This module comprises lectures (216221a), exercises (216221b) and a seminar (216221c) which have to be booked in conjunction. Note that registrations for this module open on 1.12.2018 and close on 18.01.2019 (Friday). Registrations are only possible via KVV https://kvv.imp.fu-berlin.de/vv/details?s=SS+19&lvnr=216221a bzw. https://kvv.imp.fu-berlin.de/portal/site/2843857c-01fb-4323-8afe-0fe1072ef663 You will receive an email confirming your registration within a week of the registration deadline. N.B.: For now, Master students in Computer Science can only register for the lectures and exercises (216221a and 216221b). This restriction, however, does not apply to Master students in Bioinformatics and Master students in Biochemistry. close

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 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 graduate students in Biochemistry, Bioinformatics 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 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 is English. Student participation In order to pass the entire module, you need to: give one or more presentations (you may propose 6 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 unexcused, 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) propose and defend a small potential research project of your own (including a written proposal of around 3 pages) 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 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 chair discussions Grading Grading of the module will be on a pass/fail basis. Contact In case of questions, please contact Irmtraud Meyer by email or phone (030-9406-3292), see also https://www.mdc-berlin.de/meyer for details. close

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 close