Kodama: genotype compression and matrix multiplication leveraging genetic relatedness www.biorxiv.org/content/10.6...

Introducing the 𝐎𝐩𝐞𝐧 𝐒𝐜𝐡𝐨𝐥𝐚𝐫𝐬𝐡𝐢𝐩 𝐓𝐫𝐚𝐢𝐧𝐢𝐧𝐠 𝐟𝐨𝐫 𝐑𝐞𝐬𝐞𝐚𝐫𝐜𝐡𝐞𝐫𝐬 𝐒𝐞𝐫𝐢𝐞𝐬 We’re starting with 2 online courses, with more on the way: → Fundamentals of Open Scholarship > bit.ly/4vYZVjh → Preregistration and Reregistration Reports > bit.ly/48sPpXE 🧵 (1/6)

📣 𝐖𝐞’𝐫𝐞 𝐡𝐢𝐫𝐢𝐧𝐠 𝐚 𝐩𝐨𝐬𝐭𝐝𝐨𝐜 𝐢𝐧 𝐩𝐨𝐩𝐮𝐥𝐚𝐭𝐢𝐨𝐧 & 𝐬𝐭𝐚𝐭𝐢𝐬𝐭𝐢𝐜𝐚𝐥 𝐠𝐞𝐧𝐞𝐭𝐢𝐜𝐬! 🌍📈🧬 If you’re finishing a PhD (or know someone who is) and want to work on complex trait biology + 𝑟𝑒𝑎𝑙-𝑤𝑜𝑟𝑙𝑑 𝑖𝑚𝑝𝑎𝑐𝑡, read on 👇

Excited to share our new paper in @JNCI_Now! We integrated GWAS data from 11 solid cancers with ~1,500 cell type annotations to pinpoint WHERE in the body cancer risk variants actually act. A thread 👇 @peter-kraft.bsky.social

This👇 A key to any productive collaboration between computer scientists and epidemiologists (or clinicians or biologists or…) is to learn each others’ languages. Sometimes we use different words for the same concepts, sometimes we use the same words but mean very different things.

Ewan Birney@ewanbirney.bsky.social · 3mo ago

I wrote a friendly rant about the use of causal language in AI. www.linkedin.com/posts/ewan-b...

🎉New preprint: Phenome-derived polygenic scores and social determinants jointly shape context-dependent disease risk. We evaluate disease risk along 2 complementary axes: • how genetic liability is represented • the social context in which it is expressed

medRxivpreprint@medrxivpreprint.bsky.social · 4mo ago

Phenome-derived polygenic scores and social determinants jointly shape context-dependent disease risk https://www.medrxiv.org/content/10.64898/2026.04.16.26351039v1

Ooh sorry to miss in person but glad it will be recorded. Having embarrassed myself recently blathering on about how my one undergrad “Theater of Bertolt Brecht” class formed my perspective on AI (thanks umich rc!), it will be nice to hear from folks who’ve actually studied and thought about this.

Alondra Nelson@alondra.bsky.social · 3mo ago

An #AI event with #PhiBetaKappa next Tuesday in San Diego, where I was elected to PBK. A full circle moment. Free with registration. Join us! www.eventbrite.com/e/the-human-...

Congrats and kudos to @xueyaowu.bsky.social for leading this collab with Joy Jiang, Graham Colditz, Rulla Tamimi & team—first of 🤞many projects to peek into the black box of AI mammogram risk models and see if they are telling us something about breast cancer epidemiology. 1/2

xueyaowu.bsky.social@xueyaowu.bsky.social · 4mo ago

Excited to share our recent paper in #npjBreastCancer! We investigated what drives the AI-generated mammogram risk score (MRS)—a texture feature that predicts breast cancer risk beyond breast density. A thread 👇 @peter-kraft.bsky.social

So this is a really important point- using AI to "detect" IPV without patients' consent or willing disclosure raises issues - why screen for IPV without a patient-centered framework? - what are health systems doing with these data? - how are patients being protected?

Oni Blackstock, MD MHS@oniblackstock.bsky.social · 4mo ago

One reason is that it takes away autonomy from the patient/client to disclose their experience of IPV. People experiencing IPV often strategize what to share and when. AI "disclosing" this takes away their autonomy and could put people at greater risk.

No. No I am not. But I’m gonna steal that line: “from practice for practice.”

Hey, cancer epi folks: I’m organizing an informal morning run/walk meet up at #AACR26. If you’d like to join, DM me for details!

Looking forward to #AACR26 in San Diego in less than a week! Check out these presentations from our team, including the largest ever GWAS of breast cancer & AML and a hot-off-the-presses study of mutational patterns in triple-negative breast cancer.

A propos moon bases and Mars colonies: “there will be ample provision for the elite,” Dennis Brutus, 1978.

I’m honored and excited to join the Board of Directors! IGES is home to such a vibrant and welcoming scientific community, I look forward to helping it continue to thrive! 💟🧬 Join us for IGES 2026 in beautiful Estérel, QC 🍁 Abstract submission is open until May 30 www.geneticepi.org/2026-annual-...

International Genetic Epidemiology Society@geneticepi.bsky.social · 5mo ago

Congratulations to the winners of this year's IGES leadership elections! 🎉🎉🎉 • President Elect: Elizabeth Blue • Treasurer: Cheryl Cropp • Board of Directors: @lindakachuri.bsky.social and @burcudarst.bsky.social

Failure to understand that the fundamental principle of Mendelian randomization (MR) is of gene-environment equivalence contributes to the flood of nonsense MR papers that are appearing; Shah Ebrahim, Gib Hemani and I explain why in this short commentary. journals.plos.org/plosmedicine...

Gene-environment equivalence: The fundamental principle of Mendelian randomization

In this Perspective, George Davey Smith and colleagues outline how and why gene-environment equivalence, the fundamental principle of Mendelian Randomization (MR), must be properly applied and critica...

journals.plos.org

Interested in pleiotropy dissection but not sure where to start, which methods are useful, which studies offer illustrative examples, or how to robustly validate your results? Look no further 👀 rdcu.be/eSfAZ

Dissecting pleiotropy to gain mechanistic insights into human disease

Nature Reviews Genetics - Genome-wide association studies of increasing scale have revealed the prevalence of pleiotropic genetic variants that affect multiple traits. In this Review, the authors...

rdcu.be

@ajhgnews.bsky.social sat with Julie-Alexia Dias, MSc, in the latest "Inside AJHG" to discuss her recently published paper, “Evaluating multi-ancestry genome-wide association methods: statistical power, population structure, and practical implications.”➡️ ashg.org/ajhg/inside-... #ASHG #humangenetics

This was neat work by @nmancuso.bsky.social et al developing and benchmarking a new multi-ancestry fine-mapping method (“SuShiE”). I learned something about the performance of pooled v stratified analyses but still have some Qs. 1/n

Nature Genetics@natgenet.nature.com · last yr.

📢OUT TODAY @natgenet.nature.com 📰Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk. By @zeyunlu.bsky.social, @nmancuso.bsky.social and colleagues. ⬇️ www.nature.com/articles/s41...

The observation that joint analysis can safely improve power strikes me as being a similar observation to that of @genandgenes.bsky.social et al in their Nature 2019 manuscript: www.nature.com/articles/s41...

Genetic analyses of diverse populations improves discovery for complex traits - Nature

Genetic analyses of ancestrally diverse populations show evidence of heterogeneity across ancestries and provide insights into clinical implications, highlighting the importance of including ancestral...

nature.com

Multi-ancestry GWAS can increase power and precision, but how should we analyze them? Pooled or stratified? We answer that question in a paper out today in AJHG, led by Julie Dias and Haoyu Zhang. 1/7 www.cell.com/ajhg/fulltex...

Evaluating multi-ancestry genome-wide association methods: Statistical power, population structure, and practical implications

Multi-ancestry GWASs enhance discovery in diverse populations, but optimal methods remain debated. Using theory, simulations, and analyses from the UK Biobank and All of Us, we show that pooled analys...

cell.com

An evergreen thread: Race/Ethnicity is *not the same* as genetics, and you can't use Race/Ethnicity as a sort of stand-in for genetics. These two concepts are connected via aspects like skin colour, but the connection is alot less profound and categorical than most people think.

Nice blog and good to see this also from the twins/shared environment side. We (with my colleagues in @wittbrodtlab.bsky.social) have tried to tackle the non-additive in experimental settings (in medaka fish) which we can map to human (as the medaka fish are "wild") www.biorxiv.org/content/10.1...

Discovery and characterisation of gene by environment and epistatic genetic effects in a vertebrate model

Phenotypic variation arises from the interplay between genetic and environmental factors. However, disentangling these interactions for complex traits remains challenging in observational cohorts such...

biorxiv.org

I wrote about gene-gene interactions (epistasis) and the implications for heritability, trait definitions, natural selection, and therapeutic interventions. Biology is clearly full of causal interactions, so why don't we see them in the data? A 🧵:

Beneath the surface of the sum

When genetic interactions matter and when they don't

open.substack.com

Upvoting this response to the NIH RFI on limiting publishing fees, and highlighting two points. 1/3

Chris Marcum 📖@csmarcum.sciences.social.ap.brid.gy · 11mo ago

I've made my personal response to The National Institutes of Health Request for Information on Maximizing Research Funds by Limiting Allowable Publishing Costs available to all to read here: https://doi.org/10.54900/da84n-4hx26

Congrats to Yuxi Liu & co. for showing adherence to a Mediterranean diet lowers dementia risk—especially for those who inherited risky genes. (1/4)

CNN@cnn.com · 12mo ago

Closely following the Mediterranean diet lowered the risk of dementia by at least 35% in people with two copies of the APOE4 gene, a major risk factor for Alzheimer's, according to a new study. https://cnn.it/45UbHPX