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Personal profile

Research profile

Maarten Merkx is full professor at the department of Biomedical Engineering of Eindhoven University of Techology (TU/e), where he leads the research group Protein Engineering operating at the interface of chemical biology and synthetic biology. An important research theme is to develop generic engineering concepts for the development of protein-based switches, which include fluorescent sensors for intracellular imaging of metal ions, photo-switchable proteins, and protein-based sensors for antibody detection. Combining protein engineering and DNA nanotechnology the group develops intelligent biomolecular sensors and switches for applications in intracellular imaging, optogenetics, point-of-care diagnostics and antibody-based therapies.

Academic background

Maarten Merkx studied physical organic chemistry and biochemistry at the Radboud University Nijmegen (1995, cum laude). He did his PhD with Prof. Averill (1999, University of Amsterdam) working on purple acid phosphatases, and was an HSFP post-doctoral fellow with Prof. Lippard (MIT, 1999-2001). Currently he is a professor in protein engineering at the Eindhoven University of Technology and a core member of the Institute for Complex Molecular Systems (ICMS). His group combines approaches from protein engineering, chemical biology, and synthetic biology to develop biomolecular sensors and actuators for applications in intracellular imaging, point-of-care diagnostics, optogenetics, and antibody-based therapies. An important research theme is the engineering of biomolecular switches, which include fluorescent and bioluminescent sensor proteins for intracellular imaging, photo-switchable proteins, and protein- and DNA-based sensors for antibody detection and actuation. He obtained young investigator grants from NWO (VIDI, 2006) and an ERC consolidator grant in 2011. In 2012 he received the award for the best TU/e teacher at the master's level.. Prof. Merkx has published 115+ research papers and is associate editor for ACS Sensors.


Proteins are highly efficient and sophisticated macromolecular machines that run life. By engineering new proteins with new functions we go beyond the already impressive functional diversity of natural proteins, critically testing our understanding of protein function and developing new applications for proteins in therapy and diagnosis.


External positions

associate editor ACS Sensors, American Chemical Society

1 Oct 2016 → …

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Research Output 1999 2019

DNA-functionalized supramolecular polymers: dynamic multicomponent assemblies with emergent properties

Wijnands, S. P. W., Meijer, E. W. & Merkx, M., 1 Jan 2019, In : Bioconjugate Chemistry.

Research output: Contribution to journalReview articleAcademicpeer-review

Open Access
Hybrid systems
4 Citations (Scopus)

Accelerating DNA-based computing on a supramolecular polymer

Engelen, W., Wijnands, S. P. W. & Merkx, M., 1 Aug 2018, In : Journal of the American Chemical Society. 140, 30, p. 9758-9767 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Networks (circuits)
Molecular Computers

An exciting year ahead for ACS sensors

Gooding, J. J., Mazur, A., Sailor, M., Merkx, M., Kelley, S., Tao, N., Long, Y. & Bakker, E., 26 Jan 2018, In : ACS Sensors. 3, 1, p. 1-2 2 p.

Research output: Contribution to journalEditorialAcademicpeer-review

Open Access
7 Citations (Scopus)

Controlling protein activity by dynamic recruitment on a supramolecular polymer platform

Wijnands, S. P. W., Engelen, W., Lafleur, R. P. M., Meijer, E. W. & Merkx, M., 2018, In : Nature Communications. 9, 65, 9 p., 65

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Personnel Selection
5 Citations (Scopus)

Dual-color bioluminescent sensor proteins for therapeutic drug monitoring of antitumor antibodies

van Rosmalen, M., Ni, Y., Vervoort, D. F. M., Arts, R., Ludwig, S. K. J. & Merkx, M., 6 Mar 2018, In : Analytical Chemistry. 90, 5, p. 3592-3599 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Antineoplastic Agents


Engineering protein switches: sensors and regulators for biology and diagnostics

Maarten Merkx (Recipient), 2011

Recognition: ERCStartingScientific

Protein Engineering
Synthetic Biology

Exploring the diagnostics market for simple and fast point-of-care antibody detection

Maarten Merkx (Recipient), 2013

Recognition: ERCProof of conceptScientific


Therapeutic antibody drug monitoring using bioluminescent sensors proteins and a smartphone

Maarten Merkx (Recipient), 2016

Recognition: ERCProof of conceptScientific

Luminescent Proteins
Drug Monitoring
Point-of-Care Systems
Biosimilar Pharmaceuticals



1/09/12 → …


Chemical biology



DBL Entering the lab

1/09/13 → …


iGEM project

1/09/14 → …


Molecular biosensing

1/09/15 → …


Student theses

19F MRI : methods and applications for quantitative molecular imaging

Author: Abdurrachim, D., 31 Oct 2008

Supervisor: Nicolaij, K. (Supervisor 1), Grüll, H. (Supervisor 2), Merkx, M. (Supervisor 2), Strijkers, G. (Supervisor 2), Lamerichs, R. M. (External coach), Yildirim, M. (External person) (External coach) & Kok, M. (Supervisor 2)

Student thesis: Master

Abeta-dendrimer complexes as well-defined amyloid oligomers

Author: IJsselstijn, L., 31 Jan 2006

Supervisor: van Baal, I. (Supervisor 1), Merkx, M. (Supervisor 2), Meijer, E. (Supervisor 2), van Genderen, M. (Supervisor 2) & Scheper, W. (External person) (Supervisor 2)

Student thesis: Master

Antibody detection based on a switchable reporter enzyme

Author: Aper, S., 29 Feb 2012

Supervisor: Banala, S. (Supervisor 1) & Merkx, M. (Supervisor 2)

Student thesis: Master

Antibody detection using FRET-based sensor proteins

Author: Kruis, I., 29 Feb 2012

Supervisor: Merkx, M. (Supervisor 1)

Student thesis: Master

Bioluminescent antibody conjugates for direct detection of analytes in solution

Author: van Aalen, E., 28 Mar 2019

Supervisor: Ni, Y. (Supervisor 1) & Merkx, M. (Supervisor 2)

Student thesis: Master