VariantFlux, a workflow that integrates ancestry-aware variant interpretation into genome-scale metabolic modelling to generate personalised, variant-constrained kidney reconstructions, is presented, allowing exploratory, mechanistic prediction of how naturally occurring genetic variation reshapes human metabolism.
Human genome-wide association studies have identified hundreds of thousands of variant trait associations, but interpreting their mechanistic consequences at allele resolution remains a central bottleneck. DNA foundation models pretrained on genomic sequence corpora learn features predictive of regulatory activity, yet...
The SNPannotator package is introduced, an automated post-GWAS analysis software package designed to streamline the interpretation of GWAS findings and provide a practical framework for efficiently deriving biologically meaningful insights from GWAS data.
Alireza Ani, I. Nolte, Zoha Kamali et al.· Bioinformatics· 1 citation
It is found that the abundance of both genetic and mistranslated protein variants mirrors their allele frequencies in the human population, and it is proposed that non-genetic amino acid substitutions in human proteins provide an abundant source to expanding the functional proteome.
Vyacheslav Tretyachenko, Tehila Leiman, David Morgenstern et al.· Nature· 1 citation
This Primer outlines the computational foundations of long-read whole-genome analysis in human genomics, spanning read processing, mapping, de novo assembly, multi-class variant detection, haplotype phasing, repeat analysis and epigenetic profiling, and highlights key analytical trade-offs between mapping-based and ass...
Xin-Chang Zheng, P. Sanio, Rui-Bang Luo et al.· Nature Reviews Methods Prime...· 0 citations
Structural variants (SVs), including variable number tandem repeats (VNTRs), are a major source of human genetic variation, but their impact on the proteome remains poorly characterized. Using a long-read assembly-based reference panel, we imputed 54,578 general SVs and 15,826 VNTRs in 54,306 UK Biobank participants to...
P. Yuan, W. Bai, J. Hou et al.· medRxiv· 0 citations
Abstract Interpretation of rare-disease genomes remains constrained by variant-centric analytical frameworks that insufficiently capture the cumulative impact of multiple variants within a gene. GenePy provides an individual-level, gene-based burden metric that integrates variant consequence, allele frequency, and zygo...
Iman Nazari, Guo Cheng, J. Ashton et al.· NAR Genomics and Bioinformat...· 0 citations
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