Massive single-cell study by Kanai et al (www.medrxiv.org/content/10.1...): - Once statistical power is high, constrained genes have more (though weaker) eQTLs. - Chromatin-QTLs near constrained genes have "normal" effect sizes, colocalize more with disease, but exhibit attenuated peak-gene effects.

A thread of directed acyclic graphs (DAGs) that look like record covers... because that's EXACTLY what the world needs 1. Huey Lewis and the News: link.springer.com/chapter/10.1...

Well, I found the solution Harmit!

Americans make great biologists because we are forged by the hardest challenge in all of biotech: getting flavor from a turkey

I'm a longtime fan of Affinity Designer as an affordable Illustrator-killer for figures, and... it's now free?! www.canva.com/newsroom/new... Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.

Many journal sites are down. But you know which one is NOT? That of CSH Protocols! So, check out the definitive source of technique-related reviews and laboratory protocols in the life sciences. cshprotocols.cshlp.org

"it would make sense to adopt some ground rules. In many ways, these would be similar to those adopted by geneticists after the first frenzy of candidate gene associations was found to be a waste of time and money because the area was overwhelmed by nonreplicable false positive results."🙌

We did a thing. 😬

I've done a lot of work in Python this fall, and it hasn't endeared me to the language at all. Why does stuff have to be so complicated when you're doing it in Python? blog.genesmindsmachines.com/p/python-is-...

Now a nice series of papers using genetics to "uncouple" excess adiposity from its adverse metabolic effects. Here for metabolic traits www.nature.com/articles/s42..., here including non metabolic traits elifesciences.org/articles/72452 & here using partitioned PRS www.nature.com/articles/s41...

The real question, the one many of us are avoiding, is whether we need some metric to rank publications. Be that JIF, citation count, or something akin to eLife's impact assessment. And from my recent foray onto the academic job market, the answer is an unequivocal yes. Journals provide this.

Outlook, can we have a nice email user experience? Or maybe have copilot help us parse through our inbox? Hell no, but I will flag any and all google calendar invites as phishing

#r2u now contains BioConductor 3.22 released yesterday for Ubuntu 24.04 and 22.04 (for the 500-some packages we cover, details at the site). #Rstats 4.5.2 has been built, we will update the containers in a few days as well. #r2u. Fast. Easy. Reliable. Pick All Three. eddelbuettel.github.io/r2u

I am very happy to finally share SAFE-LD, a method convert genotypes to an anonymised privacy-preserving version to be used to precisely compute LD. Led by @gdesanctis.bsky.social Claudia Gianbartolomei @sodbo.bsky.social and Davide bolognini. 📄: shorturl.at/BgXqq Github: shorturl.at/b49Wa

With so many new methods buried in results-focused papers, this thread is my encouragement to groups to also publish separate protocols papers! You'll be pleasantly surprised at the engagement these papers get, and most importantly they provide real impact aiding others in their science.

A small 🧵 encouraging people to publish protocols. Our #AutoSpectral release has made me reflect on how much the community tends to appreciate protocol papers. People rarely present protocols as their main achievements, but they are often the most impactful work. www.biorxiv.org/content/10.1...

PSA: it’s all great if you provide an interactive dashboard to browse the data you painstakingly generated. But please do back up the data on persistent archive like zenodo. It’s too bad we can’t access the database when inevitably the server goes down and you moved onto other projects/institutions

🧬 EuroBioC2026 is coming to Turku, Finland, from June 3–5, 2026! Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology. 👉 More details soon at eurobioc2026.bioconductor.org

I've been asked about this paper (www.nature.com/articles/s41...) enough times that I finally had to read it. The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma. tl;dr it's glam-slop & everyone involved should be embarrassed

#rstats : when you have a path string like "this/is/my/path", is there a formatting shortcut somewhere to quickly split it into a vector like c("this", "is", "my", "path") (even better if with {here} or {this.path}) {lintr} is harassing me for long lines and I ought to do something

Be careful, check your kids’ book, they might contain rogue pseudotime analyses 💻🧬

💡 Came across this nice tool today: 🎨 qualpal for algorithmically choosing maximally distinct colors under certain restrictions #dataviz JOSS paper, online tool, R package #rstats joss.theoj.org/papers/10.21...

Are you going to #ASHG2025 next week in Boston? Interested in getting some mentorship from leading figures in the field (and me)? Check out our speed mentoring event on Thursday! Sign-ups are online so reserve a spot ASAP. site.pheedloop.com/event/ASHG25...

One of the biggest increases in my analysis/coding productivity in recent years is completely embracing git repos 🐧 Coupled with GitHub it is *so easy* to be open, reproducible, efficient, and accountable to myself and colleagues 👨‍💻 No more chaotic servers wondering which script led to what! 😵‍💫

Is it me or now Rstudio saves files with .r instead of .R? Same goes for Rmd vs rmd. What is this heresy #rstats? Well I actually don’t know if there is one way that is more correct but

This is truly an incredible breakthrough IMO. Really exemplifies what you get when deep domain expertise (popgen/evolution/disease genetics in this case) fuses with cleverly crafted ML. What u get r sleek, well thought out architectures that absolutely destroy the behemoths. Wow!! 1/

Massive sibling regression study finds that human traits are largely environmentally driven (average heritability = 0.3)

Only single cell sequencing of the all these post docs will reveal why

@riyavsinha.bsky.social @jengreitz.bsky.social sky.social @anshulkundaje.bsky.social y.social have made the ENCODE-rE2G data available to browse through the E2G portal, a custom-built extension of the Platform 👇 We plan to further integrate their data 👀 e2g.stanford.edu

Teaching data science, data visualization, or programming is getting quite challenging when LLMs are so good at these tasks. I strongly feel students still need to do things themselves. But how do we make them do this, and not just take the AI shortcut? blog.genesmindsmachines.com/p/teaching-d...

I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.

I could have sworn I created this before on our Previous Parish, but couldn't find it so made it fresh. I present: OUR BLESSED mixed models // THEIR BARBAROUS fixed effects

Our first Fall #tidyomics meeting will be this Wed 10 September, early in US / noon in Europe / late in Australia. Feel free to join if you're interested in what we are doing to make omics data more amenable to tidy data analysis. Organized with Stefano @stemang.bsky.social

In a new work with Joseph Rich and Conrad Oakes we tackle the problem of how to best organize alluvial plots. We formalize two optimization problems and develop a solution for them based on the neighbornet algorithm, implemented in the program wompwomp: github.com/pachterlab/w...

🚨 This will become a curated list of awesome tools for complex trait genetics, **add yours**! it may become a review in which case those who contribute are invited as co-authors.

"We propose a model in which TF binding is not determined by individual binding sites, but rather by the sum of multiple, overlapping binding sites." www.nature.com/articles/s41...

I’ve been quiet for a while on here as I relocated from France to Denmark. Copenhagen is great and after lots of relocation logistics, I just started as a Researcher at @cbmr.science. I’ll work on variant to function projects in the field of obesity in the Loos group.

She published in 1936 the work that would secure her a place in the history of science. The article was titled " P’ " and used data from seismic stations around the world. On Inge Lehmann: uniavisen.dk/en/the-overl... ‪‬ @minouette.bsky.social @adalovelaceday.bsky.social ‪‪

Excited to share this preprint from first author Jon Rosen, a postdoctoral fellow in the @klmohlke.bsky.social lab and my lab. We examine eQTL study sample size and how this affects signal discovery and rates of colocalization with GWAS. www.biorxiv.org/content/10.1...

Just posting a preprint of the work should be the way to achieve such open access. The preprint is the only version that is solely the work of the fundee, and the only version over which the funder should have any say.

New post: https://jcarroll.com.au/2025/06/29/counting-digits-quickly/ What if you could just wave a magic wand over your R #rstast :rstats: code and have it transform into something that ran as fast as or faster than C? @t_kalinowski's {quickr} 'R to Fortran Transpiler' does that for you! […]

Sounds nice in theory, but how can the student be competitive for post docs and later, ECR awards without publications? It’s just setting students up for career failure in the current world. If you want to change science, change uni hiring practices first.

At least they seem to be discussing issues with reactions more complex than stirring NaCl into solution! I am, however, reminded of this incredible detective story: www.cell.com/cell-reports...

We are excited to announce that tidypopgen – a new package for rapid population genetic workflows in R – is now available at evolecolgroup.github.io/tidypopgen/ 🧬💻 Read more in the preprint describing its features here: www.biorxiv.org/content/10.1... #popgen #Rpackage #genetics 1/2

Game apps marketing has gone too far: thanks to AI, cards are randomly distributed!

Deep Learning