PhD position on iCELL: individualized CELLular models of disease diversity in the population

Excited about desigining computational methods to uncover genetic diversity in complex disease using large-scale cellular models of human donors? Read on and join us!

Every person has a unique genetic landscape, leading to individual variation in disease risk, treatment response, and other human-related phenotypes. Phenotypic diversity originates from an interplay between genetic and environmental factors, and optimal disease treatment or prevention for each individual requires a better understanding of the complex biology underlying this interplay.

The iCELL flagship consortium brings together computational scientists, molecular biologists, geneticists, and physicists with the goal of building a platform to develop large-scale individualized cellular models. These will be applied across the population to characterise (genetic) diversity among individuals in complex disease, initially focusing on DNA repair and fibrosis.

The iCELL project will use “village cultures”, where cells from many donors are co-cultured using homogeneous conditions, coupled with cellular/molecular profiling: high-throughput spatio-temporal imaging and single-cell RNA sequencing and proteomics. There will also be teams working on mimicking the natural environment of cells and tissues, to take into account intrinsic (genetic) and extrinsic (environmental) factors.

Your PhD research will focus on developing computational methods to uncover patterns of genetic and transcriptional variation associated with phenotypes or conditions of interest (e.g. exposure to ionizing radiation inducing DNA damage) from single-cell profiles of co-cultured iCELL populations. You will also develop strategies to integrate and analyze iCELL data together with multi-omics data from publicly available cohorts, focusing primarily on DNA repair and fibrosis.

You will be embedded in the research teams of Joana Gonçalves (https://goncalveslab.tudelft.nl, primary affiliation) and Joyce van Meurs (https://www.erasmusmc.nl/en/research/researchers/meurs-joyce-van), respectively in the Pattern Recognition & Bioinformatics section at Delft University of Technology (TUD) and the Molecular Genetics department at Erasmus Medical Center (EMC). You will work in close collaboration with both teams and will benefit from two vibrant research communities: on pattern recognition, algorithmics, machine learning, and bioinformatics at TUD; and on molecular genetics, biology, and bioinformatics at EMC.

Our extensive collaboration networks will further provide you with a rich and stimulating research environment, and first-hand experience with state of the art methodology. In addition to iCELL, the Gonçalves team is involved in relevant collaborations developing innovative technology and computational methods to learn new insight at the molecular level: e.g. knockout-CRISPR screens to link mutational signatures to DNA repair mechanisms (PROTON-DDR), synthetic lethality prediction models, and building of multimodal molecular atlases of different human tissues (HuBMAP, KPMP, Aging). 

The successful PhD candidate has a solid foundation in one or more of the following disciplines: algorithms and complexity, machine learning. Typically, this translates to a background in computer science or other exact sciences (physics, engineering). Extensive knowledge of biology is not required, but interest and willingness to learn will be essential to design meaningful methodology. Acquaintance with molecular biology, genetics, and bioinformatics methods for the analysis of high-throughput (single-cell) sequencing data are a plus. We require fluently spoken and written English. In addition, we are looking for creativity, critical thinking, rigour, independence, and good communication skills.

Doing a PhD at TU Delft requires English proficiency at a certain level to ensure that the candidate is able to communicate and interact well, participate in English-taught Doctoral Education courses, and write scientific articles and a final thesis. For more details please check the ://www.tudelft.nl/onderwijs/opleidingen/phd/admission">Graduate Schools Admission Requirements .

Doctoral candidates will be offered a 4-year period of employment in principle, but in the form of 2 employment contracts. An initial 1,5 year contract with an official go/no go progress assessment within 15 months. Followed by an additional contract for the remaining 2,5 years assuming everything goes well and performance requirements are met.

Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities, increasing from € 2541 per month in the first year to € 3247 in the fourth year. As a PhD candidate you will be enrolled in the TU Delft Graduate School. The TU Delft Graduate School provides an inspiring research environment with an excellent team of supervisors, academic staff and a mentor. The Doctoral Education Programme is aimed at developing your transferable, discipline-related and research skills.

The TU Delft offers a customisable compensation package, discounts on health insurance and sport memberships, and a monthly work costs contribution. Flexible work schedules can be arranged.

For international applicants, TU Delft has the Coming to Delft Service . This service provides information for new international employees to help you prepare the relocation and to settle in the Netherlands. The Coming to Delft Service offers a Dual Career Programme  for partners and they organise events to expand your (social) network.

Delft University of Technology is built on strong foundations. As creators of the world-famous Dutch waterworks and pioneers in biotech, TU Delft is a top international university combining science, engineering and design. It delivers world class results in education, research and innovation to address challenges in the areas of energy, climate, mobility, health and digital society. For generations, our engineers have proven to be entrepreneurial problem-solvers, both in business and in a social context.

At TU Delft we embrace diversity as one of our core values  and we actively engage  to be a university where you feel at home and can flourish. We value different perspectives and qualities. We believe this makes our work more innovative, the TU Delft community more vibrant and the world more just. Together, we imagine, invent and create solutions using technology to have a positive impact on a global scale. That is why we invite you to apply. Your application will receive fair consideration.

Challenge. Change. Impact!

The Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) brings together three scientific disciplines. Combined, they reinforce each other and are the driving force behind the technology we all use in our daily lives. Technology such as the electricity grid, which our faculty is helping to make completely sustainable and future-proof. At the same time, we are developing the chips and sensors of the future, whilst also setting the foundations for the software technologies to run on this new generation of equipment – which of course includes AI. Meanwhile we are pushing the limits of applied mathematics, for example mapping out disease processes using single cell data, and using mathematics to simulate gigantic ash plumes after a volcanic eruption. In other words: there is plenty of room at the faculty for ground-breaking research. We educate innovative engineers and have excellent labs and facilities that underline our strong international position. In total, more than 1000 employees and 4,000 students work and study in this innovative environment.

Click here  to go to the website of the Faculty of Electrical Engineering, Mathematics and Computer Science.

The application is ongoing until the position is filled, so interested candidates are encouraged to apply as soon as possible and no later than July 2, 2023. Applications submitted before the deadline will be given priority. Applicants submitting after the deadline may still be considered, if no suitable candidate has yet been found.

For more information about this vacancy, please contact Dr. Joana Gonçalves.

Are you interested in this vacancy? Please apply via the application button. Do not forget to include all the following documents:

The letter of application should summarise: (I) why you would like to do a PhD, (II) why you are interested in the project/topic/lab, (III) why your profile is suitable for the job, and (IV) what you hope to learn/achieve from the position. 

Please note:

• A pre-employment screening can be part of the selection procedure.
• You can apply online. We will not process applications sent by email and/or post.
• Please do not contact us for unsolicited services.