Cardio-Bioinformatics Now: Gene Regulatory Networks in the Evolution and Development of the Heart

About the project

About the Project 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 will I study? 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 already funding in place 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. (Specifically, the PhD student will be trained in structured interpretation of publicly available genomics and transcriptomics data. They will be trained to access data from data bases (e.g gnomAD, dbGaP, dbSNP, dbVar, GTEx, other NCBI/ Ensembl databases and tools, GEO, CGR, STRING, AlphaFold, etc (and if specific diseases of relevance: ClinVar, SV4GD, etc). They will be trained to establish standardised data analysis pipelines following FAIR (Findable, Accessible, Interoperable, Reusable) data principles. They will explore integrative so-called multi-omics techniques, network analysis, and examine structural annotation to understand the functional consequences of genetic variations in evolution and eventually in the future also in human disease.). (Specifically, the PhD student will be trained in structured interpretation of publicly available genomics and transcriptomics data. They will be trained to access data from data bases (e.g gnomAD, dbGaP, dbSNP, dbVar, GTEx, other NCBI/ Ensembl databases and tools, GEO, CGR, STRING, AlphaFold, etc (and if specific diseases of relevance: ClinVar, SV4GD, etc). They will be trained to establish standardised data analysis pipelines following FAIR (Findable, Accessible, Interoperable, Reusable) data principles. They will explore integrative so-called multi-omics techniques, network analysis, and examine structural annotation to understand the functional consequences of genetic variations in evolution and eventually in the future also in human 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: Year 1: An introduction to Unix and High-Performance Computing Quality Control of Sequencing Data Genome Assembly and Annotation Year 2: RNA-seq and Differential Expression Alignment, Visualisation and Variant Calling Introduction to Visualisation and Plotting with R and ggplot2 This project will also 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. Enquiries are encouraged! Please contact Professor Stefan Hoppler ( s.p.hoppler@abdn.ac.uk ) for further information. Candidate Background: Candidates should hold a minimum of a 2:1 Honours degree (Or equivalent) in a relevant subject. We actively encourage applications from diverse career paths and backgrounds and across all sections of the community, regardless of age, disability, ethnicity, gender, gender expression, sexual orientation and transgender status, amongst other protected characteristics. Aberdeen and Aberdeenshire: Scotland’s third largest city, Aberdeen sits on the coast between the mountains of Aberdeenshire and the stunning North Sea coastline. Renowned as a Global Energy Hub, Aberdeen is a vibrant, entrepreneurial region, home to a unique mix of business opportunities and specialist skills across various sectors including energy, technology, life sciences and food & drink. More than 20% of Scotland’s top businesses are located in this region which is taking great strides to ensure that it continues to compete on a world stage. Investments of more than £10 billion of public and private infrastructure is due to be delivered before 2030, marking an exciting time to be part of a genuine world-class location. --------------------------------- Application Procedure: Important note: This project is open only to applicants eligible for the Home/UK fee rate. This includes EU students who hold settled or pre-settled status and meet the relevant residency criteria. To apply, please submit the following documents via email to smmsn-pgrenquiries@abdn.ac.uk A cover letter addressed to the supervisor of the project you're applying for. An up-to-date CV detailing your academic qualifications, employment history, and any other relevant experience. Please ensure your current permanent address is clearly stated, as this will be used to determine your fee status. Clear copies of your degree certificates and transcripts (if available). Evidence of settled or pre-settled status (if applicable). Please send your application with documents attached as a single email with the subject line: "BHF Stefan Hoppler - [Your Name]" The deadline for applications is 23:59 GMT on 25th October 2026 . Please note that incomplete applications will not be considered. For any enquiries regarding your application or the application process, please contact smmsn-pgrenquiries@abdn.ac.uk

Research areas