Found: 12

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  • Cribriform and intraductal prostate cancer are associated with increased genomic instability and distinct genomic alterations.

    Published in:
    2018
    By:
    • Böttcher, René;
    • Kweldam, Charlotte F.;
    • Livingstone, Julie;
    • Lalonde, Emilie;
    • Yamaguchi, Takafumi N.;
    • Huang, Vincent;
    • Yousif, Fouad;
    • Fraser, Michael;
    • Bristow, Robert G.;
    • van der Kwast, Theodorus;
    • Boutros, Paul C.;
    • Jenster, Guido;
    • van Leenders, Geert J. L. H.
    Publication type:
    journal article

  • The telomere length landscape of prostate cancer.

    Published in:
    Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-27223-6
    By:
    • Livingstone, Julie;
    • Shiah, Yu-Jia;
    • Yamaguchi, Takafumi N.;
    • Heisler, Lawrence E.;
    • Huang, Vincent;
    • Lesurf, Robert;
    • Gebo, Tsumugi;
    • Carlin, Benjamin;
    • Eng, Stefan;
    • Drysdale, Erik;
    • Green, Jeffrey;
    • van der Kwast, Theodorus;
    • Bristow, Robert G.;
    • Fraser, Michael;
    • Boutros, Paul C.
    Publication type:
    Article

  • Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.

    Published in:
    Nature Methods, 2015, v. 12, n. 7, p. 623, doi. 10.1038/nmeth.3407
    By:
    • Ewing, Adam D;
    • Houlahan, Kathleen E;
    • Hu, Yin;
    • Ellrott, Kyle;
    • Caloian, Cristian;
    • Yamaguchi, Takafumi N;
    • Bare, J Christopher;
    • P'ng, Christine;
    • Waggott, Daryl;
    • Sabelnykova, Veronica Y;
    • Kellen, Michael R;
    • Norman, Thea C;
    • Haussler, David;
    • Friend, Stephen H;
    • Stolovitzky, Gustavo;
    • Margolin, Adam A;
    • Stuart, Joshua M;
    • Boutros, Paul C
    Publication type:
    Article

  • NFTest: automated testing of Nextflow pipelines.

    Published in:
    Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae081
    By:
    • Patel, Yash;
    • Zhu, Chenghao;
    • Yamaguchi, Takafumi N;
    • Bugh, Yuan Zhe;
    • Tian, Mao;
    • Holmes, Aaron;
    • Fitz-Gibbon, Sorel T;
    • Boutros, Paul C
    Publication type:
    Article

  • PipeVal: light-weight extensible tool for file validation.

    Published in:
    Bioinformatics, 2024, v. 40, n. 2, p. 1, doi. 10.1093/bioinformatics/btae079
    By:
    • Patel, Yash;
    • Beshlikyan, Arpi;
    • Jordan, Madison;
    • Kim, Gina;
    • Holmes, Aaron;
    • Yamaguchi, Takafumi N;
    • Boutros, Paul C
    Publication type:
    Article

  • The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact.

    Published in:
    Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-13084-7
    By:
    • van Dessel, Lisanne F.;
    • van Riet, Job;
    • Smits, Minke;
    • Zhu, Yanyun;
    • Hamberg, Paul;
    • van der Heijden, Michiel S.;
    • Bergman, Andries M.;
    • van Oort, Inge M.;
    • de Wit, Ronald;
    • Voest, Emile E.;
    • Steeghs, Neeltje;
    • Yamaguchi, Takafumi N.;
    • Livingstone, Julie;
    • Boutros, Paul C.;
    • Martens, John W. M.;
    • Sleijfer, Stefan;
    • Cuppen, Edwin;
    • Zwart, Wilbert;
    • van de Werken, Harmen J. G.;
    • Mehra, Niven
    Publication type:
    Article

  • Germline BRCA2 mutations drive prostate cancers with distinct evolutionary trajectories.

    Published in:
    Nature Communications, 2017, v. 8, n. 1, p. 13671, doi. 10.1038/ncomms13671
    By:
    • Taylor, Renea A.;
    • Fraser, Michael;
    • Livingstone, Julie;
    • Espiritu, Shadrielle Melijah G.;
    • Thorne, Heather;
    • Huang, Vincent;
    • Lo, Winnie;
    • Shiah, Yu-Jia;
    • Yamaguchi, Takafumi N.;
    • Sliwinski, Ania;
    • Horsburgh, Sheri;
    • Meng, Alice;
    • Heisler, Lawrence E.;
    • Yu, Nancy;
    • Yousif, Fouad;
    • Papargiris, Melissa;
    • Lawrence, Mitchell G.;
    • Timms, Lee;
    • Murphy, Declan G.;
    • Frydenberg, Mark
    Publication type:
    Article

  • Valection: design optimization for validation and verification studies.

    Published in:
    BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2391-z
    By:
    • Cooper, Christopher I;
    • Yao, Delia;
    • Sendorek, Dorota H;
    • Yamaguchi, Takafumi N;
    • P'ng, Christine;
    • Houlahan, Kathleen E;
    • Caloian, Cristian;
    • Fraser, Michael;
    • Ellrott, Kyle;
    • Margolin, Adam A;
    • Bristow, Robert G;
    • Stuart, Joshua M;
    • Boutros, Paul C
    Publication type:
    Article

  • Germline contamination and leakage in whole genome somatic single nucleotide variant detection.

    Published in:
    BMC Bioinformatics, 2018, v. 19, p. 1, doi. 10.1186/s12859-018-2046-0
    By:
    • Sendorek, Dorota H.;
    • Caloian, Cristian;
    • Ellrott, Kyle;
    • Bare, J. Christopher;
    • Yamaguchi, Takafumi N.;
    • Ewing, Adam D.;
    • Houlahan, Kathleen E.;
    • Norman, Thea C.;
    • Margolin, Adam A.;
    • Stuart, Joshua M.;
    • Boutros, Paul C.
    Publication type:
    Article

  • Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.

    Published in:
    Genome Biology, 2018, v. 19, n. 1, p. N.PAG, doi. 10.1186/s13059-018-1539-5
    By:
    • Lee, Anna Y.;
    • Ewing, Adam D.;
    • Ellrott, Kyle;
    • Hu, Yin;
    • Houlahan, Kathleen E.;
    • Bare, J. Christopher;
    • Espiritu, Shadrielle Melijah G.;
    • Huang, Vincent;
    • Dang, Kristen;
    • Chong, Zechen;
    • Caloian, Cristian;
    • Yamaguchi, Takafumi N.;
    • Kellen, Michael R.;
    • Chen, Ken;
    • Norman, Thea C.;
    • Friend, Stephen H.;
    • Guinney, Justin;
    • Stolovitzky, Gustavo;
    • Haussler, David;
    • Margolin, Adam A.
    Publication type:
    Article

  • Precision Radiotherapy: Reduction in Radiation for Oropharyngeal Cancer in the 30 ROC Trial.

    Published in:
    2021
    By:
    • Riaz, Nadeem;
    • Sherman, Eric;
    • Pei, Xin;
    • Schöder, Heiko;
    • Grkovski, Milan;
    • Paudyal, Ramesh;
    • Katabi, Nora;
    • Selenica, Pier;
    • Yamaguchi, Takafumi N;
    • Ma, Daniel;
    • Lee, Simon K;
    • Shah, Rachna;
    • Kumar, Rahul;
    • Kuo, Fengshen;
    • Ratnakumar, Abhirami;
    • Aleynick, Nathan;
    • Brown, David;
    • Zhang, Zhigang;
    • Hatzoglou, Vaios;
    • Liu, Lydia Y
    Publication type:
    journal article

  • Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer.

    Published in:
    Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-14318-9
    By:
    • Zhou, Stanley;
    • Hawley, James R.;
    • Soares, Fraser;
    • Grillo, Giacomo;
    • Teng, Mona;
    • Madani Tonekaboni, Seyed Ali;
    • Hua, Junjie Tony;
    • Kron, Ken J.;
    • Mazrooei, Parisa;
    • Ahmed, Musaddeque;
    • Arlidge, Christopher;
    • Yun, Hwa Young;
    • Livingstone, Julie;
    • Huang, Vincent;
    • Yamaguchi, Takafumi N.;
    • Espiritu, Shadrielle M. G.;
    • Zhu, Yanyun;
    • Severson, Tesa M.;
    • Murison, Alex;
    • Cameron, Sarina
    Publication type:
    Article