User profiles for A. A. Pai
Athma PaiAssistant 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
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 …
of common diseases and in evolution. However, until recently, we have known little about …
Understanding mechanisms underlying human gene expression variation with RNA sequencing
Understanding the genetic mechanisms underlying natural variation in gene expression is a
central goal of both medical and evolutionary genetics, and studies of expression …
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
Background DNA methylation is an essential epigenetic mechanism involved in gene
regulation and disease, but little is known about the mechanisms underlying inter-individual …
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
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 …
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
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 …
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
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 …
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
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 …
remains controversial. It is unclear if transcript degradation in low quality RNA samples …
[HTML][HTML] Noisy splicing drives mRNA isoform diversity in human cells
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 …
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
… 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 …
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
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 …
estimated to be infected with Mycobacterium tuberculosis (MTB), the etiological agent causing …