| 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 | 2270 | 2012 |
| Systematic comparison of single-cell and single-nucleus RNA-sequencing methods J Ding, X Adiconis, SK Simmons, MS Kowalczyk, CC Hession, ... Nature biotechnology 38 (6), 737-746, 2020 | 717* | 2020 |
| Chromatin potential identified by shared single-cell profiling of RNA and chromatin S Ma, B Zhang, LM LaFave, AS Earl, Z Chiang, Y Hu, J Ding, A Brack, ... Cell 183 (4), 1103-1116. e20, 2020 | 640 | 2020 |
| Distinct evolutionary trajectories of primary high‐grade serous ovarian cancers revealed through spatial mutational profiling A Bashashati, G Ha, A Tone, J Ding, LM Prentice, A Roth, J Rosner, ... The Journal of pathology 231 (1), 21-34, 2013 | 490 | 2013 |
| Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing RD Morin, K Mungall, E Pleasance, AJ Mungall, R Goya, RD Huff, ... Blood, The Journal of the American Society of Hematology 122 (7), 1256-1265, 2013 | 456 | 2013 |
| 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 | 395 | 2014 |
| Interpretable dimensionality reduction of single cell transcriptome data with deep generative models J Ding, A Condon, SP Shah Nature communications 9 (1), 2002, 2018 | 349 | 2018 |
| Use of mutation profiles to refine the classification of endometrial carcinomas MK McConechy, J Ding, MCU Cheang, KC Wiegand, J Senz, AA Tone, ... The Journal of pathology 228 (1), 20-30, 2012 | 334 | 2012 |
| Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer G Ha, A Roth, D Lai, A Bashashati, J Ding, R Goya, R Giuliany, J Rosner, ... Genome research 22 (10), 1995-2007, 2012 | 308 | 2012 |
| Ovarian and endometrial endometrioid carcinomas have distinct CTNNB1 and PTEN mutation profiles MK McConechy, J Ding, J Senz, W Yang, N Melnyk, AA Tone, LM Prentice, ... Modern pathology 27 (1), 128-134, 2014 | 290 | 2014 |
| DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer A Bashashati, G Haffari, J Ding, G Ha, K Lui, J Rosner, DG Huntsman, ... Genome biology 13, 1-14, 2012 | 279 | 2012 |
| JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data A Roth, J Ding, R Morin, A Crisan, G Ha, R Giuliany, A Bashashati, M Hirst, ... Bioinformatics 28 (7), 907-913, 2012 | 233 | 2012 |
| Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data J Ding, A Bashashati, A Roth, A Oloumi, K Tse, T Zeng, G Haffari, M Hirst, ... Bioinformatics 28 (2), 167-175, 2012 | 191 | 2012 |
| BRCA1 and BRCA2 mutations correlate with TP53 abnormalities and presence of immune cell infiltrates in ovarian high-grade serous carcinoma JN McAlpine, H Porter, M Köbel, BH Nelson, LM Prentice, SE Kalloger, ... Modern Pathology 25 (5), 740-750, 2012 | 189 | 2012 |
| Single-cell transcriptome analysis reveals disease-defining T-cell subsets in the tumor microenvironment of classic Hodgkin lymphoma T Aoki, LC Chong, K Takata, K Milne, M Hav, A Colombo, EA Chavez, ... Cancer discovery 10 (3), 406-421, 2020 | 180 | 2020 |
| Transcriptional atlas of intestinal immune cells reveals that neuropeptide α-CGRP modulates group 2 innate lymphoid cell responses H Xu, J Ding, CBM Porter, A Wallrapp, M Tabaka, S Ma, S Fu, X Guo, ... Immunity 51 (4), 696-708. e9, 2019 | 173 | 2019 |
| Gut CD4+ T cell phenotypes are a continuum molded by microbes, not by TH archetypes E Kiner, E Willie, B Vijaykumar, K Chowdhary, H Schmutz, J Chandler, ... Nature immunology 22 (2), 216-228, 2021 | 134 | 2021 |
| Systematic analysis of somatic mutations impacting gene expression in 12 tumour types J Ding, MK McConechy, HM Horlings, G Ha, F Chun Chan, T Funnell, ... Nature communications 6 (1), 8554, 2015 | 104 | 2015 |
| Identification of the epigenetic reader CBX2 as a potential drug target in advanced prostate cancer PL Clermont, F Crea, YT Chiang, D Lin, A Zhang, JZL Wang, A Parolia, ... Clinical epigenetics 8, 1-14, 2016 | 83 | 2016 |
| Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces J Ding, A Regev Nature communications 12 (1), 2554, 2021 | 78 | 2021 |
