Master thesis – Bioinformatics – RNA-Seq analysis

Belgian Nuclear Research Center
Mol, Belgium

Development of a RNA-seq analysis pipeline for bacterial transcriptomics

Introduction/framework **

Recent developments in new high-throughput technologies have revolutionized molecular biology. This technological progress has led to an explosive growth of the biological information (e.g. via DNA sequencing, RNA microarrays, proteomics), creating new opportunities in the field of bioinformatics in order to computationally deal with the dramatic increase of data. More specifically, the recent availability of next-generation sequencing (NGS) methods has opened up new horizons at the level of gene expression analysis. Where initially NGS applications were mainly focussing on the sequencing of genomic DNA, this technology is now finding its way to be used in transcriptomics studies i.e. RNAseq. Compared with microarrays, RNA seq is not dependent on the genome annotation (important e.g. for discovery of small regulatory RNA), and offers improved sensitivity and increased dynamic range.

However, these high-throughput sequencing methods produce a massive amount of data. For example, today, one run on the HiSeq2000 sequencing platform of Illumina produces gigabytes of DNA sequencing data Moreover, the domain of next-generation sequencing data analysis is still maturing, and even more powerful sequencing methods are being developed. Therefore, RNA-seq analyses will require reliable and high performance bioinformatics methods to extract the useful biological information out of these data.

Objectives of the project **

The objective of this PhD research is the development of a bioinformatics pipeline able to analyze microbial RNA-seq data based on the next-generation DNA-sequencing technologies. Main goals of the pipeline will be:

  1. Detect differential expression
  2. Reliable detection of small regulatory RNA, either starting from site-directed or regular RNA-seq data.
  3. Combining RNA-seq data to optimize the genome annotation of the studied bacteria.

As a proof of concept, the bioinformatics algorithms developed in this research proposal will be benchmarked via in-house generated and publicly available data.

  • Position: Internship
  • Job Location:
         Boeretang 200
    2400 Mol, Male, Belgium
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