Bioinformatics Research Group
We are based in both the Adrian Building on the University campus and the Data to Knowledge for Practice (DKP) Facility at the Glenfield Hospital. This means we are ideally placed to tackle our research interests, which focus on providing software to enable the safe storage and sharing of bioresearch and healthcare data. Some of our main projects are described below:
GWAS Central (formerly HGVbaseG2P) is an enhanced content graphical-based genome-wide association study (GWAS) resource which combines the best features of a database and a scientific journal.
- Beck T, Hastings RK, Gollapudi S, Free RC, Brookes AJ. (2014). GWAS Central: a comprehensive resource for the comparison and interrogation of genome-wide association studies. Eur J Hum Genet; 22(7):949-52. PubMed
- Beck T, Free RC, Thorisson GA, Brookes AJ. (2012). Semantically enabling a genome-wide association study database. J Biomed Semantics; 3(1):9. PubMed
- Thorisson GA, Lancaster O, Free RC, Hastings RK, Sarmah P, Dash D, Brahmachari SK, Brookes AJ. (2009). HGVbaseG2P: a central genetic association database. Nucleic Acids Res; 37(Database issue):D797-802. PubMed
The G2P Knowledge Centre
This is a cornerstone for the online genotype-to-phenotype (G2P) community. Its functions include:
- Centralised access to distributed G2P data, acting as the GEN2PHEN project website
- Providing dynamic online workspaces for expert knowledge exchange for the G2P community
- Providing G2P news and meeting calendars
- Webb AJ, Thorisson GA, Brookes AJ. (2011). GEN2PHEN Consortium. An informatics project and online "Knowledge Centre" supporting modern genotype-to-phenotype research. Hum Mutat; 32(5):543-50. PubMed
Cafe Variome is a complete data discovery solution designed to provide a general-purpose, web-based tool that can be quickly installed by any genotype-phenotype data owner, or network of data owners, to make safe or sensitive content appropriately discoverable.
- Lancaster O, Beck T, Atlan D, Swertz M, Veal C, Dalgleish R, Brookes AJ. (2015). Cafe Variome: General-Purpose Software for Making Genotype-Phenotype Data Discoverable in Restricted or Open Access Contexts. Hum Mutat. PubMed
OmicsConnect is a set of tools used to assist with omics data validation, management, viewing and sharing of complex omics data.
The OmicsConnect toolkit includes:
- Database Tools
- DAS Server
- Browser Server
A web-interface that provides graphical display and filtering options enabling researchers to mine extensive catalogues of human genome sequence trace files for structural variation (no public website).
Accreditation and attribution in data sharing
The issues surrounding accreditation of researchers who deposit their data in central public databases must be addressed if this practice is to be further encouraged and the origin of a specific dataset is to be correctly determined. These issues are being tackled within the group, from the promotion of Digital Identity technologies to authenticate website membership, through to the implementation of unique researcher identifications for tracking individual’s scientific contributions. The group is actively involved in the Open Researcher and Contributor ID Initiative (ORCID).