Dec 2013 – Dec 2016 Senior Leadership Fellow in Bioinformatics & Head of the Transcriptomics Core Facility at The Jenner Institute, University of Oxford
I am responsible for the Transcriptomics Core Facility for the Jenner Institute. We support Jenner Investigators and collaborators to identify transcriptomics correlates of vaccine efficacy and immunogenicity for a broad range of novel and licensed vaccines in adults, children and livestock. These findings could suggest ideas for new immunomodulatory molecules to improve vaccines for infectious diseases such as malaria, TB and influenza.
Dec 2013 – current Honorary Research Associate, King’s College London
Feb 2011 – current Honorary Research Associate, UCL Institute of Neurology
Feb 2011 – current Honorary Research Associate, Imperial College London
Feb 2011 – Nov 2013 Research Associate, King’s College London
I worked on an MRC funded project UK Brain Expression Consortium to study expression QTL (eQTL) in ten brain regions extracted in parallel from 134 healthy controls. The aim is to provide an understanding of genetic regulation of gene expression and alternative splicing in human brains. An immediate application is the follow-up of GWAs hits from Parkinson’s disease, Alzheimer’s disease and relevant phenotypes.
2008 – 2011 Biostatistician/Epidemiologist, Respiratory Epidemiology and Public Health, Imperial College London
I co-lead three genetics consortiums (asthma, hayfever and bronchial hyper responsiveness), participated in five other genetics consortiums and contributed replication data to various other projects. I am in charge of quality control and analysis of the GWAs data for the European Community Respiratory Health Survey (ECRHS) (n=2,312) and also analyze respiratory, allergy and lung function phenotypes from the Northern Finnish Birth Cohort of 1966 (NFBC66) (n=5,000). This has lead to three first-authored or joint first-authored publications among several others. I was supported by funding from an EU project and Department of Health, UK.
2004 – 2007 Medical Statistician, Centre for Statistics in Medicine, University of Oxford
I conducted research in methodologies relevant to the design and analysis stage of gene expression microarrays. I was funded by Cancer Research UK and therefore provided various analytical support to Cancer Research UK researchers in Oxford.
2002 – 2004 Research Assistant, Genome Institute of Singapore
Provided various statistical and bioinformatics support to senior researchers. I was invited to give a short presentation on my work to the Steering Advisory Committee.
2004 – 2009 DPhil* University of Oxford
2001 – 2002 MSc in Applied Statistics University of Oxford
1998 – 2001 B. Comm (Actuarial Studies) University of Melbourne
* DPhil topic: Increasing statistical power and generalizability in genomics microarray research. Supervised by Professors Douglas G. Altman and Chris C. Holmes.
2012 – 2013 Trainee American Society of Human Genetics
2011 – 2012 Member European Respiratory Society
2010 – 2011 Charted Statisitician & Fellow Royal Statistical Society
2010 – 2011 Charted Scientist Science Council
PRIZES AND AWARDS
2010 Young Scientist Sponsorship, European Respiratory Society (ERS)
2008 My ERS abstract was voted as top 5% of all the abstracts submitted
2004 3-year PhD studentship by Cancer Research UK
2001 Exchange year to Heriot-Watt University, Edinburgh
2001 Melbourne Abroad Prize Scholarship
1998 Top Student Award for achieving best results at A-levels
1994 Best Student Award and prize money for lower secondary certificate
My research interest is in applying and developing appropriate statistical techniques to reveal genetic mechanisms of diseases. Having lead and participated in numerous international genetics consortia to help identify variants associated with complex diseases, I realized that there is currently a gap in the knowledge about how these variants influence gene expression, protein levels and subsequently the individuals themselves. In my current post, I help bridge this apparent disconnect by studying the genetic regulation of gene expression in multiple brain tissues.
TEACHING AND TRAINING
2007, gave weekly tutorials to 4 MSc students during their taught course (9 months). I am in regular contact with two of them, both of whom are completing the DPhil in statistical genetics.
2012, co-supervised the research component (3 months) of two MSc in Informatics at King’s College London to develop several bioinformatics webtools. One of the project was to provide a user friendly access and visualization of the eQTL results from the UK Human Brain Expression Consortium that we are currently analyzing. The other project involved a set of general utility webtools (calculating linkage disequilibrium using the latest 1000 Genomes data, identifying probes that contain polymorphisms). I was involved in planning their research project, directed their work, trained them in Unix, PhP, R as well with writing up and providing feedback.
I have acted as demonstrator and computer practical demonstrators for the following modules
- Microarray bioinformatics module in University of Oxford (July 2005, May 2006, October 2006).
- Ad-hoc assistance with the computer practicals for students from the University of Oxford Doctoral Training Centre (Life Sciences Interface).
- STATA practical course in University of Oxford
- Summer School in Genetic Association Studies in King’s College London (June 2012)
In addition to my statistical genetics research, I provide ad hoc statistical advice to researchers in Oxford, King’s College London and externally.
Statistical languages R, Bioconductor, S-PLUS, Stata (basic), SPSS (basic)
Genetics software/tools Ensembl, ProbABEL, MACH, minimac, PLINK, QUICKTEST, QuTie, snpMatrix, SNPTEST, matrixEQTL etc.
Shell scripting awk, bash scripting, sed and other unix/linux tools
Programming languages C (basic), Perl (basic), PhP (basic)
Word processing LaTeX, Emacs (+ESS), MS Word
Presentation LaTeX package beamer, MS PowerPoint
Databases MS Excel (intermediate), MySQL (basic)
Platforms Linux (various distros), Windows (2000, XP, 7)
- Named researcher in “Using genetic variability in whole transcriptome expression in cells and tissues to understand the pathogenesis of Parkinson’s and Alzheimer’s disease” (~£1.4 million from the Medical research Council). Lead PI: Prof. John Hardy. Co-PI: Dr. Michael E Weale and Dr. Mina Ryten.
- Named researcher in “The regulation and function of MIR137 in schizophrenia” (submitted). Lead PI: Prof. John Quinn.
- DPhil funding from Cancer Research UK (2004 – 2007). With the help of Prof. Altman, I co-wrote the application request for DPhil funding.
- Ad-hoc reviewer for Nucleic Acids Research Journal, Human Molecular Genetics and Pancreatic Cancer Research UK charity
- Participation in Genetics Consortiums
- The ECRHS-SAPALDIA-EGEA collaboration
- Analysis in Population-based Cohorts of Asthma Traits (APCAT)
- The SpiroMeta Consortium
- GABRIEL consortium (A Multidisciplinary Study to Identify the Genetic and Environmental Causes of Asthma in the European Community)
- The Transnational Asthma Genetics (TAG) Consortium
- The Early Growth Genetics (EGG) and Early Genetics and Longitudinal Epidemiology (EAGLE)
- Membership in European Respiratory Society (ERS), European Academy of Allergy and Clinical Immunology (EAACI) and Fellow of the Royal Statistical Society