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Klaus-Tschira-Institute for Computational Cardiology -
Bioinformatics and Systems Cardiology

Open PostDoc / PhD positions

Biological-Technical Assistant (m/f)

Start: as soon as possible / Duration: 18 months with the option of extension

 

The main focus of the group is on the interaction of non-coding RNAs (ncRNAs), RNA-binding proteins (RBPs) and their effect on different stages of RNA processing. The position is advertised jointly with the DZHK junior research group Cardiac Proteostasis (Dr. Shirin Doroudgar). The activity mainly relates to the work with cell culture models and serves the research of circular RNA species in particular and RNA interactions as well as functions in general.

Tasks

- Cell culture (standard cell lines as well as hIPSCs and NRVMs)
- Isolation of DNA, RNA and proteins PCR (for amplicon sequencing and RNA quantification)
- Western Blots- Knock Downs (siRNAs)
- Cloning and transfection of adenoviruses and AAVs.
- Preparation and sequencing of Nanopore libraries (Oxford Nanopore Technologies)
- Capturing and evaluating microscopic images
- General laboratory tasks and organization (including orders, request for quotation,  control and
  procurement of consumables, disposal, maintenance of equipment)
- Establishment of new methods
- Evaluation, documentation and presentation of results

Qualifications required
- Experience with the development and troubleshooting of molecular biology experiments
- Experience in DNA isolation, amplification and cloning, RNA isolation and RTPCR, and  
  immunoblotting
- Experience with tissue cultures, including primary cardiac myocytes, cell lines, and iPS-cubicles
- Expertise in Immunocytofluorescence and Microscopy
- Background in cardiac biology, including expertise in in vitro and in vivo models
- Expertise in cardiac, biochemical and phenotypic analyses
- Experience in the development of gene delivery platforms such as Adenovirus and Adeno-
  associated virus
- Computer skills including expertise in the use of Excel, ImageJ,  Prism, PowerPoint and Illustrator
- You speak English well as you will work in an international team
- Strong ability to work in a team, flexibility, reliability and independence at work

* * * * *

Postdoc in Computational RNA Biology (Epitranscriptomics, m/f)

Starting date: as soon as possible / Duration: Initially 2 years; option of further extension.

All successful applicants will enter a collaborative research environment focusing on the role of RNA in cardiac disorders. The flow of genetic information from DNA to proteins has been traditionally seen as a linear pathway with an RNA intermediate. However, instead of just being an inert carrier of information, RNA performs a multitude of tasks and may even be transformed in the course of these events. We are looking for talented investigators to work on different aspects of the complex life of RNA and how it integrates with other processes within the cell and beyond.

The successful applicant will enter a collaborative research environment focusing on the role of RNA modifications in cardiac disorders. We are looking for a talented investigator to analyze Illumina and Single Molecule RNA sequencing data, to design algorithms and statistical approaches for RNA modification detection and quantitation. You will be part of the DFG-funded priority program SPP1784 “Chemical Biology of native Nucleic Acid Modifications”.

Tasks

You will implement existing and develop new bioinformatics methods to analyze RT signatures in Illumina (e.g. https://github.com/dieterich-lab/JACUSA) data and to mine Oxford Nanopore sequencing traces (e.g. https://github.com/nanoporetech/tombo) with the purpose of RNA modification detection and quantitation. You will devise new ways to integrate single molecule with miCLIP (near-base resolution) and LAIC-seq (transcript resolution) data. You will also closely interact with our experts on RNA turnover dynamics  and ribosome profiling.

Required Qualifications

The ideal candidates will have a PhD or equivalent in Bioinformatics, Physics, Statistics or a related discipline. You offer solid expertise in handling high-throughput data sets and are fully competent in managing the underlying statistical challenges. Moreover, you are happy to work in a highly interdisciplinary team. A proven competence in scripting/programming (i.e. at least two out of C/C++, R, Python, Java) is essential. Other relevant qualifications include a good understanding of RNA Biology.

What we offer

The Dieterich Lab (www.dieterichlab.org) offers a stimulating, diverse and international research environment. We are embedded in a vibrant community of cardiovascular research labs and collaborate with many experimentally or theoretically oriented labs in the Heidelberg area.

Additionally we offer:
– individual, goal-oriented further education
– ticket for public transport
– Kindergarten as well as holiday organization for schoolchildren
– Information about finding a flat
– Health promotion
– University sports / Library access

* * *

Bioinformatics Software Developer (m/f)

Starting date: as soon as possible / Duration: Initially 2 years; option of further extension.

The division of Bioinformatics and Systems Cardiology at the Klaus Tschira Institute for Integrative Computational Cardiology develops software to study the role of RNA in cardiac disorders (github.com/dieterich-lab). The flow of genetic information from DNA to proteins has been traditionally seen as a linear pathway with an RNA intermediate. However, instead of just being an inert carrier of information, RNA performs a multitude of tasks and may even be transformed in the course of these events.

Tasks

The successful applicant will enter a collaborative research environment and contribute to the group’s bioinformatic software portfolio. Software development will mainly focus on Python and R, while the applicant is also expected to be familiar with team-based software development via GitHub and project management solutions such as RedMine.

The applicant will also support the group in the administration of the Dieterich Lab Debian-based computer cluster.  In this function the applicant will aid in the supervision of automatic backups (performed with Bareos and Borg), help users of our cluster to install new specialized bioinformatics software from source and deploy system upgrades with ansible.

Required Qualifications

Applicants should have a Master’s degree in computer science, bioinformatics, or a comparable relevant background and level of expertise. In addition to very good Linux administration skills (i.e. software management, shell and scripting languages), the ideal candidate has a proven record in database programming, web application development and/or high-level language programming in established software frameworks.

Proficiency in handling large-scale scientific data sets, cluster computing, or virtualization is a plus. Fluent spoken and written English is expected. Your technical expertise is complemented by essential soft skills, the ability to communicate and work in teams, flexibility and targeted action.

Was wir anbieten

Das Dieterich Lab (www.dieterichlab.org) bietet ein anregendes, vielfältiges und internationales Forschungsumfeld. Wir sind eingebettet in eine lebendige Gemeinschaft von Herz-Kreislauf-Forschungslaboren und arbeiten mit vielen experimentell oder theoretisch ausgerichteten Laboren im Raum Heidelberg zusammen.

Zusätzlich bieten wir:

  • Individuelle, zielorientierte Weiterbildung
  • Ticket für den öffentlichen Verkehr
  • Kinderkrippe und Kindergarten, sowie Ferienorganisation für Schulkinder
  • Informationen zur Wohnungssuche
  • Gesundheitsförderung
  • Universitätssport / Bibliothek

Contact & Application

Please upload a covering letter/supporting statement, including a brief statement of research interests, CV and the details of two referees as part of your online application.

Applications including all relevant credentials should be sent to (email: in ONE pdf-file):

University Hospital Heidelberg
Department of Internal Medicine III Section of Bioinformatics & Systems Cardiology
Prof. Dr. rer. nat. Christoph Dieterich
Im Neuenheimer Feld 669
69120 Heidelberg

Email: sekretariat.dieterich@med.uni-heidelberg.de

Interested ?
Please contact us.

We are always looking for talented students with a background in bioinformatics / medical informatics who wish to do an internship, master’s thesis or similar.

We also encourage medical students who would like to pursue a computational
project in their dissertation (Medical Structured Scientific Program / MEDISS)
to contact us.

We stand for equal opportunities. People with disabilities are given priority with the same suitability. The university hospital aims at a general increase in the proportion of women in all areas and positions where women are underrepresented. Qualified women are therefore particularly encouraged to apply. Full-time positions are, in principle, divisible insofar as there are no official or legal grounds.

For specific job descriptions, please check back regularly.

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Contact

Klaus-Tschira-Institute for Computational Cardiology

 

Prof. Dr. Christoph Dieterich

 

University Hospital Heidelberg

Innere Medizin III

Im Neuenheimer Feld 669
69120 Heidelberg

 

Tel.: +49 6221 - 56 6869

Fax: +49 6221 - 56 6868

 

E-Mail: sekretariat.dieterich
@med.uni-heidelberg.de

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