Graduate School: University of Virginia
Primary Appointment: Assistant Professor, Public Health Sciences
Statistical and computational genomics, including next-gen SNP discovery, comparative gene structure prediction, functional RNA-seq and ChIP-seq analyses.
Biomedical Sciences Graduate Program(s)
- Biochemistry, Molecular Biology and Genetics
- Microbiology, Immunology and Infectious Diseases
- Structural, Computational Biology and Biophysics
The advent of ultra-high throughput second-generation DNA sequencing has provided an ever-increasingly detailed view of the human genome, from both a structural and functional perspective. Our research leverages such genomic datasets to expose the biological processes underlying complex biology. Ongoing projects in the lab include: discovery of genetic polymorphisms associated with multigenic human diseases (type 1 diabetes and cancer); genomic studies of human immune system development and response to infectious disease; and the development of bioinformatic algorithms for sensitive and accurate consensus gene structure prediction across closely-related organisms (e.g. Plasmodium, Drosophila, and primates). We also collaborate on a variety of functional genomics projects using “next-gen” sequencing methods for ChIP-seq, RNA-seq, MeDIP-seq, CLIP-seq, etc. For most projects, we develop and employ state-of-the art statistical machine learning methods, customized to integrate and interrogate genomic data specific to the particular experimental context.
- Tribolium Genome Sequencing Consortium. The genome of the model beetle and pest Tribolium castaneum. Nature. 2008 Apr 24;452(7190):949-55. Epub 2008 Mar 23. PubMed PMID: 18362917.
- Liu Q, Mackey AJ, Roos DS, Pereira FC. Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction. Bioinformatics. 2008 Mar 1;24(5):597-605. Epub 2008 Jan 10. PubMed PMID: 18187439.
- Chen F, Mackey AJ, Vermunt JK, Roos DS. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One. 2007 Apr 18;2(4):e383. PubMed PMID: 17440619; PubMed Central PMCID: PMC1849888.
- Elsik CG, Mackey AJ, Reese JT, Milshina NV, Roos DS, Weinstock GM. Creating a honey bee consensus gene set. Genome Biol. 2007;8(1):R13. PubMed PMID: 17241472; PubMed Central PMCID: PMC1839126.