Phylogenetic Quantification of Intra-tumour Heterogeneity
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DOI: 10.1371/journal.pcbi.1003535
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- Sohrab P. Shah & Ryan D. Morin & Jaswinder Khattra & Leah Prentice & Trevor Pugh & Angela Burleigh & Allen Delaney & Karen Gelmon & Ryan Guliany & Janine Senz & Christian Steidl & Robert A. Holt & Ste, 2009. "Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution," Nature, Nature, vol. 461(7265), pages 809-813, October.
- Peter J. Campbell & Shinichi Yachida & Laura J. Mudie & Philip J. Stephens & Erin D. Pleasance & Lucy A. Stebbings & Laura A. Morsberger & Calli Latimer & Stuart McLaren & Meng-Lay Lin & David J. McBr, 2010. "The patterns and dynamics of genomic instability in metastatic pancreatic cancer," Nature, Nature, vol. 467(7319), pages 1109-1113, October.
- Nicholas Navin & Jude Kendall & Jennifer Troge & Peter Andrews & Linda Rodgers & Jeanne McIndoo & Kerry Cook & Asya Stepansky & Dan Levy & Diane Esposito & Lakshmi Muthuswamy & Alex Krasnitz & W. Rich, 2011. "Tumour evolution inferred by single-cell sequencing," Nature, Nature, vol. 472(7341), pages 90-94, April.
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