Timothy Ley

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Timothy Ley

Lewis T and Rosalind B Apple Professor of Medicine, Professor of Medicine, Professor of Genetics

 https://orcid.org/0000-0002-9913-0520

    Willing to Mentor

    Available to Mentor:

    Undergraduate Students, Post-Baccalaureate Students, PhD/MSTP Students, Health Professions (Medical, OT, PT, Dental, Audiology, etc.) Students, Postdocs, Residents and Fellows

    • 82367
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    1982 …2024

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    • 2024

      PML::RARA and GATA2 proteins interact via DNA templates to induce aberrant self-renewal in mouse and human hematopoietic cells

      Katerndahl, C. D. S., Rogers, O. R. S., Day, R. B., Xu, Z., Helton, N. M., Ramakrishnan, S. M., Miller, C. A. & Ley, T. J., Apr 30 2024, In: Proceedings of the National Academy of Sciences of the United States of America. 121, 18, e2317690121.

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

      Open Access

    • Proteogenomic analysis reveals cytoplasmic sequestration of RUNX1 by the acute myeloid leukemia–initiating CBFB::MYH11 oncofusion protein

      Day, R. B., Hickman, J. A., Xu, Z., Katerndahl, C. D. S., Ferraro, F., Ramakrishnan, S. M., Erdmann-Gilmore, P., Sprung, R. W., Mi, Y., Townsend, R. R., Miller, C. A. & Ley, T. J., Feb 15 2024, In: Journal of Clinical Investigation. 134, 4, 1e176311.

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

      Open Access
      1 Scopus citations

    • Rapid and accurate remethylation of DNA in Dnmt3a-deficient hematopoietic cells with restoration of DNMT3A activity

      Li, Y., Abel, H. J., Cai, M., LaValle, T. A., Yin, T., Helton, N. M., Smith, A. M., Miller, C. A. & Ley, T. J., Feb 2024, In: Science Advances. 10, 5, eadk8598.

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

      Open Access
      1 Scopus citations

    • Stabilizing the Proteomes of Acute Myeloid Leukemia Cells: Implications for Cancer Proteomics

      Sprung, R. W., Zhang, Q., Kramer, M. H., Christopher, M. C., Erdmann-Gilmore, P., Mi, Y., Malone, J. P., Ley, T. J. & Townsend, R. R., Feb 2024, In: Molecular and Cellular Proteomics. 23, 2, 100716.

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

      Open Access
    • 2023

      Description of a novel subtype of acute myeloid leukemia defined by recurrent CBFB insertions

      Ryland, G. L., Umeda, M., Holmfeldt, L., Lehmann, S., Herlin, M. K., Ma, J., Khanlari, M., Rubnitz, J. E., Ries, R. E., Kosasih, H. J., Ekert, P. G., Goh, H. N., Tiong, I. S., Grimmond, S. M., Haferlach, C., Day, R. B., Ley, T. J., Meshinchi, S., Ma, X. & Blombery, P. & 1 others, Klco, J. M., Feb 16 2023, In: Blood. 141, 7, p. 800-805 6 p.

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

      Open Access
      2 Scopus citations

    • Genomic landscape of TP53-mutated myeloid malignancies

      Abel, H. J., Oetjen, K. A., Miller, C. A., Ramakrishnan, S. M., Day, R. B., Helton, N. M., Fronick, C. C., Fulton, R. S., Heath, S. E., Tarnawsky, S. P., Srivatsan, S. N., Duncavage, E. J., Schroeder, M. C., Payton, J. E., Spencer, D. H., Walter, M. J., Westervelt, P., DiPersio, J. F., Ley, T. J. & Link, D. C., Aug 16 2023, In: Blood Advances. 7, 16, p. 4586-4598 13 p.

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

      Open Access
      12 Scopus citations

    • Melanoma in a patient with DNMT3A overgrowth syndrome

      Chen, D. Y., Sutton, L. A., Ramakrishnan, S. M., Duncavage, E. J., Heath, S. E., Compton, L. A., Miller, C. A. & Ley, T. J., Apr 2023, In: Cold Spring Harbor molecular case studies. 9, 2, a006267.

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

      Open Access
      2 Scopus citations
    • 2022

      Convergent Clonal Evolution of Signaling Gene Mutations Is a Hallmark of Myelodysplastic Syndrome Progression

      Menssen, A. J., Khanna, A., Miller, C. A., Srivatsan, S. N., Chang, G. S., Shao, J., Robinson, J., O’Laughlin, M., Fronick, C. C., Fulton, R. S., Brendel, K., Heath, S. E., Saba, R., Welch, J. S., Spencer, D. H., Payton, J. E., Westervelt, P., DiPersio, J. F., Link, D. C. & Schuelke, M. J. & 4 others, Jacoby, M. A., Duncavage, E. J., Ley, T. J. & Walter, M. J., Jul 1 2022, In: Blood cancer discovery. 3, 4, p. 330-345 16 p.

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

      Open Access
      15 Scopus citations

    • Failure to Detect Mutations in U2AF1 due to Changes in the GRCh38 Reference Sequence

      Miller, C. A., Walker, J. R., Jensen, T. L., Hooper, W. F., Fulton, R. S., Painter, J. S., Sekeres, M. A., Ley, T. J., Spencer, D. H., Goll, J. B. & Walter, M. J., Mar 2022, In: Journal of Molecular Diagnostics. 24, 3, p. 219-223 5 p.

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

      Open Access
      13 Scopus citations

    • Focal disruption of DNA methylation dynamics at enhancers in IDH-mutant AML cells

      Wilson, E. R., Helton, N. M., Heath, S. E., Fulton, R., Payton, J. E., Welch, J., Walter, M., Westervelt, P., DiPersio, J. F., Link, D. C., Miller, C., Ley, T. J. & Spencer, D., Apr 2022, In: Leukemia. 36, 4, p. 935-945 11 p.

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

      Open Access
      16 Scopus citations

    • Genetic and Transcriptional Contributions to Relapse in Normal Karyotype Acute Myeloid Leukemia

      Petti, A. A., Khan, S. M., Xu, Z., Helton, N., Fronick, C. C., Fulton, R., Ramakrishnan, S. M., Srivatsan, S. N., Heath, S. E., Westervelt, P., Payton, J. E., Walter, M. J., Link, D. C., DiPersio, J., Miller, C. & Ley, T. J., Jan 1 2022, In: Blood cancer discovery. 3, 1, p. 32-49 18 p.

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

      Open Access
      12 Scopus citations

    • IL-1β expression in bone marrow dendritic cells is induced by TLR2 agonists and regulates HSC function

      Li, S., Yao, J. C., Oetjen, K. A., Krambs, J. R., Xia, J., Zhang, J., Schmidt, A. P., Helton, N. M., Fulton, R. S., Heath, S. E., Turnbull, I. R., Mbalaviele, G., Ley, T. J., Walter, M. J. & Link, D. C., Oct 6 2022, In: Blood. 140, 14, p. 1607-1620 14 p.

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

      Open Access
      5 Scopus citations

    • Physician-scientists in the United States at 2020: Trends and concerns

      Garrison, H. H. & Ley, T. J., May 2022, In: FASEB Journal. 36, 5, e22253.

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

      Open Access
      25 Scopus citations

    • Proteomic and phosphoproteomic landscapes of acute myeloid leukemia

      Kramer, M. H., Zhang, Q., Sprung, R., Day, R. B., Erdmann-Gilmore, P., Li, Y., Xu, Z., Helton, N. M., George, D. R., Mi, Y., Westervelt, P., Payton, J. E., Ramakrishnan, S. M., Miller, C. A., Link, D. C., DiPersio, J. F., Walter, M. J., Townsend, R. R. & Ley, T. J., Sep 29 2022, In: Blood. 140, 13, p. 1533-1548 16 p.

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

      Open Access
      40 Scopus citations

    • Recurrent transcriptional responses in AML and MDS patients treated with decitabine

      Upadhyay, P., Beales, J., Shah, N. M., Gruszczynska, A., Miller, C. A., Petti, A. A., Ramakrishnan, S. M., Link, D. C., Ley, T. J. & Welch, J. S., Jul 2022, In: Experimental Hematology. 111, p. 50-65 16 p.

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

      Open Access
      6 Scopus citations

    • Somatic Dnmt3a inactivation leads to slow, canonical DNA methylation loss in murine hematopoietic cells

      Smith, A. M., Verdoni, A. M., Abel, H. J., Chen, D. Y., Ketkar, S., Leight, E. R., Miller, C. A. & Ley, T. J., Apr 15 2022, In: iScience. 25, 4, 104004.

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

      Open Access
      2 Scopus citations
    • 2021

      Co-evolution of tumor and immune cells during progression of multiple myeloma

      Liu, R., Gao, Q., Foltz, S. M., Fowles, J. S., Yao, L., Wang, J. T., Cao, S., Sun, H., Wendl, M. C., Sethuraman, S., Weerasinghe, A., Rettig, M. P., Storrs, E. P., Yoon, C. J., Wyczalkowski, M. A., McMichael, J. F., Kohnen, D. R., King, J., Goldsmith, S. R. & O’Neal, J. & 9 others, Fulton, R. S., Fronick, C. C., Ley, T. J., Jayasinghe, R. G., Fiala, M. A., Oh, S. T., DiPersio, J. F., Vij, R. & Ding, L., Dec 1 2021, In: Nature communications. 12, 1, 2559.

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

      Open Access
      81 Scopus citations

    • Dnmt3a deficiency in the skin causes focal, canonical DNA hypomethylation and a cellular proliferation phenotype

      Chen, D. Y., Ferguson, I. M., Braun, K. A., Sutton, L. A., Helton, N. M., Ramakrishnan, S. M., Smith, A. M., Miller, C. A. & Ley, T. J., Apr 20 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 16, e2022760118.

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

      Open Access
      7 Scopus citations

    • Enhanced Efficacy and Increased Long-Term Toxicity of CNS-Directed, AAV-Based Combination Therapy for Krabbe Disease

      Li, Y., Miller, C. A., Shea, L. K., Jiang, X., Guzman, M. A., Chandler, R. J., Ramakrishnan, S. M., Smith, S. N., Venditti, C. P., Vogler, C. A., Ory, D. S., Ley, T. J. & Sands, M. S., Feb 3 2021, In: Molecular Therapy. 29, 2, p. 691-701 11 p.

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

      Open Access
      34 Scopus citations

    • Functional and epigenetic phenotypes of humans and mice with DNMT3A Overgrowth Syndrome

      Smith, A. M., LaValle, T. A., Shinawi, M., Ramakrishnan, S. M., Abel, H. J., Hill, C. A., Kirkland, N. M., Rettig, M. P., Helton, N. M., Heath, S. E., Ferraro, F., Chen, D. Y., Adak, S., Semenkovich, C. F., Christian, D. L., Martin, J. R., Gabel, H. W., Miller, C. A. & Ley, T. J., Dec 1 2021, In: Nature communications. 12, 1, 4549.

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

      Open Access
      25 Scopus citations

    • Genome sequencing as an alternative to cytogenetic analysis in myeloid cancers

      Duncavage, E. J., Schroeder, M. C., O'Laughlin, M., Wilson, R., MacMillan, S., Bohannon, A., Kruchowski, S., Garza, J., Du, F., Hughes, A. E. O., Robinson, J., Hughes, E., Heath, S. E., Baty, J. D., Neidich, J., Christopher, M. J., Jacoby, M. A., Uy, G. L., Fulton, R. S. & Miller, C. A. & 7 others, Payton, J. E., Link, D. C., Walter, M. J., Westervelt, P., DiPersio, J. F., Ley, T. J. & Spencer, D. H., Mar 11 2021, In: New England Journal of Medicine. 384, 10, p. 924-935 12 p.

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

      Open Access
      174 Scopus citations

    • Immunosuppression and outcomes in adult patients with de novo acute myeloid leukemia with normal karyotypes

      Ferraro, F., Miller, C. A., Christensen, K. A., Helton, N. M., O’Laughlin, M., Fronick, C. C., Fulton, R. S., Kohlschmidt, J., Eisfeld, A. K., Bloomfield, C. D., Ramakrishnan, S. M., Day, R. B., Wartman, L., Uy, G. L., Welch, J., Christopher, M. J., Heath, S. E., Baty, J. D., Schuelke, M. J. & Payton, J. E. & 7 others, Spencer, D. H., Rettig, M. P., Link, D. C., Walter, M. J., Westervelt, P., DiPersio, J. F. & Ley, T. J., Dec 7 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 49, e2116427118.

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

      Open Access
      27 Scopus citations

    • Impact of a 40-gene targeted panel test on physician decision making for patients with acute myeloid leukemia

      Barnell, E. K., Newcomer, K. F., Skidmore, Z. L., Krysiak, K., Anderson, S. R., Wartman, L. D., Oh, S. T., Welch, J. S., Stockerl-Goldstein, K. E., Vij, R., Cashen, A. F., Pusic, I., Westervelt, P., Abboud, C. N., Ghobadi, A., Uy, G. L., Schroeder, M. A., Dipersio, J. F., Politi, M. C. & Spencer, D. H. & 5 others, Duncavage, E. J., Ley, T. J., Griffith, M., Jacoby, M. A. & Griffith, O. L., Jan 2021, In: JCO Precision Oncology. 5, p. 191-203 13 p.

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

      Open Access
      9 Scopus citations

    • Tumor suppressor function of Gata2 in acute promyelocytic leukemia

      Katerndahl, C. D. S., Rogers, O. R. S., Day, R. B., Cai, M. A., Rooney, T. P., Helton, N. M., Hoock, M., Ramakrishnan, S. M., Nonavinkere Srivatsan, S., Wartman, L. D., Miller, C. A. & Ley, T. J., Sep 30 2021, In: Blood. 138, 13, p. 1148-1161 14 p.

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

      Open Access
      20 Scopus citations
    • 2020

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

      PCAWG Tumor Subtypes and Clinical Translation Working Group, PCAWG Consortium, Jiao, W., Atwal, G., Polak, P., Karlic, R., Cuppen, E., Al-Shahrour, F., Atwal, G., Bailey, P. J., Biankin, A. V., Boutros, P. C., Campbell, P. J., Chang, D. K., Cooke, S. L., Deshpande, V., Faltas, B. M., Faquin, W. C., Garraway, L. & Getz, G. & 182 others, Grimmond, S. M., Haider, S., Hoadley, K. A., Jiao, W., Kaiser, V. B., Karlic, R., Kato, M., Kübler, K., Lazar, A. J., Li, C. H., Louis, D. N., Margolin, A., Martin, S., Nahal-Bose, H. K., Nielsen, G. P., Nik-Zainal, S., Omberg, L., P’ng, C., Perry, M. D., Polak, P., Rheinbay, E., Rubin, M. A., Semple, C. A., Sgroi, D. C., Shibata, T., Siebert, R., Smith, J., Stein, L. D., Stobbe, M. D., Sun, R. X., Thai, K., Wright, D. W., Wu, C. L., Yuan, K., Zhang, J., Danyi, A., de Ridder, J., van Herpen, C., Lolkema, M. P., Steeghs, N., Getz, G., Morris, Q. D., Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Beroukhim, R., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Boutros, P. C., Bova, G. S., Bowen, D. T., Bowlby, R., Bowtell, D. D. L., Boyault, S., Boyce, R., Boyd, J., Brazma, A., Brennan, P., Brewer, D. S., Brinkman, A. B., Bristow, R. G., Broaddus, R. R., Brock, J. E., Brock, M., Broeks, A., Brooks, A. N., Brooks, D., Brors, B., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Dec 1 2020, In: Nature communications. 11, 1, 728.

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

      Open Access
      131 Scopus citations

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

      PCAWG Consortium, PCAWG Drivers and Functional Interpretation Working Group, PCAWG-Structural Variation Working Group, 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. & 183 others, Herrmann, C., Maruvka, Y. E., Shen, C., 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., Lehmann, K. V., Li, Y., Liu, E. M., Lochovsky, L., Park, K., Pich, O., Roberts, N. D., Saksena, G., Schumacher, S. E., Sidiropoulos, N., Sieverling, L., Sinnott-Armstrong, N., Stewart, C., Tamborero, D., Tubio, J. M. C., Umer, H. M., Uusküla-Reimand, L., Wadelius, C., Wadi, L., Yao, X., Zhang, C. Z., Zhang, J., Haber, J. E., Hobolth, A., Imielinski, M., Kellis, M., Lawrence, M. S., von Mering, C., Nakagawa, H., Raphael, B. J., Rubin, M. A., Sander, C., Stein, L. D., Stuart, J. M., Tsunoda, T., Wheeler, D. A., Johnson, R., Reimand, J., Gerstein, M., Khurana, E., Campbell, P. J., López-Bigas, N., Weischenfeldt, J., Beroukhim, R., Martincorena, I., Pedersen, J. S., Getz, G., Bader, G. D., Barenboim, J., Brunak, S., Chen, K., Choi, J. K., Deu-Pons, J., Fink, J. L., Frigola, J., Gambacorti-Passerini, C., Garsed, D. W., Gut, I. G., Haan, D., Harmanci, A. O., Helmy, M., Hodzic, E., Izarzugaza, J. M. G., Kim, J. K., Korbel, J. O., Larsson, E., Li, S., Li, X., Lou, S., Marchal, K., Martinez-Fundichely, A., McGillivray, P. D., Meyerson, W., Muiños, F., Paczkowska, M., Park, K., Pons, T., Pulido-Tamayo, S., Reyes-Salazar, I., Reyna, M. A., Rubio-Perez, C., Sahinalp, S. C., Salichos, L., Shackleton, M., Shrestha, R., Valencia, A., Vazquez, M., Verbeke, L. P. C., Wang, J., Warrell, J., Waszak, S. M., Wu, G., Yu, J., Zhang, X., Zhang, Y., Zhao, Z., Zou, L., Akdemir, K. C., Alvarez, E. G., Baez-Ortega, A., Boutros, P. C., Bowtell, D. D. L., Brors, B., Burns, K. H., Chan, K., Cortés-Ciriano, I., Dueso-Barroso, A., Dunford, A. J., Edwards, P. A., Estivill, X., Etemadmoghadam, D., Frenkel-Morgenstern, M., Gordenin, D. A., Hutter, B., Jones, D. T. W., Ju, Y. S., Kazanov, M. D., Klimczak, L. J., Koh, Y., Lee, E. A., Lee, J. J. K., Lynch, A. G., Macintyre, G., Markowetz, F., Meyerson, M., Miyano, S., Navarro, F. C. P., Ossowski, S., Park, P. J., Pearson, J. V., Puiggròs, M., Rippe, K., Roberts, S. A., Rodriguez-Martin, B., Scully, R., Torrents, D., Villasante, I., Waddell, N., Yang, L., Yoon, S. S., Zamora, J., Aaltonen, L. A., Abeshouse, A., Aburatani, H., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Feb 6 2020, In: Nature. 578, 7793, p. 102-111 10 p.

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

      Open Access
      371 Scopus citations

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

      PCAWG Drivers and Functional Interpretation Group, PCAWG Consortium, Carlevaro-Fita, J., Lanzós, A., Feuerbach, L., Hong, C., Mas-Ponte, D., Pedersen, J. S., Johnson, R., Abascal, F., Amin, S. B., Bader, G. D., Barenboim, J., Beroukhim, R., Bertl, J., Boroevich, K. A., Brunak, S., Campbell, P. J., Chakravarty, D. & Chan, C. W. Y. & 182 others, Chen, K., Choi, J. K., Deu-Pons, J., Dhingra, P., Diamanti, K., 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., Hornshøj, H., Isaev, K., Izarzugaza, J. M. G., Johnson, T. A., Juul, M., Juul, R. I., Kahles, A., Kahraman, A., Kellis, M., Khurana, E., Kim, J., Kim, J. K., Kim, Y., Komorowski, J., Korbel, J. O., Kumar, S., Larsson, E., Lawrence, M. S., Lee, D., Lehmann, K. V., Li, S., Li, X., Lin, Z., Liu, E. M., Lochovsky, L., Lou, S., Madsen, T., Marchal, K., Martincorena, I., Martinez-Fundichely, A., Maruvka, Y. E., McGillivray, P. D., Meyerson, W., Muiños, F., Mularoni, L., Nakagawa, H., Nielsen, M. M., Paczkowska, M., Park, K., Park, K., Pich, O., Pons, T., Pulido-Tamayo, S., Raphael, B. J., Reimand, J., Reyes-Salazar, I., Reyna, M. A., Rheinbay, E., Rubin, M. A., Rubio-Perez, C., Sabarinathan, R., Sahinalp, S. C., Saksena, G., Salichos, L., Sander, C., Schumacher, S. E., Shackleton, M., Shapira, O., Shen, C., Shrestha, R., Shuai, S., Sidiropoulos, N., Sieverling, L., Sinnott-Armstrong, N., Stein, L. D., Stuart, J. M., Tamborero, D., Tiao, G., Tsunoda, T., Umer, H. M., Uusküla-Reimand, L., Valencia, A., Vazquez, M., Verbeke, L. P. C., Wadelius, C., Wadi, L., Wang, J., Warrell, J., Waszak, S. M., Weischenfeldt, J., Wheeler, D. A., Wu, G., Yu, J., Zhang, J., Zhang, X., Zhang, Y., Zhao, Z., Zou, L., von Mering, C., Aaltonen, L. A., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Dec 1 2020, In: Communications Biology. 3, 1, 56.

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

      Open Access
      147 Scopus citations

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

      PCAWG Drivers and Functional Interpretation Working Group, PCAWG Consortium, 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. & 182 others, Diamanti, K., Feuerbach, L., 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., Kahraman, A., Kellis, M., Khurana, E., Kim, J., Kim, J. K., Kim, Y., Komorowski, J., Korbel, J. O., Kumar, S., Lanzós, A., Larsson, E., Lawrence, M. S., Lee, D., Lehmann, K. V., Li, S., Li, X., Lin, Z., Liu, E. M., Lochovsky, L., Lou, S., Madsen, T., Marchal, K., Martincorena, I., Martinez-Fundichely, A., Maruvka, Y. E., McGillivray, P. D., Meyerson, W., Muiños, F., Mularoni, L., Nakagawa, H., Nielsen, M. M., Paczkowska, M., Park, K., Park, K., Pedersen, J. S., Pons, T., Pulido-Tamayo, S., Raphael, B. J., Reimand, J., Reyes-Salazar, I., Reyna, M. A., Rheinbay, E., Rubin, M. A., Rubio-Perez, C., Sahinalp, S. C., Saksena, G., Salichos, L., Sander, C., Schumacher, S. E., Shackleton, M., Shapira, O., Shen, C., Shrestha, R., Shuai, S., Sidiropoulos, N., Sieverling, L., Sinnott-Armstrong, N., Stein, L. D., Stuart, J. M., Tamborero, D., Tiao, G., Tsunoda, T., Umer, H. M., Uusküla-Reimand, L., Valencia, A., Vazquez, M., Verbeke, L. P. C., Wadelius, C., Wadi, L., Wang, J., Warrell, J., Waszak, S. M., Weischenfeldt, J., Wheeler, D. A., Wu, G., Yu, J., Zhang, J., Zhang, X., Zhang, Y., Zhao, Z., Zou, L., von Mering, C., Gallinger, S., Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Dec 1 2020, In: Nature communications. 11, 1, 734.

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

      Open Access
      25 Scopus citations

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

      PCAWG-Structural Variation Working Group, PCAWG Consortium, 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. & 182 others, 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., Koh, Y., Korbel, J. O., Kumar, K., Lee, E. A., Li, Y., Lynch, A. G., Macintyre, G., Markowetz, F., Martincorena, I., Martinez-Fundichely, A., Miyano, S., Nakagawa, H., Navarro, F. C. P., Ossowski, S., Pearson, J. V., Puiggròs, M., Rippe, K., Roberts, N. D., Roberts, S. A., Rodriguez-Martin, B., Schumacher, S. E., Scully, R., Shackleton, M., Sidiropoulos, N., Sieverling, L., Stewart, C., Torrents, D., Tubio, J. M. C., Villasante, I., Waddell, N., Wala, J. A., Weischenfeldt, J., Yang, L., Yao, X., Yoon, S. S., Zamora, J., Park, P. J., Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Boutros, P. C., Bova, G. S., Bowen, D. T., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Muyas, F. & Werner, J., Mar 1 2020, In: Nature Genetics. 52, 3, p. 331-341 11 p.

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

      Open Access
      407 Scopus citations

    • Comprehensive molecular characterization of mitochondrial genomes in human cancers

      PCAWG Consortium, Yuan, Y., Ju, Y. S., Kim, Y., Li, J., Wang, Y., Yoon, C. J., Yang, Y., Martincorena, I., Creighton, C. J., Weinstein, J. N., Xu, Y., Han, L., Kim, H. L., Nakagawa, H., Park, K., Campbell, P. J., Liang, H., Aaltonen, L. A. & Abascal, F. & 181 others, Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Beroukhim, R., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Boutros, P. C., Bova, G. S., Bowen, D. T., Bowlby, R., Bowtell, D. D. L., Boyault, S., Boyce, R., Boyd, J., Brazma, A., Brennan, P., Brewer, D. S., Brinkman, A. B., Bristow, R. G., Broaddus, R. R., Brock, J. E., Brock, M., Broeks, A., Brooks, A. N., Brooks, D., Brors, B., Brunak, S., Bruxner, T. J. C., Bruzos, A. L., Buchanan, A., Buchhalter, I., Buchholz, C., Bullman, S., Burke, H., Burkhardt, B., Burns, K. H., Busanovich, J., Bustamante, C. D., Butler, A. P., Butte, A. J., Byrne, N. J., Børresen-Dale, A. L., Caesar-Johnson, S. J., Cafferkey, A., Cahill, D., Calabrese, C., Caldas, C., Calvo, F., Camacho, N., Campbell, P. J., Campo, E., Cantù, C., Cao, S., Carey, T. E., Carlevaro-Fita, J., Carlsen, R., Cataldo, I., Cazzola, M., Cebon, J., Cerfolio, R., Chadwick, D. E., Chakravarty, D., Chalmers, D., Chan, C. W. Y., Chan, K., Chan-Seng-Yue, M., Chandan, V. S., Chang, D. K., Chanock, S. J., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Mar 1 2020, In: Nature Genetics. 52, 3, p. 342-352 11 p.

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      248 Scopus citations

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

      PCAWG-Structural Variation Working Group, PCAWG Consortium, 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., Boutros, P. C., Bowtell, D. D. L., Brors, B., Burns, K. H. & Campbell, P. J. & 182 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., Lee, J. J. K., Li, Y., Lynch, A. G., Macintyre, G., Markowetz, F., Martincorena, I., Martinez-Fundichely, A., Meyerson, M., Miyano, S., Nakagawa, H., Navarro, F. C. P., Ossowski, S., Park, P. J., Pearson, J. V., Puiggròs, M., Rippe, K., Roberts, N. D., Roberts, S. A., Rodriguez-Martin, B., Schumacher, S. E., Scully, R., Shackleton, M., Sidiropoulos, N., Sieverling, L., Stewart, C., Torrents, D., Tubio, J. M. C., Villasante, I., Waddell, N., Wala, J. A., Weischenfeldt, J., Yang, L., Yao, X., Yoon, S. S., Zamora, J., Zhang, C. Z., Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Muyas, F. & Werner, J., Mar 1 2020, In: Nature Genetics. 52, 3, p. 294-305 12 p.

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

      Open Access
      157 Scopus citations

    • Divergent mutational processes distinguish hypoxic and normoxic tumours

      PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 737.

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

      Open Access
      87 Scopus citations

    • Genomic basis for RNA alterations in cancer

      PCAWG Transcriptome Core Group, PCAWG Transcriptome Working Group, PCAWG Consortium, Calabrese, C., Davidson, N. R., Demircioğlu, D., Fonseca, N. A., He, Y., Kahles, A., Lehmann, K. V., Liu, F., Shiraishi, Y., Soulette, C. M., Urban, L., Greger, L., Li, S., Liu, D., Perry, M. D., Xiang, Q. & Zhang, F. & 183 others, Zhang, J., Bailey, P., Erkek, S., Hoadley, K. A., Hou, Y., Huska, M. R., Kilpinen, H., Korbel, J. O., Marin, M. G., Markowski, J., Nandi, T., Pan-Hammarström, Q., Pedamallu, C. S., Siebert, R., Stark, S. G., Su, H., Tan, P., Waszak, S. M., Yung, C., Zhu, S., Awadalla, P., Creighton, C. J., Meyerson, M., Ouellette, B. F. F., Wu, K., Yang, H., Brazma, A., Brooks, A. N., Göke, J., Rätsch, G., Schwarz, R. F., Stegle, O., Zhang, Z., Amin, S. B., Chateigner, A., Cortés-Ciriano, I., Craft, B., Frenkel-Morgenstern, M., Goldman, M., Khurana, E., Lamaze, F. C., Li, C., Li, X., Li, X., Liu, X., Nielsen, M. M., Ojesina, A. I., Park, P. J., Pedersen, J. S., Teh, B. T., Wang, J., Xiong, H., Yakneen, S., Ye, C., Zhang, X., Zheng, L., Zhu, J., Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Beroukhim, R., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Boutros, P. C., Bova, G. S., Bowen, D. T., Bowlby, R., Bowtell, D. D. L., Boyault, S., Boyce, R., Boyd, J., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Feb 6 2020, In: Nature. 578, 7793, p. 129-136 8 p.

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      Open Access
      273 Scopus citations

    • Genomic footprints of activated telomere maintenance mechanisms in cancer

      PCAWG-Structural Variation Working Group, PCAWG Consortium, 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. & 182 others, Bowtell, D. D. L., Brors, B., 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., Lee, E. A., Lee, J. J. K., Li, Y., Lynch, A. G., Macintyre, G., Markowetz, F., Martincorena, I., Martinez-Fundichely, A., Meyerson, M., Miyano, S., Nakagawa, H., Navarro, F. C. P., Ossowski, S., Pearson, J. V., Puiggròs, M., Rippe, K., Roberts, N. D., Roberts, S. A., Rodriguez-Martin, B., Schumacher, S. E., Scully, R., Shackleton, M., Sidiropoulos, N., Sieverling, L., Stewart, C., Torrents, D., Tubio, J. M. C., Villasante, I., Waddell, N., Wala, J. A., Weischenfeldt, J., Yang, L., Yao, X., Yoon, S. S., Zamora, J., Zhang, C. Z., Brors, B., Rippe, K., Jones, D. T. W., Feuerbach, L., Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Muyas, F. & Werner, J., Dec 1 2020, In: Nature communications. 11, 1, 733.

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

      Open Access
      77 Scopus citations

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

      PCAWG Transcriptome Working Group, PCAWG-Structural Variation Working Group, PCAWG Consortium, 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. & 183 others, Craft, D., Creighton, C. J., Davidson, N. R., 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., Marin, M. G., Markowski, J., Meyerson, M., Nandi, T., Nielsen, M. M., Ojesina, A. I., Ouellette, B. F. F., Pan-Hammarström, Q., Park, P. J., Pedamallu, C. S., Pedersen, J. S., Perry, M. D., Rätsch, G., Schwarz, R. F., Shiraishi, Y., Siebert, R., Soulette, C. M., Stark, S. G., Stegle, O., Su, H., Tan, P., Teh, B. T., Urban, L., Wang, J., Waszak, S. M., Wu, K., Xiang, Q., Xiong, H., Yakneen, S., Yang, H., Ye, C., Yung, C. K., Zhang, F., Zhang, J., Zhang, X., Zhang, Z., Zheng, L., Zhu, J., Zhu, 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., Chen, K., Cortés-Ciriano, I., Dueso-Barroso, A., Dunford, A. J., Edwards, P. A., Estivill, X., Etemadmoghadam, D., Feuerbach, L., Fink, J. L., 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., Lynch, A. G., Macintyre, G., Markowetz, F., Martincorena, I., Martinez-Fundichely, A., Miyano, S., Nakagawa, H., Navarro, F. C. P., Ossowski, S., Pearson, J. V., Puiggròs, M., Rippe, K., Roberts, N. D., Roberts, S. A., Rodriguez-Martin, B., Schumacher, S. E., Scully, R., Shackleton, M., Sidiropoulos, N., Sieverling, L., Stewart, C., Torrents, D., Tubio, J. M. C., Villasante, I., Waddell, N., Wala, J. A., Weischenfeldt, J., Yang, L., Yao, X., Yoon, S. S., Zamora, J., Zhang, C. Z., Creighton, C. J., Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Muyas, F. & Werner, J., Dec 1 2020, In: Nature communications. 11, 1, 736.

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

      Open Access
      51 Scopus citations

    • Inferring structural variant cancer cell fraction

      PCAWG Evolution and Heterogeneity Working Group, PCAWG Consortium, Cmero, M., Yuan, K., Ong, C. S., Schröder, J., Adams, D. J., Anur, P., Beroukhim, R., Boutros, P. C., Bowtell, D. D. L., Campbell, P. J., Cao, S., Christie, E. L., Cun, Y., Dawson, K. J., Demeulemeester, J., Dentro, S. C., Deshwar, A. G. & Donmez, N. & 182 others, Drews, R. M., Eils, R., Fan, Y., Fittall, M. W., Garsed, D. W., Gerstung, M., Getz, G., Gonzalez, S., Ha, G., Haase, K., Imielinski, M., Jerman, L., Ji, Y., Jolly, C., Kleinheinz, K., Lee, J., Lee-Six, H., Leshchiner, I., Livitz, D., Malikic, S., Martincorena, I., Mitchell, T. J., Morris, Q. D., Mustonen, V., Oesper, L., Peifer, M., Peto, M., Raphael, B. J., Rosebrock, D., Rubanova, Y., Sahinalp, S. C., Salcedo, A., Schlesner, M., Schumacher, S. E., Sengupta, S., Shi, R., Shin, S. J., Spellman, P. T., Spiro, O., Stein, L. D., Tarabichi, M., Van Loo, P., Vembu, S., Vázquez-García, I., Wang, W., Wedge, D. C., Wheeler, D. A., Wintersinger, J. A., Yang, T. P., Yao, X., Yu, K., Zhu, H., Corcoran, N. M., Papenfuss, T., Hovens, C. M., Markowetz, F., Macintyre, G., Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Boutros, P. C., Bova, G. S., Bowen, D. T., Bowlby, R., Boyault, S., Boyce, R., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Dec 1 2020, In: Nature communications. 11, 1, 730.

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

      Open Access
      29 Scopus citations

    • Integrative pathway enrichment analysis of multivariate omics data

      PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 735.

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

      Open Access
      117 Scopus citations

    • Long non-coding RNA RAMS11 promotes metastatic colorectal cancer progression

      Silva-Fisher, J. M., Dang, H. X., White, N. M., Strand, M. S., Krasnick, B. A., Rozycki, E. B., Jeffers, G. G. L., Grossman, J. G., Highkin, M. K., Tang, C., Cabanski, C. R., Eteleeb, A., Mudd, J., Goedegebuure, S. P., Luo, J., Mardis, E. R., Wilson, R. K., Ley, T. J., Lockhart, A. C. & Fields, R. C. & 1 others, Maher, C. A., Dec 1 2020, In: Nature communications. 11, 1, 2156.

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

      Open Access
      88 Scopus citations

    • Obesity is a risk factor for acute promyelocytic leukemia: Evidence from population and cross-sectional studies and correlation with FLT3 mutations and polyunsaturated fatty acid metabolism

      Mazzarella, L., Botteri, E., Matthews, A., Gatti, E., Di Salvatore, D., Bagnardi, V., Breccia, M., Montesinos, P., Bernal, T., Gil, C., Ley, T. J., Sanz, M., Bhaskaran, K., Coco, F. L. & Pelicci, P. G., Jun 1 2020, In: Haematologica. 105, 6, p. 1559-1566 8 p.

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

      Open Access
      29 Scopus citations

    • Pan-cancer analysis of whole genomes

      The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Feb 6 2020, In: Nature. 578, 7793, p. 82-93 12 p.

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

      Open Access
      1757 Scopus citations

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

      PCAWG-Structural Variation Working Group, PCAWG Consortium, 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. & 182 others, Ardeljan, D., Tojo, M., Roberts, N. D., Zumalave, S., Edwards, P. A., Weischenfeldt, J., Puiggròs, M., Chong, Z., Chen, K., Lee, E. A., Wala, J. A., Raine, K. M., 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., Burns, K. H., Campbell, P. J., Tubio, J. M. C., Akdemir, K. C., Boutros, P. C., Bowtell, D. D. L., Brors, B., Chan, K., Cortés-Ciriano, I., Dunford, A. J., Estivill, X., Etemadmoghadam, D., Feuerbach, L., Fink, J. L., Frenkel-Morgenstern, M., Garsed, D. W., Gordenin, D. A., Haan, D., Haber, J. E., Hess, J. M., Hutter, B., Imielinski, M., Jones, D. T. W., Kazanov, M. D., Klimczak, L. J., Koh, Y., Kumar, K., Lee, J. J. K., Lynch, A. G., Macintyre, G., Markowetz, F., Martinez-Fundichely, A., Meyerson, M., Miyano, S., Nakagawa, H., Ossowski, S., Pearson, J. V., Rippe, K., Roberts, S. A., Scully, R., Shackleton, M., Sidiropoulos, N., Sieverling, L., Stewart, C., Villasante, I., Waddell, N., Yang, L., Yao, X., Yoon, S. S., Zhang, C. Z., Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Mar 1 2020, In: Nature Genetics. 52, 3, p. 306-319 14 p.

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      Open Access
      249 Scopus citations

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

      PCAWG Drivers and Functional Interpretation Working Group, PCAWG Consortium, 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. & 182 others, Khurana, E., Marchal, K., 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., Guo, Q., Gut, I. G., 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., Johnson, R., Johnson, T. A., Juul, M., Juul, R. I., Kahles, A., Kellis, M., Kim, J., Kim, J. K., Kim, Y., Komorowski, J., Korbel, J. O., Kumar, S., Lanzós, A., Larsson, E., Lee, D., Lehmann, K. V., Li, S., Li, X., Lin, Z., Liu, E. M., Lochovsky, L., Lou, S., Madsen, T., Martincorena, I., Martinez-Fundichely, A., Maruvka, Y. E., McGillivray, P. D., Meyerson, W., Muiños, F., Mularoni, L., Nakagawa, H., Nielsen, M. M., Park, K., Park, K., Pons, T., Reyes-Salazar, I., Rheinbay, E., Rubio-Perez, C., Saksena, G., Salichos, L., Sander, C., Schumacher, S. E., Shackleton, M., Shapira, O., Shen, C., Shuai, S., Sidiropoulos, N., Sieverling, L., Sinnott-Armstrong, N., Stein, L. D., Tamborero, D., Tiao, G., Tsunoda, T., Umer, H. M., Uusküla-Reimand, L., Wadelius, C., Wang, J., Warrell, J., Waszak, S. M., Weischenfeldt, J., Wu, G., Yu, J., Zhang, J., Zhang, X., Zhang, Y., Zhao, Z., Zou, L., Reimand, J., Stuart, J. M., Raphael, B. J., Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Ding, L., Fulton, L. A., Fulton, R. S., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Dec 1 2020, In: Nature communications. 11, 1, 729.

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

      Open Access
      69 Scopus citations

    • Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig

      PCAWG Evolution and Heterogeneity Working Group, PCAWG Consortium, Rubanova, Y., Shi, R., Harrigan, C. F., Li, R., Wintersinger, J., Sahin, N., Deshwar, A. G., Dentro, S. C., Leshchiner, I., Gerstung, M., Jolly, C., Haase, K., Tarabichi, M., Wintersinger, J., Deshwar, A. G., Yu, K., Gonzalez, S. & Rubanova, Y. & 182 others, Macintyre, G., Adams, D. J., Anur, P., Beroukhim, R., Boutros, P. C., Bowtell, D. D., Campbell, P. J., Cao, S., Christie, E. L., Cmero, M., Cun, Y., Dawson, K. J., Demeulemeester, J., Donmez, N., Drews, R. M., Eils, R., Fan, Y., Fittall, M., Garsed, D. W., Getz, G., Ha, G., Imielinski, M., Jerman, L., Ji, Y., Kleinheinz, K., Lee, J., Lee-Six, H., Livitz, D. G., Malikic, S., Markowetz, F., Martincorena, I., Mitchell, T. J., Mustonen, V., Oesper, L., Peifer, M., Peto, M., Raphael, B. J., Rosebrock, D., Sahinalp, S. C., Salcedo, A., Schlesner, M., Schumacher, S., Sengupta, S., Shi, R., Shin, S. J., Spiro, O., Stein, L. D., Vázquez-García, I., Vembu, S., Wheeler, D. A., Yang, T. P., Yao, X., Yuan, K., Zhu, H., Wang, W., Morris, Q. D., Spellman, P. T., Wedge, D. C., Van Loo, P., Morris, Q. D., Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S. M., Aikata, H., Akbani, R., Akdemir, K. C., Al-Ahmadie, H., Al-Sedairy, S. T., Al-Shahrour, F., Alawi, M., Albert, M., Aldape, K., Alexandrov, L. B., Ally, A., Alsop, K., Alvarez, E. G., Amary, F., Amin, S. B., Aminou, B., Ammerpohl, O., Anderson, M. J., Ang, Y., Antonello, D., Anur, P., Aparicio, S., Appelbaum, E. L., Arai, Y., Aretz, A., Arihiro, K., Ariizumi, S. I., Armenia, J., Arnould, L., Asa, S., Assenov, Y., Atwal, G., Aukema, S., Auman, J. T., Aure, M. R. R., Awadalla, P., Aymerich, M., Bader, G. D., Baez-Ortega, A., Bailey, M. H., Bailey, P. J., Balasundaram, M., Balu, S., Bandopadhayay, P., Banks, R. E., Barbi, S., Barbour, A. P., Barenboim, J., Barnholtz-Sloan, J., Barr, H., Barrera, E., Bartlett, J., Bartolome, J., Bassi, C., Bathe, O. F., Baumhoer, D., Bavi, P., Baylin, S. B., Bazant, W., Beardsmore, D., Beck, T. A., Behjati, S., Behren, A., Niu, B., Bell, C., Beltran, S., Benz, C., Berchuck, A., Bergmann, A. K., Bergstrom, E. N., Berman, B. P., Berney, D. M., Bernhart, S. H., Berrios, M., Bersani, S., Bertl, J., Betancourt, M., Bhandari, V., Bhosle, S. G., Biankin, A. V., Bieg, M., Bigner, D., Binder, H., Birney, E., Birrer, M., Biswas, N. K., Bjerkehagen, B., Bodenheimer, T., Boice, L., Bonizzato, G., De Bono, J. S., Boot, A., Bootwalla, M. S., Borg, A., Borkhardt, A., Boroevich, K. A., Borozan, I., Borst, C., Bosenberg, M., Bosio, M., Boultwood, J., Bourque, G., Boutros, P. C., Bova, G. S., Bowen, D. T., Bowlby, R., Ding, L., Fulton, L. A., Govindan, R., Jayasinghe, R., Ley, T., Miller, C. A., Mutch, D. & Wendl, M. C., Dec 1 2020, In: Nature communications. 11, 1, 731.

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

      Open Access
      30 Scopus citations

    • Remethylation of Dnmt3a−/− hematopoietic cells is associated with partial correction of gene dysregulation and reduced myeloid skewing

      Ketkar, S., Verdoni, A. M., Smith, A. M., Bangert, C. V., Leight, E. R., Chen, D. Y., Brune, M. K., Helton, N. M., Hoock, M., George, D. R., Fronick, C., Fulton, R. S., Ramakrishnan, S. M., Chang, G. S., Petti, A. A., Spencer, D. H., Miller, C. A. & Ley, T. J., Feb 11 2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 6, p. 3123-3134 12 p.

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

      Open Access
      21 Scopus citations

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

      MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 4748.

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

      Open Access
      32 Scopus citations

    • Sex differences in oncogenic mutational processes

      PCAWG Tumour Subtypes and Clinical Translation & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 4330.

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

      Open Access
      62 Scopus citations

    • The clonal evolution of metastatic colorectal cancer

      Dang, H. X., Krasnick, B. A., White, B. S., Grossman, J. G., Strand, M. S., Zhang, J., Cabanski, C. R., Miller, C. A., Fulton, R. S., Goedegebuure, S. P., Fronick, C. C., Griffith, M., Larson, D. E., Goetz, B. D., Walker, J. R., Hawkins, W. G., Strasberg, S. M., Linehan, D. C., Lim, K. H. & Lockhart, A. C. & 5 others, Mardis, E. R., Wilson, R. K., Ley, T. J., Maher, C. A. & Fields, R. C., Jun 2020, In: Science Advances. 6, 24, eaay9691.

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

      Open Access
      48 Scopus citations

    • The landscape of viral associations in human cancers

      PCAWG Pathogens & PCAWG Consortium, Mar 1 2020, In: Nature Genetics. 52, 3, p. 320-330 11 p.

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

      Open Access
      246 Scopus citations
    • 2019

      A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing

      Petti, A. A., Williams, S. R., Miller, C. A., Fiddes, I. T., Srivatsan, S. N., Chen, D. Y., Fronick, C. C., Fulton, R. S., Church, D. M. & Ley, T. J., Dec 1 2019, In: Nature communications. 10, 1, 3660.

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

      Open Access
      138 Scopus citations
    • 2018

      A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

      The Cancer Genome Atlas Research Network, Apr 9 2018, In: Cancer Cell. 33, 4, p. 690-705.e9

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

      Open Access
      417 Scopus citations