Benchmarking and methods development for spatially resolved ’omic technologies

• PhD
• Masters by Coursework

Spatial transcriptomics provides unprecedented detail into the function and cellular organisation of tissues through the capture of gene expression profiles enriched with spatial context. This project will involve analysis of an extensive benchmarking resource (SpatialBench) to provide insights about different technologies and guide development of best-in-class analysis pipelines. Spatial data pre-processing and downstream analytical pipelines will be improved through the development of open-source computational tools with enhanced baseline noise estimation and segmentation for more accurate transcript-to-cell mapping. We are seeking a student with a strong statistical or computational background (e.g. an undergraduate degree in statistics and mathematics, engineering, computer science or masters in bioinformatics), programming skills, an interest in interdisciplinary biomedical research, and a desire to develop their skills in imaging and genomic data science.

This project is eligible for the WEHI Artificial Intelligence (AI) & Machine Learning (ML) PhD Scholarship, and is open to both domestic and international students.

The Ritchie laboratory develops analysis methods and open-source software (freely available as part of the Bioconductor project) that are tailored to new applications of genomic technology in biomedical research. Our time is divided evenly between methodological work and primary data analysis of in-house experiments from our collaborators and public datasets to provide new insights into gene regulation in health and disease.

Our major interests include:
– statistical methods for modelling variation in RNA-sequencing data
– software for interactive visualisation of gene expression data
– software for the analysis of single-cell and long-read gene expression and methylation data
– applying our data analysis skills to study epigenetic and genetic regulation in development and cancer together with our collaborators.