|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
|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
|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
|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
|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
|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
|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
|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
|Interpretable dimensionality reduction of single cell transcriptome data with deep generative models|
J Ding, A Condon, SP Shah
Nature communications 9 (1), 1-13, 2018
|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
|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
|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 (12), 1-14, 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
|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
|Single-Cell Transcriptome Analysis Reveals Disease-Defining T-cell Subsets in the Tumor Microenvironment of Classic Hodgkin LymphomaSingle-Cell Characterization of Hodgkin Lymphoma|
T Aoki, LC Chong, K Takata, K Milne, M Hav, A Colombo, EA Chavez, ...
Cancer Discovery 10 (3), 406-421, 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
|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), 1-13, 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), 1-14, 2016
|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
|Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas|
A Mathelier, C Lefebvre, AW Zhang, DJ Arenillas, J Ding, WW Wasserman, ...
Genome biology 16 (1), 1-17, 2015