2024

Korsten, G. and Kapitein, L.C., 2024. Studying Selective Autophagy of Protein Aggregates Using Particles Induced by Multimerization (PIMs). In Selective Autophagy: Methods and Protocols (pp. 95-108). New York, NY: Springer US. https://doi.org/10.1007/978-1-0716-4067-8_8

Korsten, G., Osinga, M., Pelle, R.A., Serweta, A.K., Hoogenberg, B., Kampinga, H.H. and Kapitein, L.C., 2024. Nuclear poly-glutamine aggregates rupture the nuclear envelope and hinder its repair. Journal of Cell Biology, 223(11), p.e202307142. https://doi.org/10.1083/jcb.202307142

Yang, S., Bögels, B.W., Wang, F., Xu, C., Dou, H., Mann, S., Fan, C. and de Greef, T.F., 2024. DNA as a universal chemical substrate for computing and data storage. Nature Reviews Chemistry, 8(3), pp.179-194. https://doi.org/10.1038/s41570-024-00576-4

Özçelik, R., de Ruiter, S., Criscuolo, E. and Grisoni, F., 2024. Chemical language modeling with structured state space sequence models. Nature Communications, 15(1), p.6176. https://doi.org/10.1038/s41467-024-50469-9

van der Meel, R., Grisoni, F. and Mulder, W.J., 2024. Lipid discovery for mRNA delivery guided by machine learning. Nature Materials, 23(7), pp.880-881. https://doi.org/10.1038/s41563-024-01934-9

Doloman, A. and Sousa, D.Z., 2024. Mechanisms of microbial co-aggregation in mixed anaerobic cultures. Applied Microbiology and Biotechnology, 108(1), p.407. https://doi.org/10.1007/s00253-024-13246-8

van Tilborg, D., Brinkmann, H., Criscuolo, E., Rossen, L., Özçelik, R. and Grisoni, F., 2024. Deep learning for low-data drug discovery: hurdles and opportunities. Current Opinion in Structural Biology, 86, p.102818. https://doi.org/10.1016/j.sbi.2024.102818

Besteman, M.S., Doloman, A. and Sousa, D.Z., 2024. Transcriptomic evidence for an energetically advantageous relationship between Syntrophomonas wolfei and Methanothrix soehngenii. Environmental Microbiology Reports, 16(3), p.e13276. https://doi.org/10.1111/1758-2229.13276

Flaiz, M. and Sousa, D.Z., 2023. Accelerate acetogenic bioproduction: Acetogens as sustainable producers of biocommodities. Current Opinion in Systems Biology, p.100500. https://doi.org/10.1016/j.coisb.2023.100500

Boldini, D., Ballabio, D., Consonni, V., Todeschini, R., Grisoni, F. and Sieber, S.A., 2024. Effectiveness of molecular fingerprints for exploring the chemical space of natural products. Journal of Cheminformatics, 16(1), p.35. https://doi.org/10.1186/s13321-024-00830-3

Doloman, A., de Bruin, S., van Loosdrecht, M.C., Sousa, D.Z. and Lin, Y., 2024. Coupling extracellular glycan composition with metagenomic data in papermill and brewery anaerobic granular sludges. Water Research, 252, p.121240. https://doi.org/10.1016/j.watres.2024.121240

Yurchenko, A., Özkul, G., van Riel, N.A., van Hest, J.C. and de Greef, T.F., 2024. Mechanism-based and data-driven modeling in cell-free synthetic biology. Chemical Communications, 60(51), pp.6466-6475.https://doi.org/10.1039/d4cc01289e

Yang, S., Bögels, B.W., Wang, F., Xu, C., Dou, H., Mann, S., Fan, C. and de Greef, T.F., 2024. DNA as a universal chemical substrate for computing and data storage. Nature Reviews Chemistry, pp.1-16. https://doi.org/10.1038/s41570-024-00576-4

Egas, R.A., Sahonero‐Canavesi, D.X., Bale, N.J., Koenen, M., Yildiz, Ç., Villanueva, L., Sousa, D.Z. and Sánchez‐Andrea, I., 2024. Acetic acid stress response of the acidophilic sulfate reducer Acididesulfobacillus acetoxydans. Environmental Microbiology, 26(2), p.e16565. https://doi.org/10.1111/1462-2920.16565

Faquetti, M.L., Slappendel, L., Bigonne, H., Grisoni, F., Schneider, P., Aichinger, G., Schneider, G., Sturla, S.J. and Burden, A.M., 2024. Baricitinib and tofacitinib off‐target profile, with a focus on Alzheimer’s disease. Alzheimer’s & Dementia: Translational Research & Clinical Interventions, 10(1), p.e12445. https://doi.org/10.1002/trc2.12445

2023

Grisoni, F., 2023. Chemical language models for de novo drug design: Challenges and opportunities. Current Opinion in Structural Biology, 79, 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., 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., 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., Grisoni, F., 2023. Structure‐based Drug discovery with Deep Learning. ChemBioChem, p.e202200776. https://doi.org/10.1002/cbic.202200776

Volkamer, A., Riniker, S., Lanini, J., Grisoni, F., Evertsson E., Rodríguez-Pérez, R., Schneider N., 2023. Machine learning for small molecule drug discovery in academia and industry, Artificial Intelligence in the Life Sciences, 3, 100056. https://doi.org/10.1016/j.ailsci.2022.100056

Mullowney, M. W., Duncan, K. R., Elsayed, S. S., Garg, N., et al., 2023. Artificial intelligence for natural product drug discovery. Nature Reviews Drug Discovery, 1-22. https://doi.org/10.1038/s41573-023-00774-7

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

Rodenburg, L. W., van der Windt, I. S., Dreyer, H. H., Smits, S. M., et al., 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), 102337. https://doi.org/10.1016/j.xpro.2023.102337

Lefferts, J. W., Boersma, V., Nieuwenhuijze, N. D. A., Suen, S. W. F., Hajo, K., Collantes, N. S., … & Beekman, J. M., 2023. Targeted locus amplification reveals heterogeneity between and within CFTR genotypes and association with CFTR function in patient-derived intestinal organoids. Journal of Cystic Fibrosis, 22(3), 538-547. https://doi.org/10.1016/j.jcf.2023.04.003

Delpiano, L., Rodenburg, L. W., Burke, M., Nelson, G., Amatngalim, G. D., Beekman, J. M., & Gray, M. A., 2023. Dynamic regulation of airway surface liquid pH by TMEM16A and SLC26A4 in cystic fibrosis nasal epithelia with rare mutations. Proceedings of the National Academy of Sciences, 120(47), e2307551120. https://doi.org/10.1073/pnas.2307551120

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