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Computational approaches to identify functional genetic variants in cancer genomes.
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group. Gonzalez-Perez A, et al. Among authors: karchin r. Nat Methods. 2013 Aug;10(8):723-9. doi: 10.1038/nmeth.2562. Nat Methods. 2013. PMID: 23900255 Free PMC article.
Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria.
Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS, Biesecker LG, Radivojac P, Brenner SE; ClinGen Sequence Variant Interpretation Working Group. Pejaver V, et al. Among authors: karchin r. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. doi: 10.1016/j.ajhg.2022.10.013. Epub 2022 Nov 21. Am J Hum Genet. 2022. PMID: 36413997 Free PMC article.
Accumulation of driver and passenger mutations during tumor progression.
Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, Chen S, Karchin R, Kinzler KW, Vogelstein B, Nowak MA. Bozic I, et al. Among authors: karchin r. Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18545-50. doi: 10.1073/pnas.1010978107. Epub 2010 Sep 27. Proc Natl Acad Sci U S A. 2010. PMID: 20876136 Free PMC article.
Integrated genomic analyses of ovarian carcinoma.
Cancer Genome Atlas Research Network. Cancer Genome Atlas Research Network. Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166. Nature. 2011. PMID: 21720365 Free PMC article.
CRAVAT: cancer-related analysis of variants toolkit.
Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R. Douville C, et al. Among authors: karchin r. Bioinformatics. 2013 Mar 1;29(5):647-8. doi: 10.1093/bioinformatics/btt017. Epub 2013 Jan 16. Bioinformatics. 2013. PMID: 23325621 Free PMC article.
A hybrid likelihood model for sequence-based disease association studies.
Chen YC, Carter H, Parla J, Kramer M, Goes FS, Pirooznia M, Zandi PP, McCombie WR, Potash JB, Karchin R. Chen YC, et al. Among authors: karchin r. PLoS Genet. 2013;9(1):e1003224. doi: 10.1371/journal.pgen.1003224. Epub 2013 Jan 24. PLoS Genet. 2013. PMID: 23358228 Free PMC article.
141 results