I am currently a post-doc in the lab of John Hickey at the Roslin Institute, University of Edinburgh.
My current research focuses on phasing genotype data and the subsequent use of this phase information in genotype imputation. I am involved in maintaing AlphaPhase and developing it so that it can be used with the large datasets, involving hundreds of thousands animals, now becoming avaliable.
My previous position was with the Myles lab at the University of Dalhousie. Here my research focused on genotype imputation. Genotype imputation is often used with next-generation DNA sequencing to improve the results of downstream analysis such as Genome Wide Association Scans (GWAS). Most current genotype imputation methods were developed for human or other high quality data sets where there is a pool of reference samples and sequencing is often done at sufficient depth to make confident genotype calls. In non-model organisms, such as apple (Malus domestica), this is often not the case and my research focuses on evaluating existing methods on these datasets and developing new imputation methods.
From November 2011 to November 2013 I was a post doc in the lab of Mark Holder at the University of Kansas. My research focused on methods for detecting and correcting a class of alignment errors: over compression. Each column in an alignment represents residues that should be inherited from a common ancestor. Under a strict interpretation of homology, each site in an alignment can be explained at most one insertion, but possibly multiple deletions. In a compressed alignment, residues inherited from an insertion event appear in the same column as residues that did not arise from that event. Our method compares site-likelihoods under a model that allows multiple insertions to site-likelihoods under a form of stochastic Dollo model which prohibits multiple insertions in the same column. Site-likelihood comparisons that favour multiple insertions can be used to guide the splitting of a single column into two or more columns in which all of the residues do appear to be homologous.
I completed my PhD at the University of Manchester in 2011, working in the lab of Dr. Simon Whelan, who is now at Uppsala University. My PhD research was focused on two areas, linked by the common thread of phylogenetic trees:
- The Tree Search Problem - The number of possible phylogenetic trees grows super-exponentially with the number of taxa and this can make finding the tree that best fits the data very difficult. We investigated how often different methods find a “good” tree (one statistically indistinguishable from the best tree) and whether any features of the data are correlated with the difficulty of the tree search problem.
- Modelling Gene Family Evolution - Inferring gene family evolutionary is still in its infancy when compared to DNA or Protein evolution and models are still being developed. We investigated and compared the parsimony and maximum likelihood methods of inference and are currently finishing work on different models, including those with a sink state, that could be used for gene family evolution.
Previous to doing my PhD I completed a MSc in Bioinformatics, also at the University of Manchester. Between my first degree and my masters I work for the UK Ministry of Defence near Bath, for five years. I obtained my first degree, a BSc in Computer Science, from the University of Wales, Swansea (now the University of Swansea).
- Money D, Migicovsky Z Gardner K, Myles S (2017) LinkImputeR: user-guided genotype calling and imputation for non-model organisms. BMC Genomics 18: 523 DOI: 10.1186/s12864-017-3873-5 | PubMed: 28693460
- Antolin R, Nettelblad C, Gorjanc G, Money D, Hickey J M (2017) A hybrid method for the imputation of genomic data in livestock populations Genetics Selection Evolution 49:30. DOI: 10.1186/s12711-017-0300-y | PubMed: 28253858
- Migicovsky Z, Sawler J, Money D , Eibach R, Miller A J, Luby J L, Jamieson A R, Velasco D, von Kintzel S, Warner J, Wührer W, Brown P J, Myles S (2016) Genomic Ancestry Estimation QuantifiesUse of Wild Species in Grape Breeding. BMC Genomics 17:478. DOI: 10.1186/s12864-016-2834-8 | PubMed: 27357509
- Migicovsky Z, Gardner K, Money D, Sawler J, Bloom J, Moffett P, Chao C T, Schwaninger H, Fazio G, Zhong G-Y, Myles S (2016) Genome to phenome mapping in apple using historical data. The
Plant Genome 9. DOI: 10.3835/plantgenome2015.11.0113 | PubMed: 27898813
- Money D, Gardner K, Migicovsky Z, Schwaninger H, Zhong G-Y, Myles S (2015) LinkImpute: Fast and Accurate Genotype Imputation for Non-Model Organisms. G3: Genes, Genomes, Genetics 5: 2383-2390 DOI: 10.1534/g3.115.021667 | PubMed: 26377960
- Money D, Whelan S (2015) GeLL: A Generalized Likelihood Library for Phylogenetic Models. Bioinformatics 31: 2391-2393. DOI: 10.1093/bioinformatics/btv126 | PubMed: 25725494
- McClure KA, Sawler J, Gardner KM, Money D, Myles S (2014) Genomics: A potential panacea for the perennial problem. American Journal of Botany 101: 1780-1790. DOI: 10.3732/ajb.1400143 | PubMed: 25326620
- Ames RM, Money D, Lovell SC (2014) Inferring gene family histories in Yeast identifies lineage specific expansions. PLoS One 9(6): e99480. DOI: 10.1371/journal.pone.0099480 | PubMed: 24921666
- Money D, Whelan S (2012) Characterizing the phylogenetic tree-search problem. Systematic Biology 61: 228-239. DOI: 10.1093/sysbio/syr097 | PubMed: 22076302
- Ames RM, Money D, Ghatge V, Whelan S, Lovell SC (2012) Determining the evolutionary history of gene families. Bioinformatics 28: 48-55. DOI: 10.1093/bioinformatics/btr592 | PubMed: 22039210
- Whelan S, Money D (2010) The prevalence of multifurcations in tree-space and their implications for tree-search. Molecular Biology and Evolution 27: 2674-2677. DOI: 10.1093/molbev/msq163 | PubMed: 20584772
- DupliphyML A tool for modelling gene family size evolution. (Ames et al 2012)
- GeLL A Java library for general likelihood calculations. (Money and Whelan 2015)
- LinkImpute A genotype imputation tool. (Money et al 2015)
- LinkImputeR A genotype imputation tool that incoporates read data and different filtering of the data. (Money et al 2017)
My CV (PDF)