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Cracking the Regulatory Genome: which Genetic Variants Affect Gene Transcription?

Scientific Conference

Friday 12 June 2015 from 12:00 at 13:00

Speaker

Roger Pique-Regi, PhD

  • Assistant Professor, Center for Molecular Medicine and Genetics, Department of Clinical and Translational Science, Wayne State University

My research objective is to develop a better understanding of the gene regulatory language encoded both in the human genome and in the epigenetic marks that define the state of the cell. Learning the grammar that controls the molecular machinery that activates / modulates gene transcription on a given tissue / condition is a fundamental step towards understanding how the cell is wired and the molecular basis for disease. My pre-doctoral research at University of Southern California focused on the development of statistical tools for analyzing data from experiments that examined gene expression patterns and copy number alterations in neuroblastoma tumors (Asgharzadeh et al., 2006 J. Natl. Cancer Inst.; Pique-Regi et al., 2008 Bioinformatics). During my postdoctoral work at the University of Chicago, I developed a novel probabilistic framework to predict tissue-specific regulatory sites for DNA-binding proteins using DNase-seq footprinting (Pique-Regi et al., 2011 Genome Res). Subsequently, we used DNase-seq to measure chromatin accessibility in 70 Yoruba lymphoblastoid cell lines (Degner et al., 2012 Nature), for which genome-wide genotypes and estimates of gene expression levels based on RNA-seq are also available. This work represents the first study to provide direct results supporting a molecular mechanism for a large fraction of genetic determinants of gene expression. Using computational approaches, I contributed to elucidate a molecular mechanism that compartmentalizes specific DNA sequence elements to the nuclear lamina (Zullo et al., 2012 Cell). I also maintain the widely used software packages GADA (>100 registered users) and CENTIPEDE (>200 monthly accessions).

 
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Updated on 6/9/2015
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