PhD/postdoc in multimodal machine learning for molecular maps of human tissue

TU Delft
Intelligent Systems - Pattern Recognition and Bioinformatics
Netherlands Delft


There is a position available for either a PhD candidate or a postdoctoral researcher in TU Delft's computational team of HuBMAP: the international Human BioMolecular Atlas Program funded by the US National Institutes of Health (NIH). Our team at the TU Delft is one of three participating European partners amongst all 50 funded institutions.

The HuBMAP project: Deciphering the functioning of organs and tissues is crucial to advance our understanding of human health, as well as the diagnosis and treatment of disease. Such intricate biological functions result from the specialization, interaction, and spatial organization of all 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. The goal of HuBMAP is to drive the development of this methodology to molecularly map healthy cells in human tissue.

Your role: You will do research on multimodal machine learning methodology to discover and leverage patterns across heterogeneous high-throughput 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, spatial and temporal.
- Recognition of coherent and contrasting/differential patterns.
- Supervised learning of cell types and tissue structures based on molecular content.
- Interpretability of multimodal pattern recognition and prediction models.

Your embedding and collaborations: This position is in the Gonçalves lab at the TU Delft, whose research focuses on algorithmics and machine learning for precision biomedicine. We are part of the Pattern Recognition and Bioinformatics section of the Intelligent Systems department, providing direct and abundant access to experts in the field of machine learning. We actively collaborate with biomedical research teams on various topics, and are also part of initiatives like Convergence for Health and Technology. Within HuBMAP, our team works in close collaboration with the Spraggins lab at Vanderbilt University (U.S.), developing experimental protocols and generating the molecular profiles of human tissue. This will enable you to gain hands-on experience with unique and exciting data from the latest technologies, including sequencing-based spatial transcriptomics and imaging mass spectrometry. In this project we also collaborate with the Van de Plas lab at the TU Delft, with extensive expertise on computational imaging mass spectrometry and fusion across molecular imaging modalities.

Conditions of employment
TU Delft offers PhD-candidates a 4-year contract, with an official go/no go progress assessment after one year. Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities, increasing from € 2434 per month in the first year to € 3111 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 position the TU Delft offers a 2 years contract. Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities (Scale 10 € 2836 - € 4474).

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 we offer the Coming to Delft Service and Partner Career Advice to assist you with your relocation.

TU Delft (Delft University of Technology)
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 and aim to be as inclusive as possible (see our Code of Conduct). Together, we imagine, invent and create solutions using technology to have a positive impact on a global scale. Challenge. Change. Impact!

Faculty Electrical Engineering, Mathematics and Computer Science
The Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) brings together three disciplines - electrical engineering, mathematics and computer science. Combined, they reinforce each other and are the driving force behind the technology we use in our daily lives. Technology such as the electricity grid, which our faculty is helping to make future-proof. We are also working on a world in which humans and computers reinforce each other. We are mapping out disease processes using single cell data, and using mathematics to simulate gigantic ash plumes after a volcanic eruption. There is plenty of room here for ground-breaking research. We educate innovative engineers and have excellent labs and facilities that underline our strong international position. In total, more than 1,100 employees and 4,000 students work and study in this innovative environment.


For a PhD candidate position, 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 will be 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.

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

Start date

As soon as possible

How to Apply

Application procedure
Are you interested in this vacancy? Please apply no later than November 3, 2021 via the following website:

Do not forget to include 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.


Joana Gonçalves