Computational Methods for Epigenome Analysis (SoSe 2024)

Format and Time

  • Bioinformatics special lecture
  • 5 ECTS credit points
  • Course language: English
  • Block course
  • Lecture and hands-on practical workshop
  • Mandatory courses on UNIX shell and R programming via DataCamp at your own pace until July 3
  • The lecture and course will be held between July 29 and August 12 2024 (in presence).
  • Introductory meeting, July 4, 14:30 (A 4.3 Room 0.14)

Lecturers and TAs

Course outline

This course offers a practical introduction to bioinformatics methods and tools used for NGS-based (NGS = next generation sequencing) epigenome analysis. The lecture will refresh the students’ knowledge on epigenetic gene regulation, introduce a series of experimental methods to profile the epigenome and introduce into the theoretical background of bioinformatic methods and software tools used for data processing, quality control, exploratory analysis, differential analysis and integration of multiple data modalities. Four epigenomic data modalities will be discussed in detail: gene expression, DNA methylation, chromatin accessibility, histone modifications. The theoretical knowledge conveyed in the lecture will be solidified in a hands-on workshop in which the students will employ the introduced methods. Here, the students will work in groups of 2-3, each addressing one of the four epigenetic modalities mentioned above.
Students will present their results in a final presentation at the end of the course.

Content

  • Refamiliarize yourselves with the UNIX shell and R using DataCamp
  • Introduction to epigenetic gene regulation
  • Experimental techniques and bioinformatic analysis for gene expression (RNA-seq)
  • Experimental techniques and bioinformatic analysis for DNA methylation (bisulfite-seq, microarrays, enrichment-based methods, etc.)
  • Experimental techniques and bioinformatic analysis for chromatin accessibility (ATAC-seq, DNase-seq, NOMe-seq, etc.)
  • Experimental techniques and bioinformatic analysis for histone modifications (ChIP-seq, CUT&RUN, etc.)
  • Integrative data analysis: Dimension reduction, clustering, differential analysis, segmentation, imputation
  • Emerging epigenome profiling technologies (including single-cell and multiome methods)

Schedule

  • April 29 to July 3 (self-guided): Refamiliarize yourselves with the UNIX shell and R programming in the DataCamp classroom and complete the mandatory courses
  • July 4, 14:30: Introductory meeting
  • July 29 to 31: six theoretical lectures (90 minutes each) introducing into the biological and bioinformatic background.
  • August 1 to 2 (9am – 5pm): Practical introduction to the hands-on workshop
  • August 5: written exam (90 minutes)
  • August 6 to 9 (9am – 5pm): hands-on workshop
  • August 12: Presentation of results
  • August 18: Protocols handed in

All Lectures, the course and the presentation will be held in presence.

Admission

To enroll, students should have a basic knowledge in modern genomics and principles of epigenetics. They should have basic skills for script-based programming using the R language. Students will get the opportunity to (re-)familiarize themselves using a DataCamp classroom provided upon registration.

Mandatory courses on the UNIX shell and R scripting will have to be completed in that DataCamp classroom before the introductory meeting (i.e. by July 3, 2024, 23:59).

The course will be limited to 24 (bioinformatics) students. Students who attended the lecture “Principles of Epigenetics” will be given priority. Non-bioinformatics students will be accepted on an individual basis if they can show that the requirements are met.

Assessment/Exams

Students need to pass a written exam, based on the lecture content, prove that they successfully participated in the workshop by handing in a notebook-based protocol and give a 20-minute final presentation. The final grade will be given based on the exam and a check on the above criteria.

What can you do to prepare for the lecture?

Sign up

If interested, sign up by submitting the following information via email to: mijo00001@stud.uni-saarland.de AND nihit.aggarwal@uni-saarland.de

Deadline: April 28, 2024

  • Your name
  • Your UNIVERSITY email address
  • Your field of study (e.g. Bioinformatics)
  • Your current semester
  • Whether you passed the lecture Principles of Epigenetics
  • Your immatriculation number

Example:

TO: mijo00001@stud.uni-saarland.de, nihit.aggarwal@uni-saarland.de
SUBJECT: COMP_EPI_WS (SoSe2024)
BODY: John Snow, jsnow@uni-saarland.de, Bioinformatics Master, 3, Yes[WS23], 999999

You will be informed whether you have been accepted to the course after the sign-up deadline (April 28, 2024) passes

Literature

Lecture slides, workshop handouts and problem sets will be disseminated in MS Teams.