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University Medical Center Groningen

Department of Genetics

Research vacancies

For Postdoctoral and PhD work

ERIBA
ERIBA

Introduction: The Department of Genetics at the University Medical Center Groningen, the Netherlands, offers an ambitious, dynamic and international environment, with state-of-the-art facilities. There are more than 50 international researchers and PhD students on the staff, representing some 30 nationalities (see map).

The research section is located in the European Research Institute for the Biology of Aging (ERIBA) along with other departments that share an interest in applying systems biology approaches to studying the genetic factors involved in human diseases and aging, in human cells and in model organisms. The Department of Genetics c ollaborates widely with other groups in Groningen, and at a national and international level. Candidates should be fluent in English.

Students looking for internships in Genetics should look here.

Salary will depend on your level of education and experience and is based on a full-time working week of 38 hours. The terms of employment are in accordance with the Collective Bargaining Agreement for Dutch University Medical Centres ( CAO UMC ).

  • For all vacancies in the UMCG see here. Open applications to our department are welcome from excellent candidates
  • See a presentation about the department here
  • Read comments from a Polish postdoc about working in the Dept of Genetics
  • See also what a supervisor (Prof. Irene van Langen, clinical geneticist) and a specialist-in-training (AIOS, Dr. Paul van der Zwaag) had to say about their work together here (in Dutch)
  • For more info on our Systems Genetics work, the Department of Genetics and other vacancies at UMCG

How to apply Your application should include: Cover letter, Curriculum Vitae, Contact information of two references, Academic transcripts (for a PhD post).
We require: an MSc degree in biology, medical biology, bioinformatics, or a comparable discipline. Candidates should have some experience in genetics, systems biology and/or bioinformatics and:

Affinity with molecular biology methodologies
Enthusiasm, highly motivated
Excellent communication stills, team player
Excellent computer and software skills
Fluency in English

Please send your application to Prof. Cisca Wijmenga, head of the Complex genetics research group. See also Systems Genetics


2 PhD students to perform bioinformatic analyses of gut microbiota composition (Jan 2017)

PhD project 1 . This project involves multi-omics analysis of the role of the gut microbiota composition in human metabolism and immunity, and its relation to host genome, transcriptome, proteome, environment and lifestyle.

In order to identify the downstream effects of the composition of the gut microbiota on human metabolic and immunological parameters, this project will study a population cohort of 2,000 individuals for whom we have extensive information on genetics, gut microbiome (both 16S rRNA sequencing and metagenomics sequencing), gene expression (RNA-seq), methylation (450K array), proteomics, diet and lifestyle. Several studies have already been published describing the cohort and the methods used: A. Zhernakova et al, Science, 2016 (DOI:10.1126/science.aad3369), MJ Bonder et al, Nature Genetics, 2016 (doi:10.1038/ng.3663); E. Tigchelaar, BMJ open, 2015 (doi:10.1186/1756-0500-7-901)

PhD project 2 . T his new project examines t he role of the gut virome in shaping the microbiome composition during the first year of life. We will follow 1,000 mother-baby pairs from pregnancy until the babies are 1-year old. We will collect baby stool samples at seven time-points during their first year of life. Additional information, including genetics, dietary and lifestyle factors, is being collected for both mothers and babies. The project aims to identify the role of the gut virome in shaping the gut bacterial composition and in shaping babies’ health. The sample collection is ongoing. The project is covered by an ERC starting grant to Dr. A. Zhernakova.

PhD students working on these projects will be expected to:

  • Integrate and analyse the genomic-, metagenomic-, metabolomics- and proteomics datasets
  • Design, develop, implement and maintain new algorithms, applications and infrastructure components
  • Summarize and report key analytical findings in both oral and written form at work meetings, at international scientific conferences, and in scientific publications

Candidates should:

  • Have an MSc in medical biology (or equivalent), mathematics, bioinformatics or computer science
  • Be highly motivated and have excellent mathematical, statistical and computer science skills
  • Experience with advanced statistics, biology or biochemistry
  • Excellent oral and written communication skills in English

It would be a bonus to have:

  • Experience in handling large (>1 Terabyte) databases (both unstructured and structured)
  • A knowledge of developing and debugging in Java

Working environment We have an enthusiastic team and a strong bioinformatics group. Our microbiome studies have been published in leading journals such as Science, Nature Genetics, Cell, and Gut. The Department of Genetics at the University Medical Centre Groningen is an energetic, dynamic and international environment, with state-of-the-art laboratory and computing technology. We work in close collaboration with groups from MIT and the Broad Institute (Boston). Working visits to the Broad Institute are often a part of the PhD training.

For further information and to apply, please contact: Dr. Alexandra Zhernakova, email: sasha.zhernakova@gmail.com ; Dr. Jingyuan Fu, email: fjingyuan@gmail.com

Links: www.systemsgenetics.nl ; https://www.rug.nl/research/genetics/


Positions in the System Genetics group of the University Medical Center Groningen

The Department of Genetics has 3 postdoctoral vacancies and 1 postdoctoral/PhD vacancy (Systems Genetics). We are a highly interdisciplinary department working on how genetic and environmental risk factors cause disease, with a special focus on common complex diseases. To build an understanding of how genetic variation leads to disease, we are applying our expertise in bioinformatics, functional genomics and experimental validation, and we are combining data from clinical cohorts with population-based cohorts enriched for different levels of ‘omics’ data. Our goal is to develop personalized treatments and preventive strategies that preserve health.

The department is an energetic, dynamic and international environment. Our research combines bioinformatics and statistics, immunology and molecular biology, and we are supported by state-of-the-art infrastructure. We are interested in recruiting self-motivated individuals with the drive to be competitive at the international level and who will enjoy working in a multi­disciplinary team.

We are seeking 3 ambitious postdocs and 1 postdoc or PhD student to contribute to different innovative and interdisciplinary genomics projects. Please mention the specific position you wish to apply for in your application. The conditions of employment comply with the Collective Labour Agreement of Medical Centers (CAO-UMC).

All applicants should have:

-       An excellent track record in genomics, system genetics, bioinformatics and/or immunology
-       Excellent communication skills
-       Excellent knowledge of English
-       The ability to work independently in a multidisciplinary and international environment.

Postdoc position (2 years) in Prof. Morris Swertz’s group

The Swertz group (Systems Genetics) is supported by an NWO VIDI grant and many national and international infrastructure grants. This group of 25 bioinformaticians develops analysis pipelines and database support interfaces for next-generation sequencing analysis (NGS) and the integration of multi-omics datasets from biobank samples, as well as tools to support personalized medicine prediction. Our algorithms, pipelines and databases are part of the MOLGENIS open source software suite (http://github.com/molgenis).

We are seeking a postdoc to coordinate and develop research opportunities in the area of NGS data analysis at the crossroads between clinical diagnostic work and research. As the challenge of NGS lies in data interpretation, you will focus on novel pipelines and methods to enable whole-genome interpretation, automated analysis/re-analysis, and population-based ‘big data’ methods to predict health/disease outcomes. As a postdoc you will write scientific research papers and co-supervise a team of scientific programmers, PhD students and postdocs, while overseeing a large high performance computing cluster of >1000 cores and a petabyte of storage.

We are looking for someone with a PhD in bioinformatics, computer science, molecular biology, genomics, epidemiology, artificial intelligence, or another relevant computational science. You should have expertise in large-scale bioinformatics and NGS analyses, be fluent in written and spoken English with good communication skills, and be highly motivated to further biomedical research and translate the results to the clinic. We will appreciate excellence and a good track record in one or more of the following: mathematics/statistics, high performance computing, machine learning, Linux, Bash, SLURM, R, Python, Perl, Java, BWA, GATK, Jenkins, Maven, Git, R, GWAS/gene expression, biobanking, QTLs, genetics or epidemiology.

For more information, please contact Prof. Morris Swertz (m.a.swertz@rug.nl).

Postdoctoral position: A systems genetics approach towards understanding lipid and cholesterol metabolism

It is clear that over 200 genetic variants affect lipid and cholesterol levels. These include rare mutations that cause dyslipidemia and common variants that have subtle effects on lipid and cholesterol levels. For a cohort of 1,500 population-based samples we have generated high-resolution measurements on many omics levels. These include DNA, RNA (RNA-seq), methylation (450k), volatile organic compounds in exhaled breath, plasma metabolites, microbiome, and extensive phenotype information.

You will investigate how genetic variants affect these different levels, using novel statistical methodologies. You will have a proven track record in analyzing large omics datasets and excellent skills in statistics, mathematics, and programming (Java or C++). You will be part of a team consisting of PhD students with backgrounds in statistical genetics and bioinformatics.

We are looking for a team player to drive the development and application of methods to identify relationships between these different omics levels. Please contact Dr. Lude Franke , see more on Franke group


PhD position: Next-generation analysis of diseases: identifying human disease pathways by integrating genome information

The Department of Genetics performs research into multiple complex diseases. We have contributed to the identification of genetic variants that cause type 1 diabetes, rheumatoid arthitis, celiac disease, ulcerative colitis, and Crohn’s disease. We collaborate extensively with the Groningen Bioinformatics Centre, working on the development and application of novel approaches to identify genetic variants and their functional consequences.

Background
Research in life sciences is changing rapidly. With the availability of high-throughput techniques (such as DNA and RNA microarray chips) and massive parallel sequencing, we now generate gigabytes of data per day. By using these techniques for multiple common diseases like diabetes, rheumatoid arthritis, celiac disease and inflammatory bowel disease, we have identified several causal genetic variants and common genetic factors for several autoimmune diseases.

But what are the functions of these genes and how are they related? And more importantly, why do they eventually lead to disease? We can now start answering these questions by combining genotype, expression, proteomics and methylation data for over 2,000 individuals. This allows us to identify relationships between genetic variants and their effects on gene and protein expression. We expect this information to lead us to the functional ‘downstream’ effects of these genetic variants, which is likely to result in better insight into these diseases.

We offer a challenging PhD research project for a period of 4 years and require a talented and motivated person to carry out this research. You must have an MSc degree (or expect to get one soon) in Biology or Medical Biology, Biochemistry, Mathematics, Physics, Bioinformatics or Computer Science, or in a closely related field. You will work in an international team with several post-docs, PhD students and technicians.

Responsibilities
- Design, develop, implement, and maintain new algorithms, applications and infrastructure components (primarily using Java and occasionally using R)
- Analysis of genomics, proteomics and metabolomics datasets
- Summarize and report key analytical findings at work meetings and international scientific conferences, and write scientific papers

Requirements
- MSc in medical biology (or equivalent), mathematics, physics, bioinformatics or computer science. The candidate must be highly motivated and have excellent mathematical, statistical and computer science skills
- Experience with advanced statistics, biology or biochemistry
- Strong knowledge in developing and debugging in Java
- Excellent oral and written communication skills, good level of English

Bonus
- Experience with handling large (>1 Terabyte) databases (both unstructured and structured)
- Active contributor to open source software

Contact: Lude Franke, tel. +31 (0)50 3617100, email
More information on Dr. Franke's work and at Systems genetics

Laatst gewijzigd:10 januari 2017 16:22