• 3573 Citations

Research output per year

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Personal profile


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.

Research profile

Maarten Merkx is full professor at the department of Biomedical Engineering of Eindhoven University of Technology (TU/e), where he leads the research group Protein Engineering operating at the interface of chemical biology and synthetic biology. His research 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.

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, a core member of the Institute for Complex Molecular Systems (ICMS) and dean of the department of Biomedical Engineering.


He obtained young investigator grants from NWO (VIDI 2006), an ERC Consolidator grant in 2011, and an ERC Proof of Concept grant in 2014 and 2017. As the only Dutch scientist he was invited in 2015 to speak at the World Economic forum in a session on the future of synthetic biology. In 2017 he reached the media with his expertise on DNA computing, amongst others an article on wired.com. In 2019 he received an NWO Take Off grant to map the commercial possibilities of his glow-in-the-dark paper-based assays for point-of-care diagnostics. Furthermore, he was awarded multiple times as best teacher in the master’s program, and received the award for the best TU/e teacher at the master level in 2012. In November 2019, he became the dean of the TU/e department of Biomedical Engineering.

External positions

associate editor ACS Sensors, American Chemical Society

1 Oct 2016 → …

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Research Output

Continuous small-molecule monitoring with a digital single particle switch

Yan, J., van Smeden, L., Merkx, M., Zijlstra, P. & Prins, M. W. J., 19 Mar 2020, In : ACS Sensors.

Research output: Contribution to journalArticleAcademicpeer-review

  • Engineered living materials based on adhesin-mediated trapping of programmable cells

    Guo, S., Dubuc, E., Rave, Y., Verhagen, M., Twisk, S. A. E., van der Hek, T., Oerlemans, G. J. M., van den Oetelaar, M. C. M., van Hazendonk, L. S., Brüls, M., Eijkens, B. V., Joostens, P. L., Keij, S. R., Xing, W., Nijs, M., Stalpers, J., Sharma, M., Gerth, M., Boonen, R. J. E. A., Verduin, K. & 3 others, Merkx, M., Voets, I. K. & De Greef, T. F. A., 20 Mar 2020, In : ACS Synthetic Biology. 9, 3, p. 475-485 11 p.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
  • 4 Downloads (Pure)

    Programmable bivalent peptide-DNA locks for pH-based control of antibody activity

    Engelen, W., Zhu, K., Subedi, N., Idili, A., Ricci, F., Tel, J. & Merkx, M., 22 Jan 2020, In : ACS Central Science. 6, 1, p. 22-31 10 p.

    Research output: Contribution to journalArticleAcademicpeer-review

    Open Access
  • 6 Downloads (Pure)

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

    Wijnands, S. P. W., Meijer, E. W. & Merkx, M., 17 Jul 2019, In : Bioconjugate Chemistry. 30, 7, p. 1905-1914 10 p.

    Research output: Contribution to journalReview articleAcademicpeer-review

    Open Access
  • 3 Citations (Scopus)
    40 Downloads (Pure)

    Engineering sensor proteins

    Merkx, M., Smith, B. D. & Jewett, M., 27 Dec 2019, In : ACS Sensors. 4, 12, p. 3089-3091 3 p.

    Research output: Contribution to journalEditorialAcademicpeer-review

    Open Access
    1 Downloads (Pure)


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

    M. Merkx (Recipient), 2013

    Prize: ERCProof of conceptScientific

  • Courses


    1/09/12 → …


    iGEM project

    1/09/14 → …


    Molecular biosensing

    1/09/15 → …


    Molecular biosensing



    Molecular cell biology

    1/09/13 → …


    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

    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

    Aß-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

    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