Ruprecht-Karls-Universität Heidelberg
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Dieterich0118 - Scientist (f/m) / PhD position
Project no:
Dieterich0118

Project leader:

Project supervisor:
Dieterich, Christoph
Application deadline:
30. Apr 2018
Start of PhD project:
1. Jun 2018

Project description:

Title:
Computational ncRNA Biology of renal / podocyte disorders
Summary:
You will enter a collaborative research environment focusing on Non-coding RNAs in renal and cardiac disorders. We are looking for a talented investigator to analyze the sequence, structure and conservation of the long ncRNA transcriptome in mammals. You will be part of a collaborative DFG-funded research unit “Disease pathways in podocyte injury”. Our experimental partner is Dr. Roman Müller from the University Hospital Cologne.
The Dieterich Lab works on computational and statistical approaches to study

RNA modifications (i.e. RNA editing and others)
RNA-RNA and RNA-protein interactions
Circular RNAs and general splicing
Control of translation
RNA dynamics
Data integration (OMICS & clinical data)

Given previous experience, the applicant will either work on:

(1) Applying state-of-the-art bioinformatics methods to assemble cell-specific non-coding transcriptomes, assess dynamic expression and localization, as well as sequence-structure conservation from next-generation RNA sequencing data.

Moreover, (2) the applicant will develop methods to predict ncRNA interactions with protein, RNA and DNA binding partners. Herein, you will benefit from our membership in the FANTOM6 consortium, which studies lncRNA function.
References:
Metge, F.; Czaja-Hasse, L. F.; Reinhardt, R. & Dieterich, C. (2017), 'FUCHS-towards full circular RNA characterization using RNAseq.', PeerJ 5, e2934.

Malone, B.; Atanassov, I.; Aeschimann, F.; Li, X.; Grosshans, H. & Dieterich, C. (2017), 'Bayesian prediction of RNA translation from ribosome profiling.', Nucleic acids research.

Piechotta, M.; Wyler, E.; Ohler, U.; Landthaler, M. & Dieterich, C. (2017), 'JACUSA: site-specific identification of RNA editing events from replicate sequencing data.', BMC bioinformatics 18, 7.

Jakobi, T.; Czaja-Hasse, L. F.; Reinhardt, R. & Dieterich, C. (2016), 'Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts.', Genomics, proteomics & bioinformatics 14, China, 216-23.

Cheng, J.; Metge, F. & Dieterich, C. (2016), 'Specific identification and quantification of circular RNAs from sequencing data.', Bioinformatics (Oxford, England) 32, 1094-6.

Bartram, M.P., Amendola, E., Benzing, T., Schermer, B., de Vita, G. and Müller, R.-U. “Mice lack-ing microRNAs in Pax8-expressing cells develop hypothyroidism and end-stage renal failure.” BMC Mol. Biol. 2016.

Bartram MP, Höhne M, Dafinger C, Völker LA, Albersmeyer M, Heiss J, Göbel H, Brönneke H, Burst V, Liebau MC, Benzing T, Schermer B and Müller RU. Conditional loss of kidney microRNAs results in congenital anomalies of the kidney and urinary tract (CAKUT). J Mol Med (Berl). 2013 Jun;91(6):739-48.
Methods that will be used:
See https://www.ncbi.nlm.nih.gov/pubmed/27592414

Computational RNA Biology and software development
• R Programming
• Python Programing
• Bash programming
Cooperation partners:
Priv.-Doz. Dr. med. Roman-Ulrich Müller
University Hospital Cologne
Department of Internal Medicine II
Center of Molecular Medicine, University of Cologne
Kerpener Str. 62
50937 Cologne, Germany
Personal qualifications:
Candidates should possess a Master’s Degree or equivalent qualification in biophysics, biochemistry, bioinformatics, or a related discipline. Candidates should preferably have a good background in statistics, experience in scripting/programming, possess excellent communication skills, and have a genuine interest in interdisciplinary research. Moreover, you are happy to work in a highly interdisciplinary team. A proven competence in scripting/programming (e.g. at least two out of C/C++, R, Perl, Python, Java) is essential. Other relevant qualifications include a good understanding of RNA Biology.
Keywords:
Long ncRNA, Computational Biology, bioinformatics, podocyte, kidney disease