Advanced bioinformatics for biotechnology

The course will discuss the practical and methodological aspects of some of the most widely used experimental techniques based on next-generation sequencing (NGS) from a bioinformatics point of view. First, transcriptome characterisation and quantification through RNA-Seq will be discussed in detail, also introducing the case of single-cell level (scRNA-Seq) approaches. The course will then introduce and discuss some of the most broadly used techniques for the characterisation of protein-DNA interactions at the genomic level (ChIP-Seq and other DNA-enrichment based techniques). Different state of the art approaches to the bioinformatic analysis of sequencing data will be outlined both methodologically and in practice. A focus on the proper handling of sequencing data will initiate the students to the importance of FAIR principles in modern bioinformatics.

Students will apply different bioinformatic tools and pipelines to selected case studies during classes. The course is ideally linked to those dealing with functional genomics and bioinformatics.

At the end of this class, the students are expected to:
- be familiar with the most widely used protocols for sample preparation for RNA sequencing and be aware of the main principles underlying transcriptomes characterization and quantification;
- know the computational and methodological basics of standard bioinformatics protocols for RNA sequencing analysis, as well as being able to apply them to real case studies;
- know the computational and methodological basics of common bioinformatics protocols for single-cell RNA-Seq analysis and be able to apply them to real case studies;
- know the computational and methodological basics of standard bioinformatics protocols for characterising protein-DNA interactions at the genomic level and be able to apply them to real case studies.
- Be aware of the importance and role that FAIR principles have in bioinformatics data handling.