Block course 3 - 13 April 2018

Registration deadline: 19 March 2018

Registration via KVV (Department of Mathematics and Computer Science)

Comment regarding time conflicts of this module with university exams

Please note that I am happy to excuse your absence in case a University exam is overlapping a morning or afternoon session of this module. In that case, please email me your time conflict(s) as early as possible and provide written evidence for the exam by the registration deadline for this module.

Contents

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 were only published in 2016. These methods open exciting possibilities to explore transcriptomes in unprecedented ways.

Many of these methods combine novel experimental pipelines with next-generation sequencing and 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.  The corresponding computational aspects cannot be understood or optimised without considering the experimental side and vice versa.

Topic-wise, our focus will be on:

• algorithms and computational strategies including probabilistic and comparative methods
• transcriptome-wide experimental methods and protocols for investigating RNA structures and RNA-RNA interactions in vitro and in vivo

Target audience

This self-contained module is targeted at both, graduate students in Bioinformatics as well as graduate students in Biochemistry. It thus goes without saying that no participant is expected to know everything. Everyone, however, is expected to learn something outside their "official" area of expertise, as we will cover both computational and experimental methods for investigating RNA structures and RNA-RNA interactions. In-between questions will thus be encouraged throughout.

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 as well as a small research proposal of your own. Formally speaking, the module comprises

• lectures
• example classes
• seminar talks

Language

Note that the language for the entire module will be English.

Student participation and important deadlines

The registration deadline for this module is Monday, 19. March 2018. Please note that I am happy to excuse your absence in case a University exam is overlapping a morning or afternoon session of this module. In that case, please email me your time conflict(s) as early as possible and provide written evidence for the exam.

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

• give one or two presentations (if you wish, you may email me a short list of 4 preferred papers to Irmtraud Meyer by Monday, 19. March, at the very latest; the earlier you send your short-list, the higher your chance of being assigned a paper from your list (i.e. first come, first served); you may work in a team of two and give twice the presentations (as team), in that case both students need to email me to (a) confirm the other team member and (b) the same list of 4 papers; I reserve the right to assign presentations)
• clarify any questions you may have regarding your presentation by Thursday, 5. April, e.g. by emailing the contact person assigned to your paper or by arranging a face-to-face meeting. For this, please contact Stefan or Peter directly (see the list of papers for whom to contact for which paper).
• email your finalized presentation to Irmtraud Meyer by Friday, 6. April, as a single pdf-file
• attend all events (if you miss a class without a formal excuse (e.g. illness, university exam) , you may be asked to write a report)
• participate actively (e.g. by chairing a discussion, asking and/or clarifying questions)
• propose and defend a small potential research project of your own (submit 1-2 pages as pdf-file including references via email to Irmtraud Meyer by Friday, 6. April; this should ideally be done in teams of two)
• come prepared (e.g. read papers ahead of time so you could readily summarize and discuss it)
• provide feedback to fellow students via a small questionnaire to help them improve their presentation skills

For MSc students in Biochemistry: if you want to participate only in the lecture-part of the module, you have to attend all lectures and example classes and actively participate in both to pass it.

What you will learn

• fundamental principles underlying existing computational and experimental methods and their pros and cons
• critically present and discuss research concepts and strategies
• propose and defend a small original research project of your own
• hopefully, think outside the box and learn to address a wider scientific audience
• chair a discussion
• optionally: work in a team of two (presentations, research proposal)

Grading

Grading of the module will be on a pass/fail basis. Note that any teamwork will be judged as a whole.

Dates and location

The entire module will take place on the campus of the Max Delbrueck Centre in Berlin-Buch on workdays (Mo to Fr)

• 9.30 to 16.30 h from 3. April (Tuesday, first day) to 13. April 2018 (Friday, last day).

The research campus offers facilities for lunch and tee/coffee breaks.

• the first week will take place in MDC campus building C81 (FMP) in room 1.14 on the ground floor
• the second week will take place in the library of the MDC campus in building 10 in room 27.1 on the ground floor

see the directions to the MDC campus in Berlin-Buch and a map of the MDC campus.

Contact

In case of general questions including questions regarding the registration for this module, please contact Irmtraud Meyer by email or phone (030-9406-3292). For questions about specific papers, please contact Peter or Stefan directly, see the list of papers.

Background reading

• C.K. Kwok (2016): Dawn of the in vivo RNA structurome and interactome
• J.G. Aw (2016): In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

Two key papers to give you some ideas:

• Dawn of the in vivo RNA structurome and interactome
• RNA duplex map in living cells reveals higher order transcriptome structure