PhD or Postdoc multimodal machine learning for molecular maps of human tissue

Are you interested in machine learning for multimodal molecular analysis of human tissue? Join the TU Delft team and be part of this exciting international HuBMAP consortium!

There is a position available for either a PhD candidate or a postdoctoral researcher in TU Delft's computational team of a multi-grant consortium involved in multimodal molecular mapping and analysis of human tissue.

Deciphering the functioning of organs and tissues is crucial to advance our understanding of human health, as well as disease diagnosis and treatment. Such intricate biological functions result from the specialization, interaction, and spatial organization of cells into higher-order structures, tissues, and organs. Scientists estimate there are 37 trillion cells in an adult human body, each with its own rich molecular profile. Determining function and relations among these cells is therefore a significant undertaking requiring the development of advanced molecular biology technologies and computational methods. Our team further aims to accomplish this through deep integration of multimodal molecular profiles.

In this context, our team is one of few European partners involved in the following initiatives funded by the US National Institutes of Health (NIH):

• Human BioMolecular Atlas Program (HuBMAP), focusing on eye, pancreas, and kidney of healthy human donors.
• Kidney Precision Medicine Project (KPMP), focusing on kidney diseases.
• Aging Research, focusing on brain and Alzheimer's disease.

Your role: You will do research on multimodal machine learning methodology to discover and leverage patterns across high-throughput multimodal molecular profiles. Some topics of interest:

• Integration of measurements for different types of molecular species (using techniques such as transcriptomics, proteomics, and lipidomics).
• Multiscale analysis along various dimensions at different resolutions, e.g. spatial and temporal.
• Multimodal recognition of correlating and contrasting/differential patterns.
• Supervised learning, semi-supervised, and transfer learning of cell types and tissue structures based on molecular content.
• Cross-modality predictions.
• Interpretability of multimodal pattern recognition and prediction models.

Your embedding and collaborations: You'll be embedded in the Gonçalves lab at TU Delft (https://goncalveslab.tudelft.nl), whose research focuses on algorithmics and machine learning for computational biomedicine. We integrate the Pattern Recognition and Bioinformatics section in the Intelligent Systems department (EEMCS faculty), offering you ample access to experts in machine learning. Within the HuBMAP/KPMP/Aging grants, you will work in close collaboration with the Spraggins lab at Vanderbilt University (U.S.) and the Van de Plas lab at TU Delft. The Spraggings lab develops experimental protocols to generate high-quality molecular profiles of human tissue, and the Van de Plas lab does research on computational imaging mass spectrometry and fusion across molecular imaging modalities.

Next to the HuBMAP/KPMP/Aging initiatives, the Gonçalves' lab is involved in other collaborative initiatives developing innovative technology and computational methods to learn new insight from molecular profiles: e.g. knockout-CRISPR screens to link mutational signatures to DNA repair mechanisms (PROTON-DDR), synthetic lethality prediction models, and multi-donor 'village' cultures and single-cell profiling as a platform to study and screen genetic and environmental causes of phenotypic diversity at a large-scale (iCELL Convergence Flagship). This provides for a rich and stimulating research environment where you'll be able to acquire first-hand experience with state of the art methodology.

For the PhD:

The successful 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 related. Extensive knowledge of biology is not required, but interest and willingness to learn are essential to design meaningful methodology. We require fluently spoken and written English. In addition, we are looking for creativity, critical thinking, rigour, independence, ability to work in a team, 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 Graduate Schools Admission Requirements .

For the Postdoc:

The candidate meets all the requirements above and also holds a PhD in computer science, data science, machine learning, or related. In addition, the successful candidate has expertise in Bioinformatics, including the processing and analysis of high-dimensional molecular biology data generated using sequencing technologies.

For the PhD:

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 € 2.541 per month in the first year to € 3.247 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.

For the Postdoc:

TU Delft initially offers a 1-year contract, with the possibility of extending up to 3 or 4 years based on performance. Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities (based on scale 10: € 2.960 - € 4.670).

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:

• Letter of application
• CV
• List of publications, when available
• Academic transcripts (both MSc and BSc degrees)
• MSc thesis (for PhD candidate), or PhD thesis (for postdoc candidate)
• Names and contact details of two references (telephone number and email)

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