This is a block Pro-/Seminar primarily for Bioinformatics and open to interested Biotechnology students.

Overview: Epigenetic modifications, such as DNA methylation and histone modification, alter DNA accessibility as well as chromatin structure, thereby regulating gene expression patterns. These processes are crucial to the normal development and differentiation of distinct cell lineages. Mutations or deletions can result in human diseases caused by alterations in the regulation of transcription.  DNA methylation patterns, which are strongly associated with clinical phenotypes, can be used as biomarkers for diagnosing diseases and guiding treatments. To better understand human development and diseases great efforts are currently made to develop methods to measure epigenetic cell-cell differences as well as combine data sets of different epigenetic modifications to predict their impact on development and health.
In the course of this seminar, we will cover different chromatin accessibility and DNA methylation assays and bioinformatics methods that further use these data, e. g. for predictions of disease risks.

News: All topics have been assigned and participants were notified. Thanks for your interest in this course!

Due to the current pandemic situation, for the dates listed below, we will have remote meetings via Microsoft Teams conferences instead of personal meetings.

Tutor: M.Sc. Viktoria Wagner
Key dates:

Registration *09.11.2020-20.11.2020: Register here
Kick-off meeting [mandatory]08.12.2020, 14:00 remotely via Microsoft Teams (Download slides)
Deadline to register in HISPOS OR de-register from seminar *04.01.2021 (4 weeks after the kick-off meeting)
Deadline for feedback ** [optional]01.03.2021 (2 weeks before the presentations)
Presentations15.03.2021 remotely via Microsoft Teams
Summary submission deadline22.03.2021 (1 week after the presentations)

* If you want to deregister from the seminar, please send the tutor an email irrespectively whether you (de)registered in HISPOS or not.

** If you would like to get feedback about your slides, e.g. to improve your presentation before the talk, send your slides to the tutor before the feedback deadline. We strongly encourage you to take this opportunity. When asking for feedback the more complete the submitted presentation the more helpful our feedback can be. Thus, try to avoid submitting half-finished slides. Feedback will be provided at least once but at most twice per participant. Also, before sending in the slides, check out our support materials (presentation guidelines, presentation guidelines checklist). You must hand-in a (digital) copy of the completed guidelines checklist at latest when performing the presentation.

Please note: Your slides will make up a substantial part of the final grade. Reading and paying attention to the provided presentation guidelines will help you to get an impression of which aspects are relevant for the evaluation. Disregarding many of the points listed in the guidelines may negatively affect your grade.

Place and Time for Presentations:

  • E2.1 (CBI), room 206 OR remote (Microsoft Teams), starting at 10 am.

Requirements for participation (Bioinformatics):

  • Proseminar: at least in 3rd semester, Bioinformatics I & Genetics lecture
  • Seminar: no pre-requisites.

Good language skills are presumed as all talks will be held in english language.

Certificate requirements:

  • Successful presentation:
    • Talk: 30 minutes for a Pro-seminar and 40 minutes for a Seminar
    • Discussion: 5 minutes during which you should be able to answer questions from the tutor(s)/audience
  • Attendance to all presentations is mandatory
  • Submitting a summary (may have an impact on the final grade):
    • Short description of the presented topic(s)
    • Ca. 2 pages of text, excluding title (page), references, figures, tables etc..
    • No figures, tables or formulas required
    • Main structure: title page, main text (with or without subsections), references
    • It is recommended to write the report using LaTeX in order to train scientific writing

Final grade:

  • Primarily based on the given presentation & follow-up discussion
  • Might be influenced by the quality of the submitted summary report

Topics

All manuscript files are either open-access or available via the university network using a secure VPN connection.

Nr.PresentationTopicParticipantGroup
1SeminarAssessment of computational methods for the analysis of single-cell ATAC-seq dataSami Adbennour LaradjiBioinformatics
2SeminarQuantitative comparison of DNA methylation assays for biomarker development and clinical applicationsJennifer CzajaBioinformatics
3SeminarCOCOA: coordinate covariation analysis of epigenetic heterogeneityAnna HartungBioinformatics
4SeminarEpigenetic prediction of complex traits and deathGuangyi ChenBioinformatics
5SeminarDynamic changes in the epigenomic landscape regulate human organogenesis and link to developmental disordersOmar LahamBioinformatics
6ProseminarA comprehensive comparison of tools for differential
ChIP-seq analysis
Larissa Sue FeyBioinformatics
7SeminarHMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristicsMarie DetzlerBioinformatics
8SeminarMethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profilesKalanika ElamaldeniyaBioinformatics
9SeminarNoMeplot: analysis of DNA
methylation and nucleosome
occupancy at the single molecule
Jens PetermannBioinformatics
10SeminarUnique and assay specific features of NOMe-, ATAC- and DNase I-seq dataAdnan KarimBioinformatics

Recommended readings

Students who either have a shallow understanding on the topic and / or want to prepare for the course should consider reading the following papers: