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Reposted by Ryan Layer

Nature Computational Science @natcomputsci.nature.com · 31/01/2025

📢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

nature.com

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.

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Ryan Layer @ryanlayer.bsky.social · 05/12/2024

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...

biorxiv.org

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...

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Reposted by Ryan Layer

Stephen Turner @stephenturner.us · 28/11/2024

STABIX: Summary statistic-based GWAS indexing and compression www.biorxiv.org/content/10.1101/202… 🧬🖥️🧪 github.com/kristen-schneider/stabix from @ryanlayer.bsky.social lab

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Ryan Layer @ryanlayer.bsky.social · 21/11/2024

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...

biorxiv.org

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...

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