Publications

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  • 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.
  • 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. PubMed 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. 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). pii: e00067-16. 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):1114-29. 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.
  • 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 May 17;12:166. doi: 10.1186/1471-2105-12-166. PubMed PMID: 21586113; PubMed Central PMCID: PMC3118168.
  • Warden M, Pique-Regi R, Ortega A, Asgharzadeh S. Bioinformatics for copy number variation data. Methods Mol Biol. 2011;719:235-49. doi: 10.1007/978-1-61779-027-0_11. PubMed PMID: 21370087.
  • Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 2011;12(1):R10. doi: 10.1186/gb-2011-12-1-r10. Epub 2011 Jan 20. Erratum in: Genome Biol. 2011;12(6):405. PubMed PMID: 21251332; PubMed Central PMCID: PMC3091299.
  • 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. doi: 10.1101/gr.112623.110. Epub 2010 Nov 24. PubMed PMID: 21106904; PubMed Central PMCID: PMC3044858.
  • Pique-Regi R, Cáceres A, González JR. R-Gada: a fast and flexible pipeline for copy number analysis in association studies. BMC Bioinformatics. 2010 Jul 16;11:380. doi: 10.1186/1471-2105-11-380. PubMed PMID: 20637081; PubMed Central PMCID: PMC2915992.
  • Shtir C, Pique-Regi R, Siegmund K, Morrison J, Schumacher F, Marjoram P. Copy number variation in the Framingham Heart Study. BMC Proc. 2009 Dec 15;3 Suppl 7:S133. PubMed PMID: 20018000; PubMed Central PMCID: PMC2795907.
  • Pique-Regi R, Ortega A, Asgharzadeh S. Joint estimation of copy number variation and reference intensities on multiple DNA arrays using GADA. Bioinformatics. 2009 May 15;25(10):1223-30. doi: 10.1093/bioinformatics/btp119. Epub 2009 Mar 10. PubMed PMID: 19276152; PubMed Central PMCID: PMC2732310.
  • Pique-Regi R, Morrison J, Thomas DC. Bayesian hierarchical modeling of means and covariances of gene expression data within families. BMC Proc. 2007;1 Suppl 1:S111. Epub 2007 Dec 18. PubMed PMID: 18466452; PubMed Central PMCID: PMC2367475.
  • 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. doi: 10.1093/bioinformatics/btm601. Epub 2008 Jan 18. PubMed PMID: 18203770; PubMed Central PMCID: PMC2704547.
  • Swartz MD, Thomas DC, Daw EW, Albers K, Charlesworth JC, Dyer TC, Fridley BL, Govil M, Kraft P, Kwon S, Logue MW, Oh C, Pique-Regi R, Saba L, Schumacher FR, Uh HW. Model selection and Bayesian methods in statistical genetics: summary of group 11 contributions to Genetic Analysis Workshop 15. Genet Epidemiol. 2007;31 Suppl 1:S96-102. Review. PubMed PMID: 18046760.
  • 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 Sep 6;98(17):1193-203. PubMed PMID: 16954472.