pubtest

@article{asgharzadeh2006prognostic,
title={Prognostic significance of gene expression profiles of metastatic neuroblastomas lacking MYCN gene amplification},
author={Asgharzadeh, Shahab and Pique-Regi, Roger and Sposto, Richard and Wang, Hong and Yang, Yujun and Shimada, Hiroyuki and Matthay, Katherine and Buckley, Jonathan and Ortega, Antonio and Seeger, Robert C},
journal={Journal of the National Cancer Institute},
volume={98},
number={17},
pages={1193–1203},
year={2006},
publisher={Oxford University Press}
}

@article{pique2008sparse,
title={Sparse representation and Bayesian detection of genome copy number alterations from microarray data},
author={Pique-Regi, Roger and Monso-Varona, Jordi and Ortega, Antonio and Seeger, Robert C and Triche, Timothy J and Asgharzadeh, Shahab},
journal={Bioinformatics},
volume={24},
number={3},
pages={309–318},
year={2008},
publisher={Oxford Univ Press}
}

@inproceedings{pique2007wavelet,
title={Wavelet footprints and sparse Bayesian learning for DNA copy number change analysis},
author={Pique-Regi, Roger and Tsau, En-Shuo and Ortega, Antonio and Seeger, Robert and Asgharzadeh, Shahab},
booktitle={Acoustics, Speech and Signal Processing, 2007. ICASSP 2007. IEEE International Conference on},
volume={1},
pages={I–353},
year={2007},
organization={IEEE}
}

@article{pique2009joint,
title={Joint estimation of copy number variation and reference intensities on multiple DNA arrays using GADA},
author={Pique-Regi, Roger and Ortega, Antonio and Asgharzadeh, Shahab},
journal={Bioinformatics},
volume={25},
number={10},
pages={1223–1230},
year={2009},
publisher={Oxford University Press}
}

@article{pique2011accurate,
title={Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data},
author={Pique-Regi, Roger and Degner, Jacob F and Pai, Athma A and Gaffney, Daniel J and Gilad, Yoav and Pritchard, Jonathan K},
journal={Genome research},
volume={21},
number={3},
pages={447–455},
year={2011},
publisher={Cold Spring Harbor Lab}
}

@inproceedings{pique2005sequential,
title={Sequential diagonal linear discriminant analysis (seqdlda) for microarray classification and gene identification},
author={Pique-Regi, Roger and Ortega, Antonio and Asgharzadeh, Shahab},
booktitle={Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts. IEEE},
pages={112–113},
year={2005},
organization={IEEE}
}

@inproceedings{pique2006block,
title={Block diagonal linear discriminant analysis with sequential embedded feature selection},
author={Pique-Regi, Roger and Ortega, Antonio},
booktitle={Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on},
volume={5},
pages={V–V},
year={2006},
organization={IEEE}
}

@article{bell2011dna,
title={DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines},
author={Bell, Jordana T and Pai, Athma A and Pickrell, Joseph K and Gaffney, Daniel J and Pique-Regi, Roger and Degner, Jacob F and Gilad, Yoav and Pritchard, Jonathan K},
journal={Genome biology},
volume={12},
number={1},
pages={R10},
year={2011},
publisher={BioMed Central}
}

@inproceedings{sheng2009microarray,
title={Microarray classification using block diagonal linear discriminant analysis with embedded feature selection},
author={Sheng, Lingyan and Pique-Regi, Roger and Asgharzadeh, Shahab and Ortega, Antonio},
booktitle={Acoustics, Speech and Signal Processing, 2009. ICASSP 2009. IEEE International Conference on},
pages={1757–1760},
year={2009},
organization={IEEE}
}

@inproceedings{shtir2009copy,
title={Copy number variation in the Framingham Heart Study},
author={Shtir, Corina and Pique-Regi, Roger and Siegmund, Kim and Morrison, John and Schumacher, Fredrick and Marjoram, Paul},
booktitle={BMC proceedings},
volume={3},
number={7},
pages={S133},
year={2009},
organization={BioMed Central}
}

@inproceedings{pique2007bayesian,
title={Bayesian hierarchical modeling of means and covariances of gene expression data within families},
author={Pique-Regi, Roger and Morrison, John and Thomas, Duncan C},
booktitle={BMC proceedings},
volume={1},
number={1},
pages={S111},
year={2007},
organization={BioMed Central}
}

@inproceedings{pique2008bayesian,
title={Bayesian detection of recurrent copy number alterations across multiple array samples},
author={Pique-Regi, Roger and Monso-Varona, Jordi and Ortega, Antonio and Asgharzadeh, Shahab},
booktitle={Genomic Signal Processing and Statistics, 2008. GENSiPS 2008. IEEE International Workshop on},
pages={1–4},
year={2008},
organization={IEEE}
}

@inproceedings{sheng2009treelets,
title={Treelets as feature transformation tool for block diagonal linear discrimination},
author={Sheng, Lingyan and Ortega, Antonio and Pique-Regi, Roger and Asgharzadeh, Shahab},
booktitle={Genomic Signal Processing and Statistics, 2009. GENSIPS 2009. IEEE International Workshop on},
pages={1–4},
year={2009},
organization={IEEE}
}

@article{pique2010r,
title={R-Gada: a fast and flexible pipeline for copy number analysis in association studies},
author={Pique-Regi, Roger and C{\’a}ceres, Alejandro and Gonz{\’a}lez, Juan R},
journal={BMC bioinformatics},
volume={11},
number={1},
pages={380},
year={2010},
publisher={BioMed Central}
}

@article{gonzalez2011fast,
title={A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data},
author={Gonz{\’a}lez, Juan R and Rodr{\’\i}guez-Santiago, Benjam{\’\i}n and C{\’a}ceres, Alejandro and Pique-Regi, Roger and Rothman, Nathaniel and Chanock, Stephen J and Armengol, Llu{\’\i}s and P{\’e}rez-Jurado, Luis A},
journal={BMC bioinformatics},
volume={12},
number={1},
pages={166},
year={2011},
publisher={BioMed Central}
}

@article{warden2011bioinformatics,
title={Bioinformatics for copy number variation data},
author={Warden, Melissa and Pique-Regi, Roger and Ortega, Antonio and Asgharzadeh, Shahab},
journal={Bioinformatics for Omics Data: Methods and Protocols},
pages={235–249},
year={2011},
publisher={Humana Press}
}

@phdthesis{pique2009sparse,
title={Sparse representation models and applications to bioinformatics},
author={Pique-Regi, Roger},
year={2009},
school={University of Southern California}
}

@inproceedings{pique2003efficient,
title={Efficient face coding in video sequences combining adaptive principal component analysis and a hybrid codec approach},
author={Piqu{\’e}, Roger and Torres, Luis},
booktitle={Acoustics, Speech, and Signal Processing, 2003. Proceedings.(ICASSP’03). 2003 IEEE International Conference on},
volume={3},
pages={III–629},
year={2003},
organization={IEEE}
}

@inproceedings{pique2003combining,
title={Combining adaptive principal component analysis and a hybrid codec approach for face coding in video sequences},
author={Piqu{\’e}, Roger and Torres, Luis},
booktitle={Proceedings ICASSP’03},
volume={3},
year={2003}
}

@article{pique2008gada,
title={gada R package: User’s manual},
author={Pique-Regi, Roger and Gonz{\’a}lez, Juan R},
year={2008}
}

@article{pique2012detecting,
title={Detecting changes in DNA copy number: Reviewing signal processing techniques},
author={Pique-Regi, Roger and Ortega, Antonio and Tewfik, Ahmed and Asgharzadeh, Shahab},
journal={IEEE Signal Processing Magazine},
volume={29},
number={1},
pages={98–107},
year={2012},
publisher={IEEE}
}

@article{benjamin12fast,
title={A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data},
author={Benjam{\’\i}n, Rodr{\’\i}guez-Santiago and Alejandro, C{\’a}ceres and Roger, Pique-Regi and Nathaniel, Rothman and Stephen, Chanock and Llu{\’\i}s, Armengol and Luis, P{\’e}rez-Jurado},
journal={BMC Bioinformatics},
volume={12}
}

@article{gaffney2012dissecting,
title={Dissecting the regulatory architecture of gene expression QTLs},
author={Gaffney, Daniel J and Veyrieras, Jean-Baptiste and Degner, Jacob F and Roger, Pique-Regi and Pai, Athma A and Crawford, Gregory E and Stephens, Matthew and Gilad, Yoav and Pritchard, Jonathan K},
journal={Genome Biology},
volume={13},
number={1},
pages={R7},
year={2012},
publisher={BioMed Central Ltd}
}

@article{roger11r,
title={R-Gada: a fast and flexible pipeline for copy number analysis in association studies},
author={Roger, Pique-Regi and Alejandro, C{\’a}ceres},
journal={BMC Bioinformatics},
volume={11}
}

@article{degner2012dnase,
title={DNase I sensitivity QTLs are a major determinant of human expression variation},
author={Degner, Jacob F and Pai, Athma A and Pique-Regi, Roger and Veyrieras, Jean-Baptiste and Gaffney, Daniel J and Pickrell, Joseph K and De Leon, Sherryl and Michelini, Katelyn and Lewellen, Noah and Crawford, Gregory E and others},
journal={Nature},
volume={482},
number={7385},
pages={390–394},
year={2012},
publisher={Nature Publishing Group}
}

@article{zullo2012dna,
title={DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina},
author={Zullo, Joseph M and Demarco, Ignacio A and Piqu{\’e}-Regi, Roger and Gaffney, Daniel J and Epstein, Charles B and Spooner, Chauncey J and Luperchio, Teresa R and Bernstein, Bradley E and Pritchard, Jonathan K and Reddy, Karen L and others},
journal={Cell},
volume={149},
number={7},
pages={1474–1487},
year={2012},
publisher={Cell Press}
}

@article{asgharzadeh2012clinical,
title={Clinical significance of tumor-associated inflammatory cells in metastatic neuroblastoma},
author={Asgharzadeh, Shahab and Salo, Jill A and Ji, Lingyun and Oberthuer, Andr{\’e} and Fischer, Matthias and Berthold, Frank and Hadjidaniel, Michael and Liu, Cathy Wei-Yao and Metelitsa, Leonid S and Pique-Regi, Roger and others},
journal={Journal of Clinical Oncology},
volume={30},
number={28},
pages={3525–3532},
year={2012},
publisher={American Society of Clinical Oncology}
}

@article{pronold2012copy,
title={Copy number variation signature to predict human ancestry},
author={Pronold, Melissa and Vali, Marzieh and Pique-Regi, Roger and Asgharzadeh, Shahab},
journal={BMC bioinformatics},
volume={13},
number={1},
pages={336},
year={2012},
publisher={BioMed Central}
}

@article{degnersupplementary,
title={Supplementary Material for: DNaseI sensitivity QTLs are a major determinant of human expression variation.},
author={Degner, Jacob F and Pai, Athma A and Pique-Regi, Roger and Veyrieras, Jean-Baptiste and Gaffney, Daniel J and Pickrell, Joseph K and De Leon, Sherryl and Michelini, Katelyn and Lewellen, Noah and Crawford, Gregory E and others}
}

@article{moyerbrailean2014all,
title={Are all genetic variants in DNase I sensitivity regions functional?},
author={Moyerbrailean, Gregory A and Harvey, Chris T and Kalita, Cynthia A and Wen, Xiaoquan and Luca, Francesca and Pique-Regi, Roger},
journal={bioRxiv},
pages={007559},
year={2014},
publisher={Cold Spring Harbor Labs Journals}
}

@article{harvey2014quasar,
title={QuASAR: quantitative allele-specific analysis of reads},
author={Harvey, Chris T and Moyerbrailean, Gregory A and Davis, Gordon O and Wen, Xiaoquan and Luca, Francesca and Pique-Regi, Roger},
journal={Bioinformatics},
volume={31},
number={8},
pages={1235–1242},
year={2014},
publisher={Oxford University Press}
}

@misc{asgharzadeh2007prognostic,
title={Prognostic significance of genomic alterations of metastatic neuroblastomas.},
author={Asgharzadeh, Shahab and Pique-Regi, Roger and Tu, Yuexian and Sposto, Richard and Shimada, Hiroyuki and Ortega, Antonio and Seeger, Robert},
year={2007},
publisher={American Association for Cancer Research}
}

@article{wen2015cross,
title={Cross-population joint analysis of eQTLs: fine mapping and functional annotation},
author={Wen, Xiaoquan and Luca, Francesca and Pique-Regi, Roger},
journal={PLoS genetics},
volume={11},
number={4},
pages={e1005176},
year={2015},
publisher={Public Library of Science}
}

@article{pacis2015bacterial,
title={Bacterial infection remodels the DNA methylation landscape of human dendritic cells},
author={Pacis, Alain and Tailleux, Ludovic and Morin, Alexander M and Lambourne, John and MacIsaac, Julia L and Yotova, Vania and Dumaine, Anne and Danckaert, Anne and Luca, Francesca and Grenier, Jean-Christophe and others},
journal={Genome research},
volume={25},
number={12},
pages={1801–1811},
year={2015},
publisher={Cold Spring Harbor Lab}
}

@misc{pique2008bayesian,
title={Bayesian detection of genome copy number alterations from microarray data in cancer cells},
author={Pique-Regi, Roger and Monso-Varona, Jordi and Ortega, Antonio and Triche, Timothy and Seeger, Robert and Asgharzadeh, Shahab},
year={2008},
publisher={American Association for Cancer Research}
}

@article{moyerbrailean2015high,
title={A high-throughput RNA-seq approach to profile transcriptional responses},
author={Moyerbrailean, Gregory A and Davis, Gordon O and Harvey, Chris T and Watza, Donovan and Wen, Xiaoquan and Pique-Regi, Roger and Luca, Francesca},
journal={Scientific reports},
volume={5},
year={2015},
publisher={Nature Publishing Group}
}

@article{piquecentipede,
title={CENTIPEDE: application to ATAC-seq footprinting of DNA: protein interactions},
author={Pique-Regi, Roger and Estill, Molly and Watza, Donovan and Doman, Elisabeth and Luca, Francesca}
}

@article{donia2015toolbox,
title={A toolbox for microbiome engineering},
author={Donia, Mohamed S},
journal={Cell systems},
volume={1},
number={1},
pages={21–23},
year={2015},
publisher={Cell Press}
}

@article{moyerbrailean2016genetics,
title={Which genetics variants in DNase-Seq footprints are more likely to alter binding?},
author={Moyerbrailean, Gregory A and Kalita, Cynthia A and Harvey, Chris T and Wen, Xiaoquan and Luca, Francesca and Pique-Regi, Roger},
journal={PLoS genetics},
volume={12},
number={2},
pages={e1005875},
year={2016},
publisher={Public Library of Science}
}

@article{johnson2016nuclease,
title={Nuclease footprints in sperm project past and future chromatin regulatory events},
author={Johnson, Graham D and Jodar, Meritxell and Pique-Regi, Roger and Krawetz, Stephen A},
journal={Scientific reports},
volume={6},
pages={25864},
year={2016},
publisher={Nature Publishing Group}
}

@article{wen2016efficient,
title={Efficient integrative multi-SNP association analysis via deterministic approximation of posteriors},
author={Wen, Xiaoquan and Lee, Yeji and Luca, Francesca and Pique-Regi, Roger},
journal={The American Journal of Human Genetics},
volume={98},
number={6},
pages={1114–1129},
year={2016},
publisher={Cell Press}
}

@article{richards2016genetic,
title={Genetic and transcriptional analysis of human host response to healthy gut microbiota},
author={Richards, Allison L and Burns, Michael B and Alazizi, Adnan and Barreiro, Luis B and Pique-Regi, Roger and Blekhman, Ran and Luca, Francesca},
journal={mSystems},
volume={1},
number={4},
pages={e00067–16},
year={2016},
publisher={American Society for Microbiology Journals}
}

@article{sen2016traumatic,
title={Traumatic brain injury causes retention of long introns in metabolic genes via regulation of intronic Histone 3 lysine 36 methylation levels in the sub-acute phase of injury},
author={Sen, Arko and Wu, Wen and Nuga, Oluwademi Okikiolu and Liu, Jenny and Burl, Rayanne and Gurdziel, Katherine and Pique-Regi, Roger and H{\”u}ttemann, Maik and Ruden, Douglas M},
journal={bioRxiv},
pages={077214},
year={2016},
publisher={Cold Spring Harbor Labs Journals}
}

@article{valle2015epidemiology,
title={Epidemiology and surveillance of amyotrophic lateral sclerosis in two large metropolitan areas in California},
author={Valle, Jhaqueline and Roberts, Eric and Paulukonis, Susan and Collins, Natalie and English, Paul and Kaye, Wendy},
journal={Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration},
volume={16},
number={3-4},
pages={209–215},
year={2015},
publisher={Taylor \& Francis}
}

@article{wen2017integrating,
title={Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization},
author={Wen, Xiaoquan and Pique-Regi, Roger and Luca, Francesca},
journal={PLoS genetics},
volume={13},
number={3},
pages={e1006646},
year={2017},
publisher={Public Library of Science}
}

@article{moyerbrailean2016high,
title={High-throughput allele-specific expression across 250 environmental conditions},
author={Moyerbrailean, Gregory A and Richards, Allison L and Kurtz, Daniel and Kalita, Cynthia A and Davis, Gordon O and Harvey, Chris T and Alazizi, Adnan and Watza, Donovan and Sorokin, Yoram and Hauff, Nancy and others},
journal={Genome research},
volume={26},
number={12},
pages={1627–1638},
year={2016},
publisher={Cold Spring Harbor Lab}
}

@article{nedelec2016genetic,
title={Genetic ancestry and natural selection drive population differences in immune responses to pathogens},
author={N{\’e}d{\’e}lec, Yohann and Sanz, Joaqu{\’\i}n and Baharian, Golshid and Szpiech, Zachary A and Pacis, Alain and Dumaine, Anne and Grenier, Jean-Christophe and Freiman, Andrew and Sams, Aaron J and Hebert, Steven and others},
journal={Cell},
volume={167},
number={3},
pages={657–669},
year={2016},
publisher={Cell Press}
}

@article{snyder2016social,
title={Social status alters immune regulation and response to infection in macaques},
author={Snyder-Mackler, Noah and Sanz, Joaqu{\’\i}n and Kohn, Jordan N and Brinkworth, Jessica F and Morrow, Shauna and Shaver, Amanda O and Grenier, Jean-Christophe and Pique-Regi, Roger and Johnson, Zachary P and Wilson, Mark E and others},
journal={Science},
volume={354},
number={6315},
pages={1041–1045},
year={2016},
publisher={American Association for the Advancement of Science}
}

@article{piqueaccurate,
title={Accurate inference of transcription factor binding from DNA},
author={Pique-Regi, Roger and Degner, Jacob F and Pai, Athma A and others}
}

@article{pique2014luca,
title={Luca and Pique-Regi Collaborative Labs Produce Novel Results},
author={Pique-Regi, Roger},
year={2014}
}

@article{bell2011erratum,
title={Erratum to: DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines},
author={Bell, Jordana T and Pai, Athma A and Pickrell, Joseph K and Gaffney, Daniel J and Pique-Regi, Roger and Degner, Jacob F and Gilad, Yoav and Pritchard, Jonathan K},
journal={Genome biology},
volume={12},
number={6},
pages={405},
year={2011},
publisher={BioMed Central}
}

@article{kalita2017quasar,
title={QuASAR-MPRA: Accurate allele-specific analysis for massively parallel reporter assays},
author={Kalita, Cynthia A and Moyerbrailean, Gregory A and Brown, Christopher and Wen, Xiaoquan and Luca, Francesca and Pique-Regi, Roger},
journal={bioRxiv},
pages={105627},
year={2017},
publisher={Cold Spring Harbor Labs Journals}
}

@article{richards2017environmental,
title={Environmental perturbations lead to extensive directional shifts in RNA processing},
author={Richards, Allison L and Watza, Donovan and Findley, Anthony and Alazizi, Adnan and Wen, Xiaoquan and Pai, Athma A and Pique-Regi, Roger and Luca, Francesca},
journal={bioRxiv},
pages={119974},
year={2017},
publisher={Cold Spring Harbor Labs Journals}
}

@article{talreja2017rna,
title={RNA-sequencing Identifies Novel Pathways in Sarcoidosis Monocytes},
author={Talreja, Jaya and Farshi, Pershang and Alazizi, Adnan and Luca, Francesca and Pique-Regi, Roger and Samavati, Lobelia},
journal={Scientific Reports},
volume={7},
year={2017},
publisher={Nature Publishing Group}
}

@article{moyerbraileangenetic,
title={Which genetic variants in DNase I sensitive regions are functional?},
author={Moyerbrailean, Gregory A and Harvey, Chris T and Kalita, Cynthia A and Wen, Xiaoquan and Luca, Francesca and Pique-Regi, Roger}
}

@article{ruden2017identification,
title={Identification of splicing quantitative trait loci (sQTL) in lead-treated Drosophila melanogaster},
author={Ruden, Douglas Mark and Qu, Wen and Gurdziel, Katherine and Pique-Regi, Roger},
journal={Frontiers in Genetics},
volume={8},
pages={145},
year={2017},
publisher={Frontiers}
}

@article{richards2017variation,
title={Variation in gut microbiota composition impacts host gene expression},
author={Richards, Allison and Muehlbauer, Amanda L and Alazizi, Adnan and Burns, Michael B and Gould, Trevor J and Cascardo, Camilla and Pique-Regi, Roger and Blekhman, Ran and Luca, Francesca},
journal={bioRxiv},
pages={210294},
year={2017},
publisher={Cold Spring Harbor Laboratory}
}

@article{ruden2017smooth,
title={Smooth, an hnRNP-L homologue, 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},
author={Ruden, Douglas Mark and Sen, Arko and Gurdziel, Katherine and Liu, Jenny and Qu, Wen and Burl, Rayanne and Huttemann, Maik and Pique-Regi, Roger and others},
journal={Frontiers in Genetics},
volume={8},
pages={175},
year={2017},
publisher={Frontiers}
}

@article{qu2017identification,
title={Identification of Splicing Quantitative Trait Loci (sQTL) in Drosophila melanogaster with Developmental Lead (Pb2+) Exposure},
author={Qu, Wen and Gurdziel, Katherine and Pique-Regi, Roger and Ruden, Douglas M},
journal={Frontiers in genetics},
volume={8},
year={2017},
publisher={Frontiers Media SA}
}

@article{lacher2018hypermorphic,
title={A hypermorphic antioxidant response element is associated with increased MS4A6A expression and Alzheimer’s disease},
author={Lacher, Sarah E and Alazizi, Adnan and Wang, Xuting and Bell, Douglas A and Pique-Regi, Roger and Luca, Francesca and Slattery, Matthew},
journal={Redox biology},
volume={14},
pages={686–693},
year={2018},
publisher={Elsevier}
}

@article{sen2017smooth,
title={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},
author={Sen, Arko and Gurdziel, Katherine and Liu, Jenney and Qu, Wen and Nuga, Oluwademi O and Burl, Rayanne B and H{\”u}ttemann, Maik and Pique-Regi, Roger and Ruden, Douglas M},
journal={Frontiers in genetics},
volume={8},
year={2017},
publisher={Frontiers Media SA}
}