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Grisoni, F., 2023. Chemical language models for de novo drug design: Challenges and opportunities. Current Opinion in Structural Biology79, p.102527. https://doi.org/10.1016/j.sbi.2023.102527

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 Bioengineering1(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 Communications14(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 Modeling62(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 modeling62(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 Bioproducts16(1), pp.1-17.  https://doi.org/10.1186/s13068-023-02336-w

Rodenburg, L.W., van der Windt, I.S., Dreyer, H.H., Smits, S.M., den Hertog-Oosterhoff, L.A., Aarts, E.M., Beekman, J.M. and Amatngalim, G.D., 2023. Protocol for generating airway organoids from 2D air liquid interface-differentiated nasal epithelia for use in a functional CFTR assay. STAR protocols4(3), p.102337. https://doi.org/10.1016/j.xpro.2023.102337

De Poel, E., Spelier, S., Hagemeijer, M.C., van Mourik, P., Suen, S.W.F., Vonk, A.M., Brunsveld, J.E., Ithakisiou, G.N., Kruisselbrink, E., Oppelaar, H. and Berkers, G., 2023. FDA-approved drug screening in patient-derived organoids demonstrates potential of drug repurposing for rare cystic fibrosis genotypes. Journal of Cystic Fibrosis. https://doi.org/10.1016/j.jcf.2023.03.004

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 biology11(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 Communications13(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 Factories21(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 Microbiology88(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 Biology32(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. Elife11, 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 science134(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 Biology71, 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

Amatngalim, G.D., Rodenburg, L.W., Aalbers, B.L., Raeven, H.H., Aarts, E.M., Sarhane, D., Spelier, S., Lefferts, J.W., Silva, I.A., Nijenhuis, W. and Vrendenbarg, S., 2022. Measuring cystic fibrosis drug responses in organoids derived from 2D differentiated nasal epithelia. Life Science Alliance5(12). DOI: 10.26508/lsa.202101320

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 Biology221(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

Rodenburg, L.W., Delphiano, L., Railean, V., Centeio, R., Pinto, M.C., Smits, S.M.A., van der Windt, I.S., van Hugten, C.F.J., van Beuningen, S.F.B., Rodenburg, R.N.P., van der Ent, C.K., Amaral, M.D., Kunzelmann, K., Gray, M.A., Beekman, J.M., Amatngalim, G.D., 2022. Drug Repurposing for Cystic Fibrosis: Identification of Drugs that Induce CFTR-Independent Fluid Secretion in Nasal Organoids. International Journal of Molecular Sciences, 23(20), 12657; https://doi.org/10.3390/ijms232012657  

Spelier, S., de Poel, E., Ithakisiou, G.N., Suen, S.W.F., Hagemeijer, M.C., Muilwijk, D., Vonk, A.M., Brunsveld, J.E., Kruisselbrink, E., van der Ent, C.K., Beekman, J.M., 2022. High-Throughput Functional Assay in Cystic Fibrosis Patient-Derived Organoids Allows Drug Repurposing. ERJ Open Research, https://doi.org/10.1183/23120541.00495-2022

Passmore, Josiah B., Wilco Nijenhuis, and Lukas C. Kapitein. “From observing to controlling: Inducible control of organelle dynamics and interactions.” Current Opinion in Cell Biology 71 (2021): 69-76. https://doi.org/10.1016/j.ceb.2021.02.002

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

Cremers, Glenn AO, Bas JHM Rosier, Ab Meijs, Nicholas B. Tito, Sander MJ van Duijnhoven, Hans van Eenennaam, Lorenzo Albertazzi, and Tom FA de Greef. “Determinants of ligand-functionalized DNA nanostructure-cell interactions.” bioRxiv (2021). https://pubs.acs.org/doi/10.1021/jacs.1c02298

Chen, Fangrui, Jingchao Wu, Malina K. Iwanski, Daphne Jurriens, Arianna Sandron, Milena Pasolli, Gianmarco Puma et al. “Centriole-independent centrosome assembly in interphase mammalian cells.” bioRxiv (2021). https://doi.org/10.1101/2021.08.22.457259

Amatngalim, Gimano D., Lisa W. Rodenburg, Bente L. Aalbers, Henriette HM Raeven, Ellen M. Aarts, Iris AL Silva, Wilco Nijenhuis et al. “CFTR modulator response measurements in subjects with cystic fibrosis using 2D differentiated nasal epithelia converted into spheroids.” bioRxiv (2021). https://doi.org/10.1101/2021.07.20.453105