2024
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2023
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Moret, M., Pachon Angona, I., Cotos, L., Yan, S., Atz, K., Brunner, C., Baumgartner, M., Grisoni, F., 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
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Boldini, D., Grisoni, F., Kuhn, D., Friedrich, L., & Sieber, S. A., 2023. Practical guidelines for the use of gradient boosting for molecular property prediction. Journal of Cheminformatics, 15(1), 73. https://doi.org/10.1186/s13321-023-00743-7
Flaiz, M., Sousa, D.Z., 2023. Accelerate acetogenic bioproduction: acetogens as sustainable producers of biocommodities. Current Opinion in Systems Biology, 100500. https://doi.org/10.1016/j.coisb.2023.100500
Olavarria, K., Becker, M. V., Sousa, D.Z., van Loosdrecht, M.C., Wahl, S.A., 2023. Design and thermodynamic analysis of a pathway enabling anaerobic production of poly-3-hydroxybutyrate in Escherichia coli. Synthetic and Systems Biotechnology, 8(4), 629-639. https://doi.org/10.1016/j.synbio.2023.09.005
Diender, M., Dykstra, J.C., Parera Olm, I., Kengen, S.W., Stams, A J., Sousa, D Z., 2023. The role of ethanol oxidation during carboxydotrophic growth of Clostridium autoethanogenum. MicrobialBiotechnology, 16(11),2082-2093. https://doi.org/10.1111/1751-7915.14338
Parera Olm, I., 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), 1-17. https://doi.org/10.1186/s13068-023-02336-w
Liu, Q., Yang, S., Seitz, I., Pistikou, A.M.M., de Greef, T.F., Kostiainen, M.A., 2023. A Synthetic Protocell‐Based Heparin Scavenger. Small, 19(13), 2201790. https://doi.org/10.1002/smll.202201790
Bögels, B W., Nguyen, B.H., Ward, D., Gascoigne, L., et al., 2023. DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access. Nature Nanotechnology, 1-10. https://doi.org/10.1038/s41565-023-01377-4
Makri Pistikou, AM., Cremers, G.A.O., Nathalia, B.L. et al., 2023. Engineering a scalable and orthogonal platform for synthetic communication in mammalian cells. Nature Communications, 14: 7001. https://doi.org/10.1038/s41467-023-42810-5
Deckers, J., Anbergen, T., Hokke, A. M., de Dreu, A., et al., 2023. Engineering cytokine therapeutics. Nature Reviews Bioengineering, 1(4), 286-303. https://doi.org/10.1038/s44222-023-00057-1
Bartelds, M. W., García-Blay, Ó., Verhagen, P. G., Wubbolts, E. J., van Sluijs, B., Heus, H. A., … & Hansen, M. M., 2023. Noise Minimization in Cell-Free Gene Expression. ACS Synthetic Biology, 12(8), 2217-2225. https://doi.org/10.1021/acssynbio.3c00174
Leroy, C., Spelier, S., Essonghe, N.C., Poix, V., Kong, R., Gizzi, P., Bourban, C., Amand, S., Bailly, C., Guilbert, R. and Hannebique, D., 2023. Use of 2, 6-diaminopurine as a potent suppressor of UGA premature stop codons in cystic fibrosis. Molecular Therapy, 31(4), pp.970-985. https://doi.org/10.1016/j.ymthe.2023.01.014
De Poel, E., Spelier, S., Hagemeijer, M. C., van Mourik, P., Suen, S. W. F., Vonk, A. M., … & Beekman, J. M., 2023. FDA-approved drug screening in patient-derived organoids demonstrates potential of drug repurposing for rare cystic fibrosis genotypes. Journal of Cystic Fibrosis. 22(3):548-559. https://doi.org/10.1016/j.jcf.2023.03.004
Lefferts, J.W., Boersma, V., Hagemeijer, M.C., Hajo, K., Beekman, J.M., Splinter, E., 2023. Targeted Locus Amplification and Haplotyping. In: Peters, B.A., Drmanac, R. (eds) Haplotyping. Methods in Molecular Biology, vol 2590. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2819-5_2
Spelier, S., van Doorn, E. P., van der Ent, C. K., Beekman, J. M., & Koppens, M. A., 2023. Readthrough compounds for nonsense mutations: bridging the translational gap. Trends in Molecular Medicine. 29(4):297-314. https://doi.org/10.1016/j.molmed.2023.01.004
Rodenburg, L. W., Metzemaekers, M., van der Windt, I. S., Smits, S. M., et al., 2023. Exploring intrinsic variability between cultured nasal and bronchial epithelia in cystic fibrosis. Scientific Reports, 13(1), 18573. https://doi.org/10.1038/s41598-023-45201-4
Lefferts, J. W., Bierlaagh, M. C., Kroes, S., Nieuwenhuijze, N. D., Sonneveld van Kooten, et al., 2023. CFTR Function Restoration upon Elexacaftor/Tezacaftor/Ivacaftor Treatment in Patient-Derived Intestinal Organoids with Rare CFTR Genotypes. International Journal of Molecular Sciences, 24(19), 14539. https://doi.org/10.3390/ijms241914539
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Damstra, H. G., Passmore, J. B., Serweta, A. K., Koutlas, I., et al., Gelmap: intrinsic calibration and deformation mapping for expansion microscopy. Nature Methods, 20(10), 1573-1580. https://doi.org/10.1038/s41592-023-02001-y
Truong, M. A., Cané‐Gasull, P., de Vries, S. G., Nijenhuis, W., et al., 2023. A kinesin‐based approach for inducing chromosome‐specific mis‐segregation in human cells. The EMBO Journal, 42:e111559. https://doi.org/10.15252/embj.2022111559
2022
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
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 protocols, 4(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 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
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 Alliance, 5(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 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
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
2021
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