Chemistry Research: Bijvoet Centre for Biomolecular Research

2025

Acquisition of Fc-afucosylation of PfEMP1-specific IgG is age-dependent and associated with clinical protection against malaria

Lopez-Perez, M., Seidu, Z., Larsen, M. D., Wang, W., Nouta, J., Wuhrer, M., Vidarsson, G., Ofori, M. F. & Hviid, L., 2 Jan 2025, In: Nature Communications. 16, 1, 237.

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Addition and Oxidation Reactivity of a Pentacoordinate Nickelacyclobutane

Sansores-Paredes, M. L. G., Lutz, M. & Moret, M. E., 6 Mar 2025, In: Chemistry - A European Journal. 31, 14, e202404133.

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A network of interacting ciliary tip proteins with opposing activities imparts slow and processive microtubule growth

Saunders, H. A. J., van den Berg, C. M., Hoogebeen, R. A., Schweizer, D., Stecker, K. E., Roepman, R., Howes, S. C. & Akhmanova, A., 24 Jan 2025, (E-pub ahead of print) In: Nature Structural and Molecular Biology.

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Bisecting N-Acetylglucosamine of the N-Glycan of Immunoglobulin G Does Not Affect Binding to Fc Gamma Receptors

Bosman, G. P., Stoof, I. D., Bastiaansen, H. P., Quarles van Ufford, L., Dobruchowska, J. M., Langenbach, J. W. H., Boruah, B. M., Moremen, K. W., Bentlage, A. E. H., Lissenberg-Thunnissen, S. N., Vidarsson, G. & Boons, G. J., 21 Mar 2025, In: ACS Chemical Biology. 20, 3, p. 680-689 10 p.

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Cardiomyocyte SORBS2 expression increases in heart failure and regulates integrin interactions and extracellular matrix composition

Timmer, L. T., den Hertog, E., Versteeg, D., Post, H., Verdonschot, J. A. J., Monshouwer-Kloots, J., Kyriakopoulou, E., Perini, I., Koopmans, T., van der Kraak, P., Zentilin, L., Heymans, S. R. B., Vink, A., Giacca, M., Heck, A. J. R. & van Rooij, E., 17 Feb 2025, (E-pub ahead of print) In: Cardiovascular Research. 16 p., cvaf021.

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Chloride, Alkoxide, or Silicon: The Bridging Ligand Dictates the Spin State in Dicobalt Expanded Pincer Complexes

Bienenmann, R. L. M., Asundi, A. S., Lutz, M., Sarangi, R. & Broere, D. L. J., 13 Jan 2025, In: Organometallics. 44, 1, p. 94-104 11 p.

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Divergent Chemoenzymatic Synthesis of Sulfated Ganglio-Oligosaccharides for Probing Ligand Requirements of Glycan Binding Proteins

Bunyatov, M. I., Wolfert, M. A. & Boons, G.-J., 10 Mar 2025, In: Angewandte Chemie-International Edition. 64, 11, 10 p., e202415521.

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In-depth plasma N-glycoproteome profiling using narrow-window data-independent acquisition on the Orbitrap Astral mass spectrometer

Jager, S., Zeller, M., Pashkova, A., Schulte, D., Damoc, E., Reiding, K. R., Makarov, A. A. & Heck, A. J. R., 13 Mar 2025, In: Nature Communications. 16, 1, 2497.

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Liposome-Encapsulated Escherichia coli Lysates to Reconstitute Intracellular Macromolecular Crowding Effects

Kalacheva, M. S., da Silva, N. R. & Boersma, A. J., 21 Mar 2025, In: ACS Synthetic Biology. 14, 3, p. 901-908 8 p.

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Local structural flexibility drives oligomorphism in computationally designed protein assemblies

Khmelinskaia, A., Bethel, N. P., Fatehi, F., Mallik, B. B., Antanasijevic, A., Borst, A. J., Lai, S.-H., Chim, H. Y., Wang, J. Y. '., Miranda, M. C., Watkins, A. M., Ogohara, C., Caldwell, S., Wu, M., Heck, A. J. R., Veesler, D., Ward, A. B., Baker, D., Twarock, R. & King, N. P., 26 Feb 2025, (E-pub ahead of print) In: Nature Structural and Molecular Biology. 746.

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Multitiered Proteome Analysis Displays the Hyperpermeability of the Rheumatoid Synovial Compartment for Plasma Proteins

Stork, E. M., Nteak, S. K., van Rijswijck, D. M. H., Damen, J. M. A., Scherer, H. U., Toes, R. E. M., Bondt, A., Huizinga, T. W. J. & Heck, A. J. R., Feb 2025, In: Molecular and Cellular Proteomics. 24, 2, 14 p., 100900.

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NMR characterisation of the antibiotic resistance-mediating 32mer RNA from the 23S ribosomal RNA

Muhs, C., Kemper, L., Richter, C., Lavore, F., Weingarth, M., Wacker, A. & Schwalbe, H., 3 Apr 2025, (E-pub ahead of print) In: Biomolecular NMR Assignments.

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Prolonged Trapping of Adeno-Associated Virus Capsids Reveals that Genome Packaging Affects Single-Ion Mass Spectrometry Measurements

Ebberink, E. H. T. M., Yin, V. C., Deslignière, E., Barendregt, A., Wörner, T. P., Fort, K. L., Makarov, A. A. & Heck, A. J. R., 2 Apr 2025, In: Journal of the American Chemical Society. 147, 13, p. 10925-10934 10 p.

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Protein-bound and free glycation compounds in human milk: A comparative study with minimally processed infant formula and pasteurized bovine milk

Arena, S., De Pascale, S., Ciaravolo, V., Monroy, M. M., Gouw, J. W., Stahl, B., Bäuerl, C., Collado, M. C., De Filippo, C., Scaloni, A. & Troise, A. D., 15 Jan 2025, In: Food Chemistry. 463, Pt 2, 14 p., 141265.

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Regulatory effects of Lacticaseibacillus rhamnosus ZFM216 and its bacteriocin on intestinal microbiota in vitro

Zhou, Q., Lou, Y., Shan, C., Ye, Z., Wu, D., Li, P., Breukink, E. & Gu, Q., Apr 2025, In: Food Bioscience. 66, 12 p., 106136.

Research output: Contribution to journal › Article › Academic › peer-review

Spatial organization of the sperm cell glycoproteome

Ji, R., Chiozzi, R. Z., van den Toorn, H., Leung, M., Zeev-Ben-Mordehai, T., Burke, N. D., Bromfield, E. G., Reiding, K. R. & Heck, A. J. R., Jan 2025, In: Molecular and Cellular Proteomics. 24, 1, 100893.

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StableMARK-decorated microtubules in cells have expanded lattices

de Jager, L., Jansen, K. I., Hoogebeen, R., Akhmanova, A., Kapitein, L. C., Förster, F. & Howes, S. C., 6 Jan 2025, In: The Journal of cell biology. 224, 1, 12 p., e202206143.

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Structural diversity of axonemes across mammalian motile cilia

Leung, M. R., Sun, C., Zeng, J., Anderson, J. R., Niu, Q., Huang, W., Noteborn, W. E. M., Brown, A., Zeev-Ben-Mordehai, T. & Zhang, R., 30 Jan 2025, In: Nature. 637, 8048, p. 1170-1177 8 p.

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Structure-property relationships to direct the dynamic properties of acylsemicarbazide-based materials

Maessen, S. J. D., Lekanne Deprez, S., Vermeeren, P., van den Bersselaar, B. W. L., Lutz, M., Heuts, J. P. A., Fonseca Guerra, C. & Palmans, A. R. A., 2025, In: Polymer Chemistry. 16, 3, p. 290-300 11 p.

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Temperature adaptation of yeast phospholipid molecular species at the acyl chain positional level

Kelso, C., Maccarone, A. T., de Kroon, A. I. P. M., Mitchell, T. W. & Renne, M. F., Feb 2025, In: FEBS Letters. 599, 4, p. 530-544 15 p.

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2024

2,2-Difluoro Derivatives of Fucose Can Inhibit Cell Surface Fucosylation without Causing Slow Transfer to Acceptors

Liu, Y., Sweet, I. R. & Boons, G.-J., 28 Oct 2024, In: JACS Au. 4, 10, p. 3953–3963 11 p.

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A Biomimetic Synthetic Strategy Can Provide Keratan Sulfate I and II Oligosaccharides with Diverse Fucosylation and Sulfation Patterns

Wu, Y., Bosman, G. P., Chapla, D., Huang, C., Moremen, K. W., de Vries, R. P. & Boons, G.-J., 3 Apr 2024, In: Journal of the American Chemical Society. 146, 13, p. 9230-9240 11 p.

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Accelerating Protein-Protein Interaction screens with reduced AlphaFold-Multimer sampling

Bellinzona, G., Sassera, D. & Bonvin, A. M. J. J., 2024, In: Bioinformatics Advances. 4, 1, vbae153.

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Adipocyte p53 coordinates the response to intermittent fasting by regulating adipose tissue immune cell landscape

Reinisch, I., Michenthaler, H., Sulaj, A., Moyschewitz, E., Krstic, J., Galhuber, M., Xu, R., Riahi, Z., Wang, T., Vujic, N., Amor, M., Zenezini Chiozzi, R., Wabitsch, M., Kolb, D., Georgiadi, A., Glawitsch, L., Heitzer, E., Schulz, T. J., Schupp, M. & Sun, W. & 11 others, Dong, H., Ghosh, A., Hoffmann, A., Kratky, D., Hinte, L. C., von Meyenn, F., Heck, A. J. R., Blüher, M., Herzig, S., Wolfrum, C. & Prokesch, A., 15 Feb 2024, In: Nature Communications. 15, 1, p. 1-21 21 p., 1391.

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Afucosylated broadly neutralizing antibodies enhance clearance of HIV-1 infected cells through cell-mediated killing

de Taeye, S. W., Schriek, A. I., Umotoy, J. C., Grobben, M., Burger, J. A., Sanders, R. W., Vidarsson, G., Wuhrer, M., Falck, D., Kootstra, N. A. & van Gils, M. J., 9 Aug 2024, In: Communications Biology. 7, 1, 11 p., 964.

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A Handle on Mass Coincidence Errors in De Novo Sequencing of Antibodies by Bottom-up Proteomics

Schulte, D. & Snijder, J., 2 Aug 2024, In: Journal of Proteome Research. 23, 8, p. 3552-3559 8 p.

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A Hybrid Orbitrap-Nanoelectromechanical Systems Approach for the Analysis of Individual, Intact Proteins in Real Time

Neumann, A. P., Sage, E., Boll, D., Reinhardt-Szyba, M., Fon, W., Masselon, C., Hentz, S., Sader, J. E., Makarov, A. & Roukes, M. L., 12 Aug 2024, In: Angewandte Chemie-International Edition. 63, 33, 8 p., e202317064.

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Alternative splicing controls teneurin-3 compact dimer formation for neuronal recognition

Gogou, C., Beugelink, J. W., Frias, C. P., Kresik, L., Jaroszynska, N., Drescher, U., Janssen, B. J. C., Hindges, R. & Meijer, D. H., 29 Apr 2024, In: Nature Communications. 15, 1, 15 p., 3648.

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An integrated approach towards extracting structural characteristics of chlorosomes from a bchQ mutant of Chlorobaculum tepidum

Dsouza, L., Li, X., Erić, V., Huijser, A., Jansen, T. L. C., Holzwarth, A. R., Buda, F., Bryant, D. A., Bahri, S., Gupta, K. B. S. S., Sevink, G. J. A. & de Groot, H. J. M., Jun 2024, In: Physical Chemistry Chemical Physics. 26, 22, p. 15856-15867 12 p.

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Antigen-specific Fab profiling achieves molecular-resolution analysis of human autoantibody repertoires in rheumatoid arthritis

Stork, E. M., van Rijswijck, D. M. H., van Schie, K. A., Hoek, M., Kissel, T., Scherer, H. U., Huizinga, T. W. J., Heck, A. J. R., Toes, R. E. M. & Bondt, A., 10 Apr 2024, In: Nature Communications. 15, 1, 12 p., 3114.

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A Peptide Strategy for Inhibiting Different Protein Aggregation Pathways

Garfagnini, T., Ferrari, L., Koopman, M. B., Dekker, F. A., Halters, S., Van Kappel, E., Mayer, G., Bressler, S., Maurice, M. M., Rüdiger, S. G. D. & Friedler, A., 16 Sept 2024, In: Chemistry - A European Journal. 30, 52, e202400080.

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ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information

Giulini, M., Honorato, R. V., Rivera, J. L. & Bonvin, A. M. J. J., 6 Jan 2024, In: Communications Biology. 7, 1, 49.

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Assessment of IgG-Fc glycosylation from individual RhD-specific B cell clones reveals regulation at clonal rather than clonotypic level

de Graaf, E. L., Larsen, M. D., van der Bolt, N., Visser, R., Verhagen, O. J. H. M., Hipgrave Ederveen, A. L., Koeleman, C. A. M., van der Schoot, C. E., Wuhrer, M. & Vidarsson, G., Mar 2024, In: Immunology. 171, 3, p. 428-439 12 p.

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Assessment of Kinome-wide Activity Remodeling Upon Picornavirus Infection

Veth, T. S., Nouwen, L. V., Zwaagstra, M., Lyoo, H., Wierenga, K. A., Westendorp, B., Altelaar, M. A. F. M., Berkers, C., van Kuppeveld, F. J. M. & Heck, A. J. R., May 2024, In: Molecular and Cellular Proteomics. 23, 5, 100757.

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A structural and dynamic visualization of the interaction between MAP7 and microtubules

Adler, A., Bangera, M., Beugelink, J. W., Bahri, S., van Ingen, H., Moores, C. A. & Baldus, M., 2 Mar 2024, In: Nature Communications. 15, 1, 16 p., 1948.

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Asymmetrical Biantennary Glycans Prepared by a Stop-and-Go Strategy Reveal Receptor Binding Evolution of Human Influenza A Viruses

Ma, S., Liu, L., Eggink, D., Herfst, S., Fouchier, R. A. M., Vries, R. P. D. & Boons, G.-J., 23 Jan 2024, In: JACS Au. 4, 2, p. 607-618 12 p.

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Asymmetric N-Glycosylation in the Tailpiece of Recombinant IgA1.

Peris-Díaz, M. D., Deslignière, E., Jager, S., Mokiem, N., Barendregt, A., Bondt, A. & Heck, A. J. R., 18 Dec 2024, In: Journal of the American Chemical Society. 146, 50, p. 34720-34732 13 p.

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A "terminal" case of glycan catabolism: structural and enzymatic characterization of the sialidases of Clostridium perfringens

Medley, B. J., Low, K. E., Irungu, J. D. W., Kipchumba, L., Daneshgar, P., Liu, L., Garber, J. M., Klassen, L., Inglis, G. D., Boons, G.-J., Zandberg, W. F., Abbott, D. W. & Boraston, A. B., Oct 2024, In: Journal of Biological Chemistry. 300, 10, 107750.

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A π-extended β-diketiminate ligand via a templated Scholl approach

Killian, L., Lutz, M. & Thevenon, A., 2024, In: Chemical Communications. 60, 52, p. 6663–6666 4 p.

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Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders

Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W., Godwin, A., Zaki, M. S., Huang, K., Lau, T., Petree, C., Efthymiou, S., Ghayoor Karimiani, E., Hempel, M., Normand, E. A., Rudnik-Schöneborn, S., Schatz, U. A., Baggelaar, M. P., Ilyas, M., Sultan, T. & Alvi, J. R. & 69 others, Ganieva, M., Fowler, B., Aanicai, R., Akay Tayfun, G., Al Saman, A., Alswaid, A., Amiri, N., Asilova, N., Shotelersuk, V., Yeetong, P., Azam, M., Babaei, M., Bahrami Monajemi, G., Mohammadi, P., Samie, S., Banu, S. H., Basto, J. P., Kortüm, F., Bauer, M., Bauer, P., Beetz, C., Garshasbi, M., Hameed Issa, A., Eyaid, W., Ahmed, H., Hashemi, N., Hassanpour, K., Herman, I., Ibrohimov, S., Abdul-Majeed, B. A., Imdad, M., Isrofilov, M., Kaiyal, Q., Khan, S., Kirmse, B., Koster, J., Lourenço, C. M., Mitani, T., Moldovan, O., Murphy, D., Najafi, M., Pehlivan, D., Rocha, M. E., Salpietro, V., Schmidts, M., Shalata, A., Mahroum, M., Talbeya, J. K., Taylor, R. W., Vazquez, D., Vetro, A., Waterham, H. R., Zaman, M., Schrader, T. A., Chung, W. K., Guerrini, R., Lupski, J. R., Gleeson, J., Suri, M., Jamshidi, Y., Bhatia, K. P., Vona, B., Schrader, M., Severino, M., Guille, M., Tate, E. W., Varshney, G. K., Houlden, H. & Maroofian, R., Apr 2024, In: Brain. 147, 4, p. 1436-1456 21 p.

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Broccoli aptamer allows quantitative transcription regulation studies in vitro

van der Sijs, A., Visser, T., Moerman, P., Folkers, G. & Kegel, W., Jun 2024, In: PLoS One. 19, 6, 15 p., e0304677.

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CAMSAPs and nucleation-promoting factors control microtubule release from γ-TuRC

Rai, D., Song, Y., Hua, S., Stecker, K., Monster, J. L., Yin, V., Stucchi, R., Xu, Y., Zhang, Y., Chen, F., Katrukha, E. A., Altelaar, M., Heck, A. J. R., Wieczorek, M., Jiang, K. & Akhmanova, A., Mar 2024, In: Nature Cell Biology. 26, 3, p. 404-420 17 p.

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CAPRI-Q: The CAPRI resource evaluating the quality of predicted structures of protein complexes

Collins, K. W., Copeland, M. M., Brysbaert, G., Wodak, S. J., Bonvin, A. M. J. J., Kundrotas, P. J., Vakser, I. A. & Lensink, M. F., 1 Sept 2024, In: Journal of Molecular Biology. 436, 17, 8 p., 168540.

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Carbene transfer reactivity from a nickelacyclobutane

Sansores-Paredes, M. L. G., Lutz, M. & Moret, M. E., 4 Nov 2024, In: Chemical Communications. 60, 85, p. 12397-12400 4 p.

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Chemical Synthesis of Δ-4,5 Unsaturated Heparan Sulfate Oligosaccharides for Biomarker Discovery

Joshi, A., Chopra, P., Venot, A. & Boons, G.-J., 29 Mar 2024, In: Organic Letters. 26, 12, p. 2462-2466 5 p.

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Chemoenzymatic synthesis of human natural killer-1-containing glycans and application as serum antibodies probes

Bunyatov, M., Wolfert, M. A., Liu, L., Huizinga, R., Schreurs, M. W. J., Jacobs, B. C. & Boons, G. J., Jan 2024, In: Nature Synthesis. 3, 1, p. 85-98 14 p.

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Chemo-Enzymatic Synthesis of Isomeric I-branched Polylactosamines using Traceless Blocking Groups

Vos, G. M., Wu, Y., van der Woude, R., de Vries, R. P. & Boons, G.-J., 22 Jan 2024, In: Chemistry-A European Journal. 30, 5, e202302877.

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Chemoenzymatic Synthesis of Tri-antennary N-glycans Terminating in Sialyl-Lewisx Reveals the Importance of Glycan Complexity for Influenza A Virus Receptor Binding

Li, T., Spruit, C. M., Wei, N., Liu, L., Wolfert, M. A., de Vries, R. P. & Boons, G.-J., 6 Jun 2024, In: Chemistry-A European Journal. 30, 32, e202401108.

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Closed-Loop Chemical Recycling of a Biobased Poly(oxanorbornene-fused γ-butyrolactone)

Harsevoort, E., Cioc, R. C., Lutz, M., Thevenon, A. & Bruijnincx, P. C. A., 18 Dec 2024, In: Journal of the American Chemical Society. 146, 50, p. 34628-34637 10 p.

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Complex N-glycans are important for interspecies transmission of H7 influenza A viruses

Spruit, C. M., Palme, D. I., Li, T., Ríos Carrasco, M., Gabarroca García, A., Sweet, I. R., Kuryshko, M., Maliepaard, J. C. L., Reiding, K. R., Scheibner, D., Boons, G.-J., Abdelwhab, E. M. & de Vries, R. P., Apr 2024, In: Journal of Virology. 98, 4, 21 p., e0194123.

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Chemistry Research: Bijvoet Centre for Biomolecular Research

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