Vacancies

Title PhD – Machine learning to integrate genome, transcriptome and patient outcome in neurological disease
Location UMC Utrecht
Job Information

Project outline.

Work to decode the genetics of a devastating neurological disease. You will focus on the analysis of non-coding DNA variants and the implementation of novel machine learning algorithms to predict biological impact based on patient DNA sequence and multi-omic profiling of human postmortem tissue and stem cell models.

Additional background.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that causes near total paralysis. There is no cure but extensive research has revealed a central role for genetics. A deeper understanding of ALS genetics has the potential to revolutionize treatment and enable predictive counseling for patients and their families. To achieve this, the ALS community initiated project MinE, a global consortium that has generated whole genome sequencing for >10,000 patients and healthy controls. The key challenge for this PhD is working to determine which of the hundreds of millions of DNA variants revealed by whole genome sequencing are important to disease.

Candidate.

We’re looking for an enthusiastic candidate eager to engage in challenging high impact research. You will have an interest in big data, problem solving and analytical thinking. This 4year PhD project is intended to be 70% computational work (30% wetlab), but 100% computational is possible. We welcome applicants from any analytical discipline including but not limited to bioinformatics, genetics, neuroscience, data science, mathematics, engineering etc. Teamwork and basic English are essential. You are not required to speak Dutch (all meetings are in English). Preference will be given to applicants with prior experience in genomics, NGS library preps, machine learning, biostatistics or programming.

Work Environment.

Utrecht University (UMC Utrecht) is consistently ranked among the top 15 universities in Europe (1st in Netherlands) and is an internationally recognized centre of excellence for ALS research and healthcare. The project supervisors have led multiple high impact ALS gene discoveries (Nature Genetics x3, Neuron x2) and act as the coordinating centre for project MinE. You will be embedded within the UMCU Brain Centre and integrated into an extensive research programme that spans genetics, translational neuroscience, stem cell models, environmental risk factors, neuroimaging, electrophysiology, patient care and clinical trials. You will also engage with extensive expertise in the Utrecht Bioinformatics Centre.

Click for more information about Utrecht and working at UMCU.

Questions/ Applications (CV & cover letter)

Dr. Kevin Kenna (K.P.Kenna – at umcutrecht.nl) Project Start Date: 2019/2020

Techniques

  •  Statistical programming & data analytics (R, python)
  • Deep learning (Keras)
  • High performance computing (SURFsara Grid, UMCU-HPC)
  • Human genetics (disease gene discovery, variant interpretation, ancestry)
  • Analysis of DNAseq & RNAseq (bulk/ single cell)
  • Wetlab: RNAseq (bulk/single cell), target validation

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Title Bioinformatician to work on Mechanisms of mutagenesis
Location Hubrecht Institute Utrecht
Job Information

Description of the project: DNA carries the instructions of life, but is also under constant attack. The resulting damage, if not repaired, leads to mutation and disease. Common environmental mutagens include sunlight and cigarette smoke, but the integrity of DNA is also threatened by chemicals produced by our own body. Our labs seek to understand the 1) sources of DNA damage in a physiological setting and 2) molecular mechanisms of DNA repair, and how these prevent mutagenesis. In order to do this, the Garaycoechea lab uses genetics in a number of systems, including mice, to modulate metabolism and DNA repair and gain mechanistic insight into how these processes drive mutation. The candidate will set up pipelines to map, call variants and quantify mutation signatures in WGS data, and will develop novel tools to study mutation in single cells. The Knipscheer lab uses NGS to gain insight into the mutation frequency and patterns of specific repair routes recapitulated in vitro. The candidate will work closely with members of both groups and will benefit from the extensive Bioinformatician community at the Hubrecht Institute.

Requirements: We seek a highly motivated Bioinformatician holding an BSc degree in bioinformatics, or an MSc or PhD degree in bioinformatics, molecular biology or cell biology. Ideal candidates have extensive experience in analysing WGS NGS data and developing pipelines for variant calling. We seek someone with an independent attitude to problem-solving who takes initiative and is enthusiastic to engage in interdisciplinary research. The working language in our international teams is English, the candidate should therefore have excellent English communication skills and be able to work as part of a team.

Duration: 1 year with the possibility of an extension after positive evaluation.

Salary: According to “CAO-Nederlandse Universiteiten” (CAO-NU), depending on experience and level of education. We offer an extensive package of fringe benefits.

Starting date: January 1st, 2020

Location: Utrecht Science Park, De Uithof.

How to apply: Please send your application to Dr. Juan Garaycoechea juan.g@hubrecht.eu or Dr. Puck Knipscheer p.knipscheer@hubrecht.eu before December 20st, 2019. For more information you can also use these email addresses or visit the website www.hubrecht.eu

Any acquisition further to this advertisement will not be appreciated.

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