Identification of pathogenic variant enriched regions across genes and gene families
Missense variant interpretation is challenging. Essential regions for protein function are
conserved among gene-family members, and genetic variants within these regions are …
conserved among gene-family members, and genetic variants within these regions are …
A genome-wide mutational constraint map quantified from variation in 76,156 human genomes
The depletion of disruptive variation caused by purifying natural selection (constraint) has
been widely used to investigate protein-coding genes underlying human disorders, but …
been widely used to investigate protein-coding genes underlying human disorders, but …
LDassoc: an online tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation
MJ Machiela, SJ Chanock - Bioinformatics, 2018 - academic.oup.com
Motivation Existing approaches to plot association results from genome-wide association
studies (GWAS) are in the form of static Manhattan plots and often lack data integration with …
studies (GWAS) are in the form of static Manhattan plots and often lack data integration with …
DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding …
The complex system of gene expression is regulated by the cell type-specific binding of
transcription factors (TFs) to regulatory elements. Identifying variants that disrupt TF binding …
transcription factors (TFs) to regulatory elements. Identifying variants that disrupt TF binding …
DNA language models are powerful predictors of genome-wide variant effects
The expanding catalog of genome-wide association studies (GWAS) provides biological
insights across a variety of species, but identifying the causal variants behind these …
insights across a variety of species, but identifying the causal variants behind these …
Advancing variant effect prediction using protein language models
BJ Livesey, JA Marsh - Nature Genetics, 2023 - nature.com
Advancing variant effect prediction using protein language models | Nature Genetics Skip to main
content Thank you for visiting nature.com. You are using a browser version with limited support …
content Thank you for visiting nature.com. You are using a browser version with limited support …
Predicting the functional effect of amino acid substitutions and indels
As next-generation sequencing projects generate massive genome-wide sequence
variation data, bioinformatics tools are being developed to provide computational …
variation data, bioinformatics tools are being developed to provide computational …
A method to predict the impact of regulatory variants from DNA sequence
Most variants implicated in common human disease by genome-wide association studies
(GWAS) lie in noncoding sequence intervals. Despite the suggestion that regulatory element …
(GWAS) lie in noncoding sequence intervals. Despite the suggestion that regulatory element …
UCSC data integrator and variant annotation integrator
Two new tools on the UCSC Genome Browser web site provide improved ways of
combining information from multiple datasets, optionally including the user's own custom …
combining information from multiple datasets, optionally including the user's own custom …
regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants
S Zhang, Y He, H Liu, H Zhai, D Huang… - Nucleic acids …, 2019 - academic.oup.com
Predicting the functional or pathogenic regulatory variants in the human non-coding genome
facilitates the interpretation of disease causation. While numerous prediction methods are …
facilitates the interpretation of disease causation. While numerous prediction methods are …