Our recent work has focused on microRNA target prediction and validation. We are particularly interested in the role of microRNAs in lung cancer pathogenesis. As part of these efforts we have developed a computational method of predicting microRNA targets, which we use in conjunction with a microarray-based method of measuring microRNA expression profiles, high-throughput functional screens, and an assay for interaction between a microRNA and a predicted target. We have identified microRNAs that distinguish lung cancer cell lines and which correlate with resistance to widely-used anti-cancer drugs.
microRNAs represent an under-appreciated source of informative variation. Most SNP discovery methods focus on coding regions, as the predicted relative risk of a non-synonymous substitution in the protein product of a gene is very high. Since the overall frequency of such events in the genome is low, a re-prioritization of where to look may be appropriate. The ’impact’ (roughly equivalent to the expectation value that a SNP is phenotypically interesting) can be defined in terms of the product of the expected frequency of a given type of variant with the predicted relative risk of a deleterious phenotype. Ranking the types of variant in terms of impact suggests that focusing on other types of variation (such as those likely to affect splicing or expression level) may be worthwhile strategies.
RESEARCH INTERESTS
microRNA roles in lung cancer pathogenesis
microRNA target prediction and validation
polymorphism identification and characterization
RECENT PUBLICATIONS
Du L, Schageman JJ, Subauste MC, Saber B, Hammond SM, Prudkin L, Wistuba II, Ji L, Roth JA, Minna JD and Pertsemlidis A, "miR-93, miR-98, and miR-197 regulate expression of tumor suppressor gene FUS1" Mol Cancer Res, 8(7):1234-1243, August 2008
Romeo S, Kozlitina J, Xing C, Pertsemlidis A, Cox D, Pennacchio LA, Boerwinkle E, Cohen JC and Hobbs HH, "Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease" Nature Genetics, 40(12):1461-1465, December 2008
Cohen JC, Pertsemlidis A, Fahmi S, Esmail S, Vega GL, Grundy SM, Hobbs HH, "Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels" Proc Natl Acad Sci U S A, 103(6):1810-5, February 2006
Kotowski IK, Pertsemlidis A, Luke A, Cooper RS, Vega GL, Cohen JC, Hobbs HH, "A spectrum of PCSK9 alleles contributes to plasma levels of low-density lipoprotein cholesterol" Am J Hum Genet, 78(3):410-22, March 2006
Lancman JJ, Caruccio NC, Harfe BD, Pasquinelli AE, Schageman JJ, Pertsemlidis A, Fallon JF, "Analysis of the regulation of lin-41 during chick and mouse limb development" Dev Dyn, 234(4):948-60, December 2005
SIGNIFICANT PUBLICATIONS
McPherson R, Pertsemlidis A, Kavaslar N, Stewart A, Roberts R, Cox DR, Hinds DA, Pennacchio LA, Tybjaerg-Hansen A, Folsom AR, Boerwinkle E, Hobbs HH, Cohen JC, "A common allele on chromosome 9 associated with coronary heart disease" Science, 316(5830):1488-91, June 2007
Cohen JC, Pertsemlidis A, Kotowski IK, Graham R, Garcia CK and Hobbs HH, "Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9" Nature Genetics, 37(3):161-165, January 2005
Cohen JC, Kiss RS, Pertsemlidis A, Marcel YL, McPherson R and Hobbs HH, "Multiple rare alleles contribute to low plasma levels of HDL cholesterol" Science, 305(5685):869-872, August 2004
Pertsemlidis A, Sorenson JM and Head-Gordon T, "Evidence for microscopic, long-range hydration forces for a hydrophobic amino acid" Proceedings of the National Academy of Sciences of the United States of America, 96(2):481-486, January 1999
Pertsemlidis A, Saxena AM, Soper AK, Head-Gordon T and Glaeser RM, "Direct, structural evidence for modified solvent structure within the hydration shell of a hydrophobic amino acid" Proceedings of the National Academy Academy of Sciences of the United States of America, 93(20):10769-10774, October 1996
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