TY - JOUR AU - Miller, C. A. AU - White, B. S. AU - Dees, N. D. AU - Griffith, M. AU - Welch, J. S. AU - Griffith, O. L. PY - 2014 DA - 2014// TI - SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution JO - PLoS Comput Biol VL - 10 UR - https://doi.org/10.1371/journal.pcbi.1003665 DO - 10.1371/journal.pcbi.1003665 ID - Miller2014 ER - TY - JOUR AU - Roth, A. AU - Khattra, J. AU - Yap, D. AU - Wan, A. AU - Laks, E. AU - Biele, J. PY - 2014 DA - 2014// TI - PyClone: statistical inference of clonal population structure in cancer JO - Nat Methods VL - 11 UR - https://doi.org/10.1038/nmeth.2883 DO - 10.1038/nmeth.2883 ID - Roth2014 ER - TY - JOUR AU - Deshwar, A. G. AU - Vembu, S. AU - Yung, C. K. AU - Jang, G. H. AU - Stein, L. AU - Morris, Q. PY - 2015 DA - 2015// TI - PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0602-8 DO - 10.1186/s13059-015-0602-8 ID - Deshwar2015 ER - TY - JOUR AU - Oesper, L. AU - Mahmoody, A. AU - Raphael, B. J. PY - 2013 DA - 2013// TI - THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data JO - Genome Biol VL - 14 UR - https://doi.org/10.1186/gb-2013-14-7-r80 DO - 10.1186/gb-2013-14-7-r80 ID - Oesper2013 ER - TY - JOUR AU - Qiao, Y. AU - Quinlan, A. R. AU - Jazaeri, A. A. AU - Verhaak, R. G. AU - Wheeler, D. A. AU - Marth, G. T. PY - 2014 DA - 2014// TI - SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0443-x DO - 10.1186/s13059-014-0443-x ID - Qiao2014 ER - TY - STD TI - Niknafs N, Beleva-Guthrie V, Naiman DQ, Karchin R. SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing. PLoS Comput. Biol. 2015;11. ID - ref6 ER - TY - JOUR AU - Ding, L. AU - Ley, T. J. AU - Larson, D. E. AU - Miller, C. A. AU - Koboldt, D. C. AU - Welch, J. S. PY - 2012 DA - 2012// TI - Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing JO - Nature VL - 481 UR - https://doi.org/10.1038/nature10738 DO - 10.1038/nature10738 ID - Ding2012 ER - TY - JOUR AU - Engle, E. K. AU - Fisher, D. A. AU - Miller, C. A. AU - McLellan, M. D. AU - Fulton, R. S. AU - Moore, D. M. PY - 2014 DA - 2014// TI - Clonal evolution revealed by whole genome sequencing in a case of primary myelofibrosis transformed to secondary acute myeloid leukemia JO - Leukemia ID - Engle2014 ER - TY - JOUR AU - Griffith, M. AU - Miller, C. A. AU - Griffith, O. L. AU - Krysiak, K. AU - Skidmore, Z. L. AU - Ramu, A. PY - 2015 DA - 2015// TI - Optimizing cancer genome sequencing and analysis JO - Cell Syst VL - 1 UR - https://doi.org/10.1016/j.cels.2015.08.015 DO - 10.1016/j.cels.2015.08.015 ID - Griffith2015 ER - TY - JOUR AU - Wang, Y. AU - Waters, J. AU - Leung, M. L. AU - Unruh, A. AU - Roh, W. AU - Shi, X. PY - 2014 DA - 2014// TI - Clonal evolution in breast cancer revealed by single nucleus genome sequencing JO - Nature VL - 512 UR - https://doi.org/10.1038/nature13600 DO - 10.1038/nature13600 ID - Wang2014 ER - TY - JOUR AU - Lundberg, P. AU - Karow, A. AU - Nienhold, R. AU - Looser, R. AU - Hao-Shen, H. AU - Nissen, I. PY - 2014 DA - 2014// TI - Clonal evolution and clinical correlates of somatic mutations in myeloproliferative neoplasms JO - Blood VL - 123 UR - https://doi.org/10.1182/blood-2013-11-537167 DO - 10.1182/blood-2013-11-537167 ID - Lundberg2014 ER - TY - JOUR AU - Miller, C. A. AU - Gindin, Y. AU - Lu, C. AU - Griffith, O. L. AU - Griffith, M. AU - Shen, D. PY - 2016 DA - 2016// TI - Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers JO - Nat Commun VL - 7 UR - https://doi.org/10.1038/ncomms12498 DO - 10.1038/ncomms12498 ID - Miller2016 ER -