Roger Pique-Regi, PhD

Education

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.

Mentoring

Accepting new M.S. students in 2024-2025

Accepting new Ph.D. students in 2024-2025

Recent Publications

[Google Scholar] [ORCiD] [ResearcherID] [Scopus] [Pubmed]

Pique-Regi R, Romero R, Tarca AL, Luca F, Xu Y, Alazizi A, Leng Y, Hsu CD, Gomez-Lopez N. Does the human placenta express the canonical cell entry mediators for SARS-CoV-2?. Elife. 2020 Jul 14;9. doi: 10.7554/eLife.58716. PubMed PMID: 32662421; PubMed Central PMCID: PMC7367681.

Talreja J, Bauerfeld C, Sendler E, Pique-Regi R, Luca F, Samavati L. Derangement of Metabolic and Lysosomal Gene Profiles in Response to Dexamethasone Treatment in Sarcoidosis. Front Immunol. 2020;11:779. doi: 10.3389/fimmu.2020.00779. eCollection 2020. PubMed PMID: 32477331; PubMed Central PMCID: PMC7235403.

Hukku A, Quick C, Luca F, Pique-Regi R, Wen X. BAGSE: a Bayesian hierarchical model approach for gene set enrichment analysis. Bioinformatics. 2020 Mar 1;36(6):1689-1695. doi: 10.1093/bioinformatics/btz831. PubMed PMID: 31702789; PubMed Central PMCID: PMC7523653.

Tarca AL, Romero R, Pique-Regi R, Pacora P, Done B, Kacerovsky M, Bhatti G, Jaiman S, Hassan SS, Hsu CD, Gomez-Lopez N. Amniotic fluid cell-free transcriptome: a glimpse into fetal development and placental cellular dynamics during normal pregnancy. BMC Med Genomics. 2020 Feb 12;13(1):25. doi: 10.1186/s12920-020-0690-5. PubMed PMID: 32050959; PubMed Central PMCID: PMC7017452.

Liu Z, Zhang Y, Graham S, Wang X, Cai D, Huang M, Pique-Regi R, Dong XC, Chen YE, Willer C, Liu W. Causal relationships between NAFLD, T2D and obesity have implications for disease subphenotyping. J Hepatol. 2020 Aug;73(2):263-276. doi: 10.1016/j.jhep.2020.03.006. Epub 2020 Mar 10. PubMed PMID: 32165250; PubMed Central PMCID: PMC7371536.

Pique-Regi R, Romero R, Tarca AL, Sendler ED, Xu Y, Garcia-Flores V, Leng Y, Luca F, Hassan SS, Gomez-Lopez N. Single cell transcriptional signatures of the human placenta in term and preterm parturition. Elife. 2019 Dec 12;8. doi: 10.7554/eLife.52004. PubMed PMID: 31829938; PubMed Central PMCID: PMC6949028.

Sakhtemani R, Senevirathne V, Stewart J, Perera MLW, Pique-Regi R, Lawrence MS, Bhagwat AS. Genome-wide mapping of regions preferentially targeted by the human DNA-cytosine deaminase APOBEC3A using uracil-DNA pulldown and sequencing. J Biol Chem. 2019 Oct 11;294(41):15037-15051. doi: 10.1074/jbc.RA119.008053. Epub 2019 Aug 19. PubMed PMID: 31431505; PubMed Central PMCID: PMC6791317.

Findley AS, Richards AL, Petrini C, Alazizi A, Doman E, Shanku AG, Davis GO, Hauff N, Sorokin Y, Wen X, Pique-Regi R, Luca F. Interpreting Coronary Artery Disease Risk Through Gene-Environment Interactions in Gene Regulation. Genetics. 2019 Oct;213(2):651-663. doi: 10.1534/genetics.119.302419. Epub 2019 Sep 6. PubMed PMID: 31492806; PubMed Central PMCID: PMC6781890.

Richards AL, Muehlbauer AL, Alazizi A, Burns MB, Findley A, Messina F, Gould TJ, Cascardo C, Pique-Regi R, Blekhman R, Luca F. Gut Microbiota Has a Widespread and Modifiable Effect on Host Gene Regulation. mSystems. 2019 Sep 3;4(5). doi: 10.1128/mSystems.00323-18. PubMed PMID: 31481602; PubMed Central PMCID: PMC6722422.

Saad MH, Rumschlag M, Guerra MH, Savonen CL, Jaster AM, Olson PD, Alazizi A, Luca F, Pique-Regi R, Schmidt CJ, Bannon MJ. Differentially expressed gene networks, biomarkers, long noncoding RNAs, and shared responses with cocaine identified in the midbrains of human opioid abusers. Sci Rep. 2019 Feb 7;9(1):1534. doi: 10.1038/s41598-018-38209-8. PubMed PMID: 30733491; PubMed Central PMCID: PMC6367337.

Snyder-Mackler N, Sanz J, Kohn JN, Voyles T, Pique-Regi R, Wilson ME, Barreiro LB, Tung J. Social status alters chromatin accessibility and the gene regulatory response to glucocorticoid stimulation in rhesus macaques. Proc Natl Acad Sci U S A. 2019 Jan 22;116(4):1219-1228. doi: 10.1073/pnas.1811758115. Epub 2018 Dec 11. PubMed PMID: 30538209; PubMed Central PMCID: PMC6347725.

Kalita CA, Brown CD, Freiman A, Isherwood J, Wen X, Pique-Regi R, Luca F. High-throughput characterization of genetic effects on DNA-protein binding and gene transcription. Genome Res. 2018 Nov;28(11):1701-1708. doi: 10.1101/gr.237354.118. Epub 2018 Sep 25. PubMed PMID: 30254052; PubMed Central PMCID: PMC6211638.

Qu W, Gurdziel K, Pique-Regi R, Ruden DM. Lead Modulates trans- and cis-Expression Quantitative Trait Loci (eQTLs) in Drosophila melanogaster Heads. Front Genet. 2018;9:395. doi: 10.3389/fgene.2018.00395. eCollection 2018. PubMed PMID: 30294342; PubMed Central PMCID: PMC6158337.

Burl RB, Ramseyer VD, Rondini EA, Pique-Regi R, Lee YH, Granneman JG. Deconstructing Adipogenesis Induced by β3-Adrenergic Receptor Activation with Single-Cell Expression Profiling. Cell Metab. 2018 Aug 7;28(2):300-309.e4. doi: 10.1016/j.cmet.2018.05.025. Epub 2018 Jun 21. PubMed PMID: 29937373; PubMed Central PMCID: PMC6082711.

Lacher SE, Alazizi A, Wang X, Bell DA, Pique-Regi R, Luca F, Slattery M. A hypermorphic antioxidant response element is associated with increased MS4A6A expression and Alzheimer's disease. Redox Biol. 2018 Apr;14:686-693. doi: 10.1016/j.redox.2017.10.018. Epub 2017 Oct 27. PubMed PMID: 29179108; PubMed Central PMCID: PMC5705802.

Kalita CA, Moyerbrailean GA, Brown C, Wen X, Luca F, Pique-Regi R. QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays. Bioinformatics. 2018 Mar 1;34(5):787-794. doi: 10.1093/bioinformatics/btx598. PubMed PMID: 29028988; PubMed Central PMCID: PMC6049023.

Sen A, Gurdziel K, Liu J, Qu W, Nuga OO, Burl RB, Hüttemann M, Pique-Regi R, Ruden DM. Smooth, an hnRNP-L Homolog, Might Decrease Mitochondrial Metabolism by Post-Transcriptional Regulation of Isocitrate Dehydrogenase (Idh) and Other Metabolic Genes in the Sub-Acute Phase of Traumatic Brain Injury. Front Genet. 2017;8:175. doi: 10.3389/fgene.2017.00175. eCollection 2017. PubMed PMID: 29187863; PubMed Central PMCID: PMC5694756.

Qu W, Gurdziel K, Pique-Regi R, Ruden DM. Identification of Splicing Quantitative Trait Loci (sQTL) in Drosophila melanogaster with Developmental Lead (Pb2+) Exposure. Front Genet. 2017;8:145. doi: 10.3389/fgene.2017.00145. eCollection 2017. PubMed PMID: 29114259; PubMed Central PMCID: PMC5660682.

Richards AL, Watza D, Findley A, Alazizi A, Wen X, Pai AA, Pique-Regi R, Luca F. Environmental perturbations lead to extensive directional shifts in RNA processing. PLoS Genet. 2017 Oct;13(10):e1006995. doi: 10.1371/journal.pgen.1006995. eCollection 2017 Oct. PubMed PMID: 29023442; PubMed Central PMCID: PMC5667937.

Talreja J, Farshi P, Alazizi A, Luca F, Pique-Regi R, Samavati L. RNA-sequencing Identifies Novel Pathways in Sarcoidosis Monocytes. Sci Rep. 2017 Jun 2;7(1):2720. doi: 10.1038/s41598-017-02941-4. PubMed PMID: 28577019; PubMed Central PMCID: PMC5457404.

Wen X, Pique-Regi R, Luca F. Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization. PLoS Genet. 2017 Mar;13(3):e1006646. doi: 10.1371/journal.pgen.1006646. eCollection 2017 Mar. PubMed PMID: 28278150; PubMed Central PMCID: PMC5363995.

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. doi: 10.1101/gr.209759.116. Epub 2016 Oct 19. PubMed PMID: 27934696; PubMed Central PMCID: PMC5131815.

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. doi: 10.1126/science.aah3580. PubMed PMID: 27885030; PubMed Central PMCID: PMC5498102.

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. PubMed 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). doi: 10.1128/mSystems.00067-16. Epub 2016 Aug 30. PubMed PMID: 27709125; PubMed Central 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):1114-1129. 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;12(2):e1005875. doi: 10.1371/journal.pgen.1005875. eCollection 2016 Feb. PubMed PMID: 26901046; PubMed Central PMCID: PMC4764260.

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.

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.

Wen X, Luca F, Pique-Regi R. Cross-population joint analysis of eQTLs: fine mapping and functional annotation. PLoS Genet. 2015 Apr;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.