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Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline.
Patel Y, Zhu C, Yamaguchi TN, Wang N, Wiltsie N, Gonzalez A, Winata H, Zeltser N, Pan Y, Mootor MFE, Sanders T, Kandoth C, Fitz-Gibbon ST, Livingstone J, Liu LY, Carlin B, Holmes A, Oh J, Sahrmann J, Tao S, Eng S, Hugh-White R, Pashminehazar K, Park A, Beshlikyan A, Jordan M, Wu S, Tian M, Arbet J, Neilsen B, Bugh YZ, Kim G, Salmingo J, Zhang W, Haas R, Anand A, Hwang E, Neiman-Golden A, Steinberg P, Zhao W, Anand P, Tsai BL, Boutros PC. Patel Y, et al. Among authors: bugh yz. bioRxiv [Preprint]. 2025 Jan 13:2024.09.04.611267. doi: 10.1101/2024.09.04.611267. bioRxiv. 2025. PMID: 39282325 Free PMC article. Preprint.
The Proteogenomics of Prostate Cancer Radioresistance.
Haas R, Frame G, Khan S, Neilsen BK, Hong BH, Yeo CPX, Yamaguchi TN, Ong EHW, Zhao W, Carlin B, Yeo ELL, Tan KM, Bugh YZ, Zhu C, Hugh-White R, Livingstone J, Poon DJJ, Chu PL, Patel Y, Tao S, Ignatchenko V, Kurganovs NJ, Higgins GS, Downes MR, Loblaw A, Vesprini D, Kishan AU, Chua MLK, Kislinger T, Boutros PC, Liu SK. Haas R, et al. Among authors: bugh yz. Cancer Res Commun. 2024 Sep 1;4(9):2463-2479. doi: 10.1158/2767-9764.CRC-24-0292. Cancer Res Commun. 2024. PMID: 39166898 Free PMC article.
NFTest: automated testing of Nextflow pipelines.
Patel Y, Zhu C, Yamaguchi TN, Bugh YZ, Tian M, Holmes A, Fitz-Gibbon ST, Boutros PC. Patel Y, et al. Among authors: bugh yz. Bioinformatics. 2024 Feb 1;40(2):btae081. doi: 10.1093/bioinformatics/btae081. Bioinformatics. 2024. PMID: 38341660 Free PMC article.