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Ballarotto, M., Willems, S., Stiller, T., Nawa, F., Marschner, J.A., Grisoni, F. and Merk, D., 2023. De Novo Design of Nurr1 Agonists via Fragment-Augmented Generative Deep Learning in Low-Data Regime. Journal of Medicinal Chemistry. https://doi.org/10.1021/acs.jmedchem.3c00485

Deckers, J., Anbergen, T., Hokke, A.M., de Dreu, A., Schrijver, D.P., de Bruin, K., Toner, Y.C., Beldman, T.J., Spangler, J.B., de Greef, T.F. and Grisoni, F., 2023. Engineering cytokine therapeutics. Nature Reviews Bioengineering, 1(4), pp.286-303. https://doi.org/10.1038/s44222-023-00030-y

Moret, M., Pachon Angona, I., Cotos, L., Yan, S., Atz, K., Brunner, C., Baumgartner, M., Grisoni, F. and Schneider, G., 2023. Leveraging molecular structure and bioactivity with chemical language models for de novo drug design. Nature Communications, 14(1), p.114. https://doi.org/10.1038/s41467-022-35692-6

Özçelik, R., van Tilborg, D., Jiménez-Luna, J. and Grisoni, F., 2023. Structure‐based Drug discovery with Deep Learning. ChemBioChem, p.e202200776. https://doi.org/10.1002/cbic.202200776

van Tilborg, D., Alenicheva, A. and Grisoni, F., 2022. Exposing the limitations of molecular machine learning with activity cliffs. Journal of Chemical Information and Modeling, 62(23), pp.5938-5951. https://doi.org/10.1021/acs.jcim.2c01073

Moret, M., Grisoni, F., Katzberger, P. and Schneider, G., 2022. Perplexity-based molecule ranking and bias estimation of chemical language models. Journal of chemical information and modeling, 62(5), pp.1199-1206. https://doi.org/10.1021/acs.jcim.2c00079

Truong, M.A., Cané‐Gasull, P., de Vries, S.G., Nijenhuis, W., Wardenaar, R., Kapitein, L.C., Foijer, F. and Lens, S.M., 2023. A kinesin‐based approach for inducing chromosome‐specific mis‐segregation in human cells. The EMBO Journal, p.e111559. https://doi.org/10.15252/embj.2022111559

Parera Olm, I. and Sousa, D.Z., 2023. Upgrading dilute ethanol to odd-chain carboxylic acids by a synthetic co-culture of Anaerotignum neopropionicum and Clostridium kluyveri. Biotechnology for Biofuels and Bioproducts, 16(1), pp.1-17.  https://doi.org/10.1186/s13068-023-02336-w

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Liu, Q., Yang, S., Seitz, I., Pistikou, A.M.M., de Greef, T.F.A. and Kostiainen, M.A., 2022. A Synthetic Protocell‐Based Heparin Scavenger. Small, p.2201790. https://doi.org/10.1002/smll.202201790

van der Linden, A.J., Pieters, P.A., Bartelds, M.W., Nathalia, B.L., Yin, P., Huck, W.T., Kim, J. and de Greef, T.F.A., 2022. DNA Input Classification by a Riboregulator-Based Cell-Free Perceptron. ACS synthetic biology, 11(4), pp.1510-1520.  https://doi.org/10.1021/acssynbio.1c00596

Yang, S., Joesaar, A., Bögels, B.W., Mann, S. and de Greef, T.F.A., 2022. Protocellular CRISPR/Cas‐Based Diffusive Communication Using Transcriptional RNA Signaling. Angewandte Chemie International Edition, p.e202202436. https://doi.org/10.1002/anie.202202436

van Sluijs, B., Maas, R.J., van der Linden, A.J., de Greef, T.F.A. and Huck, W.T., 2022. A microfluidic optimal experimental design platform for forward design of cell-free genetic networks. Nature Communications, 13(1), pp.1-11. https://doi.org/10.1038/s41467-022-31306-3

Benito-Vaquerizo, S., Parera Olm, I., de Vroet, T., Schaap, P.J., Sousa, D.Z., Martins dos Santos, V.A. and Suarez-Diez, M., 2022. Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. Microbial Cell Factories, 21(1), pp.1-18. https://doi.org/10.1186/s12934-022-01841-1

Doloman, A., Boeren, S., Miller, C.D. and Sousa, D.Z., 2022. Stimulating Effect of Trichococcus flocculiformis on a Coculture of Syntrophomonas wolfei and Methanospirillum hungatei. Applied and Environmental Microbiology, 88(13), pp.e00391-22. https://doi.org/10.1128/aem.00391-22

Meiring, J.C., Grigoriev, I., Nijenhuis, W., Kapitein, L.C. and Akhmanova, A., 2022. Opto-katanin, an optogenetic tool for localized, microtubule disassembly. Current Biology, 32(21), pp.4660-4674. https://doi.org/10.1016/j.cub.2022.09.010

Chen, F., Wu, J., Iwanski, M.K., Jurriens, D., Sandron, A., Pasolli, M., Puma, G., Kromhout, J.Z., Yang, C., Nijenhuis, W. and Kapitein, L.C., 2022. Self-assembly of pericentriolar material in interphase cells lacking centrioles. Elife, 11, p.e77892. https://doi.org/10.7554/eLife.77892

Truong, M.A., Cané-Gasull, P., de Vries, S.G., Nijenhuis, W., Wardenaar, R., Kapitein, L.C., Foijer, F. and Lens, S.M., 2022. A motor-based approach to induce chromosome-specific mis-segregations in human cells. bioRxiv. https://doi.org/10.1101/2022.04.19.488790

Janssen, A.F., Korsten, G., Nijenhuis, W., Katrukha, E.A. and Kapitein, L.C., 2021. Direct observation of aggregate-triggered selective autophagy in human cells. Journal of cell science, 134(19), p.jcs258824. https://doi.org/10.1242/jcs.258824

Passmore, J.B., Nijenhuis, W. and Kapitein, L.C., 2021. From observing to controlling: Inducible control of organelle dynamics and interactions. Current Opinion in Cell Biology, 71, pp.69-76. https://doi.org/10.1016/j.ceb.2021.02.002

Nijenhuis, W., Damstra, H.G., van Grinsven, E.J., Iwanski, M.K., Praest, P., Soltani, Z.E., van Grinsven, M.M., Brunsveld, J.E., de Kort, T., Rodenburg, L.W. and de Jong, D.C., 2021. Optical nanoscopy reveals SARS-CoV-2-induced remodeling of human airway cells. BioRxiv. https://doi.org/10.1101/2021.08.05.455126

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Verweij, F.J., Bebelman, M.P., George, A.E., Couty, M., Bécot, A., Palmulli, R., Heiligenstein, X., Sirés-Campos, J., Raposo, G., Pegtel, D.M. and Van Niel, G., 2022. ER membrane contact sites support endosomal small GTPase conversion for exosome secretion. Journal of Cell Biology, 221(12), p.e202112032. ER membrane contact sites support endosomal small GTPase conversion for exosome secretion  https://doi.org/10.1083/jcb.202112032

Damstra, H.G.J., Passmore, J.B., Serweta, A.K., Koutlas, I., Burute, M., Meye, F.J., Akhmanova, A., Kapitein, L.C., 2022. GelMap: Intrinsic calibration and deformation mapping for expansion microscopy. bioRxiv. https://doi.org/10.1101/2022.12.21.521394

Zheng, S., de Buhr, H., Praest, P., Evers, E., Brak-Boer, I., van Grinsven., Longo, Y., de Vries, L., Nijenhuis, W., Kapitein, L.C., Beekman, J.M., Nijhuis, M., Drexler, I., Wiertz, E.J.H.J., Lebbink, R.J., 2022. The SARS-CoV-2 accessory factor ORF7A downregulates MHC class I surface expression. bioRxiv. https://doi.org/10.1101/2022.05.29.493850

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Pieters, Pascal A., Bryan L. Nathalia, Ardjan J. van der Linden, Peng Yin, Jongmin Kim, Wilhelm TS Huck, and Tom FA de Greef. “Cell-Free Characterization of Coherent Feed-Forward Loop-Based Synthetic Genetic Circuits.” ACS Synthetic Biology (2021). https://pubs.acs.org/doi/10.1021/acssynbio.1c00024

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