Daniel E. Weeks

In somebody else's words:

Accessibility score for: evalsp26_01-exam_answers 100% Accessibility score: 100 percent arrow_drop_up Perfect! This PDF has a perfect accessibility score, although further improvements may still be possible. Keep up the good work!

If you use #QuartoPub for any PDF documents for teaching and you need to meet impending PDF accessibility rules, upgrade to v1.9, add format: typst: pdf-standard: ua-1 to the YAML front matter, and it'll work!

Is there a similar option for fixing accessibility issues with a Quarto book?

#Quarto #QuartoPub

📣 SING USA 2026 applications are open!

The Summer Internship for Indigenous Peoples in Genomics (SING) workshop will be July 19–24, 2026 at UW–Madison.

⏰ Apply by March 13 (midnight Hawaiʻi time)

Learn more & apply: sing.nativebio.net

Please share with Indigenous students!

#Indigenous #Genomics

Icefish: Practical zk-SNARKs for Verifiable Genomics Individual genomic data is a uniquely sensitive type of user data. While many papers have considered using Multi-Party Computation (MPC) or Fully Homomorphic Encryption (FHE) to allow collaborators to...

Since it's not on @biorxivpreprint.bsky.social, my normal crowd might not see it, but I'm very excited about this recent work that, actually, started as class project in my graduate genomics class last year: eprint.iacr.org/2026/463 . Zero knowledge proofs for genomics; with algorithms :).

a snippet of a mini-comic, at top - straight line stretches from point A to B. Immediately below, same dot at A, then becomes a curving, meandering line that winds through the page and ends at a point with rays and a question mark emanating from it. Text reads: "Nothing can do this for you - for that robs you of experience and conflates answers with learning. Rather, it's all the decisions you make along the way, the mistakes, struggles, and surprises! These pathways you create - this is learning. https://spinweaveandcut.com/fall-2025-syllabi/

In case anyone needs it for their syllabi, my statement in gen-Ai from the minicomic I made as a syllabus for class last semester. All online and printable here spinweaveandcut.com/fall-2025-sy...

In more important spite-driven development news... sessioncheck is now on CRAN. At long last I now have something dead-simple and concrete I can point to next time I'm asked to put rm(list=ls()) in a script for no obvious reason

sessioncheck.djnavarro.net

Graph of award probability of R35 and R01 from NIH factbook as a function of review rank percentile. As is apparent, 2025 is a significant departure, with lower award probabilities at all scores <40 and significant departures from norm, where even being in the top 10% is no longer a nearly certain indicator of success. Data source: https://report.nih.gov/nihdatabook/report/302

The data is in: the NIH goalposts have shifted.

What were once almost certain fundable scores have become coin flips and what used to be likely grants have become aspirational, leading to fewer awards.

Another manifestation of how HHS policies have led to fewer awards and less science.

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.

The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...

Figure 1 shows they key result

I can't wait to try this! I'm always futzing around saving plots to different dimensions and aspect ratios, then opening the files to see if they're ok, then forgetting to close them and getting errors because the filename is in use when I try to re-save with different parameteres.

A digital CAPTCHA verification window titled "Select all squares with PIPES" against a plain white background. The window contains a 3×3 grid of numbered squares, mixing literal hardware, smoking pipes, and programming syntax.

These captchas just keep getting harder #rstats

ggview::canvas() is the best thing I have learned in 2025!

This is awesome! No more (change code -> save plot -> open file)^n just to make sure your plot is readable

The canvas() function from the ggview R package is very useful for previewing/tweaking a ggplot into publication-ready format: it renders a plot "as it would appear if saved to a file with the specified dimensions".

cran.r-project.org/web/packages...

#RStats #ggplot #ggview

Some work freshly published at EJS: projecteuclid.org/journals/ele...

'Analysis of Multiple-try Metropolis via Poincaré inequalities'
- Rocco Caprio, Sam Power, Andi Q. Wang

We conduct a convergence analysis of a specific class of MCMC procedures based on multiple-proposal strategies.

Data

Genome modelling and design across all domains of life with Evo 2 - Nature Evo 2 is an artificial intelligence-based biological foundation model trained on 9 trillion DNA base pairs spanning all domains of life that predicts functional properties from genomic sequences and p...

🤯 Evo 2, a model trained on 9 trillion DNA letters from curated genomic atlas across all domains of life “learns to accurately predict functional impact of gene variation...Model parameters, training code, inference code etc = fully open, to accelerate exploration & design of biological complexity”🧪

Are you interested in understanding how social and structural determinants of health influence estimates of genetic risk? Looking for figures for teaching these concepts?

Check out our work on considerations for modeling them together, led by Sara Cromer and Dave Conti with @prsmethods.bsky.social

“Mathematics may be compared to a mill of exquisite workmanship which grinds you stuff of any degree of fineness, but nevertheless what you get out depends on what you put in - … so pages of formulae will not get a definite result out of loose data.”
TH Huxley

🧵 New publication from the PGC Anxiety Working Group. Our GWAS meta-analysis of anxiety disorders is now published in @natgenet.nature.com! 🔗: doi.org/10.1038/s415...

I was sad to learn that my postdoctoral mentor, David Botstein, died yesterday. I started with David as a postdoc in 1998, and he had a profound effect on both my life and scientific career. He was a giant in the field of genetics, making seminal contributions in both yeast and human genetics. 1/

An important #rstats post here. (Perhaps a better title: Why tidymodels might not be so tidy)

I don't eschew this kind of discussion (|> vs %>%, ...) as R Flame Wars. In fact, it's important to continue to hone the language tools we use to express & implement our ideas/models/graphs.

Interbreeding between Neanderthals and modern humans was strongly sex biased Sex biases in admixture and other demographic processes are recurrent features throughout human evolution. For admixture between Neanderthals and anatomically modern humans (AMHs), sex bias has been p...

Many living people carry fragments of Neanderthal DNA, remnants of ancient interbreeding events, with uneven distribution across chromosomes. New work by @sarahtishkoff.bsky.social lab suggests patterns are most consistent with Neanderthal contribution to human populations being highly male biased.🧪

Specifically, the idea of source credibility just doesn't apply straightforwardly to LLM interactions. When I get info from another person I can ask: how does the content relate to their expertise? Their lived experience? Their interests and biases?

8/

What's your favourite plot type?
Extra points if it's a cool science type plot.

I really like Violin plots with swam overlays.

Happy to share our latest paper, the work of @clarajiang.bsky.social who trained brain-based predictors of depression on the UK Biobank (N=7,500 curated cases and matched controls) using AI/deeplearning as well as efficient statistical learning (BLUP).

See thread below for a summary of findings

What even is truth? Seems like it should be the purview of philosophers and poets — clearly not people (me) designing snakemake workflows.

I can't be the only one who is made /uncomfortable/ by the way that razor clams burrow into sand, right?

The final moments of this video by Kate Crump on the Oregon coastline are sort of the crowning glory of horror. 😬

But how does this even work?
Let's talk about bivalve mobility (if we must).

Retraction notice: “the authors acknowledged that their analyses include coding errors. The central error arose from the inverse hyperbolic sine being calculated based on y+1, … left over from an earlier version of the study in which a log (y+1) approach was used instead of the hyperbolic sine.”

@wytamma.bsky.social 's WASM tools have transformed my experience of teaching Python to first year undergraduate biologists this year. Since last year, I've been teaching ~400 undergrads how to code (functions, lists, dictionaries, loops) over (one hour intro lecture +) two 2-hour practicals. 1/n