SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing

by Niknafs, Noushin, Beleva-Guthrie, Violeta, Naiman, Daniel Q., Karchin, Rachel
Published in PLoS Comput Biol (2015)

Network Analysis of Protein Adaptation: Modeling the Functional Impact of Multiple Mutations

by Beleva Guthrie, Violeta, Masica, David L, Fraser, Andrew, Federico, Joseph, Fan, Yunfan, Camps, Manel, Karchin, Rachel
Published in Mol Biol Evol (2018)

A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing

by Chen, Yun-Ching, Douville, Christopher, Wang, Cheng, Niknafs, Noushin, Yeo, Grace, Beleva-Guthrie, Violeta, Carter, Hannah, Stenson, Peter D., Cooper, David N., Li, Biao, Mooney, Sean, Karchin, Rachel
Published 2014

Multi-region Whole Exome Sequencing of Intraductal Papillary Mucinous Neoplasms Reveals Frequent Somatic KLF4 Mutations Predominantly in Low-Grade Regions

by Fujikura, Kohei, Hosoda, Waki, Felsenstein, Matthäus, Song, Qianqian, Reiter, Johannes G., Zheng, Lily, Beleva Guthrie, Violeta, Rincon, Natalia, Dal Molin, Marco, Dudley, Jonathan, Cohen, Joshua D., Wang, Pei, Fischer, Catherine G., Braxton, Alicia M., Noë, Michaël, Jongepier, Martine, Fernández-del Castillo, Carlos, Mino-Kenudson, Mari, Schmidt, C. Max, Yip-Schneider, Michele T., Lawlor, Rita T., Salvia, Roberto, Roberts, Nicholas J., Thompson, Elizabeth D., Karchin, Rachel, Lennon, Anne Marie, Jiao, Yuchen, Wood, Laura D.
Published in Gut (2020)

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges

by Cai, Binghuang, Li, Biao, Kiga, Nikki, Thusberg, Janita, Bergquist, Timothy, Chen, Yun-Ching, Niknafs, Noushin, Carter, Hannah, Tokheim, Collin, Beleva-Guthrie, Violeta, Douville, Christopher, Bhattacharya, Rohit, Yeo, Hui Ting Grace, Fan, Jean, Sengupta, Sohini, Kim, Dewey, Cline, Melissa, Turner, Tychele, Diekhans, Mark, Zaucha, Jan, Pal, Lipika R., Cao, Chen, Yu, Chen-Hsin, Yin, Yizhou, Carraro, Marco, Giollo, Manuel, Ferrari, Carlo, Leonardi, Emanuela, Tosatto, Silvio C.E., Bobe, Jason, Ball, Madeleine, Hoskins, Roger A., Repo, Susanna, Church, George, Brenner, Steven E., Moult, John, Gough, Julian, Stanke, Mario, Karchin, Rachel, Mooney, Sean D.
Published in Hum Mutat (2017)

Genomic characterization of malignant progression in neoplastic pancreatic cysts

by Noë, Michaël, Niknafs, Noushin, Fischer, Catherine G., Hackeng, Wenzel M., Beleva Guthrie, Violeta, Hosoda, Waki, Debeljak, Marija, Papp, Eniko, Adleff, Vilmos, White, James R., Luchini, Claudio, Pea, Antonio, Scarpa, Aldo, Butturini, Giovanni, Zamboni, Giuseppe, Castelli, Paola, Hong, Seung-Mo, Yachida, Shinichi, Hiraoka, Nobuyoshi, Gill, Anthony J., Samra, Jaswinder S., Offerhaus, G. Johan A., Hoorens, Anne, Verheij, Joanne, Jansen, Casper, Adsay, N. Volkan, Jiang, Wei, Winter, Jordan, Albores-Saavedra, Jorge, Terris, Benoit, Thompson, Elizabeth D., Roberts, Nicholas J., Hruban, Ralph H., Karchin, Rachel, Scharpf, Robert B., Brosens, Lodewijk A. A., Velculescu, Victor E., Wood, Laura D.
Published in Nat Commun (2020)