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MFM FELLOWSHIP FACULTY
ROGER PIQUE-REGI, Ph.D.

Wayne State University/Perinatology Research Branch - Single Cell Genomics, Roger Pique-Regi, Ph.D.Title

  • Associate Professor, Center for Molecular Medicine and Genetics,
    Department of Obstetrics and Gynecology, Wayne State University School of Medicine

Education and Training

  • B.S-M.S. in Telecomunications Engineering, Universitat Politecnica de Catalunya,
    Barcelona, Catalonia
  • Ph.D. in Electrical Engineering, University of Southern California, Los Angeles, CA
  • Postdoctoral training, University of Chicago, Human Genetics Department (JK Pritchard lab)

Research Accomplishments

  • Gene by environment interactions are enriched for association with complex traits. To demonstrate this, high-throughput functional genomic assays were combined with novel computational tools to detect differences in allele specific expression across environments.
  • Identification of gene regulatory sequences using functional genomics data.  A novel probabilistic framework, CENTIPEDE, was developed to predict tissue-specific regulatory sites for DNA-binding proteins using DNase-seq footprinting.
  • Identification of genetic variants that affect transcription factor binding which is a major mechanism by which non-coding variants affect gene expression and affect highly polygenic complex phenotypes. We developed tools to analyze and integrate DNase-QTLs, eQTLs and GWAS.
  • Development of machine learning and signal processing methods to analyze genomic datasets. Developed GADA, a method that combines a maximally sparse representation for copy number signal and sparse Bayesian learning (SBL) to reconstruct the signal from noisy observations.

Awards and Recognitions

  • "La Caixa" Fellowship for doctoral studies in United States , Fundacio La Caixa
  • "Chicago Fellows" postdoctoral scholarship, The University of Chicago
  • Young Investigator Award for attending the International Congress of Human Genetics in Montreal , ASHG
  • Top Ten Papers in Regulatory and Systems Genomics 2011, ISCB/RECOMB
  • Top Ten Papers in Regulatory and Systems Genomics 2012, ISCB/RECOMB
  • Outstanding Graduate Mentor Award in the Health Sciences, Wayne State University
  • Research Excellence Award, Wayne State University School of Medicine
  • R01- GM109215 "Functional Characterization of the Genetic and Environmental Determinants of Complex Traits" NIH-NIGMS (2014 - Present)

Research Interests

  • Analysis of functional genomics data (ATAC-seq, RNA-seq) both bulk and at single cell resolution
  • Development of computational tools and statistical genetics models
  • Molecular mechanisms regulating gene transcription, chromatin accessibility and transcription factor binding
  • Genetics of molecular traits, and gene by environment interactions
  • Precision medicine for cardiovascular disease, preterm birth and pregnancy complications.

Selected Publications

  • Pique-Regi R*, Monso-Varona J, Ortega A, Seeger RC, Triche TJ, Asgharzadeh S. Sparse representation and Bayesian detection of genome copy number alterations from microarray data. Bioinformatics. 2008 Feb 1;24(3):309-18. PubMed PMID: 18203770; PubMed Central PMCID: PMC2704547.
  • Pique-Regi R*, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 2011 Mar;21(3):447-55. PubMed PMID: 21106904; PubMed Central PMCID: PMC3044858.
  • 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. PubMed PMID: 22307276; PubMed Central PMCID: PMC3501342.
  • 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. PubMed PMID: 25906321; PubMed Central PMCID: PMC4408026.
  • 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. PubMed PMID: 26901046; PubMed Central PMCID: PMC4764260.
  • 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. PubMed PMID: 27934696; PubMed Central PMCID: PMC5131815.
  • 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. 2017 Sep 22. PubMed PMID: 29028988
  • 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. PubMed PMID: 29937373; PubMed Central PMCID: PMC6082711.
  • 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 Sep 25;PubMed PMID: 30254052.

(*) Indicates corresponding author.

Courses

  • MGG 7600 "Advanced Human Genetics"
  • MGG 7030 "Functional Genomics & Systems Biology"
  • MGG 8680 "Advanced Topics in Molecular Biology and Genetics - Single Cell Genomics"
  • MGG 7010 "Molecular Biology and Genetics"
  • MGG 8010 "Quantitative Data Analysis for Biological and Medical Sciences"
  • MGG 7010 "Molecular Biology and Genetics"