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Rik Lindeboom

Quantitative Systems Biology

The Lindeboom lab uses quantitative biology to understand the interaction between tumor cells and the immune system. We use (single cell) genomics and proteomics approaches combined with advanced data analysis workflows, to measure exact amounts of cancer-associated molecules. This enables predictive and quantitative modeling of cancer cell behavior and the interaction with immune cells.

Vacancies
We welcome outstanding postdocs and PhD students to submit open applications, and invite master's students for internships of 6 months or longer. Interested candidates can contact Rik Lindeboom for more information.

Our research

Vacancies

Veni grant awarded!

August 2025

Excited to announce that Rik got awarded the Veni grant from NWO to investigate how changes in MYC concentration drive epigenetic remodeling and the transformation of healthy cells into cancer cells.

Baking pizza with the lab

August 2025

After a refreshing holiday break, the Lindeboom lab reunited for a cozy dinner at Rik’s place. With Davide sharing a taste of his heritage, we rolled up our sleeves and made delicious Neapolitan pizzas together; a perfect way to kick off the new academic year.

Ryan starts as a PhD student

July 2025

We are excited to announce that Ryan is joining this month as a PhD student in both the Vermeulen and Lindeboom group. Ryan brings extensive expertise in both computational and experimental proteomics. His work will focus on developing single-cell proteomics pipelines and applying them within the RADAR consortium to uncover insights into intratumoral heterogeneity in rare cancers. Welcome, Ryan!

Janne joins the lab

June 2025

After completing a Master’s degree in Cellular and Molecular Biotechnology at Wageningen University, Janne joined the Lindeboom lab as a PhD student in June 2025 to study transcription factor biology. Her project focuses on how changes in transcription factor concentration affect binding dynamics and epigenetic remodeling, with the aim of uncovering the molecular mechanisms underlying transcription factor–mediated gene expression regulation. We are pleased to welcome Janne to the team and look forward to her contributions.

ZonMW grant with Joo lab to study binding kinetics of antigens to MHC class II and T cell receptors

March 2025

We are grateful to have received the ZonMw Open Competition grant together with Chirlmin Joo at the TU Delft. In collaboration with the Joo lab, we will combine molecular engineering, single-molecule imaging, and genomics to investigate the binding kinetics of antigens to MHC class II and T cell receptors, with the ultimate goal of gaining a deeper understanding of CD4 T cell immunity in disease.

Lab outing: go-karting and spy training

February 2025

The Lindeboom lab outing started with a morning of scientific brainstorming, strategic planning, and updates on the financial status of the lab. In the afternoon, we competed for fasted lap in two heats of go-karting, after which we solved a murder as a team in an escape room. Concluding with dinner in Amsterdam, the first lab outing of the Lindeboom lab was a great success!

Shweta joined the lab as PhD student

January 2025

We are delighted to announce that Shweta Garg has joined us as a PhD student under the ERC-funded TF-KINETIX project.

With her strong foundation in molecular and cellular biology, and a keen interest in quantitative transcription factor biology, Shweta will contribute to uncovering how binding kinetics and energy landscapes of oncogenic transcription factors are regulated at genome- and proteome-wide scales. Her work will aim to develop predictive models that influence transcription factor binding to reprogram genome-wide binding.

We are excited to have Shweta on board and look forward to her contributions to this ambitious project. Welcome to the team, Shweta!

Young Investigator Grant

December 2024
We are incredibly grateful to have received the Young Investigator Grant from KWF Kankerbestrijding and Alpe d'HuZes! This grant will support our work on understanding how antigen presentation dynamics are regulated, with the goal of building quantitative models that enable us to select tumor antigens suitable for therapeutic targeting. We will apply these technologies to penile cancers, a very rare cancer type with many unknowns with regards to its immunogenicity, to study how these processes occur in penile cancers and identify penile tumor antigens.

Read more about the awarded KWF grants.

ERC Starting grant TF-KINETIX awarded to the Lindeboom Lab!

September 2024

Extremely happy and proud to announce that the lab will soon be ERC funded through the awarded ERC Starting grant TF-KINETIX.

In this project, we will set out to uncover how binding kinetics and energy landscapes of oncogenic transcription factors are regulated at genome- and proteome-wide scales!

Interested in joining this project? Enthusiastic and talented individuals that are interested in pursuing a PhD or post-doc in quantitative transcription factor biology are invited to apply via email or the vacancy tab at the NKI website.

Read more about this news in the NKI News and at the ERC website.

Fraser joins the lab as postdoctoral researcher

September 2024

We are happy to announce that Fraser has joined our research group this month.

He will start an exciting new project focused on profiling antigen-TCR interactions. Leveraging his experience in developing large-scale screening methodologies, Fraser aims to create a high-throughput screening platform to measure these interactions at massive scale. We warmly welcome Fraser to the team!