Adam M Gustafson, PhD

PhD, Bioinformatics, Boston University, January 2009

BS in Computer Science, Oregon State University, 2004

adam.gustafson AT

Research Interests:

My research in Dr. Spira's lab has focused on studying three important aspects of cancer progression: predisposition to lung cancer through host response to cigarette smoke, early stages of lung cancer tumorigenesis, and computational prediction of rational, targeted therapies for the treatment of breast cancer. A pathway based approach to the analysis of gene expression microarray data has been used to help identify chemopreventive and treatment opportunities for cancer.
Previously, I have been involved in studying microRNAs in the plant Arabidopsis thaliana. For this work, I conducted research ranging from computationally predicted microRNA targets, to the discovery of a mechanism for the evolutionary origin of microRNAs in plants.

Selected Publications:

Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol, 2004. 2(5): p. E104. PubMed

Allen E, Xie Z, Gustafson AM, Sung GH, Spatafora JW, Carrington JC. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet, 2004. 36(12): p. 1282-90. PubMed

Gustafson AM, Allen E, Givan S, Smith D, Carrington JC, Kasschau KD. ASRP: the Arabidopsis Small RNA Project Database. Nucleic Acids Res, 2005. 33(Database issue): p. D637-40. PubMed

Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 2005. 121(2): p. 207-21. PubMed

Snitkin ES, Gustafson AM, Mellor J, Wu J, DeLisi C.  Comparative assessment of performance and genome dependence among phylogenetic profiling methods. BMC Bioinformatics, 2006. 7: p. 420. PubMed

Gustafson AM, Snitkin ES, Parker SJ, DeLisi C, Kasif S. Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics, 2006. 7: p. 265. PubMed

Linghu B, Snitkin ES, Holloway DT, Gustafson AM, Xia Y, DeLisi C. High-precision high-coverage functional inference from integrated data sources. BMC Bioinformatics. 2008 Feb 25;9:119. PubMed

Sridhar S, Schembri F, Zeskind J, Shah V, Gustafson AM, Steiling K, Liu G, Dumas YM, Zhang X, Brody JS, Lenburg ME, Spira A. Smoking-induced gene expression changes in the bronchial airway are reflected in nasal and buccal epithelium. BMC Genomics. 2008 May 30;9:259.  PubMed


Schembri F, Sridhar S, Perdomo C, Gustafson AM, Zhang X, Ergun A, Lu Jining, Liu G, Zhang X, Bowers J, Sensinger, K, Collins J, Brody J, Getts R, Lenburg M, Spira A. MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. PNAS. 2009 Feb 17;106(7):2319-24. PubMed


Bild A, Parker JS, Gustafson AM, Acharya CR, Hoadley KA, Anders C, Marcom PK, Carey LA, Potti A, Nevins JR, Perou CM. An integration of complementary strategies for gene expression analysis to reveal novel therapeutic opportunities for breast cancer. Breast Cancer Research. 2009;11(4):R55. PubMed

Gustafson AM, Soldi R, Anderlind C, Scholand MB, Qian J, Zhang X, Cooper K, Walker D, McWilliams A, Liu G, Szabo E, Brody J, Massion PP, Lenburg ME, Lam S, Bild AH, Spira A. Airway PI3K pathway activation is an early and reversible event in lung cancer development. Science Translational Medicine. 2010 Apr 7;2(26):26ra25. PubMed