Assignments for the Comparative and Regulatory Genomics course at KU Leuven. 4 ECTS. Third Semester at KU Leuven, September 2021 - January 2022

• Comparative genomics and phylogenomics (13h, including hands-on):

• database searching and retrieval of sequence data
• multiple sequence alignment
• phylogenetic inference
• evolutionary models and their statistical comparison
• phylogenomics; challenges and opportunities for phylogenetics, lateral gene transfer and reticulate evolution.
• Orthologs, GeneTrees, synteny, genome evolution, protein domains/families
• Whole-genome alignments and visualisation tools (VISTA Browser, UCSC Genome Browser, Ensembl)
• Constraint detection (Gerp, phastCons, phyloP), the portion of the human genome under constraint & the portion being functional

• Regulatory genomics (13h, including hands-on):

• High-throughput technologies to study the regulatory genome and hands-on analysis of the data (RNA-Seq, ChIP-Seq, DNase-Seq, FAIRE-Seq) + use of publicly available data (e.g., ENCODE)
• Computational prediction of cis-regulatory elements and transcription factor binding sites: pattern discovery, pattern matching, use of comparative genomics, use of other data (e.g. gene expression data). Prokaryotes & eukaryotes.
• Computational prediction of microRNA binding sites
• Introduction to gene regulatory networks
• Outreach to other areas of functional genomics and systems biology (integrative genomics), e.g., interpretation of non-coding mutations found by whole-genome re-sequencing