Aaron J. Mackey

Primary Appointment

  • Assistant Professor, Public Health Sciences

Contact

Research Interest(s)

Statistical and computational genomics, including next-gen SNP discovery, comparative gene structure prediction, functional RNA-seq and ChIP-seq analyses.

Research Description

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.

Selected Publications

  • Adhikari N, Guan W, Capaldo B, Mackey A, Carlson M, Ramakrishnan S, Walek D, Gupta M, Mitchell A, Eckman P, John R, Ashley E, Barton P, Hall J. Identification of a new target of miR-16, Vacuolar Protein Sorting 4a. PloS one. 2014;9(7): e101509. PMID: 25033200 | PMCID: PMC4102469
  • Ames E, Lawson M, Mackey A, Holmes J. Sequencing of mRNA identifies re-expression of fetal splice variants in cardiac hypertrophy. Journal of molecular and cellular cardiology. 2013;62 99-107. PMID: 23688780 | PMCID: PMC3735658
  • Huang K, Mellor K, Paul S, Lawson M, Mackey A, Timko M. Global changes in gene expression during compatible and incompatible interactions of cowpea (Vigna unguiculata L.) with the root parasitic angiosperm Striga gesnerioides. BMC genomics. 2012;13 402. PMID: 22900582 | PMCID: PMC3505475
  • Roller D, Axelrod M, Capaldo B, Jensen K, Mackey A, Weber M, Gioeli D. Synthetic lethal screening with small molecule inhibitors provides a pathway to rational combination therapies for melanoma. Molecular cancer therapeutics. 2012. PMID: 22962324 | PMCID: NIHMS405900