I work on graphical methods for reconstructing immune-related hypervariable genomic regions in the malaria parasite, Plasmodium falciparum. Typical alignment-based strategies of reads against a reference genome do not work very well for highly divergent regions of the genome. Instead, we combine multiple reference genomes of differing quality and annotation status, targeted sequencing data, and de novo assemblies of field samples, into a graph. Paths through this data structure represent individual samples and can provide a more accurate reconstruction than alignment against a single genome.
Prior to coming to Oxford I was a computational biologist in the Medical and Population Genetics (MPG) program at the Broad Institute. I worked primarily on variant discovery in the exon sequencing pilot and whole-exome arm of the 1000 Genomes project. Later, I worked on pipelining these methods for all of MPG's human exome sequencing projects.
Kiezun A, Garimella K, Do R et al. Exome sequencing and the genetic basis of complex traits. Nat Genet. 2012 May 29;44(6):623-30. doi: 10.1038/ng.2303.
DePristo MA, Banks E, Poplin R, Garimella KV et al; A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. doi: 10.1038/ng.806.
Marth GT, Yu F, Indap AR, Garimella K et al; 1000 Genomes Project. The functional spectrum of low-frequency coding variation. Genome Biol. 2011 Sep 14;12(9):R84. doi: 10.1186/gb-2011-12-9-r84.