Research Topics
Genomes and GenesSpecies | A PertsemlidisSummaryAffiliation: University of Texas Southwestern Medical Center Country: USA Publications
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Detail Information
Publications
MicroRNA expression distinguishes SCLC from NSCLC lung tumor cells and suggests a possible pathological relationship between SCLCs and NSCLCsLiqin Du
Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas, USA
J Exp Clin Cancer Res 29:75. 2010..However, the role of miRNAs in the pathogenesis and diagnosis of small cell carcinoma (SCLC), the majority of which represent the most aggressive lung tumors, has not been investigated...- microRNAs mature with help from cancer biologyZain Paroo
Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75930 8591, USA
Genome Biol 10:310. 2009..A report of the Keystone Symposium on Molecular and Cellular Biology, 'MicroRNA and Cancer', Keystone, Colorado, USA, 10-15 June 2009... - Having a BLAST with bioinformatics (and avoiding BLASTphemy)A Pertsemlidis
Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390 8591, USA
Genome Biol 2:REVIEWS2002. 2001..This article discusses the principles, workings, applications and potential pitfalls of BLAST, focusing on the implementation developed at the National Center for Biotechnology Information... - SNPCEQer II: the integrated detection and analysis of SNPs in DNA sequencesFuqiang Tang
Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Appl Bioinformatics 2:151-4. 2003..SNPCEQer II can determine the mutation type of a coding SNP and generate data for submission to the dbSNP database. The SNP report can be edited and printed, as can the chromatograms. SNPCEQer II is implemented in Visual C++... - ARROGANT: an application to manipulate large gene collectionsAmit V Kulkarni
Program in Biomedical Engineering, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
Bioinformatics 18:1410-7. 2002.... - SNPCEQer: detecting SNPs in sequences generated by the Beckman CEQ2000 DNA Analysis SystemE M Flood
Eugene McDermott Center for Human Growth and Development, The University of Texas, Southwestern Medical Center, Dallas 75390 8591, USA
Biotechniques 33:814, 816, 818-20 passim. 2002..Each gene region was analyzed in 96-306 samples. SNPCEQer was designed to operate from Windows NT, making SNP detection more accessible to users without UNIX systems. SNPCEQer is available free of charge at http://innovation.swmed.edu... - miR-93, miR-98, and miR-197 regulate expression of tumor suppressor gene FUS1Liqin Du
Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390 8591, USA
Mol Cancer Res 7:1234-43. 2009..Finally, we found that elevated miR-93 and miR-197 expression is correlated with reduced Fus1 expression in NSCLC tumor specimens. These results suggest that the three miRNAs are negative regulators of Fus1 expression in lung cancers... - Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levelsJonathan C Cohen
Donald W Reynolds Cardiovascular Clinical Research Center, Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390 9052, USA
Proc Natl Acad Sci U S A 103:1810-5. 2006.... - Power of genetic association studies with fixed and random genotype frequenciesJulia Kozlitina
Donald W Reynolds Cardiovascular Clinical Research Center, Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390 8591, USA
Ann Hum Genet 74:429-38. 2010..We explore the effect of uncertainty in the factors that determine statistical power of association studies and propose a more economical approach to the power analysis... - Selective identification of secreted and transmembrane breast cancer markers using Escherichia coli ampicillin secretion trapDeborah A Ferguson
Center for Developmental Biology, University of Texas Southwestern Medical Center, Dallas 75390-9039, USA
Cancer Res 65:8209-17. 2005..Our results indicate that CAST is a robust, rapid, and low cost method to identify cell surface and secreted proteins and is applicable to a variety of relevant biological questions... - ELXR: a resource for rapid exon-directed sequence analysisJeoffrey J Schageman
Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Harry Hines Boulevard, Dallas, TX 75390, USA
Genome Biol 5:R36. 2004..The resulting exon-flanking PCR primer pairs have been compiled into a system called ELXRdb, which may be searched by keyword, gene name or RefSeq accession number... - Reading the fine print of the human genomeJeoffrey J Schageman
McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8591, USA
IEEE Eng Med Biol Mag 22:105-8. 2003 - Multiple rare alleles contribute to low plasma levels of HDL cholesterolJonathan C Cohen
Donald W Reynolds Cardiovascular Clinical Research Center and McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
Science 305:869-72. 2004..Thus, rare alleles with major phenotypic effects contribute significantly to low plasma HDL-C levels in the general population... - microRNAs and lung cancer: tumors and 22-mersLiqin Du
Harold C Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390 8807, USA
Cancer Metastasis Rev 29:109-22. 2010.... - Association of extensive polymorphisms in the SLAM/CD2 gene cluster with murine lupusAmy E Wandstrat
Center for Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
Immunity 21:769-80. 2004..While autoimmunity may be mediated by a combination of genes in the SLAM/CD2 family cluster, the strongest candidate is Ly108, a specific isoform of which is constitutively upregulated in B6.Sle1b lymphocytes... - A spectrum of PCSK9 alleles contributes to plasma levels of low-density lipoprotein cholesterolIngrid K Kotowski
McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, 75390 9046, USA
Am J Hum Genet 78:410-22. 2006..These findings reveal that PCSK9 activity is a major determinant of plasma levels of LDL-C in humans and make it an attractive therapeutic target for LDL-C lowering... - Predicting potential miRNA target sites within gene promotersScott T Younger
Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
Bioorg Med Chem Lett 19:3791-4. 2009..These methods will facilitate investigations of whether miRNAs interact with sequences outside of 3'-untranslated regions and suggest new targets for the design of synthetic modulators of gene expression... - Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9Jonathan Cohen
Donald W Reynolds Cardiovascular Clinical Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines, Dallas, Texas 75390 9046, USA
Nat Genet 37:161-5. 2005..1%) and were associated with a 40% reduction in plasma levels of LDL cholesterol. These data indicate that common sequence variations have large effects on plasma cholesterol levels in selected populations... - Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungiHeng Chi Lee
Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
Mol Cell 38:803-14. 2010..Taken together, these results uncover several pathways for small RNA production in filamentous fungi, shedding light on the diversity and evolutionary origins of eukaryotic small RNAs... - Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver diseaseStefano Romeo
Donald W Reynolds Cardiovascular Clinical Research Center, Eugene McDermott Center for Human Growth and Development, Dallas, TX 75390, USA
Nat Genet 40:1461-5. 2008..Thus, variation in PNPLA3 contributes to ancestry-related and inter-individual differences in hepatic fat content and susceptibility to NAFLD... - Text comparison based on dynamic programmingAlexander Pertsemlidis
IEEE Eng Med Biol Mag 23:66-71. 2004 - A common allele on chromosome 9 associated with coronary heart diseaseRuth McPherson
Division of Cardiology, University of Ottawa Heart Institute, Ottawa K1Y4W7, Canada
Science 316:1488-91. 2007..Homozygotes for the risk allele make up 20 to 25% of Caucasians and have a approximately 30 to 40% increased risk of CHD... - Analysis of the regulation of lin-41 during chick and mouse limb developmentJoseph J Lancman
Department of Anatomy, University of Wisconsin, Madison, 53706, USA
Dev Dyn 234:948-60. 2005..elegans let-7 and lin-4. Finally, we show that these miRNAs and others are expressed in the chick limb consistent with the hypothesis that they regulate chicken Lin-41 activity in vivo...