Peter J. Peters

2025

In situ and in vitro cryo-EM reveal structures of mycobacterial encapsulin assembly intermediates

Berger, C., Lewis, C., Gao, Y., Knoops, K., Lopez-Iglesias, C., Peters, P. J. & Ravelli, R. B. G., 15 Feb 2025, In: Communications Biology. 8, 1, 11 p., 245.

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Open Access

2024

Cryo-EM structure of cytochrome bo<inf>3</inf> quinol oxidase assembled in peptidiscs reveals an “open” conformation for potential ubiquinone-8 release

Gao, Y., Zhang, Y., Hakke, S., Mohren, R., Sijbers, L. J. P. M., Peters, P. J. & Ravelli, R. B. G., 1 Aug 2024, In: Biochimica et Biophysica Acta-bioenergetics. 1865, 3, 149045.

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Open Access

Description and functional validation of human enteroendocrine cell sensors

Beumer, J., Geurts, M. H., Geurts, V., Andersson-Rolf, A., Akkerman, N., Völlmy, F., Krueger, D., Busslinger, G. A., Martínez-Silgado, A., Boot, C., Yousef Yengej, F. A., Puschhof, J., Van de Wetering, W. J., Knoops, K., López-Iglesias, C., Peters, P. J., Vivié, J. A., Mooijman, D., van Es, J. H. & Clevers, H., 18 Oct 2024, In: Science. 386, 6719, p. 341-348 8 p.

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

Human conjunctiva organoids to study ocular surface homeostasis and disease

Bannier-Hélaouët, M., Korving, J., Ma, Z., Begthel, H., Giladi, A., Lamers, M. M., van de Wetering, W. J., Yawata, N., Yawata, M., LaPointe, V. L. S., Dickman, M. M., Kalmann, R., Imhoff, S. M., van Es, J. H., López-Iglesias, C., Peters, P. J., Haagmans, B. L., Wu, W. & Clevers, H., 1 Feb 2024, In: Cell Stem Cell. 31, 2, p. 227-243.e12

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Open Access

Human fetal brain self-organizes into long-term expanding organoids

Hendriks, D., Pagliaro, A., Andreatta, F., Ma, Z., van Giessen, J., Massalini, S., López-Iglesias, C., van Son, G. J. F., DeMartino, J., Damen, J. M. A., Zoutendijk, I., Staliarova, N., Bredenoord, A. L., Holstege, F. C. P., Peters, P. J., Margaritis, T., Chuva de Sousa Lopes, S., Wu, W., Clevers, H. & Artegiani, B., 1 Feb 2024, In: Cell. 187, 3, p. 712-732.e38

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Ice thickness control and measurement in the VitroJet for time-efficient single particle structure determination

Henderikx, R. J. M., Schotman, M. J. G., Shahzad, S., Fromm, S. A., Mann, D., Hennies, J., Heidler, T. V., Ashtiani, D., Hagen, W. J. H., Jeurissen, R. J. M., Mattei, S., Peters, P. J., Sachse, C. & Beulen, B. W. A. M. M., 20 Oct 2024, In: Journal of Structural Biology. 216, 4, p. 13 108139.

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Open Access

Integrin-activating Yersinia protein Invasin sustains long-term expansion of primary epithelial cells as 2D organoid sheets

Wijnakker, J. J. A. P. M., van Son, G. J. F., Krueger, D., van de Wetering, W. J., Lopez-Iglesias, C., Schreurs, R., van Rijt, F., Lim, S., Lin, L., Peters, P. J., Isberg, R. R., Janda, C. Y., de Lau, W. & Clevers, H., 30 Dec 2024, In: Proceedings of the National Academy of Sciences of the United States of America. 122, 1, e2420595121.

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Long-term in vitro expansion of a human fetal pancreas stem cell that generates all three pancreatic cell lineages

Andersson-Rolf, A., Groot, K., Korving, J., Begthel, H., Hanegraaf, M. A. J., VanInsberghe, M., Salmén, F., van den Brink, S., Lopez-Iglesias, C., Peters, P. J., Krueger, D., Beumer, J., Geurts, M. H., Alemany, A., Gehart, H., Carlotti, F., de Koning, E. J. P., Chuva de Sousa Lopes, S. M., van Oudenaarden, A. & van Es, J. H. & 1 others, Clevers, H., 26 Dec 2024, In: Cell. 187, 26, p. 7394-7413.e22

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Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets

Tzfadia, O., Gijsbers, A., Vujkovic, A., Snobre, J., Vargas, R., Dewaele, K., Meehan, C. J., Farhat, M., Hakke, S., Peters, P. J., de Jong, B. C., Siroy, A. & Ravelli, R. B. G., 6 Aug 2024, In: Microbiology spectrum. 12, 8, 19 p., e0381623.

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Symmetry and planar chirality measured with a log-polar transformation in a transmission electron microscope

Tavabi, A. H., Rosi, P., Ravelli, R. B. G., Gijsbers, A., Rotunno, E., Guner, T., Zhang, Y., Roncaglia, A., Belsito, L., Pozzi, G., Denneulin, T., Gazzadi, G. C., Ghosh, M., Nijland, R., Frabboni, S., Peters, P. J., Karimi, E., Tiemeijer, P., Dunin-Borkowski, R. E. & Grillo, V., 31 Jul 2024, In: Physical Review Applied. 22, 1, 9 p., 014083.

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Tuft cells act as regenerative stem cells in the human intestine

Huang, L., Bernink, J. H., Giladi, A., Krueger, D., van Son, G. J. F., Geurts, M. H., Busslinger, G., Lin, L., Begthel, H., Zandvliet, M., Buskens, C. J., Bemelman, W. A., López-Iglesias, C., Peters, P. J. & Clevers, H., 24 Oct 2024, In: Nature. 634, 8035, p. 929-935 7 p.

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VitroJet: new features and case studies

Henderikx, R. J. M., Mann, D., Domanska, A., Dong, J., Shahzad, S., Lak, B., Filopoulou, A., Ludig, D., Grininger, M., Momoh, J., Laanto, E., Oksanen, H. M., Bisikalo, K., Williams, P. A., Butcher, S. J., Peters, P. J. & Beulen, B. W. A. M. M., 1 Apr 2024, In: Acta Crystallographica. Section D: Structural Biology. 80, Pt 4, p. 232-246 15 p.

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2023

A Lamb1Dendra2 mouse model identifies basement-membrane-producing origins and dynamics in PyMT breast tumors

Morgner, J., Bornes, L., Hahn, K., Lopez-Iglesias, C., Kroese, L., Pritchard, C. E. J., Vennin, C., Peters, P. J., Huijbers, I. & van Rheenen, J., 10 Apr 2023, In: Developmental Cell. 58, 7, p. 535-549.e5 21 p.

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Charging of Vitreous Samples in Cryogenic Electron Microscopy Mitigated by Graphene

Zhang, Y., van Schayck, J. P., Pedrazo-Tardajos, A., Claes, N., Noteborn, W. E. M., Lu, P.-H., Duimel, H., Dunin-Borkowski, R. E., Bals, S., Peters, P. J. & Ravelli, R. B. G., 2 Aug 2023, In: ACS Nano. 17, 16, p. 15836-15846 11 p.

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Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology

Berger, C., Premaraj, N., Ravelli, R. B. G., Knoops, K., Lopez-Iglesias, C. & Peters, P. J., Apr 2023, In: Nature Methods. 20, 4, p. 499-511 13 p.

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Druggable redox pathways against Mycobacterium abscessus in cystic fibrosis patient-derived airway organoids

Leon-Icaza, S. A., Bagayoko, S., Vergé, R., Iakobachvili, N., Ferrand, C., Aydogan, T., Bernard, C., Sanchez Dafun, A., Murris-Espin, M., Mazières, J., Bordignon, P. J., Mazères, S., Bernes-Lasserre, P., Ramé, V., Lagarde, J. M., Marcoux, J., Bousquet, M. P., Chalut, C., Guilhot, C. & Clevers, H. & 7 others, Peters, P. J., Molle, V., Lugo-Villarino, G., Cam, K., Berry, L., Meunier, E. & Cougoule, C., 1 Aug 2023, In: PLOS PATHOGENS. 19, 8, 24 p., e1011559.

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Engineered human hepatocyte organoids enable CRISPR-based target discovery and drug screening for steatosis

Hendriks, D., Brouwers, J. F., Hamer, K., Geurts, M. H., Luciana, L., Massalini, S., Lopez-Iglesias, C., Peters, P. J., Rodriguez-Colman, M. J., Lopes, S. C. D., Artegiani, B. & Clevers, H., Nov 2023, In: Nature Biotechnology. 41, 11, p. 1567–1581 22 p.

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Integration of an Event-driven Timepix3 Hybrid Pixel Detector into a Cryo-EM Workflow

van Schayck, J. P., Zhang, Y., Knoops, K., Peters, P. J. & Ravelli, R. B. G., 1 Feb 2023, In: Microscopy and Microanalysis. 29, 1, p. 352-363 12 p.

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Physical association of low density lipoprotein particles and extracellular vesicles unveiled by single particle analysis

Lozano-Andrés, E., Enciso-Martinez, A., Gijsbers, A., Ridolfi, A., Van Niel, G., Libregts, S. F. W. M., Pinheiro, C., van Herwijnen, M. J. C., Hendrix, A., Brucale, M., Valle, F., Peters, P. J., Otto, C., Arkesteijn, G. J. A. & Wauben, M. H. M., 1 Nov 2023, In: Journal of Extracellular Vesicles. 12, 11, 16 p., 12376.

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The crystal structure of the EspB-EspK virulence factor-chaperone complex suggests an additional type VII secretion mechanism in Mycobacterium tuberculosis

Gijsbers, A., Eymery, M., Gao, Y., Menart, I., Vinciauskaite, V., Siliqi, D., Peters, P. J., McCarthy, A. & Ravelli, R. B. G., Jan 2023, In: Journal of Biological Chemistry. 299, 1, 14 p., 102761.

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Unbiased transcription factor CRISPR screen identifies ZNF800 as master repressor of enteroendocrine differentiation

Lin, L., DeMartino, J., Wang, D., van Son, G. J. F., van der Linden, R., Begthel, H., Korving, J., Andersson-Rolf, A., van den Brink, S., Lopez-Iglesias, C., van de Wetering, W. J., Balwierz, A., Margaritis, T., van de Wetering, M., Peters, P. J., Drost, J., van Es, J. H. & Clevers, H., 27 Oct 2023, In: Science. 382, 6669, p. 451-458 8 p.

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2022

Fat causes necrosis and inflammation in parenchymal cells in human steatotic liver

Wisse, E., Braet, F., Shami, G. J., Zapotoczny, B., Vreuls, C., Verhaegh, P., Frederik, P., Peters, P. J., Damink, S. O. & Koek, G., Jan 2022, In: Histochemistry and Cell Biology. 157, 1, p. 27-38 12 p.

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In vitro grafting of hepatic spheroids and organoids on a microfluidic vascular bed

Bonanini, F., Kurek, D., Previdi, S., Nicolas, A., Hendriks, D., de Ruiter, S., Meyer, M., Cabrer, M. C., Dinkelberg, R., Garcia, S. B., Kramer, B., Olivier, T., Hu, H. L., Lopez-Iglesias, C., Schavemaker, F., Walinga, E., Dutta, D., Queiroz, K., Domansky, K. & Ronden, B. & 6 others, Joore, J., Lanz, H. L., Peters, P. J., Trietsch, S. J., Clevers, H. & Vulto, P., Nov 2022, In: Angiogenesis. 25, 4, p. 455-470 16 p.

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Mycobacteria-host interactions in human bronchiolar airway organoids

Iakobachvili, N., Leon-Icaza, S. A., Knoops, K., Sachs, N., Mazeres, S., Simeone, R., Peixoto, A., Bernard, C., Murris-Espin, M., Mazieres, J., Cam, K., Chalut, C., Guilhot, C., Lopez-Iglesias, C., Ravelli, R. B. G., Neyrolles, O., Meunier, E., Lugo-Villarino, G., Clevers, H. & Cougoule, C. & 1 others, Peters, P. J., Mar 2022, In: Molecular Microbiology. 117, 3, p. 682-692 11 p.

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Optimized human intestinal organoid model reveals interleukin-22-dependency of paneth cell formation

He, G.-W., Lin, L., DeMartino, J., Zheng, X., Staliarova, N., Dayton, T., Begthel, H., van de Wetering, W. J., Bodewes, E., van Zon, J., Tans, S., Lopez-Iglesias, C., Peters, P. J., Wu, W., Kotlarz, D., Klein, C., Margaritis, T., Holstege, F. & Clevers, H., 1 Sept 2022, In: Cell stem cell. 29, 9, p. 1333-1345.e6 20 p.

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

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SARS-CoV-2-Specific Vaccine Candidates; the Contribution of Structural Vaccinology

Pack, S. M. & Peters, P. J., 1 Feb 2022, In: Vaccines. 10, 2, 17 p., 236.

Research output: Contribution to journal › (Systematic) Review article › peer-review

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2021

Adult mouse and human organoids derived from thyroid follicular cells and modeling of Graves' hyperthyroidism

van der Vaart, J., Bosmans, L., Sijbesma, S. F., Knoops, K., van de Wetering, W. J., Otten, H. G., Begthel, H., Rinkes, I. H. M. B., Korving, J., Lentjes, E. G. W. M., Lopez-Iglesias, C., Peters, P. J., van Santen, H. M., Vriens, M. R. & Clevers, H., 21 Dec 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 51, 11 p., e2117017118.

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An organoid-derived bronchioalveolar model for SARS-CoV-2 infection of human alveolar type II-like cells

Lamers, M. M., van der Vaart, J., Knoops, K., Riesebosch, S., Breugem, T. I., Mykytyn, A. Z., Beumer, J., Schipper, D., Bezstarosti, K., Koopman, C. D., Groen, N., Ravelli, R. B. G., Duimel, H. Q., Demmers, J. A. A., Verjans, G. M. G. M., Koopmans, M. P. G., Muraro, M. J., Peters, P. J., Clevers, H. & Haagmans, B. L., 1 Mar 2021, In: The Embo Journal. 40, 5, 19 p., 105912.

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Endocytosed nanogold fiducials for improved in-situ cryo-electron tomography tilt-series alignment

Berger, C., Ravelli, R. B. G., Lopez-Iglesias, C. & Peters, P. J., Mar 2021, In: Journal of Structural Biology. 213, 1, 7 p., 107698.

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Host phospholipid peroxidation fuels ExoU-dependent cell necrosis and supports Pseudomonas aeruginosa-driven pathology

Bagayoko, S., Leon-Icaza, S. A., Pinilla, M., Hessel, A., Santoni, K., Pericat, D., Bordignon, P. J., Moreau, F., Eren, E., Boyance, A., Naser, E., Lefevre, L., Berrone, C., Iakobachvili, N., Metais, A., Rombouts, Y., Lugo-Villarino, G., Coste, A., Attree, I. & Frank, D. W. & 5 others, Clevers, H., Peters, P. J., Cougoule, C., Planes, R. & Meunier, E., 1 Sept 2021, In: PLOS PATHOGENS. 17, 9, 29 p., e1009927.

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Modelling of primary ciliary dyskinesia using patient-derived airway organoids

Van der Vaart, J., Bottinger, L., Geurts, M. H., Van de Wetering, W. J., Knoops, K., Sachs, N., Begthel, H., Korving, J., Lopez-Iglesias, C., Peters, P. J., Eitan, K., Gileles-Hillel, A. & Clevers, H., 6 Dec 2021, In: Embo Reports. 22, 12, 16 p., e52058.

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Mycobacterium tuberculosis ferritin: a suitable workhorse protein for cryo-EM development

Gijsbers, A., Zhang, Y., Gao, Y., Peters, P. J. & Ravelli, R. B. G., 1 Aug 2021, In: Acta Crystallographica. Section D: Structural Biology. 77, p. 1077-1083 7 p.

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Priming mycobacterial ESX-secreted protein B to form a channel-like structure

Gijsbers, A., Vinciauskaite, V., Siroy, A., Gao, Y., Tria, G., Mathew, A., Sanchez-Puig, N., Lopez-Iglesias, C., Peters, P. J. & Ravelli, R. B. G., 2021, In: Current Research in Structural Biology. 3, p. 153-164 12 p.

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Recent Insights into the Structure and Function of Mycobacterial Membrane Proteins Facilitated by Cryo-EM

Bendre, A. D., Peters, P. J. & Kumar, J., Jun 2021, In: Journal of Membrane Biology. 254, 3, p. 321-341 21 p.

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Single-particle cryo-EM: alternative schemes to improve dose efficiency

Zhang, Y., Lu, P. H., Rotunno, E., Troiani, F., van Schayck, J. P., Tavabi, A. H., Dunin-Borkowski, R. E., Grillo, V., Peters, P. J. & Ravelli, R. B. G., 1 Sept 2021, In: Journal of Synchrotron Radiation. 28, p. 1343-1356 14 p.

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Structural Analysis of the Partially Disordered Protein EspK from Mycobacterium Tuberculosis

Gijsbers, A., Sanchez-Puig, N., Gao, Y., Peters, P. J., Ravelli, R. B. G. & Siliqi, D., 1 Jan 2021, In: Crystals. 11, 1, 13 p., 18.

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Structure of the Yersinia injectisome in intracellular host cell phagosomes revealed by cryo FIB electron tomography

Berger, C., Ravelli, R. B. G., Lopez-Iglesias, C., Kudryashev, M., Diepold, A. & Peters, P. J., Mar 2021, In: Journal of Structural Biology. 213, 1, 11 p., 107701.

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Open Access

Tuberculosis; Past: present and future of the treatment and drug discovery research

Bendre, A. D., Peters, P. J. & Kumar, J., 2021, In: Current research in pharmacology and drug discovery. 2, 100037.

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Understanding the invisible hands of sample preparation for cryo-EM

Weissenberger, G., Henderikx, R. J. M. & Peters, P. J., May 2021, In: Nature Methods. 18, 5, p. 463-471 9 p.

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2020

Could Egg White Lysozyme be Solved by Single Particle Cryo-EM?

Zhang, Y., Tammaro, R., Peters, P. J. & Ravelli, R. B. G., 26 May 2020, In: Journal of Chemical Information and Modeling. 60, 5, p. 2605-2613 9 p.

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Cryo-EM structures from sub-nl volumes using pin-printing and jet vitrification

Ravelli, R. B. G., Nijpels, F. J. T., Henderikx, R. J. M., Weissenberger, G., Thewessem, S., Gijsbers, A., Beulen, B. W. A. M. M., Lopez-Iglesias, C. & Peters, P. J., 22 May 2020, In: Nature Communications. 11, 1, 9 p., 2563.

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Efficient molecule discrimination in electron microscopy through an optimized orbital angular momentum sorter

Troiani, F., Rotunno, E., Frabboni, S., Ravelli, R. B. G., Peters, P. J., Karimi, E. & Grillo, R., 12 Oct 2020, In: Physical Review A. 102, 4, 10 p., 043510.

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High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells

Beumer, J., Puschhof, J., Bauza-Martinez, J., Martinez-Silgado, A., Elmentaite, R., James, K. R., Ross, A., Hendriks, D., Artegiani, B., Busslinger, G. A., Ponsioen, B., Andersson-Rolf, A., Saftien, A., Boot, C., Kretzschmar, K., Geurts, M. H., Bar-Ephraim, Y. E., Pleguezuelos-Manzano, C., Post, Y. & Begthel, H. & 12 others, van der Linden, F., Lopez-Iglesias, C., van de Wetering, W. J., van der Linden, R., Peters, P. J., Heck, A. J. R., Goedhart, J., Snippert, H., Zilbauer, M., Teichmann, S. A., Wu, W. & Clevers, H., 11 Jun 2020, In: Cell. 181, 6, p. 1291-1306.e19 35 p.

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How the observation in a new custom basis based on orbital angular momentum space could improve our dose effective reconstruction of the protein structure

Troiani, F., Rotunno, E., Frabboni, S., Ravelli, R., Peters, P., Karimi, E. & Grillo, V., 1 Aug 2020, In: Microscopy and Microanalysis. 26, S2, p. 1168–1169

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SARS-CoV-2 productively infects human gut enterocytes

Lamers, M. M., Beumer, J., van der Vaart, J., Knoops, K., Puschhof, J., Breugem, T. I., Ravelli, R. B. G., Paul van Schayck, J., Mykytyn, A. Z., Duimel, H. Q., van Donselaar, E., Riesebosch, S., Kuijpers, H. J. H., Schippers, D., van de Wetering, W. J., de Graaf, M., Koopmans, M., Cuppen, E., Peters, P. J. & Haagmans, B. L. & 1 others, Clevers, H., 3 Jul 2020, In: Science. 369, 6499, p. 50-54 5 p.

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Snake Venom Gland Organoids

Post, Y., Puschhof, J., Beumer, J., Kerkkamp, H. M., de Bakker, M. A. G., Slagboom, J., de Barbanson, B., Wevers, N. R., Spijkers, X. M., Olivier, T., Kazandjian, T. D., Ainsworth, S., Iglesias, C. L., van de Wetering, W. J., Heinz, M. C., van Ineveld, R. L., van Kleef, R. G. D. M., Begthel, H., Korving, J. & Bar-Ephraim, Y. E. & 11 others, Getreuer, W., Rios, A. C., Westerink, R. H. S., Snippert, H. J. G., van Oudenaarden, A., Peters, P. J., Vonk, F. J., Kool, J., Richardson, M. K., Casewell, N. R. & Clevers, H., 23 Jan 2020, In: Cell. 180, 2, p. 233-247.e21 36 p.

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Structural dynamics of the GluK3-kainate receptor neurotransmitter binding domains revealed by cryo-EM

Kumari, J., Bendre, A. D., Bhosale, S., Vinnakota, R., Burada, A. P., Tria, G., Ravelli, R. B. G., Peters, P. J., Joshi, M. & Kumar, J., 15 Apr 2020, In: International Journal of Biological Macromolecules. 149, p. 1051-1058 8 p.

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Sub-pixel electron detection using a convolutional neural network

van Schayck, J. P., van Genderen, E., Maddox, E., Roussel, L., Boulanger, H., Frojdh, E., Abrahams, J.-P., Peters, P. J. & Ravelli, R. B. G., Nov 2020, In: Ultramicroscopy. 218, 10 p., 113091.

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VitroJet: Bridging the gap in sample prep

Weissenberger, G., Nijpels, F., Henderikx, R., Beulen, B., Ravelli, R. & Peters, P., 1 Jan 2020, In: Microscopy and Microanalysis.

Research output: Contribution to journal › Comment/Letter to the editor › Academic › peer-review

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2019

Enteroendocrine and tuft cells support Lgr5 stem cells on Paneth cell depletion

van Es, J. H., Wiebrands, K., Lopez-Iglesias, C., de Wetering, M. V., Zeinstra, L., van den Born, M., Korving, J., Sasaki, N., Peters, P. J., van Oudenaarden, A. & Clevers, H., 26 Dec 2019, In: Proceedings of the National Academy of Sciences of the United States of America. 116, 52, p. 26599-26605 7 p.

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Peter J. Peters

Research output

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