BHF-funded PhD studentship (UK residents): Gene Regulatory Networks in the Evolution and Development of the Heart

The student will use comparative genomics to investigate the evolution of Gene Regulatory Networks that control heart development.

Now is the perfect time to benefit from the wealth of genomics (and transcriptomics) data that have become available, including from a representative range of vertebrates and related chordates. We will unearth the evolutionary assembly of Gene Regulatory Networks controlling embryonic heart development and cardiomyocyte differentiation.

Our vision is to understand emergence of cardiac cell types through the assembly of genes into Gene Regulatory Networks that control heart development, morphogenesis, anatomy and physiology (e.g., contractile function). This evolutionary perspective provides new insight into how regulator genes control heart development and establish a dependable framework for analysing cis-regulatory control of cardiac gene expression and for exploring emerging properties of the evolved Gene Regulatory Network architecture.

Where?

This PhD project is an international collaboration between the Universities of Aberdeen and St Andrews in Scotland, UK and the Universidad de Barcelona in Catalonia, Spain. While the student will be officially based in Aberdeen, there is funding for regular research meetings in St Andrews and for two longer research visits (of four weeks each) to Barcelona as part of this international collaboration.

Training:

A central focus of this PhD studentship project is training of a next generation of cardiovascular researchers with computational skills; proficient to access, further analyse and interpret genomic and transcriptomics datasets in the context of vertebrate heart development, and more widely cardiovascular biology and disease.

There is funding in place for the student to take part in the bioinformatics workshops offered by the Centre of Genome-Enabled Medicine and Biology at the University of Aberdeen, such as:

• An introduction to Unix and High-Performance Computing
• Quality Control of Sequencing Data
• Genome Assembly and Annotation
• RNA-seq and Differential Expression
• Alignment, Visualisation and Variant Calling
• Introduction to Visualisation and Plotting with R and ggplot2

Additionally, this project will involve support for advanced bioinformatics analysis by a specialist senior bioinformatician, who will introduce the PhD student to higher level analysis of single-cell RNA-seq data and inference of Gene Regulatory Networks from such transcriptomics data.