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Roger Pique-Regi, Ph.D. - Publications

Affiliations: 
2003-2009 Electrical Engineering University of Southern California, Los Angeles, CA, United States 
 2009-2012 Human Genetics University of Chicago, Chicago, IL 
 2012- Center for Molecular Medicine and Genetics Wayne State University, Detroit, MI, United States 
Area:
Computational Biology, Genetics, Genomics, Electronics and Electrical Engineering, Bioinformatics
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65 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Aracena KA, Lin YL, Luo K, Pacis A, Gona S, Mu Z, Yotova V, Sindeaux R, Pramatarova A, Simon MM, Chen X, Groza C, Lougheed D, Gregoire R, Brownlee D, ... ... Pique-Regi R, et al. Epigenetic variation impacts individual differences in the transcriptional response to influenza infection. Nature Genetics. PMID 38424460 DOI: 10.1038/s41588-024-01668-z  0.437
2024 Boye C, Kalita CA, Findley AS, Alazizi A, Wei J, Wen X, Pique-Regi R, Luca F. Characterization of caffeine response regulatory variants in vascular endothelial cells. Elife. 13. PMID 38334359 DOI: 10.7554/eLife.85235  0.465
2023 Wei J, Lambert TY, Valada A, Patel N, Walker K, Lenders J, Schmidt CJ, Iskhakova M, Alazizi A, Mair-Meijers H, Mash DC, Luca F, Pique-Regi R, Bannon MJ, Akbarian S. Single nucleus transcriptomics of ventral midbrain identifies glial activation associated with chronic opioid use disorder. Nature Communications. 14: 5610. PMID 37699936 DOI: 10.1038/s41467-023-41455-8  0.691
2023 Aquino Y, Bisiaux A, Li Z, O'Neill M, Mendoza-Revilla J, Merkling SH, Kerner G, Hasan M, Libri V, Bondet V, Smith N, de Cevins C, Ménager M, Luca F, Pique-Regi R, et al. Dissecting human population variation in single-cell responses to SARS-CoV-2. Nature. PMID 37558883 DOI: 10.1038/s41586-023-06422-9  0.679
2023 Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-Meijers HE, Wu P, Wen X, Slatcher RB, Zhou X, Luca F, Pique-Regi R. Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution. Genome Research. PMID 37442575 DOI: 10.1101/gr.276765.122  0.731
2023 Wei J, Lambert TY, Valada A, Patel N, Walker K, Lenders J, Schmidt CJ, Iskhakova M, Alazizi A, Mair-Meijers H, Mash DC, Luca F, Pique-Regi R, Bannon MJ, Akbarian S. Single Nucleus Transcriptomics Reveals Pervasive Glial Activation in Opioid Overdose Cases. Biorxiv : the Preprint Server For Biology. PMID 36945611 DOI: 10.1101/2023.03.07.531400  0.686
2023 Resztak JA, Choe J, Nirmalan S, Wei J, Bruinsma J, Houpt R, Alazizi A, Mair-Meijers HE, Wen X, Slatcher RB, Zilioli S, Pique-Regi R, Luca F. Analysis of transcriptional changes in the immune system associated with pubertal development in a longitudinal cohort of children with asthma. Nature Communications. 14: 230. PMID 36646693 DOI: 10.1038/s41467-022-35742-z  0.702
2023 Okamoto J, Wang L, Yin X, Luca F, Pique-Regi R, Helms A, Im HK, Morrison J, Wen X. Probabilistic integration of transcriptome-wide association studies and colocalization analysis identifies key molecular pathways of complex traits. American Journal of Human Genetics. 110: 44-57. PMID 36608684 DOI: 10.1016/j.ajhg.2022.12.002  0.725
2022 Hukku A, Sampson MG, Luca F, Pique-Regi R, Wen X. Analyzing and reconciling colocalization and transcriptome-wide association studies from the perspective of inferential reproducibility. American Journal of Human Genetics. 109: 825-837. PMID 35523146 DOI: 10.1016/j.ajhg.2022.04.005  0.721
2022 Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-Meijers HE, Wu P, Slatcher RB, Zhou X, Luca F, Pique-Regi R. Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution. Biorxiv : the Preprint Server For Biology. PMID 35313584 DOI: 10.1101/2021.09.30.462672  0.731
2021 Muehlbauer AL, Richards AL, Alazizi A, Burns MB, Gomez A, Clayton JB, Petrzelkova K, Cascardo C, Resztak J, Wen X, Pique-Regi R, Luca F, Blekhman R. Interspecies variation in hominid gut microbiota controls host gene regulation. Cell Reports. 37: 110057. PMID 34818542 DOI: 10.1016/j.celrep.2021.110057  0.795
2021 Findley AS, Zhang X, Boye C, Lin YL, Kalita CA, Barreiro L, Lohmueller KE, Pique-Regi R, Luca F. A signature of Neanderthal introgression on molecular mechanisms of environmental responses. Plos Genetics. 17: e1009493. PMID 34570765 DOI: 10.1371/journal.pgen.1009493  0.836
2021 Resztak JA, Farrell AK, Mair-Meijers H, Alazizi A, Wen X, Wildman DE, Zilioli S, Slatcher RB, Pique-Regi R, Luca F. Psychosocial experiences modulate asthma-associated genes through gene-environment interactions. Elife. 10. PMID 34142656 DOI: 10.7554/eLife.63852  0.693
2021 Findley AS, Monziani A, Richards AL, Rhodes K, Ward MC, Kalita CA, Alazizi A, Pazokitoroudi A, Sankararaman S, Wen X, Lanfear DE, Pique-Regi R, Gilad Y, Luca F. Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions. Elife. 10. PMID 33988505 DOI: 10.7554/eLife.67077  0.829
2020 Hukku A, Pividori M, Luca F, Pique-Regi R, Im HK, Wen X. Probabilistic colocalization of genetic variants from complex and molecular traits: promise and limitations. American Journal of Human Genetics. PMID 33308443 DOI: 10.1016/j.ajhg.2020.11.012  0.692
2020 Zhang Y, Quick C, Yu K, Barbeira A, Luca F, Pique-Regi R, Kyung Im H, Wen X. PTWAS: investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis. Genome Biology. 21: 232. PMID 32912253 DOI: 10.1186/S13059-020-02026-Y  0.724
2020 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. 9. PMID 32662421 DOI: 10.7554/Elife.58716  0.636
2020 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. Frontiers in Immunology. 11: 779. PMID 32477331 DOI: 10.3389/Fimmu.2020.00779  0.7
2019 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. 8. PMID 31829938 DOI: 10.7554/Elife.52004  0.649
2019 Hukku A, Quick C, Luca F, Pique-Regi R, Wen X. BAGSE: A Bayesian Hierarchical Model Approach for Gene Set Enrichment Analysis. Bioinformatics (Oxford, England). PMID 31702789 DOI: 10.1093/Bioinformatics/Btz831  0.72
2019 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. PMID 31492806 DOI: 10.1534/Genetics.119.302419  0.806
2019 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. 4. PMID 31481602 DOI: 10.1128/mSystems.00323-18  0.822
2019 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. The Journal of Biological Chemistry. PMID 31431505 DOI: 10.1074/Jbc.Ra119.008053  0.408
2019 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. Scientific Reports. 9: 1534. PMID 30733491 DOI: 10.1038/S41598-018-38209-8  0.684
2018 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. Proceedings of the National Academy of Sciences of the United States of America. PMID 30538209 DOI: 10.1073/Pnas.1811758115  0.383
2018 Qu W, Gurdziel K, Pique-Regi R, Ruden DM. Lead Modulates and Expression Quantitative Trait Loci (eQTLs) in Heads. Frontiers in Genetics. 9: 395. PMID 30294342 DOI: 10.3389/Fgene.2018.00395  0.536
2018 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 Research. PMID 30254052 DOI: 10.1101/Gr.237354.118  0.82
2018 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 Metabolism. PMID 29937373 DOI: 10.1016/J.Cmet.2018.05.025  0.343
2018 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 Biology. 14: 686-693. PMID 29179108 DOI: 10.1016/J.Redox.2017.10.018  0.711
2017 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. Frontiers in Genetics. 8: 175. PMID 29187863 DOI: 10.3389/Fgene.2017.00175  0.371
2017 Qu W, Gurdziel K, Pique-Regi R, Ruden DM. Identification of Splicing Quantitative Trait Loci (sQTL) in Drosophila melanogaster with Developmental Lead (Pb(2+)) Exposure. Frontiers in Genetics. 8: 145. PMID 29114259 DOI: 10.3389/Fgene.2017.00145  0.552
2017 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 (Oxford, England). PMID 29028988 DOI: 10.1093/Bioinformatics/Btx598  0.799
2017 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 Genetics. 13: e1006995. PMID 29023442 DOI: 10.1371/Journal.Pgen.1006995  0.813
2017 Talreja J, Farshi P, Alazizi A, Luca F, Pique-Regi R, Samavati L. RNA-sequencing Identifies Novel Pathways in Sarcoidosis Monocytes. Scientific Reports. 7: 2720. PMID 28577019 DOI: 10.1038/S41598-017-02941-4  0.732
2017 Wen X, Pique-Regi R, Luca F. Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization. Plos Genetics. 13: e1006646. PMID 28278150 DOI: 10.1371/Journal.Pgen.1006646  0.709
2016 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 Research. 26: 1627-1638. PMID 27934696 DOI: 10.1101/Gr.209759.116  0.8
2016 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 (New York, N.Y.). 354: 1041-1045. PMID 27885030 DOI: 10.1126/Science.Aah3580  0.348
2016 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, et al. Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens. Cell. 167: 657-669.e21. PMID 27768889 DOI: 10.1016/J.Cell.2016.09.025  0.726
2016 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. 1. PMID 27709125 DOI: 10.1128/mSystems.00067-16  0.818
2016 Wen X, Lee Y, Luca F, Pique-Regi R. Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors. American Journal of Human Genetics. PMID 27236919 DOI: 10.1016/J.Ajhg.2016.03.029  0.716
2016 Johnson GD, Jodar M, Pique-Regi R, Krawetz SA. Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events. Scientific Reports. 6: 25864. PMID 27184706 DOI: 10.1038/Srep25864  0.386
2016 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 Genetics. 12: e1005875. PMID 26901046 DOI: 10.1371/Journal.Pgen.1005875  0.784
2015 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. Scientific Reports. 5: 14976. PMID 26510397 DOI: 10.1038/Srep14976  0.788
2015 Pacis A, Tailleux L, Morin AM, Lambourne J, Maclsaac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai A, He C, ... ... Pique-Regi R, et al. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Research. PMID 26392366 DOI: 10.1101/Gr.192005.115  0.685
2015 Wen X, Luca F, Pique-Regi R. Cross-population joint analysis of eQTLs: fine mapping and functional annotation. Plos Genetics. 11: e1005176. PMID 25906321 DOI: 10.1371/Journal.Pgen.1005176  0.711
2015 Harvey CT, Moyerbrailean GA, Davis GO, Wen X, Luca F, Pique-Regi R. QuASAR: quantitative allele-specific analysis of reads. Bioinformatics (Oxford, England). 31: 1235-42. PMID 25480375 DOI: 10.1093/Bioinformatics/Btu802  0.822
2012 Pronold M, Vali M, Pique-Regi R, Asgharzadeh S. Copy number variation signature to predict human ancestry. Bmc Bioinformatics. 13: 336. PMID 23270563 DOI: 10.1186/1471-2105-13-336  0.414
2012 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, et al. Clinical significance of tumor-associated inflammatory cells in metastatic neuroblastoma. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 30: 3525-32. PMID 22927533 DOI: 10.1200/Jco.2011.40.9169  0.331
2012 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. 149: 1474-87. PMID 22726435 DOI: 10.1016/J.Cell.2012.04.035  0.613
2012 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. 482: 390-4. PMID 22307276 DOI: 10.1038/Nature10808  0.852
2012 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 Biology. 13: R7. PMID 22293038 DOI: 10.1186/Gb-2012-13-1-R7  0.833
2012 Pique-Regi R, Ortega A, Tewfik A, Asgharzadeh S. Detecting changes in DNA copy number: Reviewing signal processing techniques Ieee Signal Processing Magazine. 29: 98-107. DOI: 10.1109/Msp.2011.943010  0.486
2011 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. 12: 166. PMID 21586113 DOI: 10.1186/1471-2105-12-166  0.417
2011 Warden M, Pique-Regi R, Ortega A, Asgharzadeh S. Bioinformatics for copy number variation data. Methods in Molecular Biology (Clifton, N.J.). 719: 235-49. PMID 21370087 DOI: 10.1007/978-1-61779-027-0_11  0.579
2011 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 Biology. 12: R10. PMID 21251332 DOI: 10.1186/Gb-2011-12-1-R10  0.812
2011 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 Research. 21: 447-55. PMID 21106904 DOI: 10.1101/Gr.112623.110  0.822
2011 Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK. Correction: DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines Genome Biology. 12. DOI: 10.1186/Gb-2011-12-6-405  0.799
2010 Pique-Regi R, Cáceres A, González JR. R-Gada: a fast and flexible pipeline for copy number analysis in association studies. Bmc Bioinformatics. 11: 380. PMID 20637081 DOI: 10.1186/1471-2105-11-380  0.434
2009 Shtir C, Pique-Regi R, Siegmund K, Morrison J, Schumacher F, Marjoram P. Copy number variation in the Framingham Heart Study. Bmc Proceedings. 3: S133. PMID 20018000 DOI: 10.1186/1753-6561-3-S7-S133  0.342
2009 Pique-Regi R, Ortega A, Asgharzadeh S. Joint estimation of copy number variation and reference intensities on multiple DNA arrays using GADA. Bioinformatics (Oxford, England). 25: 1223-30. PMID 19276152 DOI: 10.1093/Bioinformatics/Btp119  0.541
2009 Sheng L, Ortega A, Pique-Regi R, Asgharzadeh S. Treelets as feature transformation tool for block diagonal linear discrimination 2009 Ieee International Workshop On Genomic Signal Processing and Statistics, Gensips 2009. DOI: 10.1109/GENSIPS.2009.5174361  0.428
2008 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 (Oxford, England). 24: 309-18. PMID 18203770 DOI: 10.1093/Bioinformatics/Btm601  0.555
2007 Pique-Regi R, Morrison J, Thomas DC. Bayesian hierarchical modeling of means and covariances of gene expression data within families. Bmc Proceedings. 1: S111. PMID 18466452 DOI: 10.1186/1753-6561-1-S1-S111  0.483
2006 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. Journal of the National Cancer Institute. 98: 1193-203. PMID 16954472 DOI: 10.1093/Jnci/Djj330  0.701
2005 Pique-Regi R, Ortega A, Asgharzadeh S. Sequential Diagonal Linear Discriminant Analysis (SeqDLDA) for microarray classification and gene identification 2005 Ieee Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. 112-113. DOI: 10.1109/CSBW.2005.124  0.539
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