Ph.D. candidate (f/m/diverse) in "Computational method development for post-transcriptional gene regulation in disease models"

As German Research Center for Environmental Health, Helmholtz Zentrum München pursues the goal of developing personalized medical approaches for the prevention and therapy of major common diseases such as diabetes mellitus, allergies and lung diseases. To achieve this, it investigates the interaction of genetics, environmental factors and lifestyle.

The Institute of Computational Biology is a globally recognized department for innovations anchored at the Helmholtz Zentrum Munich and the Technical University of Munich. We are looking for a PhD candidate in "Computational method development for post-transcriptional gene regulation in disease models"

The Ph.D. project will focus on investigating the post-transcriptional regulatory network of RNA Binding Proteins (RBPs) and its functional consequences on RNA fate in disease models. For this, the student will develop innovative computational method to analyze high-throughput NGS data (mainly CLIP-seq data) for hundreds of different proteins and investigate differences between individuals, as well as healthy versus disease samples. Ultimately, the student will contribute to define new RBP functions and potential novel biomarkers in collaboration with experimental groups.

Activities and responsibilities

Job Description
  • Significantly extend statistical and machine learning tools previously developed in the Marsico lab, such as PureCLIP (Krakau et al., Genome Biol 2018) and ssHMM (Heller et al. NAR 2017), to model differential RBP binding.
  • In the context of population genomic, investigate the effect of allele-specific binding upon SNPs significantly associated to disease phenotypes. In the context of cancer, investigate the role of cancer mutations in perturbing RBP-mediated gene regulation.
  • Application and extension of machine learning methods to the prediction of RBP binding from RNA sequences/structures.

Qualification profile

Your Qualifications
  • Master’s Degree in Bioinformatics, Biostatistics, Physics, Informatics or Mathematics. Alternatively, a Master’s Degree in Biotechnology, Biology or equivalent with significant experience and interest in Bioinformatics and Statistics.
  • Excellent programming skills in R, Python and/or C/C++
  • Excellent academic record
  • Keen interest in RNA Biology and post-transcriptional regulation
  • Basic experience with NGS data analysis and machine learning or multivariate statistics methods
  • Scientific curiosity, propensity to problem solving, ability to work independently and develop original ideas
  • Highly motivated to work in a multi-disciplinary environment and in collaborations with experimental partners
  • Excellent communication and presentation skills
  • Fluency in spoken and written English
The following skills are considered advantageous:
  • Basic knowledge of Hidden Markov Models and generalized linear models
  • Knowledge of basic RNA bioinformatics algorithms for the analysis of RNA structures and functions
  • Working in a Linux environment, with experience of shell scripting, cluster or cloud computing


Our Offer
At the Helmholtz Zentrum München, you can contribute together with leading researchers to the investigation of the development, prevention and treatment of environmental diseases such as diabetes, chronic lung diseases and allergies. In order to further promote your professional development, we offer extensive and targeted research training and career programmes. We support the reconciliation between work and private life with flexible working time models, occupational health management, day care facility for children, a childcare subsidy, Elder Care, as well as other counseling and support services.

Remuneration and benefits are in accordance with the collective agreement for the public service (EG 13 50% TV EntgO Bund). In addition, there is also the possibility of granting an allowance amounting to 15% if the necessary conditions are fulfilled.

The position is (initially) limited to three years.

The activity involves special knowledge and experience specific to own scientific skills.

As a holder of the Total E-Quality Award, we promote equality of opportunity. Applications from women are welcome. Qualified applicants with physical disabilities will be given preference.
We are looking forward to receiving your comprehensive online application (cover letter, a short summary of your present and future research interests, CV, scans of your bachelor and master certificates, contact details of 2 referees) as a single PDF document until February 28th 2019.

Send application to

Anna Sacher
Phone: 089 3187 2926

Helmholtz Zentrum München
Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)
Institute of Computational Biology
Ingolstädter Landstr. 1

85764 Neuherberg near Munich

While applying for the job please refer to jobvector and use the following reference number: 2019/0060

About Helmholtz Zentrum München

Im Mittelpunkt stehen chronische, degenerative Krankheiten wie Lungenerkrankungen, Allergien, Krebs und Herz-Kreislauf-Erkrankungen, die in erheblichem Maße durch persönliche Risikofaktoren, Lebensstil und Umweltbedingungen beeinflusst werden. Zur Entwicklung neuer individualisierter Ansätze in Prävention, Diagnostik und kausaler Therapie als Merkmale einer...

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