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Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.
Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN; ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants; Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC. Lee AY, et al. Genome Biol. 2018 Nov 6;19(1):188. doi: 10.1186/s13059-018-1539-5. Genome Biol. 2018. PMID: 30400818 Free PMC article.
Fast and accurate mapping of Complete Genomics reads.
Lee D, Hormozdiari F, Xin H, Hach F, Mutlu O, Alkan C. Lee D, et al. Among authors: hach f. Methods. 2015 Jun;79-80:3-10. doi: 10.1016/j.ymeth.2014.10.012. Epub 2014 Oct 22. Methods. 2015. PMID: 25461772 Free PMC article.
Comparison of high-throughput sequencing data compression tools.
Numanagić I, Bonfield JK, Hach F, Voges J, Ostermann J, Alberti C, Mattavelli M, Sahinalp SC. Numanagić I, et al. Among authors: hach f. Nat Methods. 2016 Dec;13(12):1005-1008. doi: 10.1038/nmeth.4037. Epub 2016 Oct 24. Nat Methods. 2016. PMID: 27776113
Robustness of Massively Parallel Sequencing Platforms.
Kavak P, Yüksel B, Aksu S, Kulekci MO, Güngör T, Hach F, Şahinalp SC; Turkish Human Genome Project; Alkan C, Sağıroğlu MŞ. Kavak P, et al. Among authors: hach f. PLoS One. 2015 Sep 18;10(9):e0138259. doi: 10.1371/journal.pone.0138259. eCollection 2015. PLoS One. 2015. PMID: 26382624 Free PMC article.
Spatial genomic heterogeneity within localized, multifocal prostate cancer.
Boutros PC, Fraser M, Harding NJ, de Borja R, Trudel D, Lalonde E, Meng A, Hennings-Yeomans PH, McPherson A, Sabelnykova VY, Zia A, Fox NS, Livingstone J, Shiah YJ, Wang J, Beck TA, Have CL, Chong T, Sam M, Johns J, Timms L, Buchner N, Wong A, Watson JD, Simmons TT, P'ng C, Zafarana G, Nguyen F, Luo X, Chu KC, Prokopec SD, Sykes J, Dal Pra A, Berlin A, Brown A, Chan-Seng-Yue MA, Yousif F, Denroche RE, Chong LC, Chen GM, Jung E, Fung C, Starmans MH, Chen H, Govind SK, Hawley J, D'Costa A, Pintilie M, Waggott D, Hach F, Lambin P, Muthuswamy LB, Cooper C, Eeles R, Neal D, Tetu B, Sahinalp C, Stein LD, Fleshner N, Shah SP, Collins CC, Hudson TJ, McPherson JD, van der Kwast T, Bristow RG. Boutros PC, et al. Among authors: hach f. Nat Genet. 2015 Jul;47(7):736-45. doi: 10.1038/ng.3315. Epub 2015 May 25. Nat Genet. 2015. PMID: 26005866
94 results