Jobs

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.

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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 (https://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.

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Biologisch-Technischer Assistent (m/w)

Beginn: so bald wie möglich / Dauer: 18 Monate mit der Option auf Verlängerung

Der Hauptfokus der Arbeitsgruppe liegt auf dem Zusammenspiel von nichtkodierenden RNAs (ncRNAs), RNA-bindenden Proteinen (RBPs) und ihrer Wirkung auf verschiedene Stufen der RNA Prozessierung. Die Stelle wird gemeinsam mit der DZHK Nachwuchsgruppe Cardiac Proteostasis  (Dr. Shirin Doroudgar) ausgeschrieben. Die Tätigkeit bezieht sich hauptsächlich auf die Arbeit mit Zellkulturmodellen und dient der Erforschung von zirkulären RNA Spezien im Speziellen und RNA Interaktionen sowie Funktionen im Allgemeinen.

Aufgaben

  • Zellkultur (sowohl Standardzelllinien, als auch hIPSCs und NRVMs)
  • Isolierung von DNA, RNA und Proteinen
  • PCR (für Amplikonsequenzierung und RNA-Quantifizierung)
  • Western Blots
  • Knock Downs (siRNAs)
  • Klonierung und Transfektion von Adenoviren und AAVs.
  • Vorbereitung und Sequenzierung von Nanopore-Bibliotheken (Oxford Nanopore Technologies)
  • Erfassen und Bewerten von mikroskopischen Abbildungen
  • Allgemeine Laboraufgaben und Organisation (darunter fallen Bestellungen, Angebotsanfrage, Kontrolle und Beschaffung von Verbrauchsmaterialien, Entsorgung, Instandhaltung der Geräte)
  • Etablierung neuer Methoden
  • Auswertung, Dokumentation und Darstellung der Ergebnisse

Benötigte Qualifikationen

  • Sie haben bereits Erfahrung mit der Arbeit in einem Forschungslabor
  • Erfahrung mit der Entwicklung und Fehlerbehebung von Molekularbiologieexperimenten
  • Erfahrung in DNA-Isolierung, Amplifikation und Klonierung, RNA-Isolierung und RTPCR sowie Immunoblotting
  • Erfahrungen mit Gewebekulturen, einschließlich primärer kardialer Myozyten, Zelllinien und iPS-Zellen
  • Expertise in Immunozytofluoreszenz und Mikroskopie
  • Hintergrund in der Herzbiologie, einschließlich Expertise bei in vitro und in vivo Modellen
  • Expertise in kardialen, biochemischen und phänotypischen Analysen
  • Erfahrung in der Entwicklung von Gene-Delivery-Plattformen wie Adenovirus und Adeno-assoziiertem Virus
  • Computerkenntnisse einschließlich Fachwissen in Bezug auf die Verwendung von Excel, ImageJ, Prism, PowerPoint und Illustrator
  • Sie sprechen gut Englisch, da Sie in einem internationalen Team arbeiten werden
  • Ausgeprägte Teamfähigkeit, Flexibilität, Zuverlässigkeit und Selbstständigkeit beim Arbeiten

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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