Group De Ridder, section Genetics

2025

Dissemination of IncQ1 Plasmids Harboring NTE_KPC-IId in a Brazilian Hospital

Boralli, C. M. D. S., Paganini, J. A., Meneses, R. S., Mata, C. P. S. M. D., Leite, E. M. M., Schürch, A. C., Paganelli, F. L., Willems, R. J. L. & Camargo, I. L. B. C., Jan 2025, In: Microorganisms. 13, 1, 16 p., 180.

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Long-range enhancer-controlled genes are hypersensitive to regulatory factor perturbations

Tjalsma, S. J. D., Rinzema, N. J., Verstegen, M. J. A. M., Robers, M. J., Nieto-Aliseda, A., Gremmen, R. A., Allahyar, A., Muraro, M. J., Krijger, P. H. L. & de Laat, W., 12 Mar 2025, In: Cell genomics. 5, 3, 100778.

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Long-read sequencing identifies copy-specific markers of SMN gene conversion in spinal muscular atrophy

Zwartkruis, M. M., Elferink, M. G., Gommers, D., Signoria, I., Blasco-Pérez, L., Costa-Roger, M., van der Sel, J., Renkens, I. J., Green, J. W., Kortooms, J. V., Vermeulen, C., Straver, R., van Deutekom, H. W. M., Veldink, J. H., Asselman, F., Tizzano, E. F., Wadman, R. I., van der Pol, W. L., van Haaften, G. W. & Groen, E. J. N., 21 Mar 2025, In: Genome Medicine. 17, 1, 26.

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NGS-based Aspergillus detection in plasma and lung lavage of children with invasive pulmonary aspergillosis

Wesdorp, E., Rotte, L., Chen, L.-T., Jager, M., Besselink, N., Vermeulen, C., Hagen, F., van der Bruggen, T., Lindemans, C., Wolfs, T., Bont, L. & de Ridder, J., 17 Mar 2025, In: npj Genomic Medicine. 10, 1, 24.

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2024

Co-expression in tissue-specific gene networks links genes in cancer-susceptibility loci to known somatic driver genes

Urzúa-Traslaviña, C. G., van Lieshout, T., Boulogne, F., Domanegg, K., Zidan, M., Bakker, O. B., Claringbould, A., de Ridder, J., Zwart, W., Westra, H. J., Deelen, P. & Franke, L., 15 Jul 2024, In: BMC Medical Genomics. 17, 1, 14 p., 186.

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Evidence of survival bias in the association between APOE-Є4 and age at ischemic stroke onset

von Berg, J., McArdle, P. F., Häppölä, P., Haessler, J., Kooperberg, C., Lemmens, R., Pezzini, A., Thijs, V., Pulit, S. L., Kittner, S. J., Mitchell, B. D., de Ridder, J., van der Laan, S. W. & SiGN, FinnGen, Women’s Health Initiative, 2 Sept 2024, In: Frontiers in Genetics. 15, 10 p., 1392061.

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2023

Characterization of bla_KPC-2 and bla_NDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone

Boralli, C. M. D. S., Paganini, J. A., Meneses, R. S., Mata, C. P. S. M. D., Leite, E. M. M., Schürch, A. C., Paganelli, F. L., Willems, R. J. L. & Camargo, I. L. B. C., May 2023, In: Antibiotics. 12, 5, 926.

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Comprehensive benchmark and architectural analysis of deep learning models for nanopore sequencing basecalling

Pagès-Gallego, M. & de Ridder, J., 11 Apr 2023, In: Genome Biology. 24, 1, p. 1-18 18 p., 71.

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Corneal Transplantation for Infectious Keratitis: A Prospective Dutch Registry Study

Veugen, J. M. J., Dunker, S. L., Wolffs, P. F. G., Savelkoul, P. H. M., Winkens, B., van den Biggelaar, F. J. H. M., Nuijts, R. M. M. A. & Netherlands Cornea Transplant Network (NCTN), 1 Nov 2023, In: Cornea. 42, 11, p. 1414-1421 8 p.

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Echtvar: compressed variant representation for rapid annotation and filtering of SNPs and indels

Pedersen, B. S. & de Ridder, J., 11 Jan 2023, In: Nucleic acids research. 51, 1, p. 1-8 8 p., e3.

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Formalin-Fixed, Paraffin-Embedded-Targeted Locus Capture: A Next-Generation Sequencing Technology for Accurate DNA-Based Gene Fusion Detection in Bone and Soft Tissue Tumors

Stelloo, E., Meijers, R. W. J., Swennenhuis, J. F., Allahyar, A., Hajo, K., Cangiano, M., de Leng, W. W. J., van Helvert, S., Van der Meulen, J., Creytens, D., van Kempen, L. C., Cleton-Jansen, A.-M., Bovee, J. V. M. G., de Laat, W., Splinter, E. & Feitsma, H., Oct 2023, In: Journal of Molecular Diagnostics. 25, 10, p. 758-770 13 p.

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Genetic immune escape landscape in primary and metastatic cancer

Martínez-Jiménez, F., Priestley, P., Shale, C., Baber, J., Rozemuller, E. & Cuppen, E., May 2023, In: Nature Genetics. 55, 5, p. 820-831 12 p.

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Multi-country metabolic signature discovery for chicken health classification

Wolthuis, J. C., Magnúsdóttir, S., Stigter, E., Tang, Y. F., Jans, J., Gilbert, M., van der Hee, B., Langhout, P., Gerrits, W., Kies, A., de Ridder, J. & van Mil, S., 2 Feb 2023, In: Metabolomics. 19, 2, 9.

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Pan-cancer whole-genome comparison of primary and metastatic solid tumours

Martínez-Jiménez, F., Movasati, A., Brunner, S. R., Nguyen, L., Priestley, P., Cuppen, E. & Van Hoeck, A., 8 Jun 2023, In: Nature. 618, 7964, p. 333-341 9 p.

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Predicting response to enzalutamide and abiraterone in metastatic prostate cancer using whole-omics machine learning

de Jong, A. C., Danyi, A., van Riet, J., de Wit, R., Sjöström, M., Feng, F., de Ridder, J. & Lolkema, M. P., 8 Apr 2023, In: Nature Communications. 14, 1, p. 1-19 19 p., 1968.

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Targeted locus amplification reveals heterogeneity between and within CFTR genotypes and association with CFTR function in patient-derived intestinal organoids

Lefferts, J. W., Boersma, V., Nieuwenhuijze, N. D. A., Suen, S. W. F., Hajo, K., Collantes, N. S., Vermeulen, C., Groeneweg, T., Hagemeijer, M. C., de Jonge, H. R., van der Ent, C. K., Splinter, E. & Beekman, J. M., May 2023, In: Journal of Cystic Fibrosis. 22, 3, p. 538-547 10 p.

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The genome-wide mutational consequences of DNA hypomethylation

Besselink, N., Keijer, J., Vermeulen, C., Boymans, S., de Ridder, J., van Hoeck, A., Cuppen, E. & Kuijk, E., 27 Apr 2023, In: Scientific Reports. 13, 1, 6874.

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Ultra-fast deep-learned CNS tumour classification during surgery

Vermeulen, C., Pagès-Gallego, M., Kester, L., Kranendonk, M. E. G., Wesseling, P., Verburg, N., de Witt Hamer, P., Kooi, E. J., Dankmeijer, L., van der Lugt, J., van Baarsen, K., Hoving, E. W., Tops, B. B. J. & de Ridder, J., 26 Oct 2023, In: Nature. 622, p. 842-849 8 p.

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WEE1 inhibitor adavosertib in combination with carboplatin in advanced TP53 mutated ovarian cancer: A biomarker-enriched phase II study

Embaby, A., Kutzera, J., Geenen, J. J., Pluim, D., Hofland, I., Sanders, J., Lopez-Yurda, M., Beijnen, J. H., Huitema, A. D. R., Witteveen, P. O., Steeghs, N., van Haaften, G., van Vugt, M. A. T. M., de Ridder, J. & Opdam, F. L., Jul 2023, In: Gynecologic Oncology. 174, p. 239-246 8 p.

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2022

A multi-platform reference for somatic structural variation detection

Espejo Valle-Inclan, J., Besselink, N. J. M., de Bruijn, E., Cameron, D. L., Ebler, J., Kutzera, J., van Lieshout, S., Marschall, T., Nelen, M., Priestley, P., Renkens, I., Roemer, M. G. M., van Roosmalen, M. J., Wenger, A. M., Ylstra, B., Fijneman, R. J. A., Kloosterman, W. P. & Cuppen, E., 8 Jun 2022, In: Cell genomics. 2, 6, 100139.

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Anti-Müllerian Hormone and Cardiometabolic Disease in Women: A Two-Sample Mendelian Randomization Study

Verdiesen, R. M. G., von Berg, J., Said, M. A., van der Harst, P., Mahajan, A., van Gils, C. H., van der Schouw, Y. T. & Onland-Moret, N. C., 25 Jul 2022, In: Reviews in Cardiovascular Medicine. 23, 8, 269.

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Different responses to DNA damage determine ageing differences between organs

Vougioukalaki, M., Demmers, J., Vermeij, W. P., Baar, M., Bruens, S., Magaraki, A., Kuijk, E., Jager, M., Merzouk, S., Brandt, R. M. C., Kouwenberg, J., van Boxtel, R., Cuppen, E., Pothof, J. & Hoeijmakers, J. H. J., Apr 2022, In: Aging Cell. 21, 4, p. 1-18 e13562.

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Distinct Genomic Profiles Are Associated with Treatment Response and Survival in Ovarian Cancer

de Witte, C. J., Kutzera, J., van Hoeck, A., Nguyen, L., Boere, I. A., Jalving, M., Ottevanger, P. B., van Schaik-van de Mheen, C., Stevense, M., Kloosterman, W. P., Zweemer, R. P., Cuppen, E. & Witteveen, P. O., 2 Mar 2022, In: Cancers. 14, 6, p. 1-18 1511.

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PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics

von Berg, J., Ten Dam, M., van der Laan, S. W. & de Ridder, J., 1 Jul 2022, In: Bioinformatics (Oxford, England). 38, 1, p. i212-i219

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2021

Accurate detection of circulating tumor DNA using nanopore consensus sequencing

Marcozzi, A., Jager, M., Elferink, M., Straver, R., van Ginkel, J. H., Peltenburg, B., Chen, L.-T., Renkens, I., van Kuik, J., Terhaard, C., de Bree, R., Devriese, L. A., Willems, S. M., Kloosterman, W. P. & de Ridder, J., 9 Dec 2021, In: npj Genomic Medicine. 6, 1, p. 1-11 106.

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Allele-specific expression of GATA2 due to epigenetic dysregulation in CEBPA double-mutant AML

Mulet-Lazaro, R., van Herk, S., Erpelinck, C., Bindels, E., Sanders, M. A., Vermeulen, C., Renkens, I., Valk, P., Melnick, A. M., de Ridder, J., Rehli, M., Gebhard, C., Delwel, R. & Wouters, B. J., 15 Jul 2021, In: Blood. 138, 2, p. 160-177 18 p.

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Familial Occurrence of Adult Granulosa Cell Tumors: Analysis of Whole-Genome Germline Variants

Roze, J. F., Kutzera, J., Koole, W., Ausems, M. G. E. M., Engelstad, K., Piek, J. M. J., de Kroon, C. D., Verheijen, R. H. M., van Haaften, G., Zweemer, R. P. & Monroe, G. R., 2 May 2021, In: Cancers. 13, 10, 13 p., 2430.

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Healthcare professionals' perspectives on a blended care program in primary care; A qualitative study

Toonders, S. A. J., Poolman, E. Y., Nieboer, M. E., Pisters, M. F. & Veenhof, C., Dec 2021, In: Internet Interventions. 26, 6 p., 100440.

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Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression

Vos, E. S. M., Valdes-Quezada, C., Huang, Y., Allahyar, A., Verstegen, M. J. A. M., Felder, A. K., van der Vegt, F., Uijttewaal, E. C. H., Krijger, P. H. L. & de Laat, W., 5 Aug 2021, In: Molecular Cell. 81, 15, p. 3082-3095.e6

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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, 1301.

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Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning

Nieboer, M. M., Nguyen, L. & de Ridder, J., Dec 2021, In: Scientific Reports. 11, 1, 14411.

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Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns

Bollen, Y., Stelloo, E., van Leenen, P., van den Bos, M., Ponsioen, B., Lu, B., van Roosmalen, M. J., Bolhaqueiro, A. C. F., Kimberley, C., Mossner, M., Cross, W. C. H., Besselink, N. J. M., van der Roest, B., Boymans, S., Oost, K. C., de Vries, S. G., Rehmann, H., Cuppen, E., Lens, S. M. A. & Kops, G. J. P. L. & 6 others, Kloosterman, W. P., Terstappen, L. W. M. M., Barnes, C. P., Sottoriva, A., Graham, T. A. & Snippert, H. J. G., Aug 2021, In: Nature Genetics. 53, 8, p. 1187-1195 9 p.

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Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing

Allahyar, A., Pieterse, M., Swennenhuis, J., Los-de Vries, G. T., Yilmaz, M., Leguit, R., Meijers, R. W. J., van der Geize, R., Vermaat, J., Cleven, A., van Wezel, T., Diepstra, A., van Kempen, L. C., Hijmering, N. J., Stathi, P., Sharma, M., Melquiond, A. S. J., de Vree, P. J. P., Verstegen, M. J. A. M. & Krijger, P. H. L. & 9 others, Hajo, K., Simonis, M., Rakszewska, A., van Min, M., de Jong, D., Ylstra, B., Feitsma, H., Splinter, E. & de Laat, W., 7 Jun 2021, In: Nature Communications. 12, 1, p. 1-15 3361.

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2020

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

PCAWG Tumor Subtypes and Clinical Translation Working Group, 5 Feb 2020, In: Nature Communications. 11, 1, 12 p., 728.

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Alternate approach to stroke phenotyping identifies a genetic risk locus for small vessel stroke

von Berg, J., van der Laan, S. W., McArdle, P. F., Malik, R., Kittner, S. J., Mitchell, B. D., Worrall, B. B., de Ridder, J. & Pulit, S. L., Jul 2020, In: European Journal of Human Genetics. 28, 7, p. 963-972 10 p.

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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.

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Gene networks constructed through simulated treatment learning can predict proteasome inhibitor benefit in multiple myeloma

Ubels, J., Sonneveld, P., van Vliet, M. H. & de Ridder, J., 15 Nov 2020, In: Clinical Cancer Research. 26, 22, p. 5952-5961 10 p.

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Human extrahepatic and intrahepatic cholangiocyte organoids show region-specific differentiation potential and model cystic fibrosis-related bile duct disease

Verstegen, M. M. A., Roos, F. J. M., Burka, K., Gehart, H., Jager, M., de Wolf, M., Bijvelds, M. J. C., de Jonge, H. R., Ardisasmita, A. I., van Huizen, N. A., Roest, H. P., de Jonge, J., Koch, M., Pampaloni, F., Fuchs, S. A., Schene, I. F., Luider, T. M., van der Doef, H. P. J., Bodewes, F. A. J. A. & de Kleine, R. H. J. & 6 others, Spee, B., Kremers, G.-J., Clevers, H., IJzermans, J. N. M., Cuppen, E. & van der Laan, L. J. W., 14 Dec 2020, In: Scientific Reports. 10, 1, p. 1-16 16 p., 21900.

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MetaboShiny: interactive analysis and metabolite annotation of mass spectrometry-based metabolomics data

Wolthuis, J. C., Magnusdottir, S., Pras-Raves, M., Moshiri, M., Jans, J. J. M., Burgering, B., van Mil, S. & de Ridder, J., 11 Sept 2020, In: Metabolomics. 16, 9, p. 99

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Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies

Vermeulen, C., Allahyar, A., Bouwman, B. A. M., Krijger, P. H. L., Verstegen, M. J. A. M., Geeven, G., Valdes-Quezada, C., Renkens, I., Straver, R., Kloosterman, W. P., de Ridder, J. & de Laat, W., 1 Feb 2020, In: Nature Protocols. 15, 2, p. 364-397 34 p.

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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., 5 Jun 2020, In: Nature Communications. 11, 1, 2861.

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10 Citations (Scopus)

Patient-Derived Ovarian Cancer Organoids Mimic Clinical Response and Exhibit Heterogeneous Inter- and Intrapatient Drug Responses

de Witte, C. J., Espejo Valle-Inclan, J., Hami, N., Lõhmussaar, K., Kopper, O., Vreuls, C. P. H., Jonges, G. N., van Diest, P., Nguyen, L., Clevers, H., Kloosterman, W. P., Cuppen, E., Snippert, H. J. G., Zweemer, R. P., Witteveen, P. O. & Stelloo, E., 16 Jun 2020, In: Cell Reports. 31, 11, 8 p., 107762.

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Position Paper ETFAD: Behandeling constitutioneel eczeem rondom zwangerschap

Translated title of the contribution: Position Paper ETFAD: Treatment of atopic dermatitis during pregnancyde Bruin-Weller, M. S., van Beek, D. & Schuttelaar, M. L. A., 2020, In: Nederlands Tijdschrift voor Dermatologie en Venereologie. 30, 7, p. 10-13 4 p.

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Rainforest: A random forest approach to predict treatment benefit in data from (failed) clinical drug trials

Ubels, J., Schaefers, T., Punt, C., Guchelaar, H. J. & de Ridder, J., 1 Dec 2020, In: Bioinformatics. 36, S2, p. I601-I609

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sv-callers: A highly portable parallel workflow for structural variant detection in whole-genome sequence data

Kuzniar, A., Maassen, J., Verhoeven, S., Santuari, L., Shneider, C., Kloosterman, W. P. & de Ridder, J., 6 Jan 2020, In: PeerJ. 8, e8214.

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svMIL: Predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning

Nieboer, M. M. & de Ridder, J., 1 Dec 2020, In: Bioinformatics. 36, p. I692-I699

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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., 1 Dec 2020, In: Nature Communications. 11, 1, 12 p., 2493.

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Whole Genome Analysis of Ovarian Granulosa Cell Tumors Reveals Tumor Heterogeneity and a High-Grade TP53-Specific Subgroup

Roze, J., Monroe, G., Kutzera, J., Groeneweg, J., Stelloo, E., Paijens, S., Nijman, H., Meurs, H. V., Lonkhuijzen, L. V., Piek, J., Lok, C., Jonges, G., Witteveen, P., Verheijen, R., Haaften, G. V. & Zweemer, R., 21 May 2020, In: Cancers. 12, 5, 22 p., 1308.

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2019

A data-driven interactome of synergistic genes improves network-based cancer outcome prediction

Allahyar, A., Ubels, J. & de Ridder, J., Feb 2019, In: PLoS Computational Biology. 15, 2, e1006657.

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Causal relationships between obesity and the leading causes of death in women and men

Censin, J. C., Peters, S. A. E., Bovijn, J., Ferreira, T., Pulit, S. L., Mägi, R., Mahajan, A., Holmes, M. V. & Lindgren, C. M., Oct 2019, In: PLoS Genetics. 15, 10, e1008405.

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Group De Ridder, section Genetics

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