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Published in 2022 at "Proteomics"
DOI: 10.1002/pmic.202200176
Abstract: It is challenging to study regulatory genetic variants as gene expression is affected by both genetic polymorphisms and non‐genetic regulators. The mRNA allele‐specific expression (ASE) assay has been increasingly used for the study of cis‐acting…
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Keywords:
regulatory variants;
allele specific;
expression;
acting regulatory ... See more keywords
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Published in 2022 at "Proceedings of the National Academy of Sciences of the United States of America"
DOI: 10.1073/pnas.2206069119
Abstract: Significance Genetic association studies have identified widespread DNA methylation (DNAm) quantitative trait loci (mQTLs) that may illuminate causal genetic variations underlying human complex traits. However, due to extensive linkage disequilibrium (LD) of the genome, it…
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Keywords:
regulatory variants;
dna methylation;
human brain;
deep learning ... See more keywords
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Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbab189
Abstract: Understanding the functional consequence of noncoding variants is of great interest. Though genome-wide association studies or quantitative trait locus analyses have identified variants associated with traits or molecular phenotypes, most of them are located in…
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Keywords:
framework;
statistical learning;
regulatory variants;
novel statistical ... See more keywords
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Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac157
Abstract: SUMMARY To address the difficulty in assessing the implication of regulatory variants in diseases, a scoring scheme published by Van der Lee et al., 2020 allows the calculation of the Regulatory Variant Evidence score (RVE-score).…
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Keywords:
scoring system;
regulatory variants;
revup online;
score ... See more keywords
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Published in 2019 at "Bioinformatics"
DOI: 10.1093/bioinformatics/bty992
Abstract: Abstract Motivation Deciphering the functional roles of cis-regulatory variants is a critical challenge in genome analysis and interpretation. It has been hypothesized that altered transcription factor (TF) binding events are a central mechanism by which…
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Keywords:
binding events;
regulatory variants;
cis regulatory;
gene expression ... See more keywords
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2
Published in 2022 at "Clinical and Translational Science"
DOI: 10.1111/cts.13398
Abstract: The cytochrome P450 3As (CYP3As) are abundantly expressed in the liver and metabolize many commonly prescribed medications. Their expression is highly variable between individuals with little known genetic cause. Despite extensive investigation, cis‐acting genetic elements…
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Keywords:
regulatory variants;
expression;
cyp3a4 cyp3a5;
cyp3a4 ... See more keywords
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Published in 2020 at "Journal of Psychopharmacology"
DOI: 10.1177/0269881119895539
Abstract: Background: Dopamine-β-hydroxylase (DBH, EC 1.14.17.1), which converts dopamine to norepinephrine, is a candidate gene in neuropsychiatric diseases. Aim: To assess the effect of regulatory variants in DBH on schizophrenia and its endophenotypes –cognition and tardive…
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Keywords:
association;
regulatory variants;
tardive dyskinesia;
cognition ... See more keywords
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Published in 2017 at "Genome Biology"
DOI: 10.1186/s13059-017-1322-z
Abstract: BackgroundMost cancer risk-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) are noncoding and it is challenging to assess their functional impacts. To systematically identify the SNPs that affect gene expression by modulating…
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Keywords:
risk;
cancer risk;
regulatory variants;
cancer ... See more keywords
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Published in 2020 at "Genome Biology"
DOI: 10.1186/s13059-020-02069-1
Abstract: Background Gene expression is a key determinant of cellular response. Natural variation in gene expression bridges genetic variation to phenotypic alteration. Identification of the regulatory variants controlling the gene expression in response to drought, a…
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Keywords:
drought;
response;
gene expression;
regulatory variants ... See more keywords
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Published in 2020 at "Molecular Autism"
DOI: 10.1186/s13229-020-00333-6
Abstract: Genetic factors contribute to the development of autism spectrum disorder (ASD), and although non-protein-coding regions of the genome are being increasingly implicated in ASD, the functional consequences of these variants remain largely uncharacterized. Induced pluripotent…
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Keywords:
autism;
regulatory variants;
pluripotent stem;
induced pluripotent ... See more keywords
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Published in 2017 at "PLoS ONE"
DOI: 10.1371/journal.pone.0174738
Abstract: Utilizing data from published tuberculosis (TB) genome-wide association studies (GWAS), we use a bioinformatics pipeline to detect all polymorphisms in linkage disequilibrium (LD) with variants previously implicated in TB disease susceptibility. The probability that these…
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Keywords:
tuberculosis susceptibility;
post gwas;
predicted regulatory;
regulatory variants ... See more keywords