Jacob F Degner

Summary

Affiliation: University of Chicago
Country: USA

Publications

  1. 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
  2. pmc Dissecting the regulatory architecture of gene expression QTLs
    Daniel J Gaffney
    Department of Human Genetics, University of Chicago, 920 E58th Street, Chicago, IL 60637, USA
    Genome Biol 13:R7. 2012
  3. 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
  4. doi request reprint Identification of genetic variants that affect histone modifications in human cells
    Graham McVicker
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Science 342:747-9. 2013
  5. pmc DNase‚ÄČI 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
  6. 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
  7. 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
  8. pmc Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    Roger Pique-Regi
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 21:447-55. 2011

Detail Information

Publications8

  1. 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)...
  2. pmc Dissecting the regulatory architecture of gene expression QTLs
    Daniel J Gaffney
    Department of Human Genetics, University of Chicago, 920 E58th Street, Chicago, IL 60637, USA
    Genome Biol 13:R7. 2012
    ..Using the HapMap lymphoblastoid cell lines, we combine 1000 Genomes genotypes and an extensive catalogue of human functional elements to investigate the biological mechanisms that eQTLs perturb...
  3. 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...
  4. doi request reprint Identification of genetic variants that affect histone modifications in human cells
    Graham McVicker
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Science 342:747-9. 2013
    ..Furthermore, variants that affect chromatin at distal regulatory sites frequently also direct changes in chromatin and gene expression at associated promoters. ..
  5. pmc DNase‚ÄČI 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...
  6. 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...
  7. 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...
  8. pmc Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    Roger Pique-Regi
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 21:447-55. 2011
    ..We anticipate that this approach will be a valuable tool for genome-wide studies of gene regulation in a wide variety of cell types or tissues under diverse conditions...