Topics dealt with in the Advanced Genomics module held by Prof. Matteo Brilli The module is part of the Advanged Genomics and Epigenomics Course, owner: Prof. Giulio Pavesi
Twitter: @CompSysBiolUnit
Twitter: @MatteoBip
Orcid: https://orcid.org/0000-0001-9891-4617
Website: https://comparativesystemsbiologygroup.github.io/CSB.github.io/
Advanced genomic techniques, bioinformatic processing and models: • ChIP-Seq and the like -ChIP-Seq on bacterial transcription factors; -Computational approaches for the reconstruction of gene regulatory networks with DNA pattern scanning (Information Theory, Position weight matrices) and gene expression com- pendia (CLR and the like) and the integration of ChIP-Seq data. -Case studies +ChIP-Seq analysis with identification of transcription binding site within peaks, +CLR on a gene expression compendium of E. coli). • Tn-mutagenesis for the discovery of essential genes or genes involved in specific processes(Tn-Seq, Tn-seq circle, TraDIS, Rb-Tn-seq…) and bioinformatic analysis • Introducing the sRNA world in Bacteria, bioinformatic prediction of gene coding sRNAs, bioinformatic prediction of target transcripts, example of dynamical modelling. • Metataxonomics, metagenomics, for the characterization and the engineering of microbial communities
Network Theory • Definitions and concepts • Distinctive characteristics of biological networks • Topological analysis for the identification of essential/important genes, hubs and bottlenecks • Network motifs and their dynamical properties • The concept of community in graphs: characterization and resolution limit
Group Practical project on published data. This is the most part of the course, and is scattered throughout the frontal lessons. It is taking more and more space, so be ready with your laptop and Rstudio!