VVZ API is not affiliated with ETH Zurich. Data might be outdated or incorrect. Please view the official ETHZ Vorlesungsverzeichnis for binding information.

376-1347-00L 4 Credits DR , MSC D-HEST

Bioinformatic Approaches to Regulatory Genomics and Epigenomics

Lecturers & Examiners: Dr. Pierre-Luc Germain

VVZ CR n/a

Last Updated: 2026-06-03 00:14:16

Abstract

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.

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

General Information

Language: English
Levels: DR , MSC
Frequency: Yearly recurring

Examination

Type: graded semester performance

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.

Registration & Places

Max Places: 25
Signup End: 01.03.2026

Course Components

Type	Title	Time & Place	Hours
lecture with exercise	Bioinformatic Approaches to Regulatory Genomics and Epigenomics	Fri 14:00-15:45 (Y17 M 5)	2 h weekly
independent project	Bioinformatic Approaches to Regulatory Genomics and Epigenomics	No time listed	2 h weekly