• 4904 Citations
20052019
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Personal profile

Research profile

Tom de Greef is Associate Professor of Synthetic Biology in the department of Biomedical Engineering. Work in the Synthetic Biology group (7 PhD students, 2 post-docs) is directed at the bottom-up construction of basic cellular functions from well-characterized biological components, and the development of novel biological computing devices that can enhance signal-processing capabilities of natural and synthetic cells. This involves the design and construction of integrated genetic, protein or DNA-based circuits, either in a cell-free environment or in living cells, capable of autonomously performing useful functions. To achieve this goal, a multidisciplinary approach is employed that combines elements from DNA/RNA nanotechnology, genetic engineering, microengineering and the modelling and simulation of biomolecular networks. Ultimately, advances in synthetic biology will allow the development of functional living and hybrid technologies such as biological robots, synthetic cells or augmented natural cells, that can be interfaced with the human body to detect disease biomarkers and allow autonomous, closed-loop therapeutic functions. 

Academic background

Tom de Greef studied Biomedical Engineering at Eindhoven University of Technology (TU/e, the Netherlands), where he received his MSc degree cum laude in 2004. He then started his PhD research at the TU/e department of Chemical Engineering and Chemistry, where he graduated in 2008 on a thesis on novel polymeric materials based on quadruple hydrogen-bonding motifs, supervised by professors E. W. (Bert) Meijer and Rint Sijbesma. He subsequently moved to the Computational Biology group at the TU/e department of Biomedical Engineering (TU/e) headed by Prof. Peter Hilbers, for postdoctoral research on self-assembling systems from a computational perspective. In 2010, he became assistant professor and in 2016 he was promoted to associate professor. In 2013, Tom de Greef was a visiting scholar in the group of Prof. David Weitz at Harvard University (Cambridge, USA), working on protein affinity screening using droplet microfluidics.

In 2012 and 2013 the Netherlands Organization of Scientific Research (NWO) awarded him a VENI grant and an ECHO-STIP grant, respectively. In 2015 he received an ERC starting Grant and in 2016 an NWO VIDI grant. Tom de Greef is a core member of the Institute for Complex Molecular Systems (ICMS), a core member of the Dutch Gravitation program "Functional Molecular Systems" and a junior faculty member of the Gravitation program "Materials-Driven Regeneration". He received the 2017 Cram Lehn Pedersen prize in supramolecular chemistry, and in 2018 he was awarded a Microsoft PhD scholarship for the development of a DNA computer.

Quote

"When we learn to control the flow of biological information and use it to our advantage, we will reach the pinnacle of the Information Age."

External positions

Visiting Scholar, Harvard University

1 Apr 201310 Oct 2013

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Research Output 2005 2019

A multilayer microfluidic platform for the conduction of prolonged cell-free gene expression

van der Linden, A., Pieters, P., Yelleswarapu, M., Swank, Z., Huck, W. T. S., Maerkl, S. & de Greef, T., 2019, (Accepted/In press) In : Journal of Visualized Experiments (JoVE).

Research output: Contribution to journalArticleAcademicpeer-review

File
Lab-On-A-Chip Devices
Microfluidics
Transcription
Gene expression
Multilayers
2 Citations (Scopus)
Open Access
File
Transcription
Telecommunication networks
Communication
Cells
Networks (circuits)

Counterion dependent mechanisms of DNA origami nanostructure stabilization revealed by atomistic molecular simulation

Roodhuizen, J., Hendrikx, P. J. T. M., Hilbers, P. A. J., de Greef, T. & Markvoort, B., 2019, (Accepted/In press) In : ACS Nano.

Research output: Contribution to journalArticleAcademicpeer-review

3 Citations (Scopus)

DNA-based communication in populations of synthetic protocells

Joesaar, A. H., Yang, S., Bögels, B. W. A., van der Linden, A. J., Pieters, P. A., Kumar, P., Dachau, N., Phillips, A., Mann, S. & de Greef, T. F. A., 1 Apr 2019, In : Nature Nanotechnology. 14, p. 369-378

Research output: Contribution to journalArticleAcademicpeer-review

DNA
deoxyribonucleic acid
communication
Communication
Networks (circuits)

Pathway control in cooperative vs. anti-cooperative supramolecular polymers

Herkert, L., Droste, J., Kartha, K. K., Korevaar, P. A., de Greef, T. F. A., Hansen, M. R. & Fernández, G., 5 Aug 2019, In : Angewandte Chemie - International Edition. 58, 33, p. 11344-11349

Research output: Contribution to journalArticleAcademicpeer-review

File
Polymers
Self assembly
Functional materials
Solubility
Monomers

Prizes

COST Action CM0703

Tom de Greef (Recipient), 2011

Recognition: OtherDiscipline relatedProfessional

Cram Lehn Pedersen Prize

Tom de Greef (Recipient), 2017

Recognition: OtherDiscipline relatedScientific

Supramolecular chemistry

Microsoft PhD Scholarship

Tom de Greef (Recipient), 2018

Recognition: OtherScholarshipsScientific

NWO Veni Award : Folding and aggregation in biohybrid macromolecules

Tom de Greef (Recipient), 2012

Recognition: NWOVeniScientific

Macromolecules
Self assembly
Agglomeration
Polymers
Mathematical models
Synthetic Biology

Courses

Chemical biology

1/09/1331/08/19

Course

iGEM project

1/09/14 → …

Course

Introduction Organic Chemistry

1/09/12 → …

Course

Project Computational biology

1/09/14 → …

Course

Press / Media

Record number of seven Vidi grants at TU/e of which three at ICMS

Tom de Greef & Patricia Dankers

30/05/17

1 item of media coverage

Press/Media: Expert Comment

Definition Of Cohesion In Biology

Bart Markvoort & Tom de Greef

26/04/17

1 item of media coverage

Press/Media: Expert Comment

Resolution Definition Biology

Bart Markvoort & Tom de Greef

26/04/17

1 item of media coverage

Press/Media: Expert Comment

What Does Atp Mean In Biology

Bart Markvoort & Tom de Greef

26/04/17

1 item of media coverage

Press/Media: Expert Comment

Gold medal for TU/e iGEM team

Tom de Greef & Luc Brunsveld

20/10/15

1 item of media coverage

Press/Media: Expert Comment

Student theses

A microfluidic toolbox for supramolecular chemistry and chemical biology

Author: Rosier, B., 31 Oct 2014

Supervisor: de Greef, T. (Supervisor 1) & Meijer, E. (Supervisor 2)

Student thesis: Master

Cationic stabilization of DNA origami investigated through atomistic simulations

Author: Hendrikx, P., 29 Nov 2018

Supervisor: Roodhuizen, J. (Supervisor 1), Markvoort, B. (Supervisor 2), de Greef, T. (Supervisor 2) & Hilbers, P. (Supervisor 2)

Student thesis: Master

Coupling of an enzymatic actuator to an oscillating PEN-based DNA network

Author: Nijenhuis, M., 25 Jan 2018

Supervisor: Meijer, L. (Supervisor 1), de Greef, T. (Supervisor 2) & Hilbers, P. (Supervisor 2)

Student thesis: Master

Creating a non-linear response in dCas9-based gene repression: tuning the sgRNA concentration with the use of enzymatic coupled degradation

Author: Uittenbogaard, P., 20 May 2019

Supervisor: Hilbers, P. (Supervisor 1), de Greef, T. (Supervisor 2), Ottmann, C. (Supervisor 2) & Dubuc, E. (Supervisor 2)

Student thesis: Master

Design of a DNA-based tension probe for the quantification of cellular traction forces at a molecular level

Author: van der Putten, C., 25 Jan 2018

Supervisor: Kurniawan, N. (Supervisor 1), de Greef, T. (Supervisor 2) & Bouten, C. (Supervisor 2)

Student thesis: Master