CRAVAT: cancer-related analysis of variants toolkit. - Christopher Douville; Hannah Carter; Rick Kim; Noushin Niknafs; Mark Diekhans; Peter D. Stenson; David N. Cooper; Michael C. Ryan; Rachel Karchin (Bioinform., 2013)

A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing. - Yun-Ching Chen; Christopher Douville; Cheng Wang; Noushin Niknafs; Grace H. T. Yeo; Violeta Beleva Guthrie; Hannah Carter; Peter D. Stenson; David N. Cooper; Biao Li; Sean D. Mooney; Rachel Karchin (PLoS Comput. Biol., 2014)

SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing. - Noushin Niknafs; Violeta Beleva Guthrie; Daniel Q. Naiman; Rachel Karchin (PLoS Comput. Biol., 2015)

Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors. - Lily Zheng; Noushin Niknafs; Laura D. Wood; Rachel Karchin; Robert B. Scharpf (Bioinform., 2022)

3D genomic mapping reveals multifocality of human pancreatic precancers. - Alicia M. Braxton; Ashley L. Kiemen; Mia P. Grahn; André Forjaz; Jeeun Parksong; Jaanvi Mahesh Babu; Jiaying Lai; Lily Zheng; Noushin Niknafs; Liping Jiang; Haixia Cheng; Qianqian Song; et al. (Nat., 2024)