Athma A Pai

Summary

Affiliation: University of Chicago
Country: USA

Publications

  1. 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
  2. pmc A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues
    Athma A Pai
    Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 7:e1001316. 2011
  3. 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
  4. 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
  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 Controls of nucleosome positioning in the human genome
    Daniel J Gaffney
    Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 8:e1003036. 2012
  8. pmc The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes
    Darren A Cusanovich
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Hum Mol Genet 21:2111-23. 2012
  9. 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
  10. 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

Collaborators

Detail Information

Publications13

  1. 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...
  2. pmc A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues
    Athma A Pai
    Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 7:e1001316. 2011
    ..In particular, we estimate that, in the tissues we studied, inter-species differences in promoter methylation might underlie as much as 12%-18% of differences in gene expression levels between humans and chimpanzees...
  3. 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...
  4. 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...
  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 Controls of nucleosome positioning in the human genome
    Daniel J Gaffney
    Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
    PLoS Genet 8:e1003036. 2012
    ....
  8. pmc The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes
    Darren A Cusanovich
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Hum Mol Genet 21:2111-23. 2012
    ..Our results, therefore, establish a new set of asthma susceptibility candidate genes. More generally, our observations support the notion that many loci of small effects influence variation in lymphocyte count and asthma susceptibility...
  9. 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)...
  10. 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...
  11. 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...
  12. pmc Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection
    Luis B Barreiro
    Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 109:1204-9. 2012
    ..We thus identified a number of candidate loci, including the MAPK phosphatase DUSP14 in particular, that are promising susceptibility genes to pulmonary TB...
  13. pmc RNA-seq: impact of RNA degradation on transcript quantification
    Irene Gallego Romero
    Department of Human Genetics, University of Chicago, 920 E 58th St, CLSC 317, Chicago, IL 60637, USA
    BMC Biol 12:42. 2014
    ..Yet, low quality samples (for example, samples collected in the course of fieldwork) are at times the sole means of addressing specific questions...