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A community approach to the cancer-variant-interpretation bottleneck.
Krysiak K, Danos AM, Kiwala S, McMichael JF, Coffman AC, Barnell EK, Sheta L, Saliba J, Grisdale CJ, Kujan L, Pema S, Lever J, Spies NC, Chiorean A, Rieke DT, Clark KA, Jani P, Takahashi H, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Lamping M, Marr AR, Li BV, Lin WH, Terraf P, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith OL, Griffith M. Krysiak K, et al. Among authors: kiwala s. Nat Cancer. 2022 May;3(5):522-525. doi: 10.1038/s43018-022-00379-w. Nat Cancer. 2022. PMID: 35624339 Free PMC article.
Cancer Immunogenomics: Computational Neoantigen Identification and Vaccine Design.
Hundal J, Miller CA, Griffith M, Griffith OL, Walker J, Kiwala S, Graubert A, McMichael J, Coffman A, Mardis ER. Hundal J, et al. Among authors: kiwala s. Cold Spring Harb Symp Quant Biol. 2016;81:105-111. doi: 10.1101/sqb.2016.81.030726. Epub 2017 Apr 7. Cold Spring Harb Symp Quant Biol. 2016. PMID: 28389595 Free PMC article. Review.
DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.
Cotto KC, Wagner AH, Feng YY, Kiwala S, Coffman AC, Spies G, Wollam A, Spies NC, Griffith OL, Griffith M. Cotto KC, et al. Among authors: kiwala s. Nucleic Acids Res. 2018 Jan 4;46(D1):D1068-D1073. doi: 10.1093/nar/gkx1143. Nucleic Acids Res. 2018. PMID: 29156001 Free PMC article.
Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards.
Danos AM, Ritter DI, Wagner AH, Krysiak K, Sonkin D, Micheel C, McCoy M, Rao S, Raca G, Boca SM, Roy A, Barnell EK, McMichael JF, Kiwala S, Coffman AC, Kujan L, Kulkarni S, Griffith M, Madhavan S, Griffith OL; Clinical Genome Resource Somatic Working Group and Clinical Interpretation of Variants in Cancer team members. Danos AM, et al. Among authors: kiwala s. Hum Mutat. 2018 Nov;39(11):1721-1732. doi: 10.1002/humu.23651. Hum Mutat. 2018. PMID: 30311370 Free PMC article.
Accounting for proximal variants improves neoantigen prediction.
Hundal J, Kiwala S, Feng YY, Liu CJ, Govindan R, Chapman WC, Uppaluri R, Swamidass SJ, Griffith OL, Mardis ER, Griffith M. Hundal J, et al. Among authors: kiwala s. Nat Genet. 2019 Jan;51(1):175-179. doi: 10.1038/s41588-018-0283-9. Epub 2018 Dec 3. Nat Genet. 2019. PMID: 30510237 Free PMC article.
Standard operating procedure for curation and clinical interpretation of variants in cancer.
Danos AM, Krysiak K, Barnell EK, Coffman AC, McMichael JF, Kiwala S, Spies NC, Sheta LM, Pema SP, Kujan L, Clark KA, Wollam AZ, Rao S, Ritter DI, Sonkin D, Raca G, Lin WH, Grisdale CJ, Kim RH, Wagner AH, Madhavan S, Griffith M, Griffith OL. Danos AM, et al. Among authors: kiwala s. Genome Med. 2019 Nov 29;11(1):76. doi: 10.1186/s13073-019-0687-x. Genome Med. 2019. PMID: 31779674 Free PMC article. Review.
pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens.
Hundal J, Kiwala S, McMichael J, Miller CA, Xia H, Wollam AT, Liu CJ, Zhao S, Feng YY, Graubert AP, Wollam AZ, Neichin J, Neveau M, Walker J, Gillanders WE, Mardis ER, Griffith OL, Griffith M. Hundal J, et al. Among authors: kiwala s. Cancer Immunol Res. 2020 Mar;8(3):409-420. doi: 10.1158/2326-6066.CIR-19-0401. Epub 2020 Jan 6. Cancer Immunol Res. 2020. PMID: 31907209 Free PMC article.
CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase.
Krysiak K, Danos AM, Saliba J, McMichael JF, Coffman AC, Kiwala S, Barnell EK, Sheta L, Grisdale CJ, Kujan L, Pema S, Lever J, Ridd S, Spies NC, Andric V, Chiorean A, Rieke DT, Clark KA, Reisle C, Venigalla AC, Evans M, Jani P, Takahashi H, Suda A, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Kesserwan C, Lamping M, Shen H, Marr AR, Hoang MH, Singhal K, Khanfar M, Li BV, Lin WH, Terraf P, Corson LB, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, King I, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith M, Griffith OL. Krysiak K, et al. Among authors: kiwala s. Nucleic Acids Res. 2023 Jan 6;51(D1):D1230-D1241. doi: 10.1093/nar/gkac979. Nucleic Acids Res. 2023. PMID: 36373660 Free PMC article.
17 results