Testing significance relative to a fold-change threshold is a TREAT. - Davis J. McCarthy; Gordon K. Smyth (Bioinform., 2009)

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. - Mark D. Robinson; Davis J. McCarthy; Gordon K. Smyth (Bioinform., 2010)

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. - Davis J. McCarthy; Kieran R. Campbell; Aaron T. L. Lun; Quin F. Wills (Bioinform., 2017)

12 Grand Challenges in Single-Cell Data Science. - David Laehnemann; Johannes Köster; Ewa Szczurek; Davis J. McCarthy; Stephanie C. Hicks; Mark D. Robinson; Catalina A. Vallejos; Niko Beerenwinkel; Kieran R. Campbell; Ahmed Mahfouz; Luca Pinello; Pavel Skums; et al. (PeerJ Prepr., 2019)

Multi-view Local Co-occurrence and Global Consistency Learning Improve Mammogram Classification Generalisation. - Yuanhong Chen; Hu Wang 005; Chong Wang 012; Yu Tian 001; Fengbei Liu; Yuyuan Liu; Michael Elliott; Davis J. McCarthy; Helen Frazer; Gustavo Carneiro 001 (MICCAI (3), 2022)

Knowledge Distillation to Ensemble Global and Interpretable Prototype-Based Mammogram Classification Models. - Chong Wang 012; Yuanhong Chen; Yuyuan Liu; Yu Tian 001; Fengbei Liu; Davis J. McCarthy; Michael Elliott; Helen Frazer; Gustavo Carneiro 001 (MICCAI (3), 2022)

Trade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomics. - Hui Li; Davis J. McCarthy; Heejung Shim; Susan Wei (BMC Bioinform., 2022)

Multi-view Local Co-occurrence and Global Consistency Learning Improve Mammogram Classification Generalisation. - Yuanhong Chen; Hu Wang 005; Chong Wang 012; Yu Tian 001; Fengbei Liu; Michael Elliott; Davis J. McCarthy; Helen Frazer; Gustavo Carneiro 001 (CoRR, 2022)

Learning Support and Trivial Prototypes for Interpretable Image Classification. - Chong Wang 012; Yuyuan Liu; Yuanhong Chen; Fengbei Liu; Yu Tian 001; Davis J. McCarthy; Helen Frazer; Gustavo Carneiro 001 (ICCV, 2023)

Technical outlier detection via convolutional variational autoencoder for the ADMANI breast mammogram dataset. - Hui Li; Carlos A. Peña-Solórzano; Susan Wei; Davis J. McCarthy (CoRR, 2023)

Mixture of Gaussian-distributed Prototypes with Generative Modelling for Interpretable Image Classification. - Chong Wang 012; Yuanhong Chen; Fengbei Liu; Davis James McCarthy; Helen Frazer; Gustavo Carneiro 001 (CoRR, 2023)

BRAIxDet: Learning to detect malignant breast lesion with incomplete annotations. - Yuanhong Chen; Yuyuan Liu; Chong Wang 012; Michael Elliott; Chun Fung Kwok; Carlos A. Peña-Solórzano; Yu Tian 001; Fengbei Liu; Helen Frazer; Davis J. McCarthy; Gustavo Carneiro 001 (Medical Image Anal., 2024)

An Interpretable and Accurate Deep-Learning Diagnosis Framework Modeled With Fully and Semi-Supervised Reciprocal Learning. - Chong Wang 012; Yuanhong Chen; Fengbei Liu; Michael Elliott; Chun Fung Kwok; Carlos A. Peña-Solórzano; Helen Frazer; Davis James McCarthy; Gustavo Carneiro 001 (IEEE Trans. Medical Imaging, 2024)

Mixture of Gaussian-Distributed Prototypes With Generative Modelling for Interpretable and Trustworthy Image Recognition. - Chong Wang 012; Yuanhong Chen; Fengbei Liu; Yuyuan Liu; Davis James McCarthy; Helen Frazer; Gustavo Carneiro 001 (IEEE Trans. Pattern Anal. Mach. Intell., 2025)

Progressive Mining and Dynamic Distillation of Hierarchical Prototypes for Disease Classification and Localisation. - Chong Wang 012; Fengbei Liu; Yuanhong Chen; Chun Fung Kwok; Michael Elliott; Carlos A. Peña-Solórzano; Davis James McCarthy; Helen Frazer; Gustavo Carneiro 001 (IEEE J. Biomed. Health Informatics, 2025)