Publications

See also an equivalent list of publications from Google Scholar, and Pubmed.

Journal papers: (*) Denotes equal contribution as first author.

  • *Degner JF, *Pai AA, *Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, de Leon S, Michelini K, Lewellen N, Crawford G, Stephens M, Gilad Y, and Pritchard JK. "Variation in chromatin accessibility is a key determinant of heritable variation in gene expression". Nature, 2012. [Early access] [Pubmed] [F1000 exceptional]
  • Zullo JM, Demarco IA, Pique-Regi R, Gaffney DJ, Epstein CB, Bernstein KL, Pritchard JK, Reddy KL, and Singh H. "A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina". Cell. 2012 Jun;149(7):1474-87. [Pubmed][F1000 recommended]
  • 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 Aug 27. [Pubmed]
  • Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, and Pritchard JK. "Dissecting the regulatory architecture of gene expression QTLs." Genome Biol., 2012. [Pubmed][F1000 recommended]
  • Pique-Regi R, Ortega A, Tewfik A., Asgharzadeh S. "Detecting Changes in DNA Copy Number: Reviewing signal processing techniques". IEEE Signal Processing Magazine. 2012 Jan; 29 (1): 98-107. [IEEE Xplore]

  • 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(1):166. [Pubmed]
  • Pique-Regi R, Degner JF, Pai AA, Gaffney DG, Gilad Y, Pritchard JK. "Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data", Genome Research 2011 Mar;21(3):447-55. [Pubmed] [CENTIPEDE Website] [F1000 recommended]
  • 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 Jan 20;12(1):R10. [Pubmed]
  • Warden M, Pique-Regi R, Ortega A, Asgharzadeh S. "Bioinformatics for copy number variation data". Methods Mol Biol. 2011;719:235-49. [Pubmed]

  • 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. [Pubmed] [Full] [GADA Website]
  • 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. [Pubmed] [Full] [GADA Website]
  • Pique-Regi R, Monso-Varona J,Ortega A, Seeger RC, Triche TJ, Asgharzadeh S: "Sparse representation and Bayesian detection of the genome copy number alterations from microarray data", Bioinformatics, Feb 2008, [Pubmed] [Full] [GADA Website]
  • 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] [JNCI] [JNCI comment]

Conference Papers: (peer reviewed)

  • Sheng L, Pique-Regi R, Asgharzadeh S, Ortega A: " Microarray Classification using Block Diagonal Linear Discriminant Analysis with Embedded Feature Selection ", ICASSP 2009
  • Shtir L, Pique-Regi R, Siegmund K, Morrison J, Schumacher F, Marjoram P: "Copy Number Variation in the Framingham Heart Study ", Genetic Analysis Workshop 16, Sept. 2008. BMC Proceedings, 2009 Dec 15;3 Suppl 7:S133. [Pubmed] [Full]
  • Pique-Regi R, Monso-Varona J,Ortega A, Asgharzadeh S: " Bayesian Detection of Recurrent Copy Number Alterations across Multiple Array Samples ", Gensips 2008 [pdf]
  • Roger Pique-Regi, John Morrison, Duncan C Thomas: " Bayesian hierarchical modelling of means and covariances of gene expression data within families " BMC Proceedings , 2007. 1(Suppl 1): p. S111. [pdf] [Full]
  • Pique-Regi R, Tsau ES,Ortega A, Seeger RC, Asgharzadeh S: "Wavelet footprints and sparse Bayesian learning for DNA copy number change analysis ", in International Conference on Acoustics Speech and Signal Processing (ICASSP), Hawaii 2007. [pdf] [Best Paper Award Finalist]
  • Roger Pique-Regi, Antonio Ortega: "Block Diagonal Linear Discriminant Analysis with Sequential Embedded Feature Selection ", in International Conference on Acoustics Speech and Signal Processing (ICASSP), Tolouse, France, 2006. [pdf]
  • Roger Pique-Regi, Antonio Ortega, Shahab Asgharzadeh: " Sequential Diagonal Linear Discriminant Analysis (SeqDLDA) for Microarray Classification and Gene Identification", CSB 2005: 112-116. [pdf]
  • Roger Pique , Luis Torres, "Efficient face coding in videosequences combining adaptative Principal Component Analysis and a Hybrid Codec Approach", in International Conference on Acoustics Speech and Signal Processing (ICASSP), Hong Kong, China, 2003.

Conference meetings:

    Oral presentations:
  • "Variation in transcription factor activity inferred by DNase-seq assays provide a trans-acting mechanism for gene expression variation in humans". 4th RECOMB Conference on Regulatory Genomics, Systems Biology, and DREAM Challenges. Barcelona, Catalonia, Spain, Oct. 2011 
  • "DNaseI sensitivity QTLs are a major determinant of human expression variation". Biology of Genomes. Cold Spring Harbor, NY, May 2011. 
  • "SNPs affecting chromatin accessibility are important contributors to gene expression variation". High Throughput Biology. Cold Spring Harbor Asia, Suzhhou, China, April 2011. 
  • "Mapping of cell-type specific transcription factor binding from DNase-seq assays and variation across HapMap individuals". 3rd Annual Joint Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges. New York, NY, Nov. 2010.
    Poster presentations:
  • "Variation in transcription factor activity inferred by DNase-seq assays provide a trans-acting mechanism for gene expression variation in humans". 61st Annual meeting of the American Society of Human Genetics, Montreal, QC, Canada, October 2011 
  • "DNaseI sensitivity QTLs are a major determinant of human expression variation". Mechanisms of eukaryotic regulation. Cold Spring Harbor, NY, August 2011.
  • "Bayesian detection of recurrent copy number variation across multiple array samples", Human Genome Variation Meeting , October 2008, Toronto, Canada.
  • "Bayesian Detection of Genome Copy Number Alterations from Microarray Analysis of Neuroblastoma Cell Lines", Advances in Neuroblastoma Research, ANR 2008 , Chiba, Japan.
  • "Bayesian detection of genome copy number alterations from microarray data in cancer cells", AACR anual meeting , April 2008, San Diego, California.

Invited talks/seminars:

  • "Mapping of cell-type specific transcription factor binding from DNase-seq assays and variation across HapMap individuals", Department of Computational Biology, University of Southern California, Los Angeles, Fabruary 2011
  • "Sparse representations and application to genome copy number alteration detection from microarray data ", Human Genetics Department Seminar, University of Chicago, October 2008
  • "Bayesian Detection of Copy Number Alterations", Biostatistics Seminar, Keck School of Medicine -- Preventive Medicine, University of Southern California, Los Angeles, February 2008
  • "Improved feature selection for LDA in microarrays", Biostatistics Seminar, Keck School of Medicine -- Preventive Medicine, University of Southern California, Los Angeles, 2005