A complete 4 year PhD program focused on the development and application of computational tools to predict and analyze personalized RNA signaling profiles from an individual’s genetic code. You will work to build tools that can be transferable to any genetic disorder, but your primary application will be to identify mutations, genes and biological pathways involved in ALS - a devastating neurodegenerative disease that effects 1 in 300 people. Your work is intended to highlight therapeutic targets for drug development and to enable more extensive genetic counselling for families affected by ALS (currently causal genetic factors are known for only 15% of patients). You will utilize clinical and large scale whole genome sequencing data for ~20,000 ALS patients and matched healthy controls. These data are provided by project MinE, the world’s largest ALS sequencing consortium (involving partners across 21 countries) which is coordinated in UMCU. Your work will also incorporate single cell/ bulk transcriptome and epigenome profiling of ALS cell types derived from stem cell models and post mortem tissue and here you will interact closely with functional biologists. Much of your work will involve use of the UMCU and SURFsara high performance computing systems and you will disseminate your work through scientific publications, github and presentation at international scientific conferences.
We offer a full-time 4 year PhD position in genomics and machine learning. This can be 70% computational + 30% wetlab work OR 100% computational depending on skills of the selected applicant. Your efforts will focus on implementing novel solutions to interpret large scale whole genome sequencing of patients with amyotrophic lateral sclerosis (ALS), a fatal and incurable neurodegenerative disease that effects 1 in 300 people. You will be based in the Brain Centre of University Medical Centre Utrecht (UMCU), an internationally recognized centre of excellence for ALS research and healthcare. Here, you will be integrated into an extensive research programme that spans bioinformatics, genetics, translational neuroscience, stem cell models, biobanks, environmental risk factors, neuroimaging, electrophysiology, advanced transcriptomics, patient care and clinical trials. UMCU / Utrecht University is consistently ranked among the top 15 universities in Europe (1st in Netherlands). The project supervisors have an extensive background in ALS, bioinformatics, human genetics and related topics (see publications by K. Kenna/ J.Veldink), and have led multiple high impact ALS gene discoveries and analyses of 10’s of thousands of patients and healthy controls (Nature Genetics x3, Neuron x2). The supervisors also act as the coordinating centre for project MinE: the world’s largest ALS whole genome sequencing initiative. You will work with state of the art facilities for genomics research, high performance computing (UMCU/SURFsara), postmortem tissue/blood biobanks and a strong network of local and international collaborators.
We are looking for a motivated candidate eager to engage in challenging high impact research. You are methodical and will have an interest in big data, complex problem solving and analytical thinking. All necessary training will be provided and we welcome applicants from any analytical discipline including but not limited to bioinformatics, genetics, neuroscience, data science, life sciences, mathematics, engineering. 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, machine learning, biostatistics and/or general programming (preferably any of R/python/keras/shiny/linux). Prior wetlab experience is not essential but is desirable, particularly if this relates to preparation of libraries for DNA/RNA sequencing (bulk/ single cell/ChIP).
The maximum salary for this position (100%) is € 3.103,00 gross per month based on full-time employment (work week 36 hours). This job is based on a temporary position for 1 jaar.
In addition, we offer an annual benefit of 8.3%, holiday allowance, travel expenses and career opportunities. The terms of employment are in accordance with the Cao University Medical Centers (UMC).
For more information contact Dr Kevin Kenna (K.P.Kenna@umcutrecht.nl). Applications should include a copy of your CV, a letter of motivation and contact details for 2 references. Please visit our website for more about the ALS centre (www.als-centrum.nl), project MinE (www.projectmine.com), UMCU (www.umcutrecht.nl/en/1) or genomics/ computational biology in Utrecht (https://ubc.uu.nl/).
If you have any questions about this vacancy, please contact Mr.K. Kenna, senior onderzoeker, phone number: 088-7568877, e‑mail adress: K.P.Kenna@umcutrecht.nl.
Acquisition based on this jobopening is not appreciated.