Your job in a nutshell
As a PhD student in Bioinformatics, you will leverage state-of-the-art machine learning and artificial intelligence to discover new molecular signatures that can be translated into reliable medical assays for diagnosis, prognosis, and treatment benefit prediction, and that will ultimately contribute to improved patient care.
This PhD position is part of the Oncode Accelerator (https://www.oncodeaccelerator.nl/). Oncode Accelerator is a public-private partnership funded by the Dutch National Growth Fund (NGF). The mission of this research program is to innovate and accelerate the development of new cancer therapies to address unmet clinical needs. The Oncode Accelerator hinges on three key platforms: well-defined patient cohorts, organoid models, and Artificial Intelligence.
In Work Package 7, you will advance patient stratification & personalized medicine. About half of phase 3 clinical trials fail, most often due to a lack of efficacy of the drug tested. However, trials that adopt a biomarker strategy (i.e. attempt to identify a subset of patients most likely to benefit) have a significantly higher success rate. To discover novel biomarkers, it is essential to exploit the large molecular datasets generated through pre-clinical models such as cell lines and organoids. To this end, you will use machine learning and artificial intelligence: i) to learn a consensus space to transfer drug response predictors from pre-clinical models to tumors, and ii) to identify treatment benefit biomarkers from patient data by training patient embeddings. In particular, you will investigate whether we can leverage foundation models pre-trained on these large-scale molecular datasets to improve and accelerate the discovery of novel biomarkers.
You will be working within the Department of Bioinformatics at SkylineDx and in Jeroen de Ridder’s group at the University Medical Center Utrecht (UMCU). At SkylineDx, you will interact with multidisciplinary teams: scientists, lab technicians, a clinical study team, software engineers, and the QA/RA department. In the de Ridder’s group, you will be embedded in a bioinformatics lab that creates and applies innovative data science methods to advance our understanding of disease biology and molecular medicine.
You have
- a MSc degree in Bioinformatics, or related fields. We specifically encourage you to apply if you have a background in quantitative disciplines.
- fundamental knowledge of statistics, machine learning, and artificial intelligence
- programming skills (R, MATLAB, Python, etc.) and shell scripting.
- keen interest in oncology and genomics.
- a service and result-oriented attitude.
- excellent communication and organization skills.
- intrinsic motivation to make a positive contribution to health care and provide solutions for patients.
- strong analytical skills and creative approach to problem-solving.
- an entrepreneurial mindset and can work in an environment with high-quality standards.
- an excellent command of written and spoken English.
We offer
- a full-time position (one year contract that can be extended up to 4 years), a market-competitive salary, and market-competitive secondary conditions of employment.
- opportunities for personal growth.
- the best of two worlds: joint appointments in a leading academic bioinformatics group and an innovative biotech company with an emphasis on clinical diagnostics
- the ability to serve society with science-based solutions.
At SkylineDx
We live to make a difference. It is our mission to improve a patient’s quality of life by enabling them to benefit from personal insights at the genomic level of their disease. That means we are continuously innovating the world of gene signature-based diagnostic testing. That also means we have a unique blend of characteristics. We have our soft side. Our culture is oftentimes described as familial, warm, loyal and highly engaged. We have our rational side where exact sciences are driving our mission. And when needed our passionate side surfaces to clear the way so we can serve society with science based solutions.
Our quotes
#serviceisjoy
#valueformoney
#playtogethertowin
#amazingthingshappen
#cogitoergosum
#itsyourparty
Do apply!
Send your resume and motivation letter to [email protected]. If you have questions or want more information, don’t hesitate to contact us. You’ll find the contact details on our website. We will make sure it lands on the right desk!
