of PDAC organoids as a clinically relevant model for in vitro studies of tumor heterogeneity

lncRNA Regulation of IFNɣ and Its Effect on Checkpoint Inhibitor Expression Enhances Understanding of Therapeutic Cancer Target

Detection of atherosclerosis by small RNA-sequencing analysis of extracellular vesicle enriched serum samples

Mayo Clinic collaborates with Personalis to to offer clinical-grade comprehensive cancer genomic sequencing

Isoform variability is an important source of latent information in RNA-seq data that can be used to improve clinical prediction models.

Transcriptome-wide RNA-protein interaction predictions