Daniel E. Weeks

Out now in @natgenet.nature.com, our Comment analyzing uses of the Human Genome Diversity Project (HGDP), a controversial dataset in human genomics research. A 🧵

rdcu.be/eRu65

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New paper “Proteome-wide model for human disease genetics” is now live at Nature Genetics: rdcu.be/eRu7K
popEVE (pop.evemodel.org) finds the needles in the haystacks of human genetic variation:

INCEPTION Symposium 2025 - Research INCEPTION symposium 2025 - Focus on GWAS: paving the way for the future of genetics.

The INCEPTION is organizing its Annual Symposium. This year is about GWAS & beyond! We're happy to have @bpasaniuc.bsky.social, @caina89.bsky.social, Iuliana Ionita-Laza , Sriram Sankararaman, and others, who will talk about tools for understanding the genetic determinants of complex diseases

Incredible story of tracking down the real human behind AI slop stories, by @nickhunebrown.bsky.social

The missing heritability question is now (mostly) answered Not with a bang but with a whimper

I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵

Interesting answers, and striking that I never asked myself that question until now.

#rstats Please welcome Jarl, a new R linter.

Jarl is a CLI tool with extensions in VS Code, Positron, and Zed. It can check thousands of lines of R code in milliseconds.

Jarl provides several output formats, a Github Actions workflow, and more.

Blog post: www.etiennebacher.com/posts/2025-1...

Proteome-wide in silico screening for human protein-protein interactions Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...

Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp

Aaah! New preprint from the Sethuraman Lab has dropped! Tamsen and I have been working on this for a while, and we can’t wait for your feedback. Short thread on our swanky new polyploid genome simulator, DemographiKs, and its functionality.

Genome-wide association analyses identify distinct genetic architectures for early-onset and late-onset depression - Nature Genetics Genome-wide association analyses leveraging Nordic biobanks with longitudinal health registries identify differences in the genetic architectures of early-onset and late-onset major depressive disorde...

The results of the study were published in Nature Genetics: @natgenet.nature.com
www.nature.com/articles/s41...

How do genetic association studies rank genes? Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology.

@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪

www.nature.com/articles/d41...

Researchers publish paper about the promise and perils of post-publication peer review (e.g. Pubpeer). Turns out the paper has several hallucinated citations, which are pointed out on... Pubpeer.

Commenters have also spotted that the last author (and EIC of the journal) has 11 retractions. 🤷‍♂️

Is there a link for this paper?

The DOI in the Eureka Alert does not work.

www.eurekalert.org/news-release...

Genomic Investigations of Spoken and Written Language Abilities: A Guide to Advances in Approaches, Technologies, and Discovery Purpose: The aim of this tutorial is to show how the rise of molecular technologies and analytical methods in human genetics yields exciting new ...

Advances in genomics are giving exciting new perspectives on biology of speech, language & reading. My latest peer-reviewed paper is a tutorial, guiding readers from different backgrounds through the history of the field, current state-of-the-art, & where we’re heading. A taster in this thread.🧪
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OK.

DOES THIS WESTERN BLOT LOOK MORE LIKE A FISH OR A SHOE.

This is another example of why I think default priors are generally inappropriate for professional work. They're still great for teaching, though.

Nice thread about why CI won't help to solve the p-value problem

Nice to see all these confidence intervals. I use Wilson as a default but should be using Bayes. Challenge: figure out why “exact” confidence intervals are not recommended.

a giant graph with moderately increasing performance with age on 'percent correct'

relatedly, your images, text, and especially graphs/figures can almost always be bigger than you're making them

one thing I force myself to do is never present multi-panel figures in talks. just put each panel on its own slide then it will be huge. it's hard to read graphs from far away!

eg:

Hello bluesky community!

I'm hiring a postdoc to do machine learning in population genetics.
Starting to build up a lab at Indiana University Bloomington where I just started a faculty position.
Apply with the below link: indiana.peopleadmin.com/postings/30325

We strongly suggest using the following labels: praise: Praises highlight something positive. Try to leave at least one of these comments per review. Do not leave false praise (which can actually be damaging). Do look for something to sincerely praise. nitpick: Nitpicks are trivial preference-based requests. These should be non-blocking by nature. suggestion: Suggestions propose improvements to the current subject. It’s important to be explicit and clear on what is being suggested and why it is an improvement. Consider using patches and the blocking or non-blocking decorations to further communicate your intent. issue: Issues highlight specific problems with the subject under review. These problems can be user-facing or behind the scenes. It is strongly recommended to pair this comment with a suggestion. If you are not sure if a problem exists or not, consider leaving a question. todo: TODO’s are small, trivial, but necessary changes. Distinguishing todo comments from issues: or suggestions: helps direct the reader’s attention to comments requiring more involvement. question: Questions are appropriate if you have a potential concern but are not quite sure if it’s relevant or not. Asking the author for clarification or investigation can lead to a quick resolution. thought: Thoughts represent an idea that popped up from reviewing. These comments are non-blocking by nature, but they are extremely valuable and can lead to more focused initiatives and mentoring opportunities. chore: Chores are simple tasks that must be done before the subject can be “officially” accepted. Usually, these comments reference some common process. Try to leave a link to the process description so that the reader knows how to resolve the chore. note: Notes are always non-blocking and simply highlight something the reader should take note of.

I recently discovered Conventional Comments (conventionalcomments.org) for providing a pseudo-standard set of labels for feedback and just tried it for an article review and it was really helpful to specify issues vs. thoughts vs. suggestions, etc. Hopefully it's helpful for the authors too!

High-resolution mapping of a rapidly evolving complex trait reveals genotype-phenotype stability and an unpredictable genetic architecture of adaptation The extent to which adaptation can be predicted, particularly for traits with complex genetic bases, is unknown. Here, we leveraged a model complex trait, model species, and high-powered longitudinal ...

Thrilled to finally share the magnum opus of my PhD that focuses on the genetic basis of evolutionary change! Specifically, we know we can map the genetic basis of a trait, but can we tell which genes will underlie the trait shift when it evolves? doi.org/10.1101/2025...

#rstats
🌈🌈 Do you ever need/want to print text in color in markdown/Quarto documents, so you can easily refer to red points or blue lines in a graph?
A start on this is in the {colorize} 📦, friendly.github.io/colorize/

YouTube video by Todd Snider - Topic Statistician's Blues (Live)

RIP Todd Snider. He wrote the greatest song about #statistics you'll ever hear: Statistician's Blues.
www.youtube.com/watch?v=HPlD...

Great work led by Andrew Castillo extending sample size stability analyses to interactions! We've also added a function implementing these analyses to the InteractionPoweR R package: dbaranger.github.io/InteractionP... #rstats

Cool resource for the #rstats #spatial crowd #econsky

worldbank.github.io/ntl-training...

An overview shot of a portion of the collection: a long window box with wooden frames filled with glass models of plants carefully arranged and labeled on white backgrounds, as though part of a 3D herbarium. From this distance, they are indistinguishable from real plants.

Glass model of maple leaves, featuring blended molten glass that mimics the red hues of autumn foliage

A glass model of a Columbine (Aquilegia) with parsley-like leaves and pendulous, faintly red and yellow flowers that look like swans huddled together, necks touching and wings flared out.

Glass model of a Potentilla with almost ferny foliage and simple, open-faced yellow flowers with fuzzy centers.

Recently visited the Glass Flowers at Harvard, a collection of 4,300 extraordinarily realistic glass models of plants crafted by the Blaschkas, a father and son team of sculptors

That’s right, these are all made primarily of GLASS — a fact difficult to accept given how accurate & lifelike they are

There must be some fundamental law of the universe that no matter how many times you go over the galley proofs, no matter how intensively you & your coauthors examine them, a glaring typo will sneak its way through in plain sight. I just caught one at the final hurdle, next time may not be so lucky.

Claude R Tidyverse Expert Claude R Tidyverse Expert. GitHub Gist: instantly share code, notes, and snippets.

I was loving Claude Code... until I tried it with #rstats. Constant errors, wouldn't use the tidyverse even when asked, "optimized" functions were slower.

Frustrated, I started a session just to teach R to Claude and summarize what it learned into a CLAUDE.md file gist.github.com/sj-io/3828d6...

Photographic portrait of Bertrand Russell, and a quote : "Mathematics may be defined as the subject in which we never know what we are talking about, nor whether what we are saying is true."

"Mathematics may be defined as the subject in which we never know what we are talking about, nor whether what we are saying is true." – Bertrand Russell (1872–1970)
#quote #mathematics #maths #math