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Items: 35

1.

Deconstructing Adipogenesis Induced by β3-Adrenergic Receptor Activation with Single-Cell Expression Profiling.

Burl RB, Ramseyer VD, Rondini EA, Pique-Regi R, Lee YH, Granneman JG.

Cell Metab. 2018 Aug 7;28(2):300-309.e4. doi: 10.1016/j.cmet.2018.05.025. Epub 2018 Jun 21.

PMID:
29937373
2.

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.

Sen A, Gurdziel K, Liu J, Qu W, Nuga OO, Burl RB, Hüttemann M, Pique-Regi R, Ruden DM.

Front Genet. 2017 Nov 15;8:175. doi: 10.3389/fgene.2017.00175. eCollection 2017.

3.

A hypermorphic antioxidant response element is associated with increased MS4A6A expression and Alzheimer's disease.

Lacher SE, Alazizi A, Wang X, Bell DA, Pique-Regi R, Luca F, Slattery M.

Redox Biol. 2018 Apr;14:686-693. doi: 10.1016/j.redox.2017.10.018. Epub 2017 Oct 27.

4.

Identification of Splicing Quantitative Trait Loci (sQTL) in Drosophila melanogaster with Developmental Lead (Pb2+) Exposure.

Qu W, Gurdziel K, Pique-Regi R, Ruden DM.

Front Genet. 2017 Oct 24;8:145. doi: 10.3389/fgene.2017.00145. eCollection 2017.

5.

QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays.

Kalita CA, Moyerbrailean GA, Brown C, Wen X, Luca F, Pique-Regi R.

Bioinformatics. 2018 Mar 1;34(5):787-794. doi: 10.1093/bioinformatics/btx598.

PMID:
29028988
6.

Environmental perturbations lead to extensive directional shifts in RNA processing.

Richards AL, Watza D, Findley A, Alazizi A, Wen X, Pai AA, Pique-Regi R, Luca F.

PLoS Genet. 2017 Oct 12;13(10):e1006995. doi: 10.1371/journal.pgen.1006995. eCollection 2017 Oct.

7.

RNA-sequencing Identifies Novel Pathways in Sarcoidosis Monocytes.

Talreja J, Farshi P, Alazizi A, Luca F, Pique-Regi R, Samavati L.

Sci Rep. 2017 Jun 2;7(1):2720. doi: 10.1038/s41598-017-02941-4.

8.

Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization.

Wen X, Pique-Regi R, Luca F.

PLoS Genet. 2017 Mar 9;13(3):e1006646. doi: 10.1371/journal.pgen.1006646. eCollection 2017 Mar.

9.

High-throughput allele-specific expression across 250 environmental conditions.

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.

Genome Res. 2016 Dec;26(12):1627-1638. Epub 2016 Oct 19.

10.

Social status alters immune regulation and response to infection in macaques.

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.

Science. 2016 Nov 25;354(6315):1041-1045.

11.

Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens.

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.

Cell. 2016 Oct 20;167(3):657-669.e21. doi: 10.1016/j.cell.2016.09.025.

12.

Genetic and transcriptional analysis of human host response to healthy gut microbiota.

Richards AL, Burns MB, Alazizi A, Barreiro LB, Pique-Regi R, Blekhman R, Luca F.

mSystems. 2016 Jul-Aug;1(4). pii: e00067-16. Epub 2016 Aug 30.

13.

Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors.

Wen X, Lee Y, Luca F, Pique-Regi R.

Am J Hum Genet. 2016 Jun 2;98(6):1114-1129. doi: 10.1016/j.ajhg.2016.03.029. Epub 2016 May 26.

14.

Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events.

Johnson GD, Jodar M, Pique-Regi R, Krawetz SA.

Sci Rep. 2016 May 17;6:25864. doi: 10.1038/srep25864.

15.

Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding?

Moyerbrailean GA, Kalita CA, Harvey CT, Wen X, Luca F, Pique-Regi R.

PLoS Genet. 2016 Feb 22;12(2):e1005875. doi: 10.1371/journal.pgen.1005875. eCollection 2016 Feb.

16.

A high-throughput RNA-seq approach to profile transcriptional responses.

Moyerbrailean GA, Davis GO, Harvey CT, Watza D, Wen X, Pique-Regi R, Luca F.

Sci Rep. 2015 Oct 29;5:14976. doi: 10.1038/srep14976.

17.

Bacterial infection remodels the DNA methylation landscape of human dendritic cells.

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.

Genome Res. 2015 Dec;25(12):1801-11. doi: 10.1101/gr.192005.115. Epub 2015 Sep 21.

18.

Cross-population joint analysis of eQTLs: fine mapping and functional annotation.

Wen X, Luca F, Pique-Regi R.

PLoS Genet. 2015 Apr 23;11(4):e1005176. doi: 10.1371/journal.pgen.1005176. eCollection 2015 Apr.

19.

QuASAR: quantitative allele-specific analysis of reads.

Harvey CT, Moyerbrailean GA, Davis GO, Wen X, Luca F, Pique-Regi R.

Bioinformatics. 2015 Apr 15;31(8):1235-42. doi: 10.1093/bioinformatics/btu802. Epub 2014 Dec 4.

20.

Copy number variation signature to predict human ancestry.

Pronold M, Vali M, Pique-Regi R, Asgharzadeh S.

BMC Bioinformatics. 2012 Dec 27;13:336. doi: 10.1186/1471-2105-13-336.

21.

Clinical significance of tumor-associated inflammatory cells in metastatic neuroblastoma.

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.

J Clin Oncol. 2012 Oct 1;30(28):3525-32. Epub 2012 Aug 27.

22.

DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina.

Zullo JM, Demarco IA, Piqué-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, Singh H.

Cell. 2012 Jun 22;149(7):1474-87. doi: 10.1016/j.cell.2012.04.035.

23.

DNase I sensitivity QTLs are a major determinant of human expression variation.

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.

Nature. 2012 Feb 5;482(7385):390-4. doi: 10.1038/nature10808.

24.

Dissecting the regulatory architecture of gene expression QTLs.

Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, Pritchard JK.

Genome Biol. 2012 Jan 31;13(1):R7. doi: 10.1186/gb-2012-13-1-r7.

25.

A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data.

González JR, Rodríguez-Santiago B, Cáceres A, Pique-Regi R, Rothman N, Chanock SJ, Armengol L, Pérez-Jurado LA.

BMC Bioinformatics. 2011 May 17;12:166. doi: 10.1186/1471-2105-12-166.

26.

Bioinformatics for copy number variation data.

Warden M, Pique-Regi R, Ortega A, Asgharzadeh S.

Methods Mol Biol. 2011;719:235-49. doi: 10.1007/978-1-61779-027-0_11.

PMID:
21370087
27.

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines.

Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK.

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.

28.

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.

Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK.

Genome Res. 2011 Mar;21(3):447-55. doi: 10.1101/gr.112623.110. Epub 2010 Nov 24.

29.

R-Gada: a fast and flexible pipeline for copy number analysis in association studies.

Pique-Regi R, Cáceres A, González JR.

BMC Bioinformatics. 2010 Jul 16;11:380. doi: 10.1186/1471-2105-11-380.

30.

Copy number variation in the Framingham Heart Study.

Shtir C, Pique-Regi R, Siegmund K, Morrison J, Schumacher F, Marjoram P.

BMC Proc. 2009 Dec 15;3 Suppl 7:S133.

31.

Joint estimation of copy number variation and reference intensities on multiple DNA arrays using GADA.

Pique-Regi R, Ortega A, Asgharzadeh S.

Bioinformatics. 2009 May 15;25(10):1223-30. doi: 10.1093/bioinformatics/btp119. Epub 2009 Mar 10.

32.

Bayesian hierarchical modeling of means and covariances of gene expression data within families.

Pique-Regi R, Morrison J, Thomas DC.

BMC Proc. 2007;1 Suppl 1:S111. Epub 2007 Dec 18.

33.

Sparse representation and Bayesian detection of genome copy number alterations from microarray data.

Pique-Regi R, Monso-Varona J, Ortega A, Seeger RC, Triche TJ, Asgharzadeh S.

Bioinformatics. 2008 Feb 1;24(3):309-18. doi: 10.1093/bioinformatics/btm601. Epub 2008 Jan 18.

34.

Model selection and Bayesian methods in statistical genetics: summary of group 11 contributions to Genetic Analysis Workshop 15.

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.

Genet Epidemiol. 2007;31 Suppl 1:S96-102. Review.

PMID:
18046760
35.

Prognostic significance of gene expression profiles of metastatic neuroblastomas lacking MYCN gene amplification.

Asgharzadeh S, Pique-Regi R, Sposto R, Wang H, Yang Y, Shimada H, Matthay K, Buckley J, Ortega A, Seeger RC.

J Natl Cancer Inst. 2006 Sep 6;98(17):1193-203.

PMID:
16954472

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