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Genome Biology|February 26, 2024
A comparison of marker gene selection methods for single-cell RNA sequencing dataJeffrey M Pullin, Davis J McCarthyPlos Genetics|May 8, 2026
Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluationGuillermo Reales, Jeffrey M Pullin, Ichcha Manipur, et al.Bioinformatics (Oxford, England)|January 30, 2009
Testing significance relative to a fold-change threshold is a TREATDavis J McCarthy, Gordon K SmythBiorxiv : the Preprint Server for Biology|October 3, 2025
simPIC:flexible simulation of paired-insertion counts for single-cell ATAC sequencing dataSagrika Chugh, Heejung Shim, Davis J McCarthyGenome Biology|December 15, 2019
Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype referenceYuanhua Huang, Davis J McCarthy, Oliver StegleNucleic Acids Research|January 31, 2012
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variationDavis J McCarthy, Yunshun Chen, Gordon K SmythBioinformatics (Oxford, England)|November 14, 2009
edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataMark D Robinson, Davis J McCarthy, Gordon K SmythBiorxiv : the Preprint Server for Biology|December 23, 2024
Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data?Aaron Wing Cheung Kwok, Heejung Shim, Davis J McCarthyGenome Biology|April 20, 2021
Personalized genome structure via single gamete sequencingRuqian Lyu, Vanessa Tsui, Davis J McCarthy, et al.BMC Bioinformatics|November 4, 2022
Trade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomicsHui Li, Davis J McCarthy, Heejung Shim, et al.Pageof 6