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Bioinformatics and cellular genomics

We are interested in solving the challenges of analysing and interpreting large-scale biological data. We develop methods and software for the analysis of data produced by modern sequencing technologies, in particular single-cell genomic data. Further, we are interested in studying the effects of changes in DNA on gene expression in individual cells.

Research Overview

We are broadly interested in how computational approaches can drive biological discovery. In particular, we are interested in developing statistical and machine learning methods and software tools for the analysis of high-throughput sequencing data, with a focus on single-cell genomic data. We are also interested in the ways in which DNA variation contributes to variation in gene expression at the level of individual cells. We study “single-cell genetics” in this sense by looking at single-cell quantitative trait loci and at the effects of somatic mutations in healthy ageing and cancer. We work closely with biological collaborators to contribute computational expertise to studies motivated by specific biologically-focused questions.

Honours and PhD Projects

If you are interested in our work and are seeking Honours or PhD opportunities please contact Davis McCarthy on [email protected] to enquire about available projects.

Upcoming Positions

We are keen to hear from postdoctoral scientists with a PhD in a relevant computational discipline (up to 3 years postdoctoral). This position, under the direction of Dr Davis McCarthy, is advertised on our Careers page.

Research Themes

Analysis methods for single-cell genetics

Clonal cell populations at the single-cell level

Single-cell quantitative trait locus mapping

Bioinformatics software development

Honours and PhD Projects

Staff

Publication Highlights

  1. Buettner F, Pratanwanich N, MCCARTHY DJ, Marioni JC, Stegle O. f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq. Genome Biol. 2017;18: 212.
  2. Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, et al. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature. 2017;546: 370–375.
  3. MCCARTHY DJ, Campbell KR, Lun ATL, Wills QF. Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. Bioinformatics. 2017;33: 1179–1186.
  4. Lun ATL, MCCARTHY DJ, Marioni JC. A step-by-step workflow for low-level analysis of single-cell RNA-seq data. F1000Res. 2016;5. doi:10.12688/f1000research.9501.
  5. Fuchsberger C, Flannick J, Teslovich TM, Mahajan A, Agarwala V, Gaulton KJ, et al. The genetic architecture of type 2 diabetes. Nature. 2016;536: 41–47.
  6. MCCARTHY DJ, Humburg P, Kanapin A, Rivas MA, Gaulton K, Cazier J-B, et al. Choice of transcripts and software has a large effect on variant annotation. Genome Med. 2014;6: 26.
  7. MCCARTHY DJ*, Chen Y*, Smyth GK. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res. 2012;40: 4288–4297.
  8. Lund SP, Nettleton D, MCCARTHY DJ, Smyth GK. Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Stat Appl Genet Mol Biol. 2012;11. doi:10.1515/1544-6115.1826.
  9. Robinson MD*, MCCARTHY DJ*, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26: 139–140.
  10. MCCARTHY DJ, Smyth GK. Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics. 2009;25: 765–771.