Selected publications

Here you can find selected scientific publications from the Dutch synthetic cell community.

Would you like to add a publication to this page? Please send an email with the publication details (title, authors, journal, publication date, and link) to SynCellNL@tudelft.nl

We welcome relevant publications from researchers affiliated with SynCellNL projects or institutions.

2026

Charlotte C. Koster, Henrique da Costa Oliveira, Fabian van Beveren, Joep Houkes, Jolien J.E. van Hooff, Thijs J.G. Ettema, John van der Oost and Nico J. Claassens
De novo design of synthetic microbial genomes
23 February 2026, Nature Reviews Bioengineering, Review Article
https://rdcu.be/e5jpX

Zainab M. Rashid, Misha Klein, Thor van Heesch, Salina Quack, Quinte Smitskamp, Pim P. B. America, Paula Rivas, Marvin A. Albers, Jannik Paulus, Jocelyne Vreede, Tom N. Grossmann, and David Dulin
TAV2b Peptide Derivatives Underwind and Stabilize Double-Stranded RNA upon Binding
20 February 2026, Journal of the American Chemical Society
https://doi.org/10.1021/jacs.5c18586

Ziyang Xiao, Arnab Das, Abha Jain, Thomas K. Anderson, Craig E. Cameron, Jamie J. Arnold, David Dulin and Robert N. Kirchdoerfer
Incorporation of arabinose-CTP and arabinose-UTP inhibits viral polymerases by inducing long pauses
January 2026, JBC Journal of Biological Chemistry, 302, 1
https://doi.org/10.1016/j.jbc.2025.111027

2025

Roman Barth, Richard Janissen, Laura Muras, Jaco van der Torre, Gabriele Litos, Eli van der Sluis, Ashmiani van den Berg, Iain F. Davidson, Jan-Michael Peters and Cees Dekker
Two CTCF motifs impede cohesin-mediated DNA loop extrusion
4 December 2025, Molecular Cell, 85, 4304–4317
https://doi.org/10.1016/j.molcel.2025.11.001

‍Cleij, C.V.
Building the genome of a minimal synthetic cell
18 September 2025, doctoral thesis, Delft University of Technology
https://doi.org/10.4233/uuid:bb76ad6b-e36e-4793-b1c9-54c0e6527ba7

Jawale, Y.K.
Building Minimal Spindles: Reconstituting spindle positioning in synthetic cells
12 September 2025, doctoral thesis, Delft University of Technology
https://doi.org/10.4233/uuid:f4e25106-cb82-4706-90b7-88800d45c8d2

Lorenzo Olivi, Stephan Köstlbacher, Christina Ludwig, Mees Langendoen, Nico J. Claassens, Thijs J. G. Ettema, John van der Oost, Pieter Rein ten Wolde, Johannes Hohlbein and Raymond H. J. Staals
The Escherichia coli replication initiator DnaA is titrated on the chromosome
21 August 2025, Nature Communications, 16, 7813
https://doi.org/10.1038/s41467-025-63147-1 ‍

Brian T. Analikwu, Alice Deshayes, Jaco van der Torre, Thomas M. Guérin, Allard J. Katan, Claire Béneut, Roman Barth, Jamie Phipps, Vittore Scolari, Xavier Veaute, Didier Busso, Karine Dubrana, Stefano Mattarocci, Cees Dekker and Stéphane Marcand, Alex Joesaar, Martin Holub, Leander Lutze, Marco Emanuele, Jacob Kerssemakers, Martin Pabst and Cees Dekker
Telomeres stall DNA loop extrusion by condensin
22 July 2025, Cell Reports, 44, 115900
https://doi.org/10.1016/j.celrep.2025.115900

Dmitrii Linnik and Bert Poolman
Spatiotemporal organization of the bacterial cytoplasm
17 July 2025, Current Opinion in Microbiology, 87:102635, Review
https://doi.org/10.1016/j.mib.2025.102635

Reinhardt, M.
Quantifying the Flow of Information
13 June 2025, doctoral thesis, Vrije Universiteit Amsterdam
https://doi.org/10.5463/thesis.1092

‍M. Klein, A. Das, S. C. Bera, T. K. Anderson, D. Kocincova, H. W. Lee, B. Wang, F. S. Papini, J. C. Marecki, J. J. Arnold, C. E. Cameron, K. D. Raney, I. Artsimovitch, M. Gotte, R. N. Kirchdoerfer, M. Depken and D. Dulin
A post-assembly conformational change makes the SARS-CoV-2 polymerase elongation-competent
10 June 2025, Nucleic Acids Research, 53, 10, gkaf450
https://doi.org/10.1093/nar/gkaf450

Ettema, T.
Structural and functional characterization of the antimicrobial peptide transporter SbmA
10 June 2025, doctoral thesis, University of Groningen
https://doi.org/10.33612/diss.1307107299

Marijn van den Brink, Timotheus Y. Althuis, Christophe Danelon and Nico J. Claassens
MOSAIC: A Highly Efficient, One-Step Recombineering Approach to Plasmid Editing and Diversification
5 June 2025, ACS Synthetic Biology
https://doi.org/10.1021/acssynbio.4c00657

‍Simona Della Valle, Enrico Orsi, Sjoerd C.A. Creutzburg, Luc F.M. Jansen, Evangelia-Niki Pentari, Chase L. Beisel, Harrison Steel, Pablo I. Nikel, Raymond H.J. Staals, Nico J. Claassens, John van der Oost, Wei E. Huang and Constantinos Patinios
Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system
June 2025, Trends in Biotechnology, 43, 6, 1470-1491 deze staat wel online, maar op een datum in maart
https://doi.org/10.1016/j.tibtech.2025.02.006

‍Bogatyr, V.
Light & Sound: a study on building blocks for bottum-up synthetic cells
10 April 2025, doctoral thesis, Vrije Universiteit Amsterdam
https://doi.org/10.5463/thesis.1042

Caterina Presutti, Edo Vreeker, Sajitha Sasidharan, Zanetta Ferdinando, Marc Stuart, Joanna Juhaniewicz-Dębińska, Giovanni Maglia, Wouter H. Roos and Bert Poolman
Balancing Permeability and Stability: A Study of Hybrid Membranes for Synthetic Cells Using Lipids and PBd-b-PEO Block Copolymers
8 April 2025, Biomacromolecules, 26, 5, 2868-2881
https://doi.org/10.1021/acs.biomac.4c01651

Olga Rook, Hub Zwart and Marileen Dogterom
Public attitudes to potential synthetic cells applications: Pragmatic support and ethical acceptance
27 February 2025, PLoS ONE, 20(2): e0319337
https://doi.org/10.1371/journal.pone.0319337

Alex Joesaar, Martin Holub, Leander Lutze, Marco Emanuele, Jacob Kerssemakers, Martin Pabst and Cees Dekker
A microfluidic platform for extraction and analysis of bacterial genomic DNA
23 February 2025, Lab on a chip
https://doi.org/10.1039/d4lc00839a

Roman Barth, Iain F. Davidson, Jaco van der Torre, Michael Taschner, Stephan Gruber, Jan-Michael Peters, Cees Dekker
SMC motor proteins extrude DNA asymmetrically and can switch directions
06 February 2025, Cell, 188, 749-763
https://doi.org/10.1016/j.cell.2024.12.020

Nicola De Franceschi, Alberto Blanch-Jover and Cees Dekker
Interaction hierarchy among Cdv proteins drives recruitment to membrane necks
16 January 2025, eLife, 1-19
https://doi.org/10.7554/eLife.104226.1.sa4

Holub, M.
Single-chromosome biophysics
8 January 2025, doctoral thesis, Delft University of Technology
https://doi.org/10.4233/uuid:08912541-02f4-44af-b8a6-c3b7a3647f17

Vadim G. Bogatyr and Gijs J. L. Wuite
Challenges in observing transcription–translation for bottom-up synthetic biology
3 January 2025, QRB Discovery, 6: e5, 1-9
https://doi.org/10.1017/qrd.2024.27

For publications published before 2025, please visit the BaSyC website.