Welcome


Thanks for visiting my website. Here you can find details of my published 
research, teaching materials and links to R packages and other things. 

Do get in touch if you would like to discuss any of the content here.

Contact:

Twitter:   @davisjmcc
Email:     [reveal email] (protected by a reCAPTCHA)



I am an NHMRC Early Career Research Fellow, currently working with Dr Oliver Stegle in the Statistical Genomics group at the European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK. My current research interests include methods for the analysis of single-cell genomic data and their use in understanding gene expression regulation in induced pluripotent stem cells.

In 2015 I completed my DPhil (PhD) in Statistics in the Department of Statistics at the University of OxfordI was supervised by Professor Peter Donnelly, Director of the Wellcome Trust Centre for Human Genetics (which was where I spent most of my time). I was a member of Balliol College and for the 2012/13 academic year I was the President of the Balliol MCRMy studies were supported by funding from the General Sir John Monash Foundation.

YouTube Video



My academic CV is available here.

More information:
Google Scholar (publications)
ORCiD (publications and profile)
figshare (datasets)
GitHub (source code)





Research Interests

Statistics, Single-cell Genomics, Statistical Genetics, Bioinformatics, RNA Sequencing, High-Throughput DNA Sequencing, Gene Expression, Human Genetics, Statistical Computing



Selected Publications

  • Fuchsberger C., Flannick J., Teslovich T.M., Mahajan A., Agarwala V., Gaulton K.J., Ma C., Fontanillas P., Moutsianas L., McCarthy D.J., et al. (2016) The genetic architecture of type 2 diabetes. Nature. doi:10.1038/nature18642 [ABSTRACT]
  • McCarthy, D.J., Humburg, P., Kanapin, A., Rivas, M.A., Gaulton, K., The WGS500 Consortium, Cazier, J-B. and Donnelly, P. (2014) Choice of transcripts and software has a large effect on variant annotation. Genome Medicine. 6:26. doi:10.1186/gm543 [ABSTRACT][PDF][OpenAccess]
  • Anders, S., McCarthy, D.J., Chen Y., Okoniewski, M., Smyth, G.K., Huber, W. and Robinson, M.D. (2013). Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nature Protocols. Volume 8, 1765-1786, doi:10.1038/nprot.2013.099 [HTML][PDF]
  • McCarthy, D.J.*, Chen, Y.* and Smyth, G.K. (2012) Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research. 40 (10):4288-4297. doi:10.1093/nar/gks042 [HTML][PDF][OpenAccess]
  • Robinson, M.D.*, McCarthy, D.J.* and Smyth, G.K. (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140. doi:10.1093/bioinformatics/btp616 [HTML][PDF][OpenAccess]
  • McCarthy, D.J. and Smyth, G.K. (2009) Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics, 25(6), 765-771. doi: 10.1093/bioinformatics/btp053 [HTML][PDF][OpenAccess]

(* Joint First Authors)

Full details of my published research and more can be found here



Software


I have produced the R package scater for pre-processing, quality control and visualisation of single-cell RNA-seq data. 

I have been a developer and maintainer of the R/Bioconductor package edgeR, for differential expression analysis of RNA-Seq data (and differential analysis of other genomic count data). 

I have also contributed methods to the R/Bioconductor package limma, a very widely used package for differential expression analysis of microarray data.

There is a little bit more information about the software available here.