Joseph K Pickrell

Summary

Affiliation: University of Chicago
Country: USA

Publications

  1. pmc Understanding mechanisms underlying human gene expression variation with RNA sequencing
    Joseph K Pickrell
    Department of Human Genetics, The University of Chicago, Chicago 60637, USA
    Nature 464:768-72. 2010
  2. pmc Noisy splicing drives mRNA isoform diversity in human cells
    Joseph K Pickrell
    Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 6:e1001236. 2010
  3. doi Comment on "Widespread RNA and DNA sequence differences in the human transcriptome"
    Joseph K Pickrell
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Science 335:1302; author reply 1302. 2012
  4. pmc A mixture model approach to multiple testing for the genetic analysis of gene expression
    Cyril Dalmasso
    JE 2492 Universite Paris Sud, , 16 Avenue Paul Vaillant Couturier, Villejuif Cedex 94807, France
    BMC Proc 1:S141. 2007
  5. pmc False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions
    Joseph K Pickrell
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Bioinformatics 27:2144-6. 2011
  6. pmc Signals of recent positive selection in a worldwide sample of human populations
    Joseph K Pickrell
    Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
    Genome Res 19:826-37. 2009
  7. pmc Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
    Jacob F Degner
    Department of Human Genetics, University of Chicago, 920 E 58th St, CLSC 507, Chicago, IL 60637, USA
    Bioinformatics 25:3207-12. 2009
  8. pmc The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels
    Athma A Pai
    Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
    PLoS Genet 8:e1003000. 2012
  9. pmc Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data
    Jean Baptiste Veyrieras
    Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 7:e30629. 2012
  10. pmc DNase I sensitivity QTLs are a major determinant of human expression variation
    Jacob F Degner
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Nature 482:390-4. 2012

Detail Information

Publications16

  1. pmc Understanding mechanisms underlying human gene expression variation with RNA sequencing
    Joseph K Pickrell
    Department of Human Genetics, The University of Chicago, Chicago 60637, USA
    Nature 464:768-72. 2010
    ..Our results illustrate the power of high-throughput sequencing for the joint analysis of variation in transcription, splicing and allele-specific expression across individuals...
  2. pmc Noisy splicing drives mRNA isoform diversity in human cells
    Joseph K Pickrell
    Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 6:e1001236. 2010
    ..7% and show that introns in highly expressed genes are spliced more accurately, likely due to their shorter length. These results implicate noisy splicing as an important property of genome evolution...
  3. doi Comment on "Widespread RNA and DNA sequence differences in the human transcriptome"
    Joseph K Pickrell
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Science 335:1302; author reply 1302. 2012
    ..We found that at least 88% of these sequence mismatches can likely be explained by technical artifacts such as errors in mapping sequencing reads to a reference genome, sequencing errors, and genetic variation...
  4. pmc A mixture model approach to multiple testing for the genetic analysis of gene expression
    Cyril Dalmasso
    JE 2492 Universite Paris Sud, , 16 Avenue Paul Vaillant Couturier, Villejuif Cedex 94807, France
    BMC Proc 1:S141. 2007
    ..The contribution of our model to estimation of FDR and related criteria is illustrated on the microarray expression profiles data set provided by the Genetic Analysis Workshop 15 Problem 1...
  5. pmc False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions
    Joseph K Pickrell
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Bioinformatics 27:2144-6. 2011
    ..Here, we consider whether false positive peak calls can be caused by particular type of error in the reference genome: multicopy sequences which have been incorrectly assembled and collapsed into a single copy...
  6. pmc Signals of recent positive selection in a worldwide sample of human populations
    Joseph K Pickrell
    Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
    Genome Res 19:826-37. 2009
    ..Finally, we search for local adaptation between geographically close populations, and highlight several examples...
  7. pmc Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
    Jacob F Degner
    Department of Human Genetics, University of Chicago, 920 E 58th St, CLSC 507, Chicago, IL 60637, USA
    Bioinformatics 25:3207-12. 2009
    ..Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE)...
  8. pmc The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels
    Athma A Pai
    Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
    PLoS Genet 8:e1003000. 2012
    ..By analyzing our data within the context of known steady-state eQTLs, we estimate that a substantial fraction of eQTLs are associated with inter-individual variation in mRNA decay rates...
  9. pmc Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data
    Jean Baptiste Veyrieras
    Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
    PLoS ONE 7:e30629. 2012
    ..Nonetheless, we do observe an overall enrichment of eQTLs in exons versus introns in all three data sets, consistent with an important role for exonic sequences in gene regulation...
  10. pmc DNase I sensitivity QTLs are a major determinant of human expression variation
    Jacob F Degner
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Nature 482:390-4. 2012
    ..Our observations indicate that dsQTLs are highly abundant in the human genome and are likely to be important contributors to phenotypic variation...
  11. pmc The role of geography in human adaptation
    Graham Coop
    Department of Human Genetics, University of Chicago, Chicago, IL, USA
    PLoS Genet 5:e1000500. 2009
    ..These patterns suggest that selection is often weak enough that neutral processes -- especially population history, migration, and drift -- exert powerful influences over the fate and geographic distribution of selected alleles...
  12. pmc DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
    Jordana T Bell
    Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
    Genome Biol 12:R10. 2011
    ..Here we measured methylation levels at 22,290 CpG dinucleotides in lymphoblastoid cell lines from 77 HapMap Yoruba individuals, for which genome-wide gene expression and genotype data were also available...
  13. pmc The CFTR Met 470 allele is associated with lower birth rates in fertile men from a population isolate
    Gülüm Kosova
    University of Chicago, Illinois, United States of America
    PLoS Genet 6:e1000974. 2010
    ..003, consistent with a selective sweep outside of Africa. The fertility advantage conferred by Val470 relative to Met470 may provide a selective mechanism for these population genetic observations...
  14. pmc Comparative RNA sequencing reveals substantial genetic variation in endangered primates
    George H Perry
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 22:602-10. 2012
    ..Our observations imply that many endangered lemur populations still harbor considerable genetic variation. Timely efforts to conserve these species alongside their habitats have, therefore, strong potential to achieve long-term success...
  15. pmc The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation
    Jonathan K Pritchard
    Department of Human Genetics, The University of Chicago, Room 507, 929 E 58th St, Chicago, IL 60637, USA
    Curr Biol 20:R208-15. 2010
    ..We close by discussing some of the likely opportunities for progress in the field...
  16. pmc Inference of population splits and mixtures from genome-wide allele frequency data
    Joseph K Pickrell
    Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 8:e1002967. 2012
    ..Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com...