Content & Motivation

The last few years have seen an explosion of methods for investigating RNA structures and RNA-RNA interactions. In fact, general methods for examining the RNA structurome and RNA-RNA interactome in vivo and on a transcriptome-wide scale were only published in 2016. These methods open exciting possibilities to explore transcriptomes and to discover entirely novel mechanisms of gene regulation on RNA level.

Many of these new methods combine novel experimental protocols with dedicated computational analysis pipelines in order to make discoveries. Both aspects (experimental and computational) typically require sophisticated protocols that are both key to discovery-making. Typically, the computational aspects cannot be understood (or optimised) without considering the experimental protocol and vice versa.

The goal of this inter-disciplinary Bioinformatics module, consisting of lectures, exercises and a seminar, is to introduce you to:

  • key theoretical concepts, computational strategies and algorithms for predicting RNA secondary structures and related features, covering probabilistic and comparative machine learning methods
  • key experimental concepts for transcriptome-wide RNA structure and RNA-RNA interaction probing
  • key research contributions published in recent years

Target audience

This inter-disciplinary module is targeted at Master students in Biochemistry, Bioinformatics, Data Science and Computer Science.

It provides a self-contained, intense introduction covering both computational and experimental aspects ranging from key concepts to the latest research literature.

Interactions between students from different scientific backgrounds are actively encouraged via team-work during all aspects of the module. It goes without saying that no participant is expected to know everything, but everyone is expected to learn something outside their official area of expertise.

Format

The module comprises a lecture-part where we will cover the basics you need to know in order to understand the currently existing approaches as well as a seminar-part where you will present and discuss ongoing research in this field.

Formally speaking, the module comprises:

  • lectures
  • exercises
  • seminar talks

Important dates

This module will be taught during the lecture-free time in March and April in order to allow for different types of master students to participate.

You need to register for this module from 1. October to 20. November 2020. Please be sure to register both, via Whiteboard and via Campus Management. The module comprises lectures (216221a), exercises (216221b) and a seminar (216221c) which have to be booked in conjunction.

The key teaching dates for spring 2021 are as follows:

  • 1. to 5. March 2021: lectures and exercises (entire days from Mo to Fr)
  • then one week without any teaching activities to allow time for preparing the seminar
  • 15. to 19. March 2021: seminar (entire days from Mo to Fr)
  • 22. to 24. March 2021: seminar (entire days from Mo to We)

We will start each day at 9 h and finish around 17 h with lunch and coffee breaks in-between.

Location

All teaching will take place in the new building of the Berlin Institute of Medical Systems Biology (BIMSB) located at Hannoversche Str. 28, 10115 Berlin in Berlin Mitte (see map), detailed rooms to be confirmed nearer the date. Due to the ongoing pandemic, all teaching activities this winter term will take place online, see the email announcements.

Language

Please note that the entire module will be held in English.

Student participation

In order to pass the entire module, you need to:

  • give one or more presentations (you may propose several papers to avoid conflicts; you may work in teams of two)
  • meet with one of the instructors at least 3 working days before your presentation to finalize your draft presentation and clarify any remaining questions
  • attend all events (if you miss a class without a valid excuse, you may be asked to write a report; select exceptions are made for documented university exams)
  • participate actively throughout (e.g. by chairing a discussion)
  • come prepared (e.g. read papers ahead of time so you could readily summarize and discuss them)
  • provide feedback to fellow students via a small questionnaire to help them improve their presentation skills

What you will learn

In this module, you will learn:

  • fundamental principles underlying existing computational and experimental methods and their pros and cons
  • how to critically present and discuss research concepts and strategies
  • how to chair discussions

How to register for this module

This module comprises lectures (216221a), exercises (216221b) and a seminar (216221c) which have to be booked in conjunction.

You need to register for this module from 1. October to 20. November 2020. Please be sure to register both, via Whiteboard and via Campus Management. The module comprises lectures (216221a), exercises (216221b) and a seminar (216221c) which have to be booked in conjunction.

You will receive an email confirming your registration shortly after the registration deadline.

Recommended background reading

Contact

In case of questions, please contact Irmtraud Meyer by email or phone (030-9406-3292), see also for contact details.