| A survey of best practices for RNA-seq data analysis A Conesa, P Madrigal, S Tarazona, D Gomez-Cabrero, A Cervera, ... Genome biology 17, 1-19, 2016 | 3279 | 2016 |
| The clonal and mutational evolution spectrum of primary triple-negative breast cancers SP Shah, A Roth, R Goya, A Oloumi, G Ha, Y Zhao, G Turashvili, J Ding, ... Nature 486 (7403), 395-399, 2012 | 2334 | 2012 |
| ARID1A Mutations in Endometriosis-Associated Ovarian Carcinomas KC Wiegand, SP Shah, OM Al-Agha, Y Zhao, K Tse, T Zeng, J Senz, ... New England Journal of Medicine 363 (16), 1532-1543, 2010 | 1977 | 2010 |
| MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers C Steidl, SP Shah, BW Woolcock, L Rui, M Kawahara, P Farinha, ... Nature 471 (7338), 377-381, 2011 | 712 | 2011 |
| Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution P Eirew, A Steif, J Khattra, G Ha, D Yap, H Farahani, K Gelmon, S Chia, ... Nature 518 (7539), 422-426, 2015 | 673 | 2015 |
| deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data A McPherson, F Hormozdiari, A Zayed, R Giuliany, G Ha, MGF Sun, ... PLoS computational biology 7 (5), e1001138, 2011 | 625 | 2011 |
| Spatial genomic heterogeneity within localized, multifocal prostate cancer PC Boutros, M Fraser, NJ Harding, R De Borja, D Trudel, E Lalonde, ... Nature genetics 47 (7), 736-745, 2015 | 551 | 2015 |
| TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data G Ha, A Roth, J Khattra, J Ho, D Yap, LM Prentice, N Melnyk, ... Genome research 24 (11), 1881-1893, 2014 | 418 | 2014 |
| Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer A McPherson, A Roth, E Laks, T Masud, A Bashashati, AW Zhang, G Ha, ... Nature genetics 48 (7), 758-767, 2016 | 364 | 2016 |
| Genomic rearrangements involving programmed death ligands are recurrent in primary mediastinal large B-cell lymphoma DDW Twa, FC Chan, S Ben-Neriah, BW Woolcock, A Mottok, KL Tan, ... Blood, The Journal of the American Society of Hematology 123 (13), 2062-2065, 2014 | 339 | 2014 |
| Interfaces of malignant and immunologic clonal dynamics in ovarian cancer AW Zhang, A McPherson, K Milne, DR Kroeger, PT Hamilton, A Miranda, ... Cell 173 (7), 1755-1769. e22, 2018 | 329 | 2018 |
| Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling AW Zhang, C O’Flanagan, EA Chavez, JLP Lim, N Ceglia, A McPherson, ... Nature methods 16 (10), 1007-1015, 2019 | 308 | 2019 |
| Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes YK Wang, A Bashashati, MS Anglesio, DR Cochrane, DS Grewal, G Ha, ... Nature genetics 49 (6), 856-865, 2017 | 271 | 2017 |
| 14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma CH Lee, WB Ou, A Mariņo-Enriquez, M Zhu, M Mayeda, Y Wang, X Guo, ... Proceedings of the National Academy of Sciences 109 (3), 929-934, 2012 | 261 | 2012 |
| Histological transformation and progression in follicular lymphoma: a clonal evolution study R Kridel, FC Chan, A Mottok, M Boyle, P Farinha, K Tan, B Meissner, ... PLoS medicine 13 (12), e1002197, 2016 | 250 | 2016 |
| Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses CH O’Flanagan, KR Campbell, AW Zhang, F Kabeer, JLP Lim, J Biele, ... Genome biology 20, 1-13, 2019 | 239 | 2019 |
| From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer AV Lapuk, C Wu, AW Wyatt, A McPherson, BJ McConeghy, S Brahmbhatt, ... The Journal of pathology 227 (3), 286-297, 2012 | 219 | 2012 |
| Clonal decomposition and DNA replication states defined by scaled single-cell genome sequencing E Laks, A McPherson, H Zahn, D Lai, A Steif, J Brimhall, J Biele, B Wang, ... Cell 179 (5), 1207-1221. e22, 2019 | 217 | 2019 |
| Clonality inference in multiple tumor samples using phylogeny S Malikic, AW McPherson, N Donmez, CS Sahinalp Bioinformatics 31 (9), 1349-1356, 2015 | 210 | 2015 |
| Genome-wide identification of human microRNAs located in leukemia-associated genomic alterations DT Starczynowski, R Morin, A McPherson, J Lam, R Chari, J Wegrzyn, ... Blood, The Journal of the American Society of Hematology 117 (2), 595-607, 2011 | 170 | 2011 |
