Roger Pique-Regi (fe0105)

 Assistant Professor - Center for Molecular Medicine & Genetics and Obstetrics & Gynecology (Joint)

3309 Scott Hall

Dr. Pique-Regi laboratory aims to further our understanding of the human genome by developing computational methods and statistical models that integrate large genomic datasets. They 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 their 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, they aim to tackle problems where careful analysis seems likely to yield new biological insights. They also distribute a number of programs and software packages, including CENTIPEDE (for DNase-I foot printing) and GADA (for segmentation and copy number analysis).

• Moyerbrailean GA, Richards AL, Kurtz D, Kalita CA, Davis GO, Harvey CT, Alazizi A, Watza D, Sorokin Y, Hauff N, Zhou X, Wen X, Pique-Regi R, Luca F. High-throughput allele-specific expression across 250 environmental conditions. Genome Res. 2016 Dec;26(12):1627-1638. PMID: 27934696.
• Snyder-Mackler N, Sanz J, Kohn JN, Brinkworth JF, Morrow S, Shaver AO, Grenier JC, Pique-Regi R, Johnson ZP, Wilson ME, Barreiro LB, Tung J. Social status alters immune regulation and response to infection in macaques. Science. 2016 Nov 25;354(6315):1041-1045. PMID: 27885030.
• Nédélec Y, Sanz J, Baharian G, Szpiech ZA, Pacis A, Dumaine A, Grenier JC, Freiman A, Sams AJ, Hebert S, Pagé Sabourin A, Luca F, Blekhman R, Hernandez RD, Pique-Regi R, Tung J, Yotova V, Barreiro LB. Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens. Cell. 2016 Oct 20;167(3):657-669.e21. doi: 10.1016/j.cell.2016.09.025. PMID:
  27768889.
• Richards AL, Burns MB, Alazizi A, Barreiro LB, Pique-Regi R, Blekhman R, Luca F. Genetic and transcriptional analysis of human host response to healthy gut microbiota. mSystems. 2016 Jul-Aug;1(4). pii: e00067-16. PMID: 27709125; PMCID: PMC5047527.
• 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. PMID: 27236919; 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. PMID: 27184706; 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. PMID: 26901046; 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. PMID: 26510397; 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. PMID: 26392366; 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. 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. PubMed PMID: 25480375; PubMed Central PMCID: PMC4393517.
• 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.
• 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.

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 Pique-Regi Laboratory