Bioinformatics & Statistical Genetics
The Bioinformatics and Statistical Genetics Core provides support and services to Centre staff in the areas of bioinformatics, statistical genetics, functional genomics, databases and scientific computing; and undertakes collaborative and independent research. In the past it has focused on statistical genetics (eg association and linkage analysis), functional genomics (eg gene expression and other types of microarrays), genome analysis and annotation (DNA and protein analysis and textual data mining), relational databases (eg the Integrated Genotyping System, a database for genotype and phenotype observations), and the management of servers and clusters. More recently it has developed a new focus on next-generation sequencing, in order to support the Centre’s Illumina GA-II and Roche FLX sequencers, and manages a new 1000-core computer cluster.
Staff
Head: Prof Gil McVean
| Senior Members: | |
| Richard Copley | Sequence Analysis |
| John Broxholme | Scientific Computing |
| Jean-Baptiste Cazier | Statistical Genetics |
| Helen Lockstone | Functional Genomics |
| Gerton Lunter | High Throughput Sequencing |
| Alexander Kanapin | High Throughput Sequencing |
| Simon Fiddy | Databases |
| Kate Elliott | Genetic Association, Textual Data mining |
| Junior Members: | |
| Dong Xie | Database Development |
| Linda Hughes | High-throughput sequencing |
| Natasha Saghal | Functional Genomics |
| Andy Rimmer | Statistical Geneticist/ High-throughput sequencing. |
Services & Activities
1. Statistical Genetics support
- Provision of advice on statistical genetics analysis, use of appropriate software and databases.
- Provision of training seminars on statistical genetics
- Perform statistical genetics analyses using existing software for Centre staff.
- Develop novel methods and software to solve statistical genetics problems.
2. Sequence Analysis support
- Give advice and instruction on the selection and use of sequence analysis software and databases
- Perform sequence analyses for Centre staff
- Develop novel methods and software to solve sequence analysis problems
3. Scientific Computing support
- Management of the bioinformatics core’s compute servers and linux cluster.
- Maintenance of Sequence and other Databanks
- Maintenance of Sequence Analysis and Statistical Genetics software packages.
- Maintenance of the Sequence Analysis Web Server.
- Write scripts to automate analyses for Centre staff.
4. Database Development and Curation and General Programming
- Management of the bioinformatics core’s genotyping and microarray database servers.
- Maintenance and curation of the database content, including regular off-site backup.
- General Database maintenance tasks.
- Provide training to users in the use of database interfaces.
- Reformatting data into a form suitable for upload.
- Construct and perform complex database queries to extract data in forms not covered by standard GUI.
- Development of databases and interfaces to integrate with new genotyping and microarray instrumentation, and with external data sources.
- Development of new database functionality (eg data analyses, small-scale databases for particular experiments) on request.
5. Microarrays and Functional Genomics
- Maintenance of microarray analysis software packages.
- Provide guidance and help with design and analysis of microarray experiments.
- Perform microarray analyses for Centre staff.
- Collaborate with the Genomics Core over the development of new functional assays.
- Devise and develop new methodologies for the analysis of microarray and functional data, particularly in regard to their integration with genetic data.
6. Next Generation Sequencing
- Implement and maintain analysis pipelines to process raw NGS data
- Manage very large volumes of raw data, including deletion policy
- Analyse different types of NGS data appropriately (eg genomic sequence, digital transcriptomics, methylation etc)
- Develop databases to track NGS runs and interface with LIMS
- Develop new algorithms to analyse NGS data in response to the centre’s requirements
7. Research
- Undertake research collaborations in statistical genetics, sequence analysis and functional genomics analysis in collaboration with groups within the Centre.
- Senior staff initiate and publish independent research in peer-reviewed journals, and write grants to perform research.
The group has current research foci in the areas of sequence alignment statistics, comparative genomics, ancestral haplotype construction, LIMS database development, QTL linkage and association methods, variability in patterns of linkage disequilibrium and multivariate modelling of quantitative traits.
To contact us:
Bioinformatics and Statistical Genetics
University of Oxford
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Tel: +44 (0)1865 287 500
Fax: +44 (0)1865 287 501
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