|Roger Pique-Regi, PhD
Assistant Professor of Molecular Medicine and Genetics
540 E. Canfield, 3224 Scott Hall
Tel: (313) 577-0719
Assistant Professor (also with DCaTS, Department of Clinical and Translational Sciences); PhD, University of Southern California, 2009.
Research interestsMy research group aims to further our understanding of the human genome by developing computational methods and statistical models that integrate large datasets. We tackle questions such as: Where are the DNA sequences that control gene expression in a given tissue or cell-type? What are the chromatin marks that characterize the state of the cell and are associated with these regulatory sequences? How can genetic variation disrupt the regulatory code and affect the molecular processes leading to a disease condition?
Much of our statistical work makes use of computationally intensive approaches that are designed to be effective for extracting subtle signals from large and complex data sets. This requires using or developing new advanced state-of-the-art methods in statistics, computer science and signal processing and applying them to comparative genomics, functional genomics and population genetics. In general, we aim to tackle problems where careful analysis seems likely to yield new biological insights.
We also distribute a number of programs and software packages, including CENTIPEDE (for DNase-I foot printing) and GADA (for segmentation and copy number analysis). See [Pique-Regi Lab website] for more information.
Selected publications*Degner JF, *Pai AA, *Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, de Leon S, Michelini K, Lewellen N, Crawford G, Stephens M, Gilad Y, and Pritchard JK. "Variation in chromatin accessibility is a key determinant of heritable variation in gene expression". Nature, 2012.
Zullo JM, Demarco IA, Pique-Regi R, Gaffney DJ, Epstein CB, Bernstein KL, Pritchard JK, Reddy KL, and Singh H. "A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina". Cell 2012.
Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, and Pritchard JK. "Dissecting the regulatory architecture of gene expression QTLs." Genome Biol., 2012.
Pique-Regi R, Ortega A, Tewfik A., Asgharzadeh S. "Detecting Changes in DNA Copy Number: Reviewing signal processing techniques". IEEE Signal Processing Magazine, 2012.
González JR, Rodríguez-Santiago B, Cáceres A, Pique-Regi R, Rothman N, Chanock SJ, Armengol L, Pérez-Jurado LA. "A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data”. BMC Bioinformatics, 2011.
Pique-Regi R, Degner JF, Pai AA, Gaffney DG, Gilad Y, Pritchard JK. "Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data", Genome Research, 2011.
Pique-Regi R, Ortega A, Asgharzadeh S: "Joint estimation of copy number variation and reference intensities on multiple DNA arrays using GADA", Bioinformatics, 2009.
Pique-Regi R, Monso-Varona J,Ortega A, Seeger RC, Triche TJ, Asgharzadeh S: "Sparse representation and Bayesian detection of the genome copy number alterations from microarray data", Bioinformatics, 2008.
Asgharzadeh S, Pique-Regi R, Sposto R, Wang H, Yang Y, Shimada H, Matthay K, Buckley J, Ortega A, Seeger RC. - " Prognostic significance of gene expression profiles of metastatic neuroblastomas lacking MYCN gene amplification. " - J Natl Cancer Inst 2006.