Epigenomics offers a genome-wide perspective on how changes in chromatin regulate gene expression and cellular phenotype. This course introduces the underlying biological notions through a hands-on exploration of such data, providing an introduction to (R-based) tools necessary to explore, visualize and interpret it.
Learning objective
The objective of the course is two-fold:
1) to enable students, if not to be wholly independent with respect to NGS chromatin data analysis, at least to be able to autonomously explore, visualize and interpret such data;
2) to understand and critically appraise, from a genomics perspective and through hands-on data exploration, the key concepts underlying chromatin regulation of transcription and its impact on various biological phenomena.
Content
- Introduction to the Bioconductor ecosystem for genomic data analysis, with a focus on flexible and re-usable tools (e.g. standard data structures and visualization techniques) - How to find and re-use data from the literature - Basic analysis pipelines for ATAC-seq, ChIP-seq, and related assays, with a focus on data manipulation, exploration and visualization, motif analysis, etc. (Single-cell ATAC-seq is presented but not included in the practicals) - Introduction to regulatory genomics, with critical discussions of some of its conceptual issues: types of functional elements, the histone code, sequence recognition and binding specificity, transcriptor factor (TF) activation and binding, DNA accessibility, topological domains and chromatin loops, etc. - Importance of chromatin regulation in differentiation and neurological conditions
Prerequisites / Notice
Familiarity with R (as can be obtained from statistics courses, dedicated R courses, or some bioinformatic courses); some basic bioinformatics knowledge is beneficial but not required. Students bring their own computer to run the analyses (in case of old computers, please contact the teachers to evaluate the need for an alternative solution).
Competencies
Subject-specific Competencies
Concepts and Theories
assessed
Techniques and Technologies
assessed
Method-specific Competencies
Analytical Competencies
assessed
Decision-making
fostered
Media and Digital Technologies
assessed
Problem-solving
assessed
Social Competencies
Communication
fostered
Cooperation and Teamwork
fostered
Personal Competencies
Adaptability and Flexibility
assessed
Creative Thinking
fostered
Critical Thinking
assessed
Performance assessment
Performance assessment information (valid until the course unit is held again)
Repetition only possible after re-enrolling for the course unit.
Additional information on mode of examination
50% biweekly homework, 50% independent final project. The independent project will consist in either critically replicating an analysis from a selected publication or performing an original data analysis and description on a biological problem of the student's choice.
Performance assessment as a semester course