Bioinformatics
In Bioinformatics and Computational Biology,
projects include development of programs for copy number variation
(CNV) allelic frequency estimation (CoNVEM, Human Mutation 2010),
evaluation of "missingness" for Mendelian Randomization (AJHG, 2009),
exact solution of Hill's cubic equation for pairwise haplotype
frequency estimation (CubeX, BMC Bioinformatics 2007), interallelic
linkage disequilibrium between bi- and multi-allelic
markers (MIDAS, BMC Bioinformatics 2006) and the mining of EST
databases for splicing information (Diabetes 2006). See
http://apps.biocompute.org.uk/
for further details and access to programs. A
sample of publications:
- Raistrick CA, Alharbi KK, Day IN, Gaunt TR. Analysis of Potential Genomic Confounding in Genetic Association Studies and an
Online Genomic Confounding Browser (GCB). Ann Hum Genet. 2011 Nov;75(6):723-31.
- Raistrick CA, Day IN, Gaunt TR. Genome-Wide Data-Mining of Candidate Human Splice Translational Efficiency Polymorphisms (STEPs) and an Online Database. PLoS One. 2010 Oct 11;5(10). pii: e13340.
- Gaunt TR, Rodriguez S, Guthrie PA, Day IN. An
expectation-maximization program for determining allelic spectrum from
CNV data (CoNVEM): insights into population allelic architecture and
its mutational history. Hum Mutat. 2010
Jan 14. [Epub ahead of print]
- Rodriguez S, Gaunt TR, Day IN. Hardy-Weinberg
equilibrium
testing of biological ascertainment for Mendelian randomization
studies. Am
J Epidemiol. 2009 Feb 15;169(4):505-14. Epub 2009 Jan 6.
- Gaunt TR, Rodríguez S, Day IN. Cubic exact
solutions
for the estimation of pairwise haplotype frequencies: implications for
linkage disequilibrium analyses and a web tool 'CubeX'. BMC
Bioinformatics. 2007 Nov 2;8:428.
- Gaunt TR, Rodriguez S, Zapata C, Day IN. MIDAS:
software
for analysis and visualisation of interallelic disequilibrium between
multiallelic markers. BMC
Bioinformatics. 2006 Apr 27;7:227.
- Kralovicova J,
Gaunt TR, Rodriguez S, Wood PJ, Day IN, Vorechovsky I. Variants in the
human insulin gene that affect pre-mRNA splicing: is -23HphI a
functional single nucleotide polymorphism at IDDM2? Diabetes.
2006 Jan;55(1):260-4
