Group van Boxtel

  • 47 Article
  • 6 Review article
  • 2 Comment/debate
  • 1 Meeting Abstract
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  • 2024

    Recapitulating the adenoma-carcinoma sequence by selection of four spontaneous oncogenic mutations in mismatch-repair-deficient human colon organoids

    Mizutani, T., Boretto, M., Lim, S., Drost, J., González, D. M., Oka, R., Geurts, M. H., Begthel, H., Korving, J., van Es, J. H., van Boxtel, R. & Clevers, H., 2024, In: Nature Cancer.

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

    Open Access
  • 2023

    A multidimensional analysis reveals distinct immune phenotypes and tertiary lymphoid structure-like aggregates in the bone marrow of pediatric acute myeloid leukemia

    Koedijk, J. B., van der Werf, I., Penter, L., Vermeulen, M. A., Barneh, F., Perzolli, A., Meesters-Ensing, J. I., Fiocco, M., de Groot-Kruseman, H. A., Moeniralam, R., Christensen, K. B., Porter, B., Pfaff, K., Garcia, J. S., Rodig, S. J., Wu, C. J., Hasle, H., Nierkens, S., Belderbos, M. E. & Zwaan, C. M. & 1 others, Heidenreich, O., 30 Oct 2023, In: medRxiv : the preprint server for health sciences.

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

  • Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox

    Middelkamp, S., Manders, F., Peci, F., van Roosmalen, M. J., González, D. M., Bertrums, E. J. M., van der Werf, I., Derks, L. L. M., Groenen, N. M., Verheul, M., Trabut, L., Pleguezuelos-Manzano, C., Brandsma, A. M., Antoniou, E., Reinhardt, D., Bierings, M., Belderbos, M. E. & van Boxtel, R., 13 Sept 2023, In: Cell genomics. 3, 9, p. 100389

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

    Open Access

  • One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids

    Geurts, M. H., Gandhi, S., Boretto, M. G., Akkerman, N., Derks, L. L. M., van Son, G., Celotti, M., Harshuk-Shabso, S., Peci, F., Begthel, H., Hendriks, D., Schürmann, P., Andersson-Rolf, A., Chuva de Sousa Lopes, S. M., van Es, J. H., van Boxtel, R. & Clevers, H., 17 Aug 2023, In: Nature communications. 14, 1, p. 4998

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

    Open Access
  • 2022

    A recurrent somatic missense mutation in GNAS gene identified in familial thyroid follicular cell carcinomas in German longhaired pointer dogs

    Yu, Y., Manders, F., Grinwis, G. C. M., Groenen, M. A. M. & Crooijmans, R. P. M. A., 23 Sept 2022, In: BMC Genomics. 23, 1, p. 669 669.

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

    Open Access
    1 Citation (Scopus)

  • Colon Tumors in Enterotoxigenic Bacteroides fragilis (ETBF)-Colonized Mice Do Not Display a Unique Mutational Signature but Instead Possess Host-Dependent Alterations in the APC Gene

    Allen, J., Rosendahl Huber, A., Pleguezuelos-Manzano, C., Puschhof, J., Wu, S., Wu, X., Boot, C., Saftien, A., O'Hagan, H. M., Wang, H., van Boxtel, R., Clevers, H. & Sears, C. L., 29 Jun 2022, In: Microbiology spectrum. 10, 3, p. e0105522

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

    Open Access
    19 Citations (Scopus)

  • Efficient and error-free fluorescent gene tagging in human organoids without double-strand DNA cleavage

    Bollen, Y., Hageman, J. H., van Leenen, P., Derks, L. L. M., Ponsioen, B., Buissant des Amorie, J. R., Verlaan-Klink, I., van den Bos, M., Terstappen, L. W. M. M., van Boxtel, R. & Snippert, H. J. G., Jan 2022, In: PLoS biology. 20, 1, p. e3001527

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

    Open Access
    10 Citations (Scopus)

  • Elevated mutational age in blood of children treated for cancer contributes to therapy-related myeloid neoplasms

    Bertrums, E. J. M., Rosendahl Huber, A. K. M., de Kanter, J. K., Brandsma, A. M., van Leeuwen, A. J. C. N., Verheul, M., van den Heuvel-Eibrink, M. M., Oka, R., van Roosmalen, M. J., de Groot-Kruseman, H. A., Zwaan, C. M., Goemans, B. F. & van Boxtel, R., 1 Aug 2022, In: Cancer discovery. 12, 8, p. 1860-1872 13 p.

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

    Open Access
    21 Citations (Scopus)

  • Human induced pluripotent stem cells display a similar mutation burden as embryonic pluripotent cells in vivo

    Hasaart, K. A. L., Manders, F., Ubels, J., Verheul, M., van Roosmalen, M. J., Groenen, N. M., Oka, R., Kuijk, E., Lopes, S. M. C. D. S. & Boxtel, R. V., 18 Feb 2022, In: iScience. 25, 2, 103736.

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

    Open Access
    7 Citations (Scopus)

  • Mesenchymal tumor organoid models recapitulate rhabdomyosarcoma subtypes

    Meister, M. T., Groot Koerkamp, M. J. A., de Souza, T., Breunis, W. B., Frazer-Mendelewska, E., Brok, M., DeMartino, J., Manders, F., Calandrini, C., Kerstens, H. H. D., Janse, A., Dolman, M. E. M., Eising, S., Langenberg, K. P. S., van Tuil, M., Knops, R. R. G., van Scheltinga, S. T., Hiemcke-Jiwa, L. S., Flucke, U. & Merks, J. H. M. & 9 others, van Noesel, M. M., Tops, B. B. J., Hehir-Kwa, J. Y., Kemmeren, P., Molenaar, J. J., van de Wetering, M., van Boxtel, R., Drost, J. & Holstege, F. C. P., 10 Oct 2022, In: EMBO molecular medicine. 14, 10, p. e16001 e16001.

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

    Open Access
    25 Citations (Scopus)

  • Mutation accumulation in mtDNA of cancers resembles mutagenesis in normal stem cells

    Manders, F., van Dinter, J. & van Boxtel, R., 22 Dec 2022, In: iScience. 25, 12, p. 105610 105610.

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

    Open Access
    1 Citation (Scopus)

  • MutationalPatterns: the one stop shop for the analysis of mutational processes

    Manders, F., Brandsma, A. M., de Kanter, J., Verheul, M., Oka, R., van Roosmalen, M. J., van der Roest, B., van Hoeck, A., Cuppen, E. & van Boxtel, R., 15 Feb 2022, In: BMC genomics. 23, 1, p. 134

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

    Open Access
    68 Citations (Scopus)

  • Sister chromatid exchanges induced by perturbed replication can form independently of BRCA1, BRCA2 and RAD51

    Heijink, A. M., Stok, C., Porubsky, D., Manolika, E. M., de Kanter, J. K., Kok, Y. P., Everts, M., de Boer, H. R., Audrey, A., Bakker, F. J., Wierenga, E., Tijsterman, M., Guryev, V., Spierings, D. C. J., Knipscheer, P., van Boxtel, R., Ray Chaudhuri, A., Lansdorp, P. M. & van Vugt, M. A. T. M., 7 Nov 2022, In: Nature Communications. 13, 1, p. 6722 6722.

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

    Open Access
    19 Citations (Scopus)

  • Whole-genome sequencing and mutational analysis of human cord-blood derived stem and progenitor cells

    Rosendahl Huber, A., van Leeuwen, A. J. C. N., Peci, F., de Kanter, J. K., Bertrums, E. J. M. & van Boxtel, R., 17 Jun 2022, In: STAR protocols. 3, 2, p. 101361 101361.

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

    Open Access
    3 Citations (Scopus)
  • 2021

    Antiviral treatment causes a unique mutational signature in cancers of transplantation recipients

    de Kanter, J. K., Peci, F., Bertrums, E., Rosendahl Huber, A., van Leeuwen, A., van Roosmalen, M. J., Manders, F., Verheul, M., Oka, R., Brandsma, A. M., Bierings, M., Belderbos, M. & van Boxtel, R., 7 Oct 2021, In: Cell stem cell. 28, 10, p. 1726-1739.e6

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

    Open Access
    28 Citations (Scopus)

  • Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

    van den Boogaard, M. L., Oka, R., Hakkert, A., Schild, L., Ebus, M. E., van Gerven, M. R., Zwijnenburg, D. A., Molenaar, P., Hoyng, L. L., Dolman, M. E. M., Essing, A. H. W., Koopmans, B., Helleday, T., Drost, J., van Boxtel, R., Versteeg, R., Koster, J. & Molenaar, J. J., 7 Sept 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 36, e2007898118.

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

    Open Access
    10 Citations (Scopus)

  • Evaluating CRISPR-based prime editing for cancer modeling and CFTR repair in organoids

    Geurts, M. H., de Poel, E., Pleguezuelos-Manzano, C., Oka, R., Carrillo, L., Andersson-Rolf, A., Boretto, M., Brunsveld, J. E., van Boxtel, R., Beekman, J. M. & Clevers, H., Oct 2021, In: Life science alliance. 4, 10, e202000940.

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

    Open Access
    72 Citations (Scopus)

  • In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels

    Rothgangl, T., Dennis, M. K., Lin, P. J. C., Oka, R., Witzigmann, D., Villiger, L., Qi, W., Hruzova, M., Kissling, L., Lenggenhager, D., Borrelli, C., Egli, S., Frey, N., Bakker, N., Walker, J. A., Kadina, A. P., Victorov, D. V., Pacesa, M., Kreutzer, S. & Kontarakis, Z. & 12 others, Moor, A., Jinek, M., Weissman, D., Stoffel, M., van Boxtel, R., Holden, K., Pardi, N., Thöny, B., Häberle, J., Tam, Y. K., Semple, S. C. & Schwank, G., Aug 2021, In: Nature biotechnology. 39, 8, p. 949-957 9 p.

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

    Open Access
    220 Citations (Scopus)

  • In vivo cytidine base editing of hepatocytes without detectable off-target mutations in RNA and DNA

    Villiger, L., Rothgangl, T., Witzigmann, D., Oka, R., Lin, P. J. C., Qi, W., Janjuha, S., Berk, C., Ringnalda, F., Beattie, M. B., Stoffel, M., Thöny, B., Hall, J., Rehrauer, H., van Boxtel, R., Tam, Y. K. & Schwank, G., Feb 2021, In: Nature biomedical engineering. 5, 2, p. 179-189 11 p.

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

    70 Citations (Scopus)

  • Molecular characterization of Barrett's esophagus at single-cell resolution

    Busslinger, G. A., de Barbanson, B., Oka, R., Weusten, B. L. A., de Maat, M., van Hillegersberg, R., Brosens, L. A. A., van Boxtel, R., van Oudenaarden, A. & Clevers, H., 23 Nov 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 47

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

    Open Access
    12 Citations (Scopus)

  • Mutation signatures of pediatric acute myeloid leukemia and normal blood progenitors associated with differential patient outcomes

    Brandsma, A. M., Bertrums, E. J. M., van Roosmalen, M. J., Hofman, D. A., Oka, R., Verheul, M., Manders, F., Ubels, J., Belderbos, M. E. & van Boxtel, R., Sept 2021, In: Blood cancer discovery. 2, 5, p. 484-499 16 p.

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

    Open Access

  • Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients

    Valle-Inclan, J. E., Stangl, C., de Jong, A. C., van Dessel, L. F., van Roosmalen, M. J., Helmijr, J. C. A., Renkens, I., Janssen, R., de Blank, S., de Witte, C. J., Martens, J. W. M., Jansen, M. P. H. M., Lolkema, M. P. & Kloosterman, W. P., Dec 2021, In: Genome Medicine. 13, 1, 86.

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

    Open Access
    20 Citations (Scopus)

  • Patient-derived organoids model cervical tissue dynamics and viral oncogenesis in cervical cancer

    Lõhmussaar, K., Oka, R., Espejo Valle-Inclan, J., Smits, M. H. H., Wardak, H., Korving, J., Begthel, H., Proost, N., van de Ven, M., Kranenburg, O. W., Jonges, T. G. N., Zweemer, R. P., Veersema, S., van Boxtel, R. & Clevers, H., 5 Aug 2021, In: Cell Stem Cell. 28, 8, p. 1380-1396.e6

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

    Open Access
    116 Citations (Scopus)

  • Precancerous liver diseases do not cause increased mutagenesis in liver stem cells

    Nguyen, L., Jager, M., Lieshout, R., de Ruiter, P. E., Locati, M. D., Besselink, N., van der Roest, B., Janssen, R., Boymans, S., de Jonge, J., IJzermans, J. N. M., Doukas, M., Verstegen, M. M. A., van Boxtel, R., van der Laan, L. J. W., Cuppen, E. & Kuijk, E., 18 Nov 2021, In: Communications biology. 4, 1, p. 1301

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

    Open Access
    7 Citations (Scopus)

  • Single-cell atlas reveals meningeal leukocyte heterogeneity in the developing mouse brain

    Zelco, A., Börjesson, V., De Kanter, J. K., Lebrero-Fernandez, C., Lauschke, V. M., Rocha-Ferreira, E., Nilsson, G., Nair, S., Svedin, P., Bemark, M., Hagberg, H., Mallard, C., Holstege, F. C. P. & Wang, X., 1 Aug 2021, In: Genes and Development. 35, 15-16, p. 1190-1207 18 p.

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

    Open Access
    18 Citations (Scopus)

  • The mutational landscape of human somatic and germline cells

    Moore, L., Cagan, A., Coorens, T. H. H., Neville, M. D. C., Sanghvi, R., Sanders, M. A., Oliver, T. R. W., Leongamornlert, D., Ellis, P., Noorani, A., Mitchell, T. J., Butler, T. M., Hooks, Y., Warren, A. Y., Jorgensen, M., Dawson, K. J., Menzies, A., O'Neill, L., Latimer, C. & Teng, M. & 8 others, van Boxtel, R., Iacobuzio-Donahue, C. A., Martincorena, I., Heer, R., Campbell, P. J., Fitzgerald, R. C., Stratton, M. R. & Rahbari, R., Sept 2021, In: Nature. 597, 7876, p. 381-386 6 p.

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

    167 Citations (Scopus)
  • 2020

    An organoid biobank for childhood kidney cancers that captures disease and tissue heterogeneity

    Calandrini, C., Schutgens, F., Oka, R., Margaritis, T., Candelli, T., Mathijsen, L., Ammerlaan, C., van Ineveld, R. L., Derakhshan, S., de Haan, S., Dolman, E., Lijnzaad, P., Custers, L., Begthel, H., Kerstens, H. H. D., Visser, L. L., Rookmaaker, M., Verhaar, M., Tytgat, G. A. M. & Kemmeren, P. & 11 others, de Krijger, R. R., Al-Saadi, R., Pritchard-Jones, K., Kool, M., Rios, A. C., van den Heuvel-Eibrink, M. M., Molenaar, J. J., van Boxtel, R., Holstege, F. C. P., Clevers, H. & Drost, J., 11 Mar 2020, In: Nature communications. 11, 1, p. 1310 1310.

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

    Open Access
    196 Citations (Scopus)

  • CRISPR-Based Adenine Editors Correct Nonsense Mutations in a Cystic Fibrosis Organoid Biobank

    Geurts, M. H., de Poel, E., Amatngalim, G. D., Oka, R., Meijers, F. M., Kruisselbrink, E., van Mourik, P., Berkers, G., de Winter-de Groot, K. M., Michel, S., Muilwijk, D., Aalbers, B. L., Mullenders, J., Boj, S. F., Suen, S. W. F., Brunsveld, J. E., Janssens, H. M., Mall, M. A., Graeber, S. Y. & van Boxtel, R. & 3 others, van der Ent, C. K., Beekman, J. M. & Clevers, H., 2 Apr 2020, In: Cell stem cell. 26, 4, p. 503-510.e7

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

    149 Citations (Scopus)

  • Diverse BRAF gene fusions confer resistance to EGFR-Targeted therapy via differential modulation of BRAF activity

    Stangl, C., Post, J. B., Van Roosmalen, M. J., Hami, N., Verlaan-Klink, I., Vos, H. R., Van Es, R. M., Koudijs, M. J., Voest, E. E., Snippert, H. J. G. & Kloosterman, W. P., 1 Apr 2020, In: Molecular Cancer Research. 18, 4, p. 537-548 12 p.

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

    15 Citations (Scopus)

  • Mutation accumulation and developmental lineages in normal and Down syndrome human fetal haematopoiesis

    Hasaart, K. A. L., Manders, F., van der Hoorn, M.-L., Verheul, M., Poplonski, T., Kuijk, E., de Sousa Lopes, S. M. C. & van Boxtel, R., 31 Jul 2020, In: Scientific Reports. 10, 1, p. 12991 12991.

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

    Open Access
    21 Citations (Scopus)

  • Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia

    Waanders, E., Gu, Z., Dobson, S. M., Antić, Ž., Crawford, J. C., Ma, X., Edmonson, M. N., Payne-Turner, D., van de Vorst, M., Jongmans, M. C. J., McGuire, I., Zhou, X., Wang, J., Shi, L., Pounds, S., Pei, D., Cheng, C., Song, G., Fan, Y. & Shao, Y. & 23 others, Rusch, M., McCastlain, K., Yu, J., van Boxtel, R., Blokzijl, F., Iacobucci, I., Roberts, K. G., Wen, J., Wu, G., Ma, J., Easton, J., Neale, G., Olsen, S. R., Nichols, K. E., Pui, C.-H., Zhang, J., Evans, W. E., Relling, M. V., Yang, J. J., Thomas, P. G., Dick, J. E., Kuiper, R. & Mullighan, C. G., Jul 2020, In: Blood cancer discovery. 1, 1, p. 96-111 16 p.

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

    Open Access

  • Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli

    Genomics England Research Consortium, Apr 2020, In: Nature. 580, 7802, p. 269-273 5 p.

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

    650 Citations (Scopus)

  • Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing

    Stangl, C., de Blank, S., Renkens, I., Westera, L., Verbeek, T., Valle-Inclan, J. E., González, R. C., Henssen, A. G., van Roosmalen, M. J., Stam, R. W., Voest, E. E., Kloosterman, W. P., van Haaften, G. & Monroe, G. R., 1 Dec 2020, In: Nature Communications. 11, 1, 2861.

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

    Open Access
    41 Citations (Scopus)

  • Prime editing for functional repair in patient-derived disease models

    Schene, I. F., Joore, I. P., Oka, R., Mokry, M., van Vugt, A. H. M., van Boxtel, R., van der Doef, H. P. J., van der Laan, L. J. W., Verstegen, M. M. A., van Hasselt, P. M., Nieuwenhuis, E. E. S. & Fuchs, S. A., 23 Oct 2020, In: Nature communications. 11, 1, p. 5352 5352.

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

    Open Access
    140 Citations (Scopus)

  • The mutational impact of culturing human pluripotent and adult stem cells

    Kuijk, E., Jager, M., van der Roest, B., Locati, M. D., Van Hoeck, A., Korzelius, J., Janssen, R., Besselink, N., Boymans, S., van Boxtel, R. & Cuppen, E., 19 May 2020, In: Nature communications. 11, 1, p. 2493 2493.

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

    Open Access
    71 Citations (Scopus)
  • 2019

    Characterizing Mutational Load and Clonal Composition of Human Blood

    Huber, A. R., Manders, F., Oka, R. & van Boxtel, R., 11 Jul 2019, In: Journal of visualized experiments : JoVE. 2019, 149, e59846.

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

    6 Citations (Scopus)

  • CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing

    de Kanter, J. K., Lijnzaad, P., Candelli, T., Margaritis, T. & Holstege, F. C. P., 19 Sept 2019, In: Nucleic Acids Research. 47, 16, p. E95

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

    Open Access
    160 Citations (Scopus)

  • Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer

    Jager, M., Blokzijl, F., Kuijk, E., Bertl, J., Vougioukalaki, M., Janssen, R., Besselink, N., Boymans, S., de Ligt, J., Pedersen, J. S., Hoeijmakers, J., Pothof, J., van Boxtel, R. & Cuppen, E., Jul 2019, In: Genome research. 29, 7, p. 1067-1077 11 p.

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

    Open Access
    56 Citations (Scopus)

  • Early divergence of mutational processes in human fetal tissues

    Kuijk, E., Blokzijl, F., Jager, M., Besselink, N., Boymans, S., Chuva de Sousa Lopes, S. M., van Boxtel, R. & Cuppen, E., May 2019, In: Science advances. 5, 5, p. eaaw1271 eaaw1271.

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

    Open Access
    23 Citations (Scopus)

  • Oral mucosal organoids as a potential platform for personalized cancer therapy

    Driehuis, E., Kolders, S., Spelier, S., Lõhmussaar, K., Willems, S. M., Devriese, L. A., de Bree, R., de Ruiter, E. J., Korving, J., Begthel, H., van Es, J. H., Geurts, V., He, G. W., van Jaarsveld, R. H., Oka, R., Muraro, M. J., Vivié, J., Zandvliet, M. M. J. M., Hendrickx, A. P. A. & Iakobachvili, N. & 8 others, Sridevi, P., Kranenburg, O., van Boxtel, R., Kops, G. J. P. L., Tuveson, D. A., Peters, P. J., van Oudenaarden, A. & Clevers, H., Jul 2019, In: Cancer Discovery. 9, 7, p. 852-871 20 p.

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

    258 Citations (Scopus)

  • Probing the Tumor Suppressor Function of BAP1 in CRISPR-Engineered Human Liver Organoids

    Artegiani, B., van Voorthuijsen, L., Lindeboom, R. G. H., Seinstra, D., Heo, I., Tapia, P., López-Iglesias, C., Postrach, D., Dayton, T., Oka, R., Hu, H., van Boxtel, R., van Es, J. H., Offerhaus, J., Peters, P. J., van Rheenen, J., Vermeulen, M. & Clevers, H., 6 Jun 2019, In: Cell stem cell. 24, 6, p. 927-943.e6

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

    146 Citations (Scopus)

  • Tubuloids derived from human adult kidney and urine for personalized disease modeling

    Schutgens, F., Rookmaaker, M. B., Margaritis, T., Rios, A., Ammerlaan, C., Jansen, J., Gijzen, L., Vormann, M., Vonk, A., Viveen, M., Yengej, F. Y., Derakhshan, S., de Winter-de Groot, K. M., Artegiani, B., van Boxtel, R., Cuppen, E., Hendrickx, A. P. A., van den Heuvel-Eibrink, M. M., Heitzer, E. & Lanz, H. & 7 others, Beekman, J., Murk, J.-L., Masereeuw, R., Holstege, F., Drost, J., Verhaar, M. C. & Clevers, H., Mar 2019, In: Nature biotechnology. 37, 3, p. 303-313 11 p.

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

    300 Citations (Scopus)
  • 2018

    Measuring mutation accumulation in single human adult stem cells by whole-genome sequencing of organoid cultures

    Jager, M., Blokzijl, F., Sasselli, V., Boymans, S., Janssen, R., Besselink, N., Clevers, H., Van Boxtel, R. & Cuppen, E., 1 Jan 2018, In: Nature Protocols. 13, 1, p. 59-78 20 p.

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

    50 Citations (Scopus)

  • MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

    Blokzijl, F., Janssen, R., van Boxtel, R. & Cuppen, E., 2018, In: Genome Medicine. 10, 1, 33.

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

    Open Access
    415 Citations (Scopus)

  • Somatic Mutations Reveal Lineage Relationships and Age-Related Mutagenesis in Human Hematopoiesis

    Osorio, F. G., Rosendahl Huber, A., Oka, R., Verheul, M., Patel, S. H., Hasaart, K., de la Fonteijne, L., Varela, I., Camargo, F. D. & van Boxtel, R., 27 Nov 2018, In: Cell reports. 25, 9, p. 2308-2316.e4

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

    Open Access
    159 Citations (Scopus)
  • 2015

    Circulating microRNAs in sera correlate with soluble biomarkers of immune activation but do not predict mortality in ART treated individuals with HIV-1 infection: A case control study

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D., Matthews, C., Mollerup, D., Pearson, M., Phillips, A., Reilev, S., Tillmann, K., Varea, S., Angus, B., Babiker, A., Cordwell, B., Darbyshire, J., Dodds, W., Fleck, S., Horton, J., Hudson, F., Moraes, Y., Pacciarini, F., Palfreeman, A., Paton, N., Smith, N., Van Hooff, F., Bebchuk, J., Collins, G., Denning, E., DuChene, A., Fosdick, L., Harrison, M., Herman-Lamin, K., Krum, E., Larson, G., Neaton, J., Nelson, R., Quan, K., Quan, S., Schultz, T., Thompson, G., Wyman, N., Carey, C., Chan, F., Cooper, D., Courtney-Rodgers, D., Drummond, F., Harrod, M., Jacoby, S., Kearney, L., Lin, E., Pett, S., Robson, R., Seneviratne, N., Stewart, M., Watts, E., Finley, E., Gordin, F., Sánchez, A., Standridge, B., Belloso, W., Davey, R., Duprez, D., Gatell, J., Hoy, J., Lifson, A., Pederson, C., Perez, G., Price, R., Prineas, R., Rhame, F., Sampson, J., Worley, J., Modlin, J., Beral, V., Chaisson, R., Fleming, T., Hill, C., Kim, K., Murray, B., Pick, B., Seligmann, M., Weller, I., Cahill, K., Fox, L., Luzar, M., Martinez, A., McNay, L., Pierson, J., Tierney, J., Vogel, S., Costas, V., Eckstrand, J., Brown, S., Abusamra, L., Angel, E., Aquilia, S., Benetucci, J., Bittar, V., Bogdanowicz, E., Cahn, P., Casiro, A., Contarelli, J., Corral, J., Daciuk, L., David, D., Dobrzanski, W., Duran, A., Ebenrstejin, J., Ferrari, I., Fridman, D., Galache, V., Guaragna, G., Ivalo, S., Krolewiecki, A., Lanusse, I., Laplume, H., Lasala, M., Lattes, R., Lazovski, J., Lopardo, G., Losso, M., Lourtau, L., Lupo, S., Maranzana, A., Marson, C., Massera, L., Moscatello, G., Olivia, S., Otegui, I., Palacios, L., Parlante, A., Salomon, H., Sanchez, M., Somenzini, C., Suarez, C., Tocci, M., Toibaro, J., Zala, C., Agrawal, S., Ambrose, P., Anderson, C., Anderson, J., Baker, D., Beileiter, K., Blavius, K., Bloch, M., Boyle, M., Bradford, D., Britton, P., Brown, P., Busic, T., Cain, A., Carrall, L., Carson, S., Chenoweth, I., Chuah, J., Clark, F., Clemons, J., Clezy, K., Cortissos, P., Cunningham, N., Curry, M., Daly, L., D'Arcy-Evans, C., Del Rosario, R., Dinning, S., Dobson, P., Donohue, W., Doong, N., Downs, C., Edwards, E., Edwards, S., Egan, C., Ferguson, W., Finlayson, R., Forsdyke, C., Foy, L., Franic, T., Frater, A., French, M., Gleeson, D., Gold, J., Habel, P., Haig, K., Hardy, S., Holland, R., Hudson, J., Hutchison, R., Hyland, N., James, R., Johnston, C., Kelly, M., King, M., Kunkel, K., Lau, H., Leamy, J., Lester, D., Leung, J., Lohmeyer, A., Lowe, K., MacRae, K., Magness, C., Martinez, O., Maruszak, H., Medland, N., Miller, S., Murray, J., Negus, P., Newman, R., Ngieng, M., Nowlan, C., Oddy, J., Orford, N., Orth, D., Patching, J., Plummer, M., Price, S., Primrose, R., Prone, I., Ree, H., Remington, C., Richardson, R., Robinson, S., Rogers, G., Roney, J., Roth, N., Russell, D., Ryan, S., Sarangapany, J., Schmidt, T., Schneider, K., Shields, C., Silberberg, C., Shaw, D., Skett, J., Smith, D., Soo, T. 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  • Development and Validation of a Risk Score for Chronic Kidney Disease in HIV Infection Using Prospective Cohort Data from the D:A:D Study

    D:A:D study group, the Royal Free Hospital Clinic Cohort, and the INSIGHT, SMART, and ESPRIT study groups, 1 Mar 2015, In: PLoS Medicine. 12, 3, e1001809.

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