CURRENT STUDENT PROJECTS
Student Project
Enhancer elements in human disease
Student Project
Enhancer elements in human disease
Project Outline
Contact
Professor Alistair Forrest – [email protected]
Chief supervisor
Professor Alistair Forrest
Project suitable for
PhD
Student Project
Single cell transcriptomics
Student Project
Single cell transcriptomics
Project Outline
- Examining cellular heterogeneity in cancer samples
- Examining cell-to-cell communication in cancer samples (working with bioinformaticians in the team)
- Generating reference expression profiles of rare cell types. These have the potential to identify new genes and deepen our understanding of genetic disorders.
- Identification of new cell types based on their expression profiles (a fundamental question in human biology is; How many different cell types do we have in our bodies?)
The candidate would work with a molecular biology postdoctoral researcher on establishing single cell profiling methods and apply it to tumour samples or normal tissue from surgery waste. They would also work with bioinformaticians in the group and would have the opportunity to be trained in analysis of single cell RNA-seq data.
Contact
Professor Alistair Forrest – [email protected]
Chief supervisor
Professor Alistair Forrest
Project suitable for
PhD
Student Project
Multicellularity and disease
Student Project
Multicellularity and disease
Project Outline
The project would predominantly be a bioinformatics one with mining of large expression and genotype/phenotype datasets from human and mouse to systematically examine the relationships between cell-type-specific expression and tissue-specific disorders.
Additionally we have recently published an active enhancer atlas (Andersson et al. 2014 Nature). Enhancers show highly specific activation in different cell types (more specific than ‘genes’). By integration of the enhancer activity data with Genome wide association studies (GWAS) we are beginning to dissect out regulatory SNPs in cell-type-specific enhancers.
The candidate would work closely with a bioinformatics postdoc and would learn (and need to become proficient in dry techniques)
- Data curation and databasing
- Mining expression datasets (microarrays, RNA-seq or CAGE)
- Mining GWAS and eQTL datasets
- Data integration and statistical testing
- Sample ontology enrichment analysis
- Variant calling in whole exome and whole genome sequence datasets
Suitable candidates from both biostatistics/bioinformatics, biological/medical/veterinary sciences and computer sciences will be considered.
Contact
Professor Alistair Forrest – [email protected]
Chief supervisor
Professor Alistair Forrest
Project suitable for
PhD
Student Project
ZENBU Genome browser – data visualisation, statistics, peer-to-peer, cloud, integration
Student Project
ZENBU Genome browser – data visualisation, statistics, peer-to-peer, cloud, integration
Project Outline
- additional data visualizations
- region based statistics
- peer-to-peer (enterprise ZENBU)
- ZENBU cloud
- Data integration
- Interoperability with tools such as Galaxy
This would best suit computer science and information technology graduates. For this project there is potential for short visits to RIKEN Yokohama Japan to work with the developer/collaborator Jessica Severin.
Contact
Professor Alistair Forrest – [email protected]
Chief supervisor
Professor Alistair Forrest
Other supervisor
Jessica Severin – RIKEN Japan
Project suitable for
Honours, Masters, PhD
Essential qualifications
Computer science/information technology
Student Project
General call – Systems Biology, genomics, transcriptomics and bioinformatics
Student Project
General call – Systems Biology, genomics, transcriptomics and bioinformatics
Project Outline
Basic research:
- Transcript discovery
- Non-coding RNAs
- Primary cell biology
- Mammalian transcriptional networks and evolution of multicellularity
- Building transcriptional regulatory network models (bioinformatics and NGS data)
Applied:
- Comparing broken networks in cancer
- Cancer Biomarkers
- Tissue specificity of drug targets
- Disease gene prioritization
Contact
Professor Alistair Forrest – [email protected]
Chief supervisor
Professor Alistair Forrest
Project suitable for
Honours, MsC, PhD
Start date
continually open