Biologically inspired graphs to explore massive genetic datasets - Nature Computational Science A recent study proposes a data structure that addresses crucial challenges related to storage and computation of large genome databases.

📢In a recent News & Views, @ryanlayer.bsky.social discusses a data structure introduced by @aprilwei.bsky.social and colleagues for reducing storage and computational costs for phased whole-genome polymorphisms. www.nature.com/articles/s43...

🔓https://rdcu.be/d8ay3

GenoSiS: A Biobank-Scale Genotype Similarity Search Architecture for Creating Dynamic Patient-Match Cohorts Many patients do not experience optimal benefits from medical advances because clinical research does not adequately represent them. While the diversity of biomedical research cohorts is improving, en...

We have preprint GenoSiS: A Biobank-Scale Genotype Similarity Search Architecture for Creating Dynamic Patient-Match Cohorts led by Kristen Schneider (who defended!)that can search +70k samples in the Campus Colorado Center for Personalized Medicine biobank in <1 sec

www.biorxiv.org/content/10.1...

STABIX: Summary statistic-based GWAS indexing and compression www.biorxiv.org/content/10.1101/2024.11.... 🧬🖥️🧪 https://github.com/kristen-schneider/stabix from @ryanlayer.bsky.social lab

STABIX: Summary statistic-based GWAS indexing and compression Genome-Wide Association Studies (GWAS) are widely used to investigate the role of genetics in disease traits, but the resulting file sizes from these studies are large, posing barriers to efficient st...

We have a method for fast GWAS data access. STABIX adds a p-value index that with a position index (what TABIX has) allows you to quickly retrieve, eg. all significant SNPs in a target gene. Also column compression to reduce the size. www.biorxiv.org/content/10.1...

github.com/kristen-schn...