Joachim Lütken Weischenfeldt

Search results

• 2025

  Epigenomics-guided precision oncology: Chromatin variants in prostate tumor evolution

  Furlano, K., Keshavarzian, T., Biernath, N., Fendler, A., de Santis, M., Weischenfeldt, J. & Lupien, M., 2025, (Accepted/In press) In: International Journal of Cancer.

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

  Open Access

• GATA3 amplification is associated with high grade disease in non-invasive urothelial bladder cancer but unrelated to patient prognosis

  Plage, H., Frericks, A., Hofbauer, S., Furlano, K., Weinberger, S., Roßner, F., Schallenberg, S., Elezkurtaj, S., Lennartz, M., Marx, A., Samtleben, H., Fisch, M., Rink, M., Slojewski, M., Kaczmarek, K., Ecke, T., Koch, S., Simon, R., Sauter, G. & Zecha, H. & 6 others, Weischenfeldt, J., Klatte, T., Minner, S., Horst, D., Schlomm, T. & Kluth, M., 2025, In: BMC Urology. 25, 1, 8 p., 37.

  Research output: Contribution to journal › Journal article › Research › peer-review

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• 2024

  17p13 (TP53) Deletions Are Associated With an Aggressive Phenotype but Unrelated to Patient Prognosis in Urothelial Bladder Carcinomas

  Kluth, M., Hitzschke, M., Furlano, K., Plage, H., Hofbauer, S., Weinberger, S., Ralla, B., Fendler, A., de Martino, M., Roßner, F., Schallenberg, S., Elezkurtaj, S., Lennartz, M., Marx, A., Samtleben, H., Fisch, M., Rink, M., Slojewski, M., Kaczmarek, K. & Ecke, T. & 10 others, Koch, S., Adamini, N., Weischenfeldt, J., Klatte, T., Minner, S., Simon, R., Sauter, G., Schlomm, T., Horst, D. & Zecha, H., 2024, In: Genes Chromosomes and Cancer. 63, 9, 9 p., e23271.

  Research output: Contribution to journal › Journal article › Research › peer-review

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• CEA (CEACAM5) expression is common in muscle-invasive urothelial carcinoma of the bladder but unrelated to the disease course

  Plage, H., Furlano, K., Neymeyer, J., Weinberger, S., Gerdes, B., Hubatsch, M., Ralla, B., Franz, A., Fendler, A., de Martino, M., Roßner, F., Schallenberg, S., Elezkurtaj, S., Kluth, M., Lennartz, M., Blessin, N. C., Marx, A. H., Samtleben, H., Fisch, M. & Rink, M. & 14 others, Kaczmarek, K., Ecke, T., Hallmann, S., Koch, S., Adamini, N., Minner, S., Simon, R., Sauter, G., Weischenfeldt, J., Klatte, T., Schlomm, T., Horst, D., Zecha, H. & Slojewski, M., 2024, In: BJUI Compass. 5, 6, p. 585–592

  Research output: Contribution to journal › Journal article › Research › peer-review

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  1 Citation (Scopus)

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• Endomucin marks quiescent long-term multi-lineage repopulating hematopoietic stem cells and is essential for their transendothelial migration

  Engelhard, S., Estruch, M., Qin, S., Engelhard, C. A., Rodriguez-Gonzalez, F. G., Drilsvik, M., Martin-Gonzalez, J., Lu, J. W., Bryder, D., Nerlov, C., Weischenfeldt, J., Reckzeh, K. & Theilgaard-Mönch, K., 2024, In: Cell Reports. 43, 7, 22 p., 114475.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  1 Citation (Scopus)

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• Glioblastoma cells increase expression of notch signaling and synaptic genes within infiltrated brain tissue

  Harwood, D. S. L., Pedersen, V., Bager, N. S., Schmidt, A. Y., Stannius, T. O., Areškevičiūtė, A., Josefsen, K., Nørøxe, D. S., Scheie, D., Rostalski, H., Lü, M. J. S., Locallo, A., Lassen, U., Bagger, F. O., Weischenfeldt, J., Heiland, D. H., Vitting-Seerup, K., Michaelsen, S. R. & Kristensen, B. W., 2024, In: Nature Communications. 15, 1, 14 p., 7857.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  4 Citations (Scopus)

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• Immunotherapy drives mesenchymal tumor cell state shift and TME immune response in glioblastoma patients

  Hendriksen, J. D., Locallo, A., Maarup, S., Debnath, O., Ishaque, N., Hasselbach, B., Skjøth-Rasmussen, J., Yde, C. W., Poulsen, H. S., Lassen, U. & Weischenfeldt, J., 2024, In: Neuro-Oncology. 26, 8, p. 1453–1466 14 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  5 Citations (Scopus)

• Loss of Upk1a and Upk1b expression is linked to stage progression in urothelial carcinoma of the bladder

  Kaczmarek, K., Plage, H., Furlano, K., Hofbauer, S., Weinberger, S., Ralla, B., Franz, A., Fendler, A., de Martino, M., Roßner, F., Schallenberg, S., Elezkurtaj, S., Kluth, M., Lennartz, M., Blessin, N. C., Marx, A. H., Samtleben, H., Fisch, M., Rink, M. & Slojewski, M. & 12 others, Ecke, T., Hallmann, S., Koch, S., Adamini, N., Minner, S., Simon, R., Sauter, G., Weischenfeldt, J., Klatte, T., Schlomm, T., Horst, D. & Zecha, H., 2024, In: International Urology and Nephrology. 56, p. 499-508 10 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  1 Citation (Scopus)

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• MDB-19. THE 3D CHROMATIN LANDSCAPE OF MEDULLOBLASTOMA

  Wu, S. C., Diaz, E. F. M., Mileti, E., Bihannic, L., Smith, K. S., Rodríguez-gonzález, F. G., Sidiropoulos, N., Weischenfeldt, J. & Northcott, P. A., 2024, In: Neuro-Oncology. 26, Supplement_4, p. iv137 1 p.

  Research output: Contribution to journal › Conference abstract in journal › Research

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• PD-L1 expression in tumor and inflammatory cells is associated with favorable tumor features and favorable prognosis in muscle-invasive urothelial carcinoma of the bladder not treated by immune checkpoint inhibitors

  Plage, H., Furlano, K., Hofbauer, S., Weinberger, S., Ralla, B., Franz, A., Fendler, A., de Martino, M., Roßner, F., Elezkurtaj, S., Kluth, M., Lennartz, M., Blessin, N. C., Marx, A. H., Samtleben, H., Fisch, M., Rink, M., Slojewski, M., Kaczmarek, K. & Ecke, T. & 12 others, Hallmann, S., Koch, S., Adamini, N., Zecha, H., Minner, S., Simon, R., Sauter, G., Weischenfeldt, J., Klatte, T., Schlomm, T., Horst, D. & Schallenberg, S., 2024, In: BMC Urology. 24, 9 p., 96.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  1 Citation (Scopus)

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• PLAP expression is linked to invasive tumor growth in urothelial carcinoma of the bladder

  Plage, H., Furlano, K., Hofbauer, S., Roßner, F., Schallenberg, S., Elezkurtaj, S., Lennartz, M., Marx, A., Samtleben, H., Fisch, M., Rink, M., Slojewski, M., Kaczmarek, K., Ecke, T., Klatte, T., Koch, S., Adamini, N., Minner, S., Simon, R. & Sauter, G. & 6 others, Weischenfeldt, J., Schlomm, T., Horst, D., Zecha, H., Kluth, M. & Weinberger, S., 2024, (Accepted/In press) In: International Urology and Nephrology.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

• Reduced p63 expression is linked to unfavourable prognosis in muscle-invasive urothelial carcinoma of the bladder

  Furlano, K., Plage, H., Hofbauer, S., Weinberger, S., Ralla, B., Fendler, A., Roßner, F., Schallenberg, S., Elezkurtaj, S., Kluth, M., Lennartz, M., Blessin, N. C., Marx, A. H., Samtleben, H., Fisch, M., Rink, M., Slojewski, M., Kaczmarek, K., Ecke, T. & Koch, S. & 9 others, Adamini, N., Minner, S., Simon, R., Sauter, G., Weischenfeldt, J., Klatte, T., Schlomm, T., Horst, D. & Zecha, H., 2024, In: BJUI Compass. 5, 11, p. 1081-1089 9 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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• Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer

  Flynn, A., Waszak, S. M. & Weischenfeldt, J., 2024, In: Molecular Systems Biology. 20, 9, p. 1006–1024 19 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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• 2023

  A polygenic two-hit hypothesis for prostate cancer

  Houlahan, K. E., Livingstone, J., Fox, N. S., Kurganovs, N., Zhu, H., Sietsma Penington, J., Jung, C.-H., Yamaguchi, T. N., Heisler, L. E., Jovelin, R., Costello, A. J., Pope, B. J., Kishan, A. U., Corcoran, N. M., Bristow, R. G., Waszak, S. M., Weischenfeldt, J., He, H. H., Hung, R. J. & Hovens, C. M. & 1 others, Boutros, P. C., 2023, In: Journal of the National Cancer Institute. 115, 4, p. 468-472 5 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  2 Citations (Scopus)

• Epithelial specific splicing regulator proteins as emerging oncogenes in aggressive prostate cancer

  Advani, R., Luzzi, S., Scott, E., Dalgliesh, C., Weischenfeldt, J., Munkley, J. & Elliott, D. J., 2023, In: Oncogene. 42, p. 3161-3168 8 p.

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

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  4 Citations (Scopus)

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• Frequency and Functional Characterization of RUNX1 Germline Variants in Myeloid Neoplasms

  Nitschke, N. J., Almosailleakh, M., Niu, Y., Hansen, J. W., Raaschou-Jensen, K., Jespersen, J. S., Severinsen, M. T., Roug, A. S., Frödin, M., Weischenfeldt, J. L., Andersen, M. K. & Grønbæk, K., 2023, In: Human Mutation. 2023, 11 p., 4738660.

  Research output: Contribution to journal › Journal article › Research › peer-review

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• Hunting for the elusive target antigen in gestational alloimmune liver disease (GALD)

  Rieneck, K., Rasmussen, K. K., Schoof, E. M., Clausen, F. B., Holze, H., Bergholt, T., Jørgensen, M. H., Christensen, V. B., Almaas, R., Jordal, P. L., Locard-Paulet, M., Runager, K., Nielsen, L. K., Schlotmann, B. C., Weischenfeldt, J. L., Jensen, L. J. & Dziegiel, M. H., 2023, In: PLoS ONE. 18, 10, 25 p., e0286432.

  Research output: Contribution to journal › Journal article › Research › peer-review

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• The Neurogenome study: Comprehensive molecular profiling to optimize treatment for Danish glioblastoma patients

  Nørøxe, D. S., Maarup, S., Fougner, V., Muhic, A., Møller, S., Urup, T., Lü, M. J. S., Weischenfeldt, J., Hansen, A. E., Skovgaard Poulsen, H., Lassen, U. & Hasselbalch, B., 2023, In: Neuro-Oncology Advances. 5, 1, 8 p., vdad137.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  1 Citation (Scopus)

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• When 3D genome changes cause disease: the impact of structural variations in congenital disease and cancer

  Weischenfeldt, J. & Ibrahim, D. M., 2023, In: Current Opinion in Genetics and Development. 80, 102048.

  Research output: Contribution to journal › Review › peer-review
  3 Citations (Scopus)
• 2022

  Clonal Hematopoiesis and Epigenetic Age Acceleration in Elderly Danish Twins

  Sørensen, M., Tulstrup, M., Hansen, J. W., Weischenfeldt, J., Gronbaek, K. & Christensen, K., 2022, In: HemaSphere. 6, 9, 6 p., 768.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  6 Citations (Scopus)

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• Clonal hematopoiesis is associated with hematological toxicity during lenalidomide-based therapy for MCL

  Husby, S., Bæch-Laursen, C., Eskelund, C. W., Favero, F., Jespersen, J. S., Hutchings, M., Pedersen, L. B., Niemann, C. U., Weischenfeldt, J., Räty, R., Larsen, T. S., Kolstad, A., Jerkeman, M. & Grønbæk, K., 2022, In: Leukemia. 36, p. 2912-2916

  Research output: Contribution to journal › Journal article › Research › peer-review
  3 Citations (Scopus)

• Implementing targeted therapies in the treatment of glioblastoma: Previous shortcomings, future promises, and a multimodal strategy recommendation

  Fougner, V., Hasselbalch, B., Lassen, U., Weischenfeldt, J., Poulsen, H. S. & Urup, T., 2022, In: Neuro-Oncology Advances. 4, 1, vdac157.

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

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  7 Citations (Scopus)

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• Level of unique T cell clonotypes is associated with clonal hematopoiesis and survival in patients with lymphoma undergoing ASCT

  Husby, S., Jørgensen, G. Ø., Favero, F., Jespersen, J. S., Rodriguez-Gonzalez, F. G., Nielsen, C., Sorensen, B., Ebbesen, L. H., Bæch, J., Haastrup, E. K., Josefsson, P., Thorsgaard, M., Brown, P., El-Galaly, T. C., Larsen, T. S., Weischenfeldt, J. & Grønbæk, K., 2022, In: Bone Marrow Transplantation. 57, p. 674-677

  Research output: Contribution to journal › Letter › peer-review
  2 Citations (Scopus)

• Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study

  Burns, D., Anokian, E., Saunders, E. J., Bristow, R. G., Fraser, M., Reimand, J., Schlomm, T., Sauter, G., Brors, B., Korbel, J., Weischenfeldt, J., Waszak, S. M., Corcoran, N. M., Jung, C. H., Pope, B. J., Hovens, C. M., Cancel-Tassin, G., Cussenot, O., Loda, M. & Sander, C. & 16 others, Hayes, V. M., Dalsgaard Sorensen, K., Lu, Y. J., Hamdy, F. C., Foster, C. S., Gnanapragasam, V., Butler, A., Lynch, A. G., Massie, C. E., Woodcock, D. J., Cooper, C. S., Wedge, D. C., Brewer, D. S., Kote-Jarai, Z., Eeles, R. A. & CR-UK/Prostate Cancer UK, ICGC, The PPCG, 2022, In: European Urology. 82, 2, p. 201-211 11 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

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• Somatic structural variant formation is guided by and influences genome architecture

  Sidiropoulos, N., Mardin, B. R., Rodríguez-González, F. G., Bochkov, I. D., Garg, S., Stuetz, A. M., Korbel, J. O., Aiden, E. L. & Weischenfeldt, J., 2022, In: Genome Research. 32, 4, p. 643-655

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  14 Citations (Scopus)

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• Structural variations in cancer and the 3D genome

  Dubois, F., Sidiropoulos, N., Weischenfeldt, J. & Beroukhim, R., 2022, In: Nature Reviews Cancer. 22, p. 533-546

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

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  43 Citations (Scopus)

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• Tumor mutational burden and purity adjustment before and after treatment with temozolomide in 27 paired samples of glioblastoma: a prospective study

  Nørøxe, D. S., Flynn, A., Yde, C. W., Østrup, O., Cilius Nielsen, F., Skjøth-Rasmussen, J., Brennum, J., Hamerlik, P., Weischenfeldt, J., Skovgaard Poulsen, H. & Lassen, U., 2022, In: Molecular Oncology. 16, 1, p. 206-218

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• 2021

  Mutations known from B-cell lymphoid malignancies are not found in CD34⁺ stem cells from patients with lymphoma

  Husby, S., Favero, F., Rodriguez-Gonzalez, F. G., Sutton, L. A., Haastrup, E. K., Ørskov, A. D., Hansen, J. W., Arboe, B., Aslan, D., Clasen-Linde, E., Rahbek Gjerdrum, L. M., Gørlev, J. S., Brown, P., Fischer-Nielsen, A., Rosenquist, R., Weischenfeldt, J. & Grønbæk, K., 2021, In: Leukemia and Lymphoma. 62, 11, p. 2808-2811

  Research output: Contribution to journal › Journal article › Research › peer-review
  2 Citations (Scopus)

• Systematic dissection of transcriptional regulatory networks by genome-scale and single-cell CRISPR screens

  Lopes, R., Sprouffske, K., Sheng, C., Uijttewaal, E. C. H., Wesdorp, A. E., Dahinden, J., Wengert, S., Diaz-Miyar, J., Yildiz, U., Bleu, M., Apfel, V., Mermet-Meillon, F., Krese, R., Eder, M., Olsen, A. V., Hoppe, P., Knehr, J., Carbone, W., Cuttat, R. & Waldt, A. & 8 others, Altorfer, M., Naumann, U., Weischenfeldt, J., deWeck, A., Kauffmann, A., Roma, G., Schübeler, D. & Galli, G. G., 2021, In: Science Advances. 7, 27, eabf5733.

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• TET2 mutations are associated with hypermethylation at key regulatory enhancers in normal and malignant hematopoiesis

  Tulstrup, M., Soerensen, M., Hansen, J. W., Gillberg, L., Needhamsen, M., Kaastrup, K., Helin, K., Christensen, K., Weischenfeldt, J. & Grønbæk, K., 2021, In: Nature Communications. 12, 1, 10 p., 6061.

  Research output: Contribution to journal › Journal article › Research › peer-review

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  52 Citations (Scopus)

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• 2020

  Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

  Rheinbay, E., Nielsen, M. M., Abascal, F., Wala, J. A., Shapira, O., Tiao, G., Hornshøj, H., Hess, J. M., Juul, R. I., Lin, Z., Feuerbach, L., Sabarinathan, R., Madsen, T., Kim, J., Mularoni, L., Shuai, S., Lanzós, A., Herrmann, C., Maruvka, Y. E. & Shen, C. & 31 others, Amin, S. B., Bandopadhayay, P., Bertl, J., Boroevich, K. A., Busanovich, J., Carlevaro-Fita, J., Chakravarty, D., Chan, C. W. Y., Craft, D., Dhingra, P., Diamanti, K., Fonseca, N. A., Gonzalez-Perez, A., Guo, Q., Hamilton, M. P., Haradhvala, N. J., Hong, C., Isaev, K., Johnson, T. A., Juul, M., Kahles, A., Kahraman, A., Kim, Y., Komorowski, J., Kumar, K., Kumar, S., Lee, D., Sidiropoulos, N., Weischenfeldt, J., Pedersen, J. S. & PCAWG Drivers and Functional Interpretation Working Group, Feb 2020, In: Nature. 578, 7793, p. 102-111 10 p.

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• A Novel Gene Signature-Based Model Predicts Biochemical Recurrence-Free Survival in Prostate Cancer Patients after Radical Prostatectomy

  Shi, R., Bao, X., Weischenfeldt, J., Schaefer, C., Rogowski, P., Schmidt-Hegemann, N.-S., Unger, K., Lauber, K., Wang, X., Buchner, A., Stief, C., Schlomm, T., Belka, C. & Li, M., 2020, In: Cancers. 12, 1, p. 1-12 12 p.

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• Butler enables rapid cloud-based analysis of thousands of human genomes

  Weischenfeldt, J., PCAWG Technical Working Group & PCAWG Consortium, 2020, In: Nature Biotechnology. 38, 3, p. 288-292 5 p.

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• Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

  Carlevaro-Fita, J., Lanzós, A., Feuerbach, L., Hong, C., Mas-Ponte, D., Pedersen, J. S., Johnson, R., Sidiropoulos, N., Weischenfeldt, J. L. & Brunak, S., 2020, In: Communications Biology. 3, 1, p. 1-16 56.

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  150 Citations (Scopus)

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• Clinical impact of clonal hematopoiesis in patients with lymphoma undergoing ASCT: a national population-based cohort study

  Husby, S., Favero, F., Nielsen, C., Sørensen, B. S., Bæch, J., Grell, K., Hansen, J. W., Rodriguez-Gonzalez, F. G., Haastrup, E. K., Fischer-Nielsen, A., Andersen, P., Arboe, B., Sækmose, S. G., Hansen, P. B., Christiansen, I., Clasen-Linde, E., Meldgaard, L., Ebbesen, L. H., Segel, E. K. & Josefsson, P. & 6 others, Thorsgaard, M., El-Galaly, T. C., Brown, P., Weischenfeldt, J., Larsen, T. S. & Grønbæk, K., 2020, In: Leukemia. 34, p. 3256-3268 13 p.

  Research output: Contribution to journal › Journal article › Research › peer-review
  63 Citations (Scopus)

• Clonal hematopoiesis evolves from pretreatment clones and stabilizes after end of chemotherapy in patients with MCL

  Eskelund, C. W., Husby, S., Favero, F., Klausen, T. W., Rodriguez-gonzalez, F. G., Kolstad, A., Pedersen, L. B., Räty, R. K., Geisler, C. H., Jerkeman, M., Weischenfeldt, J. & Grønbæk, K., 2020, In: Blood. 135, 22, p. 2000-2004

  Research output: Contribution to journal › Comment/debate › Research › peer-review
  29 Citations (Scopus)

• Clonal hematopoiesis in elderly twins: concordance, discordance, and mortality

  Hansen, J. W., Pedersen, D. A., Larsen, L. A., Husby, S., Clemmensen, S. B., Hjelmborg, J., Favero, F., Weischenfeldt, J., Christensen, K. & Grønbæk, K., 2020, In: Blood. 135, 4, p. 261-268

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• Combined burden and functional impact tests for cancer driver discovery using DriverPower

  Shuai, S., Abascal, F., Amin, S. B., Bader, G. D., Bandopadhayay, P., Barenboim, J., Beroukhim, R., Bertl, J., Boroevich, K. A., Brunak, S., Campbell, P. J., Carlevaro-Fita, J., Chakravarty, D., Chan, C. W. Y., Chen, K., Choi, J. K., Deu-Pons, J., Dhingra, P., Diamanti, K. & Feuerbach, L. & 32 others, Fink, J. L., Fonseca, N. A., Frigola, J., Gambacorti-Passerini, C., Garsed, D. W., Gerstein, M., Getz, G., Guo, Q., Gut, I. G., Haan, D., Hamilton, M. P., Haradhvala, N. J., Harmanci, A. O., Helmy, M., Herrmann, C., Hess, J. M., Hobolth, A., Hodzic, E., Hong, C., Hornshøj, H., Isaev, K., Izarzugaza, J. M. G., Johnson, R., Johnson, T. A., Juul, M., Juul, R. I., Kahles, A., Pedersen, J. S., Sidiropoulos, N., Weischenfeldt, J., PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium, 2020, In: Nature Communications. 11, 1, 12 p., 734.

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• Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

  Cortés-Ciriano, I., Lee, J. J. K., Xi, R., Jain, D., Jung, Y. L., Yang, L., Gordenin, D., Klimczak, L. J., Zhang, C. Z., Pellman, D. S., Akdemir, K. C., Alvarez, E. G., Baez-Ortega, A., Beroukhim, R., Boutros, P. C., Bowtell, D. D. L., Brors, B., Burns, K. H., Campbell, P. J. & Chan, K. & 32 others, Chen, K., Cortés-Ciriano, I., Dueso-Barroso, A., Dunford, A. J., Edwards, P. A., Estivill, X., Etemadmoghadam, D., Feuerbach, L., Fink, J. L., Frenkel-Morgenstern, M., Garsed, D. W., Gerstein, M., Gordenin, D. A., Haan, D., Haber, J. E., Hess, J. M., Hutter, B., Imielinski, M., Jones, D. T. W., Ju, Y. S., Kazanov, M. D., Klimczak, L. J., Koh, Y., Korbel, J. O., Kumar, K., Lee, E. A., Lee, J. J. K., Li, Y., Sidiropoulos, N., Weischenfeldt, J., PCAWG Structural Variation Working Group & PCAWG Consortium, 6 Feb 2020, In: Nature Genetics.

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• Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

  Akdemir, K. C., Le, V. T., Chandran, S., Li, Y., Verhaak, R. G., Beroukhim, R., Campbell, P. J., Chin, L., Dixon, J. R., Futreal, P. A., Akdemir, K. C., Alvarez, E. G., Baez-Ortega, A., Beroukhim, R., Boutros, P. C., Bowtell, D. D. L., Brors, B., Burns, K. H., Campbell, P. J. & Chan, K. & 32 others, Chen, K., Cortés-Ciriano, I., Dueso-Barroso, A., Dunford, A. J., Edwards, P. A., Estivill, X., Etemadmoghadam, D., Feuerbach, L., Fink, J. L., Frenkel-Morgenstern, M., Garsed, D. W., Gerstein, M., Gordenin, D. A., Haan, D., Haber, J. E., Hess, J. M., Hutter, B., Imielinski, M., Jones, D. T. W., Ju, Y. S., Kazanov, M. D., Klimczak, L. J., Koh, Y., Korbel, J. O., Kumar, K., Lee, E. A., Lee, J. J. K., Li, Y., Sidiropoulos, N., Weischenfeldt, J., PCAWG Structural Variation Working Group & PCAWG Consortium, 2020, In: Nature Genetics. p. 294-305

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• Genomic footprints of activated telomere maintenance mechanisms in cancer

  Sieverling, L., Hong, C., Koser, S. D., Ginsbach, P., Kleinheinz, K., Hutter, B., Braun, D. M., Cortés-Ciriano, I., Xi, R., Kabbe, R., Park, P. J., Eils, R., Schlesner, M., Akdemir, K. C., Alvarez, E. G., Baez-Ortega, A., Beroukhim, R., Boutros, P. C., Bowtell, D. D. L. & Brors, B. & 32 others, Burns, K. H., Campbell, P. J., Chan, K., Chen, K., Cortés-Ciriano, I., Dueso-Barroso, A., Dunford, A. J., Edwards, P. A., Estivill, X., Etemadmoghadam, D., Feuerbach, L., Fink, J. L., Frenkel-Morgenstern, M., Garsed, D. W., Gerstein, M., Gordenin, D. A., Haan, D., Haber, J. E., Hess, J. M., Hutter, B., Imielinski, M., Jones, D. T. W., Ju, Y. S., Kazanov, M. D., Klimczak, L. J., Koh, Y., Korbel, J. O., Kumar, K., Sidiropoulos, N., Weischenfeldt, J., PCAWG Structural Variation Working Group & PCAWG Consortium, 2020, In: Nature Communications. 11, 1, 733.

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• High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

  Zhang, Y., Chen, F., Fonseca, N. A., He, Y., Fujita, M., Nakagawa, H., Zhang, Z., Brazma, A., Amin, S. B., Awadalla, P., Bailey, P. J., Brazma, A., Brooks, A. N., Calabrese, C., Chateigner, A., Cortés-Ciriano, I., Craft, B., Craft, D., Creighton, C. J. & Davidson, N. R. & 33 others, Demircioğlu, D., Erkek, S., Fonseca, N. A., Frenkel-Morgenstern, M., Goldman, M. J., Greger, L., Göke, J., He, Y., Hoadley, K. A., Hou, Y., Huska, M. R., Kahles, A., Khurana, E., Kilpinen, H., Korbel, J. O., Lamaze, F. C., Lehmann, K. V., Li, C., Li, S., Li, X., Li, X., Liu, D., Liu, F., Liu, X., Nielsen, M. M., Pedersen, J. S., Wu, K., Zhu, S., Sidiropoulos, N., Weischenfeldt, J., PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group & PCAWG Consortium, 2020, In: Nature Communications. 11, 1, p. 1-14 736.

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• Identification of unique and shared mitochondrial DNA mutations in neurodegeneration and cancer by single-cell mitochondrial DNA structural variation sequencing (MitoSV-seq)

  Jaberi, E., Tresse, E., Grønbæk, K., Weischenfeldt, J. & Issazadeh-Navikas, S., 2020, In: EBioMedicine. 57, p. 1-17 102868.

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• Integrative pathway enrichment analysis of multivariate omics data

  Paczkowska, M., Barenboim, J., Sintupisut, N., Fox, N. S., Zhu, H., Abd-Rabbo, D., Mee, M. W., Boutros, P. C., Abascal, F., Amin, S. B., Bader, G. D., Beroukhim, R., Bertl, J., Boroevich, K. A., Brunak, S., Campbell, P. J., Carlevaro-Fita, J., Chakravarty, D., Chan, C. W. Y. & Chen, K. & 30 others, Choi, J. K., Deu-Pons, J., Dhingra, P., Diamanti, K., Feuerbach, L., Fink, J. L., Fonseca, N. A., Frigola, J., Gambacorti-Passerini, C., Garsed, D. W., Gerstein, M., Getz, G., Gonzalez-Perez, A., Guo, Q., Gut, I. G., Haan, D., Hamilton, M. P., Haradhvala, N. J., Harmanci, A. O., Helmy, M., Herrmann, C., Hess, J. M., Hobolth, A., Hodzic, E., Hong, C., Hornshøj, H., Nielsen, M. M., Pedersen, J. S., Sidiropoulos, N. & Weischenfeldt, J., 5 Feb 2020, In: Nature Communications. 11, 1, 735.

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• Pan-cancer analysis of whole genomes

  ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Weischenfeldt, J. L., Sidiropoulos, N., Brunak, S. & Rodriguez Gonzalez, F. G., 2020, In: Nature. 578, 7793, p. 82-93 12 p.

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• Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

  Rodriguez-Martin, B., Alvarez, E. G., Baez-Ortega, A., Zamora, J., Supek, F., Demeulemeester, J., Santamarina, M., Ju, Y. S., Temes, J., Garcia-Souto, D., Detering, H., Li, Y., Rodriguez-Castro, J., Dueso-Barroso, A., Bruzos, A. L., Dentro, S. C., Blanco, M. G., Contino, G., Ardeljan, D. & Tojo, M. & 32 others, Roberts, N. D., Zumalave, S., Edwards, P. A. W., Weischenfeldt, J., Puiggròs, M., Chong, Z., Chen, K., Lee, E. A., Wala, J. A., Raine, K., Butler, A., Waszak, S. M., Navarro, F. C. P., Schumacher, S. E., Monlong, J., Maura, F., Bolli, N., Bourque, G., Gerstein, M., Park, P. J., Wedge, D. C., Beroukhim, R., Torrents, D., Korbel, J. O., Martincorena, I., Fitzgerald, R. C., Van Loo, P., Kazazian, H. H., Sidiropoulos, N., Weischenfeldt, J., PCAWG Structural Variation Working Group & PCAWG Consortium, 2020, In: Nature Genetics. 52, 3, p. 306-319 14 p.

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• Pathway and network analysis of more than 2500 whole cancer genomes

  Reyna, M. A., Haan, D., Paczkowska, M., Verbeke, L. P. C., Vazquez, M., Kahraman, A., Pulido-Tamayo, S., Barenboim, J., Wadi, L., Dhingra, P., Shrestha, R., Getz, G., Lawrence, M. S., Pedersen, J. S., Rubin, M. A., Wheeler, D. A., Brunak, S., Izarzugaza, J. M. G., Khurana, E. & Marchal, K. & 32 others, von Mering, C., Sahinalp, S. C., Valencia, A., Abascal, F., Amin, S. B., Bader, G. D., Bandopadhayay, P., Beroukhim, R., Bertl, J., Boroevich, K. A., Busanovich, J., Campbell, P. J., Carlevaro-Fita, J., Chakravarty, D., Chan, C. W. Y., Chen, K., Choi, J. K., Deu-Pons, J., Diamanti, K., Feuerbach, L., Fink, J. L., Fonseca, N. A., Frigola, J., Gambacorti-Passerini, C., Garsed, D. W., Gerstein, M., Larsson, E., Nielsen, M. M., Sidiropoulos, N., Weischenfeldt, J., PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium, 2020, In: Nature Communications. 11, 1, p. 1-17 729.

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• Patterns of somatic structural variation in human cancer genomes

  Li, Y., Roberts, N. D., Wala, J. A., Shapira, O., Schumacher, S. E., Kumar, K., Khurana, E., Waszak, S., Korbel, J. O., Haber, J. E., Imielinski, M., Akdemir, K. C., Alvarez, E. G., Baez-Ortega, A., Beroukhim, R., Boutros, P. C., Bowtell, D. D. L., Brors, B., Burns, K. H. & Campbell, P. J. & 29 others, Chan, K., Chen, K., Cortés-Ciriano, I., Dueso-Barroso, A., Dunford, A. J., Edwards, P. A., Estivill, X., Etemadmoghadam, D., Feuerbach, L., Fink, J. L., Frenkel-Morgenstern, M., Garsed, D. W., Gerstein, M., Gordenin, D. A., Haan, D., Haber, J. E., Hess, J. M., Hutter, B., Imielinski, M., Jones, D. T. W., Ju, Y. S., Kazanov, M. D., Klimczak, L. J., Koh, Y., Korbel, J. O., Kumar, K., Lee, E. A., Sidiropoulos, N. & Weischenfeldt, J., 2020, In: Nature. 578, 7793, p. 112-121 10 p.

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• Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

  Bailey, M. H., Meyerson, W. U., Dursi, L. J., Wang, L. B., Dong, G., Liang, W. W., Weerasinghe, A., Li, S., Kelso, S., Akbani, R., Anur, P., Bailey, M. H., Buchanan, A., Chiotti, K., Covington, K., Creason, A., Ding, L., Weischenfeldt, J., Brunak, S. & Ding, L. & 4 others, Favero, F., MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium, 2020, In: Nature Communications. 11, 1, 4748.

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• 2019

  Regulation of ETAA1-mediated ATR activation couples DNA replication fidelity and genome stability

  Achuthankutty, D., Thakur, R. S., Haahr, P., Hoffmann, S., Drainas, A. P., Bizard, A. H., Weischenfeldt, J., Hickson, I. D. & Mailand, N., 2019, In: The Journal of Cell Biology. 218, 12, 11 p., 3943.

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