SAIGE-GPU — Accelerating Genome- and Phenome-Wide Association Studies using GPUs Open Access
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btag032/8438945
"We developed SAIGE-GPU, a GPU-accelerated version of SAIGE that replaces CPU-intensive matrix operations with GPU-optimized kernels. The core innovation is distributing genetic relationship matrix calculations across GPUs and communication layers. "
Learn the full GWAS workflow in our 5-day online course (26–30 Jan 2026)
@OscarGenomics
From study design to data analysis with R & Linux tools, gain hands-on skills to run your own GWAS.
https://www.physalia-courses.org/courses-workshops/course49/
I am starting to thread into the structural implication of #aminoacid changes across recent #evolution. Wandering how many methods like these are out there and how they can help us selecting those mutations with structural and functional implications. https://www.biorxiv.org/content/10.64898/2025.12.03.692053v1 #proteins #genomics #genomephenome #GWAS
For once I did not spend much time on biological networks (maybe inadvisable at a course whose subtitle contains the words "network modeling"), but instead presented SMuGLasso, a sparse multitask group lasso for GWAS in diverse populations that we developed with Asma Nouira and that was published just last week. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012734
SMuGlasso groups SNPs by LD blocks (as done by Alia Dehman, Christophe Ambroise and Pierre Neuvial in 2015), and treats genetically homogeneous subpopulations of a heterogeneous data set as different but interlinked tasks. An additional sparsity constraints allows us to identify population-specific loci.
On simulations, we show that SMuGLasso has much better recall than classical GWAS (at the expense of more false positives, but fewer than other comparison partners).
On real data, we observe that SMuGLasso recovers all the genes identified by a classical GWAS, as well as some that were identified by a meta-GWAS that included our dataset. All in all, only 2 of the 27 identified genes look likely to be false positives.
Course Alert!😍
Curious about #GWAS? This course will guide you through the entire process — from study design and data prep to statistical analysis and interpreting results.
@OscarGenomics @gwascatalog
https://www.physalia-courses.org/courses-workshops/course49/
"GWAS SVatalog: a visualization tool to aid fine-mapping of GWAS loci with structural variations"
https://www.biorxiv.org/content/10.1101/2025.09.03.674075v1?rss=1
What determines the human gut fungal community? Emily van Syoc, @erdavenport @symbionticism &co present the first #GWAS of human genetic loci that influence the relative abundance of gut #fungi, linking these to disease risk #mycobiome @PLOSBiology https://plos.io/42bCKou
We are just one week away from Let’s Get Quizzical: Trivia, #Bioblitz & Food by the Gorge, happening on Saturday, August 30, 2025, from 11 AM to 5 PM at #GorgeEsquimaltPark - right outside the Gorge Nature House.
This exciting, #free #FamilyFriendly event is packed with activities for all ages:
🧠 Sustainable Smarts #Trivia – Three rounds of engaging trivia with fantastic #prizes from local favourites like HAVN, Axe & Grind, and Quazar’s Arcade + some of Esquimalt's finest, Warm Gift Shop, Errant Empire, and 4Cats Esquimalt!
🌿 Bioblitz #CommunityScience – Join guided walks and help document local plants, bugs, birds, and more on iNaturalist.
🐞 #BugWalk & #PlantWalks – Led by the #GWAS team to connect you with the biodiversity of our beautiful #GorgeWaterway.
🎟️ Passport to Science Wrap-Up – Explore hands-on science with our friends from Passport to Science, Victoria Bug Zoo, Centre of the Universe, and more!
And, of course… delicious food all day long:
🍦 Hazel’s Ice Cream – Serving cold treats and smiles.
🌯 Greek on the Street – Flavour-packed eats and street-side classics.
🥗 Naked Dressings – Fresh, healthy bites made with love.
Whether you are coming for the science, the food, the trivia, or simply to enjoy the community atmosphere, there is something for everyone. So, choose your favourite method of Active Transportation and come get quizzical on Saturday, August 30!
Support Your Local #NatureHouse
This #fundraiser helps support much-needed improvements to the Gorge Nature House, enabling us to continue providing #environmental #education and #CommunityPrograms for years to come.
Mark your calendars, bring your friends and family, and come celebrate the Gorge with us!
Learn More →
http://triviabythegorge.eventbrite.com
Unable to make the event but still want to support the cause?
No problem – Donate today!
https://www.gorge.ca/donate?link_id=14&can_id=885c887d51f4f2992844bbc18a1523b7&source=email-one-week-until-lets-get-quizzical-trivia-bioblitz-food-by-the-gorge&email_subject=_-one-week-until-lets-get-quizzical-trivia-bioblitz-food-by-the-gorge-_&&
#Saanich #VictoriaBC #Esquimalt #YYJ #Songhees #VancouverIsland #VanIsle #PacificNorthwest #PNW #Nature #HandsOnLearning #CitizenScience #YYJParks #AllAges #InclusiveEvents #AccessibleEvents #FreeEvent #FunAtThePark #Naturalists #LearnAboutNature #CommunityEvent #CommunityBuilding
Need an overview before the webinar? Here are 2 links from the DecodeME website:
1. Initial DecodeME DNA Results:
https://www.decodeme.org.uk/initial-dna-results/
2. X marks the spot where ME/CFS biology can be discovered:
🚨 DecodeME Genetic Results Webinar tomorrow, Thursday, Aug 14, 2:30 PM BST
Register here:
https://us02web.zoom.us/webinar/register/WN_C82NbFK_TYGnJ_T6edmV-w#/registration
(registration link will show time in your time zone)
Note from DecodeME:
"There are limited spots to join on Zoom (registering does not guarantee a spot).
Don’t worry though, we will be recording it and we will also be sharing it live on Facebook at the time."
💊 Think your prescription changes are random? Your genes might be calling the shots.
🔗 Genome-wide associations spanning 194 in-hospital drug dosage change phenotypes highlight diverse genetic backgrounds in concurrent drug therapy. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.06.042
📚 CSBJ Smart Hospital: https://www.csbj.org/smarthospital
#Genomics #Polypharmacy #PersonalizedMedicine #Pharmacogenomics #DrugSafety #GWAS #PrecisionMedicine #Pharmacology #Genetics #MedTech
"Lack of ME research because of ‘medical misogyny’, says top scientist"
https://www.thetimes.com/uk/scotland/article/chris-ponting-misogyny-me-research-c09hp0hfg
"Professor Chris Ponting, who led a groundbreaking study into the disease (DecodeME) says it is 'highly stigmatised and incredibly female-biased'"
"…clinicians and scientists should be asking why his work was not done 15 years ago"
Association of myalgic encephalomyelitis / chronic fatigue syndrome (#ME / #CFS) with genetic mutations found. Preprint. #GWAS https://www.research.ed.ac.uk/en/publications/initial-findings-from-the-decodeme-genome-wide-association-study-
#Stutter associated with mutations in specific neurologically important genes.
#gwas
https://www.science.org/content/article/genome-wide-study-makes-quantum-leap-understanding-stuttering
NEW!
🧬 Rare Variants in Crops: Theoretical Insights and Emerging Detection Strategies
from Talissa Floriani & Alexander Lipka
https://doi.org/10.1093/insilicoplants/diaf012 #PlantScience #GWAS
The 9th edition of our Introduction to #GWAS course with @OscarGenomics Filippo Biscarini, and Christian Werner is live!
Participants are diving into GWAS essentials — from study design to analysis — building a complete, efficient workflow.
🚨 Last seats alert! 🚨
Our GWAS course kicks off next week (23–27 June)💥
Learn the full pipeline—from study design to result interpretation—with hands-on sessions using R and PLINK. 💻🧬
👉 Grab your spot: https://www.physalia-courses.org/courses-workshops/course49/
