Unique transcriptional architecture in airway epithelial cells and macrophages shapes distinct responses following influenza virus infection ex vivo

Airway epithelial cells and macrophages differ markedly in their responses to influenza A virus (IAV) infection. To investigate transcriptional responses underlying these differences, purified subsets of type II airway epithelial cells (ATII) and …

Evaluation of variability in human kidney organoids

The utility of human pluripotent stem cell–derived kidney organoids relies implicitly on the robustness and transferability of the protocol. Here we analyze the sources of transcriptional variation in a specific kidney organoid protocol. Although …

Tools, simulations and trees for scRNA-seq

Presentation at the Institute of Computational Biology where I described my PhD projects.

Using clustering trees to visualise scRNA-seq data

Selected talk at the Genome Informatics 2018 conference where I described how clustering trees can be used with scRNA-seq data.

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data has dramatically increased. Navigating the vast sea of tools now available is becoming increasingly challenging for …

Splatter, a package for simulating single-cell RNA sequencing data

Selected talk at the 2017 Bioconductor Asia Meeting where I presented technical details of the Splatter package.

Simulation and analysis tools for single-cell RNA sequencing data

Selected talk at the Genome Informatics 2017 conference describing Splatter and the scRNA-tools database.

Single cells, simulation and kidneys in a dish

Presentation at the Berkeley Statistics and Genomics Seminar describing my PhD projects.

Splatter: simulation of single-cell RNA sequencing data

As single-cell RNA sequencing (scRNA-seq) technologies have rapidly developed, so have analysis methods. Many methods have been tested, developed, and validated using simulated datasets. Unfortunately, current simulations are often poorly documented, …

Single-cells, simulation and kidneys in a dish

WEHI Bioinformatics seminar series presenting my PhD projects.