02/01/06
Our analysis pipeline was part of a study of the contribution of rare variants in NPC1L1 to sterol absorption and plasma levels of LDL-C.

05/01/05
Liqin Du, Ph.D. joined the lab as a postdoctoral fellow.

02/01/05
Our analysis pipeline for association studies was part of a study on the contribution of nonsense mutations in PCSK9 to LDL-C levels in African Americans.

12/01/04
Our analysis pipeline for SNP discovery and characterization was part of a study on the contribution of polymorphisms in the SLAM/CD2 gene cluster to murine lupus.

09/01/04
Our analysis pipeline for association studies was part of a study on the contribution of rare alleles to HDL-C levels.

06/01/04
A paper describing ELXR is in Genome Biology.

Publications

Spirin V, Schmidt S, Pertsemlidis A, Cooper RS, Cohen JC, Sunyaev SR. Common Single-Nucleotide Polymorphisms Act in Concert to Affect Plasma Levels of High-Density Lipoprotein Cholesterol. Am J Hum Genet 2007;81(6).

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 2007;316(5830):1488-91.

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 2006;78(3):410-422.

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 2006;103(6):1810-1815.

Pertsemlidis A, Zelinka J, Fondon JW, 3rd., Henderson RKH, Otwinowski Z. Bayesian statistical studies of the Ramachandran distribution. Statistical Applications in Genetics and Molecular Biology 2005;4(1):1-16.

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. 2005 Dec;234(4):948-60.

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. 2005 Sep 15;65(18):8209-17.

Cohen J, Pertsemlidis A, Kotowski IK, Graham R, Garcia CK, Hobbs HH. Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9. Nat Genet. 2005 Feb;37(2):161-165.

Wandstrat AE, Nguyen C, Limaye N, Chan AY, Subramanian S, Tian XH, Yim YS, Pertsemlidis A, Garner HR Jr, Morel L, Wakeland EK. Association of Extensive Polymorphisms in the SLAM/CD2 Gene Cluster with Murine Lupus. Immunity. 2004 Dec;21(6):769-80.

Cohen JC, Kiss RS, Pertsemlidis A, Marcel YL, McPherson R, Hobbs HH. Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science. 2004 Aug 6;305(5685):869-72.

Schageman JJ, Horton CJ, Niu S, Garner HR, Pertsemlidis A. ELXR: a resource for rapid exon-directed sequence analysis. Genome Biology. 2004 Apr 28;5(5):R36. [PDF]

Schageman JJ, Ferguson DA, Zang Q, Spencer JA, Huff JW, Graff JM, Lian Y, Garner HR, Pertsemlidis A. Reading the fine print of the human genome. IEEE Eng Med Biol Mag. 2003 Mar-Apr;22(2):105-8. PMID: 12733468

Kulkarni AV, Williams NS, Lian Y, Wren JD, Mittelman D, Pertsemlidis A, Garner HR. ARROGANT: an application to manipulate large gene collections. Bioinformatics. 2002 Nov;18(11):1410-7. PMID: 12424110 [PDF]

Flood EM, Tang F, Horvath MM, Pertsemlidis A, Garner HR. SNPCEQer: detecting SNPs in sequences generated by the Beckman CEQ2000 DNA Analysis System. Biotechniques. 2002 Oct;33(4):814, 816, 818-20 passim. PMID: 12398190

Pertsemlidis A, Fondon JW 3rd. Having a BLAST with bioinformatics (and avoiding BLASTphemy). Genome Biol. 2001;2(10):REVIEWS2002. Epub 2001 Sep 27. PMID: 11597340 [PDF]

Pertsemlidis A, Pande A, Miller B, Schilling P, Wei MH, Lerman MI, Minna JD, Garner HR, Mittelman D. PANORAMA: an integrated Web-based sequence analysis tool and its role in gene discovery. Genomics. 2000 Dec 15;70(3):300-6. Erratum in: Genomics 2001 Oct;77(3):208. PMID: 11161780 [PDF]

Wren JD, Forgacs E, Fondon JW 3rd, Pertsemlidis A, Cheng SY, Gallardo T, Williams RS, Shohet RV, Minna JD, Garner HR. Repeat polymorphisms within gene regions: phenotypic and evolutionary implications. Am J Hum Genet. 2000 Aug;67(2):345-56. Epub 2000 Jul 07. PMID: 10889045 [PDF]

Pertsemlidis A, Soper AK, Sorenson JM, Head-Gordon T. Evidence for microscopic, long-range hydration forces for a hydrophobic amino acid. Proc Natl Acad Sci U S A. 1999 Jan 19;96(2):481-6. PMID: 9892659 [PDF]

Head-Gordon T, Sorenson JM, Pertsemlidis A, Glaeser RM. Differences in hydration structure near hydrophobic and hydrophilic amino acids. Biophys J. 1997 Oct;73(4):2106-15. PMID: 9336206

Pertsemlidis A, Saxena AM, Soper AK, Head-Gordon T, Glaeser RM. Direct evidence for modified solvent structure within the hydration shell of a hydrophobic amino acid. Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):10769-74. PMID: 8855255 [PDF]

VanBogelen R, Clark R, Pertsemlidis A, Abshire K, Neidhardt F. Chapter 115: Gene-protein database of Escherichia coli K-12: edition 6. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, Second edition. Neidhardt, F. et al., editors. ASM Press, Washington, D. C. 1996.