We are particularly interested in non-coding regions of the genome and are currently investigating how variation in microRNA genes and their corresponding targets may play a role in human disease. As part of this effort we have developed a computational method of predicting microRNA targets, which we use in conjunction with microarray- and qPCR-based methods of measuring microRNA expression profiles, and assays for microRNA function and interaction between a microRNA and a predicted target.
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, expression level, or the interaction between a microRNA and its target) may be worthwhile strategies.
RESEARCH INTERESTS
microRNA roles in lung cancer pathogenesis
microRNA target prediction and validation
polymorphism identification and characterization
RECENT PUBLICATIONS
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
Pertsemlidis A, Zelinka J, Fondon JW 3rd, Henderson RK, Otwinowski Z, "Bayesian statistical studies of the Ramachandran distribution" Stat Appl Genet Mol Biol, 4(1):article35, November 2005
Ferguson DA, Muenster MR, Zang Q, Spencer JA, Schageman JJ, Lian Y, Garner HR, Gaynor RB, Huff JW, Pertsemlidis A, Ashfaq R, Schorge J, Becerra C, Williams NS, Graff JM, "Selective identification of secreted and transmembrane breast cancer markers using Escherichia coli ampicillin secretion trap." Cancer Res, 65(18):8209-17, September 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
Jonathan C. Cohen, Alexander Pertsemlidis, Ingrid K. Kotowski, Randall Graham, Christine K. Garcia, Helen H. Hobbs, "Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9" Nature Genetics, 37(3):161-165, January 2005
Jonathan C. Cohen, Robert S. Kiss, Alexander Pertsemlidis, Yves L. Marcel, Ruth McPherson, Helen H. Hobbs, "Multiple rare alleles contribute to low plasma levels of HDL cholesterol" Science, 305(5685):869-872, August 2004
Alexander Pertsemlidis, Jon M. Sorenson, and Teresa Head-Gordon, "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
Alexander Pertsemlidis, Anand M. Saxena, Alan K. Soper, Teresa Head-Gordon, and Robert M. Glaeser, "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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