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 …
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
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 …
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
Translating genome-wide association study (GWAS) loci into causal variants and genes
requires accurate cell-type-specific enhancer–gene maps from disease-relevant tissues …
requires accurate cell-type-specific enhancer–gene maps from disease-relevant tissues …
SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty
Detecting allelic imbalance at the isoform level requires accounting for inferential
uncertainty, caused by multi-mapping of RNA-seq reads. Our proposed method, SEESAW …
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 …
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
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 …
in part, by changing the molecular regulators of transcription that are described as …
Perspectives on allele-specific expression
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 …
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
Allele-specific gene expression can influence disease traits. Non-coding germline genetic
variants that alter regulatory elements can cause allele-specific gene expression and …
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
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 …
phenotypes. To maximize the potential of such studies, efficient methods to identify …
Methods for statistical fine-mapping and their applications to auto-immune diseases
Although genome-wide association studies (GWAS) have identified thousands of loci in the
human genome that are associated with different traits, understanding the biological …
human genome that are associated with different traits, understanding the biological …