Background Current RNA-seq analysis software for RNA-seq data tends to use similar
parameters across different species without considering species-specific differences …

Alternative splicing is a major contributor to transcriptome and proteome diversity in health
and disease. A plethora of tools have been developed for studying alternative splicing in …

Under fluctuating conditions, plants have evolved complex systems for sensing
environmental changes to maximize reproductive success. By utilizing seasonal cues, such …

Background Differential isoform usage is an important driver of inter-individual phenotypic
diversity and is linked to various diseases and traits. However, accurately detecting the …

Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and
development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little …

RNA sequencing offers unique insights into transcriptome diversity, and a plethora of tools
have been developed to analyze alternative splicing. One important task is to detect …

We present novoRNABreak, a unified framework for cancer specific novel splice junction
and fusion transcript detection in RNA-seq data obtained from human cancer samples …

ABSTRACT A key parameter in the experimental design of RNA-seq projects is the choice of
sequencing depth. Considering a limited budget, one needs to find a tradeoff between the …

Pangenomes are becoming a powerful framework to perform many bioinformatics analyses
taking into account the genetic variability of a population, thus reducing the bias introduced …

Alternative Splicing (AS) gives rise to a diversity of proteins from a gene by editing RNA and
reshuffling the protein coding sequences. This thesis presents 3 new tools to the study of AS …