User profiles for A. A. Pai

Athma Pai

Assistant Professor, UMass Chan Medical School
Verified email at umassmed.edu
Cited by 8839

[HTML][HTML] The genetic and mechanistic basis for variation in gene regulation

AA Pai, JK Pritchard, Y Gilad - PLoS genetics, 2015 - journals.plos.org
It is now well established that noncoding regulatory variants play a central role in the genetics
of common diseases and in evolution. However, until recently, we have known little about …

Understanding mechanisms underlying human gene expression variation with RNA sequencing

JK Pickrell, JC Marioni, AA Pai, JF Degner… - Nature, 2010 - nature.com
Understanding the genetic mechanisms underlying natural variation in gene expression is a
central goal of both medical and evolutionary genetics, and studies of expression …

[HTML][HTML] DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

JT Bell, AA Pai, JK Pickrell, DJ Gaffney, R Pique-Regi… - Genome biology, 2011 - Springer
Background DNA methylation is an essential epigenetic mechanism involved in gene
regulation and disease, but little is known about the mechanisms underlying inter-individual …

DNase I sensitivity QTLs are a major determinant of human expression variation

JF Degner, AA Pai, R Pique-Regi, JB Veyrieras… - Nature, 2012 - nature.com
The mapping of expression quantitative trait loci (eQTLs) has emerged as an important tool
for linking genetic variation to changes in gene regulation 1 , 2 , 3 , 4 , 5 . However, it remains …

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

JF Degner, JC Marioni, AA Pai, JK Pickrell… - …, 2009 - academic.oup.com
Motivation: Next-generation sequencing has become an important tool for genome-wide
quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short …

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

R Pique-Regi, JF Degner, AA Pai, DJ Gaffney… - Genome …, 2011 - genome.cshlp.org
Accurate functional annotation of regulatory elements is essential for understanding global
gene regulation. Here, we report a genome-wide map of 827,000 transcription factor binding …

[HTML][HTML] RNA-seq: impact of RNA degradation on transcript quantification

I Gallego Romero, AA Pai, J Tung, Y Gilad - BMC biology, 2014 - Springer
Background The use of low quality RNA samples in whole-genome gene expression profiling
remains controversial. It is unclear if transcript degradation in low quality RNA samples …

[HTML][HTML] Noisy splicing drives mRNA isoform diversity in human cells

JK Pickrell, AA Pai, Y Gilad, JK Pritchard - PLoS genetics, 2010 - journals.plos.org
While the majority of multiexonic human genes show some evidence of alternative splicing,
it is unclear what fraction of observed splice forms is functionally relevant. In this study, we …

[HTML][HTML] Controls of nucleosome positioning in the human genome

DJ Gaffney, G McVicker, AA Pai… - PLoS …, 2012 - journals.plos.org
… These dinucleotides also influence the rotational positioning of nucleosomes—AA/AT/TA/TT
dinucleotides are favored where the DNA minor groove faces inwards towards the histone …

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection

LB Barreiro, L Tailleux, AA Pai… - Proceedings of the …, 2012 - National Acad Sciences
Tuberculosis (TB) is a major public health problem. One-third of the world's population is
estimated to be infected with Mycobacterium tuberculosis (MTB), the etiological agent causing …