Regulatory SNPs: altered transcription factor binding sites implicated in complex traits and diseases

AO Degtyareva, EV Antontseva… - International journal of …, 2021 - mdpi.com
The vast majority of the genetic variants (mainly SNPs) associated with various human traits
and diseases map to a noncoding part of the genome and are enriched in its regulatory …

Computational methods for allele-specific expression in single cells

G Qi, A Battle - Trends in Genetics, 2024 - cell.com
Allele-specific expression (ASE) is a powerful signal that can be used to investigate multiple
molecular mechanisms, such as cis-regulatory effects and imprinting. Single-cell RNA …

Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles

S Sakaue, K Weinand, S Isaac, KK Dey, K Jagadeesh… - Nature …, 2024 - nature.com
Translating genome-wide association study (GWAS) loci into causal variants and genes
requires accurate cell-type-specific enhancer–gene maps from disease-relevant tissues …

SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty

EY Wu, NP Singh, K Choi, M Zakeri, M Vincent… - Genome biology, 2023 - Springer
Detecting allelic imbalance at the isoform level requires accounting for inferential
uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW …

RNA-seq data science: From raw data to effective interpretation

D Deshpande, K Chhugani, Y Chang… - Frontiers in …, 2023 - frontiersin.org
RNA sequencing (RNA-seq) has become an exemplary technology in modern biology and
clinical science. Its immense popularity is due in large part to the continuous efforts of the …

Using epigenomics to understand cellular responses to environmental influences in diseases

JJ Wattacheril, S Raj, DA Knowles, JM Greally - PLoS genetics, 2023 - journals.plos.org
It is a generally accepted model that environmental influences can exert their effects, at least
in part, by changing the molecular regulators of transcription that are described as …

Perspectives on allele-specific expression

S Cleary, C Seoighe - Annual Review of Biomedical Data …, 2021 - annualreviews.org
Diploidy has profound implications for population genetics and susceptibility to genetic
diseases. Although two copies are present for most genes in the human genome, they are …

[HTML][HTML] Allele-specific expression: applications in cancer and technical considerations

CD Robles-Espinoza, P Mohammadi, X Bonilla… - Current opinion in …, 2021 - Elsevier
Allele-specific gene expression can influence disease traits. Non-coding germline genetic
variants that alter regulatory elements can cause allele-specific gene expression and …

A scalable unified framework of total and allele-specific counts for cis-QTL, fine-mapping, and prediction

Y Liang, F Aguet, AN Barbeira, K Ardlie… - Nature communications, 2021 - nature.com
Genetic studies of the transcriptome help bridge the gap between genetic variation and
phenotypes. To maximize the potential of such studies, efficient methods to identify …

Methods for statistical fine-mapping and their applications to auto-immune diseases

QS Wang, H Huang - Seminars in immunopathology, 2022 - Springer
Although genome-wide association studies (GWAS) have identified thousands of loci in the
human genome that are associated with different traits, understanding the biological …