216221a
Lecture
SoSe 19: Methods for investigating the RNA structurome and RNA-RNA interactome
Irmtraud Meyer
Information for students
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.
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Comments
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.
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Suggested 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
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12 Class schedule
Regular appointments
Mon, 2019-03-04 09:00 - 17:00
Tue, 2019-03-05 09:00 - 17:00
Wed, 2019-03-06 09:00 - 17:00
Thu, 2019-03-07 09:00 - 17:00
Mon, 2019-03-25 09:00 - 17:00
Tue, 2019-03-26 09:00 - 17:00
Wed, 2019-03-27 09:00 - 17:00
Thu, 2019-03-28 09:00 - 17:00
Fri, 2019-03-29 09:00 - 17:00
Mon, 2019-04-01 09:00 - 17:00
Tue, 2019-04-02 09:00 - 17:00
Wed, 2019-04-03 09:00 - 17:00