rna-seq

Benchmarking atlas-level data integration in single-cell genomics

Cell atlases often include samples that span locations, labs, and conditions, leading to complex, nested batch effects in data. Thus, joint analysis of atlas datasets requires reliable data integration. Choosing a data integration method is a …

Tools and techniques for single-cell RNA sequencing data

RNA sequencing of individual cells allows us to take a snapshot of the dynamic processes within a cell and explore differences between cell types. As this technology has developed over the last few years it has been rapidly adopted by researchers in …

Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk

Recent advances in the generation of kidney organoids and the culture of primary nephron progenitors from mouse and human have been based on knowledge of the molecular basis of kidney development in mice. Although gene expression during kidney …

Tools and techniques for single-cell RNA sequencing data

My PhD completion seminar

Kidney micro-organoids in suspension culture as a scalable source of human pluripotent stem cell-derived kidney cells

Kidney organoids have potential uses in disease modelling, drug screening and regenerative medicine. However, novel cost-effective techniques are needed to enable scaled-up production of kidney cell types in vitro. We describe here a modified …

Nephron progenitor commitment is a stochastic process influenced by cell migration

**Background** Human kidney organoids hold promise for studying development, disease modelling and drug screening. However, the utility of stem cell-derived kidney tissues will depend on how faithfully these replicate normal fetal development at …

Single-cell analysis reveals congruence between kidney organoids and human fetal kidney

**Background** Human kidney organoids hold promise for studying development, disease modelling and drug screening. However, the utility of stem cell-derived kidney tissues will depend on how faithfully these replicate normal fetal development at …

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.