Works matching AU Yamaguchi, Takafumi N

Results: 13
    1
    2

    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
    3
    4

    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
    5

    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
    6

    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
    7
    8

    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
    9

    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
    10
    11

    RNA transcripts serve as a template for double-strand break repair in human cells.

    Published in:
    Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-59510-x
    By:
    • Jalan, Manisha;
    • Brambati, Alessandra;
    • Shah, Hina;
    • McDermott, Niamh;
    • Patel, Juber;
    • Zhu, Yingjie;
    • Doymaz, Ahmet;
    • Wu, Julius;
    • Anderson, Kyrie S.;
    • Gazzo, Andrea;
    • Pareja, Fresia;
    • Yamaguchi, Takafumi N.;
    • Vougiouklakis, Theodore;
    • Ahmed-Seghir, Sana;
    • Steinberg, Philippa;
    • Neiman-Golden, Anna;
    • Azeroglu, Benura;
    • Gomez-Aguilar, Joan;
    • da Silva, Edaise M.;
    • Hussain, Suleman
    Publication type:
    Article
    12

    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
    13

    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