Roger Pique-Regi, PhD

Roger Pique-Regi, PhD
Associate Professor of Molecular Medicine and Genetics and of Obstetrics and Gynecology
Scott Hall, Rm 3309
540 E. Canfield Avenue
Detroit, MI 48201


University of Southern California, PhD, 2009

Research Focus

My research group aims to further our understanding of the human genome by developing computational methods and statistical models that integrate large genomics 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.

Recent Publications

Wen X, Lee Y, Luca F, Pique-Regi R. Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors. Am J Hum Genet. 2016 Jun 2;98(6):1114-29. doi: 10.1016/j.ajhg.2016.03.029. Epub 2016 May 26. PubMed PMID: 27236919; PubMed Central PMCID: PMC4908152.

Johnson GD, Jodar M, Pique-Regi R, Krawetz SA. Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events. Sci Rep. 2016 May 17;6:25864. doi: 10.1038/srep25864. PubMed PMID: 27184706; PubMed Central PMCID: PMC4869110.

Moyerbrailean GA, Kalita CA, Harvey CT, Wen X, Luca F, Pique-Regi R. Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding? PLoS Genet. 2016 Feb 22;12(2):e1005875. doi: 10.1371/journal.pgen.1005875. eCollection 2016 Feb. PubMed PMID: 26901046; PubMed Central PMCID: PMC4764260.

Moyerbrailean GA, Davis GO, Harvey CT, Watza D, Wen X, Pique-Regi R, Luca F. A high-throughput RNA-seq approach to profile transcriptional responses. Sci Rep. 2015 Oct 29;5:14976. doi: 10.1038/srep14976. PubMed PMID: 26510397; PubMed Central PMCID: PMC4625130.

Pacis A, Tailleux L, Morin AM, Lambourne J, MacIsaac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai A, He C, Tung J, Pastinen T, Kobor MS, Pique-Regi R, Gilad Y, Barreiro LB. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Res. 2015 Dec;25(12):1801-11. doi: 10.1101/gr.192005.115. Epub 2015 Sep 21. PubMed PMID: 26392366; PubMed Central PMCID: PMC4665002.

Wen X, Luca F, Pique-Regi R. Cross-population joint analysis of eQTLs: fine mapping and functional annotation. PLoS Genet. 2015 Apr 23;11(4):e1005176. doi: 10.1371/journal.pgen.1005176. eCollection 2015 Apr. PubMed PMID: 25906321; PubMed Central PMCID: PMC4408026.

Harvey CT, Moyerbrailean GA, Davis GO, Wen X, Luca F, Pique-Regi R. QuASAR: quantitative allele-specific analysis of reads. Bioinformatics. 2015 Apr 15;31(8):1235-42. doi: 10.1093/bioinformatics/btu802. Epub 2014 Dec 4. PubMed PMID: 25480375; PubMed Central PMCID: PMC4393517.

Pronold M, Vali M, Pique-Regi R, Asgharzadeh S. Copy number variation signature to predict human ancestry. BMC Bioinformatics. 2012 Dec 27;13:336. doi: 10.1186/1471-2105-13-336. PubMed PMID: 23270563; PubMed Central PMCID: PMC3598683.

Asgharzadeh S, Salo JA, Ji L, Oberthuer A, Fischer M, Berthold F, Hadjidaniel M, Liu CW, Metelitsa LS, Pique-Regi R, Wakamatsu P, Villablanca JG, Kreissman SG, Matthay KK, Shimada H, London WB, Sposto R, Seeger RC. Clinical significance of tumor-associated inflammatory cells in metastatic neuroblastoma. J Clin Oncol. 2012 Oct 1;30(28):3525-32. Epub 2012 Aug 27. PubMed PMID: 22927533; PubMed Central PMCID: PMC3675667.

Zullo JM, Demarco IA, Piqué-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, Singh H. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell. 2012 Jun 22;149(7):1474-87. doi: 10.1016/j.cell.2012.04.035. PubMed PMID: 22726435.

Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature. 2012 Feb 5;482(7385):390-4. doi: 10.1038/nature10808. PubMed PMID: 22307276; PubMed Central PMCID: PMC3501342.

Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, Pritchard JK. Dissecting the regulatory architecture of gene expression QTLs. Genome Biol. 2012 Jan 31;13(1):R7. doi: 10.1186/gb-2012-13-1-r7. PubMed PMID: 22293038; PubMed Central PMCID: PMC3334587.