Matt Holt

I may play around a bit more tonight, but this is a good checkpoint: github.com/COMBINE-lab/.... All features implemented, unit and integration tests, dedicated aarch64 & avx2 backends, a driver CLI! Still a bit slower than the C version, but we're closing the gap quick!

I’ll be presenting on long-read pharmacogenomics at #ACMGMtg26 next week. Let me know if you want to connect while there!

Introducing kuva: A scientific plotting library in rust, along with cli binary with the option to plot directly into the terminal.

Feel free to drop me some feedback as an issue on the repo

github.com/Psy-Fer/kuva

crates.io/crates/kuva/...

GitHub - zaeleus/noodles: Bioinformatics I/O libraries in Rust Bioinformatics I/O libraries in Rust. Contribute to zaeleus/noodles development by creating an account on GitHub.

Also *highly* recommend noodles for a Rust native crate: github.com/zaeleus/nood...

The screenshot of the release notes reads: A new version of TeX Live Utility is available! TeX Live Utility 1.55 is now available-you have 1.54. Would you like to download it now? Release Notes: Changes Since 1.54 • Fix bug 137, homepage link in Help Book. • First release in a long time, since I don't use TeX anymore and resent the very idea of paying Apple annually for the privilege of giving away free and open-source software. Also, I'm really lazy. Please accept my apologies for all the annoying issues you've encountered in this mission-critical software. • Updated mirror list, which was three years out of date. • Added missing legacy mirrors, which was even more out of date. • Added an alert on startup when user tries Homebrew's lobotomized MacTex, because those lunatics left timgr but removed its database. Thanks for nothing, guys. Bug 142 and 144. • Use a custom user-agent to work around the Anubis bot trap on texlive.info. Can't wait to see what else breaks because of this, thanks to the profusion of degenerate Artificial Insemination fetishists scraping websites to feed their models. • Lists of countries in Repository/Continent are now sorted. No idea how you people let me get away with that one for the last fifteen years.

There's a "is anyone even reading this" sort of honesty you get in the software update release notes from a project that's been around for a long time.

Portello: Making global assembly more effective for rare-disease whole genome sequencing www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/PacificBiosc...

Small variant basepair errors comparison between conventionally mapped reads and portello-mapped reads.

We demonstrate that variant calling shows improved accuracy given these assembly-based read mappings. For instance, given the same set of input reads, DeepVariant calling from portello-mapped reads shows a 47% reduction in errors compared to calls from a conventional mapping process. (3/5)

Comparison of read mappings at HG002 chr4:40,294,825-40,295,700, showing conventional (pbmm2) read mappings (above) and portello mappings (below). The same set of unaligned input reads were input into each mapping process.

What if you could improve small variant accuracy, CNV inference, and interpretability of your HiFi WGS data by taking a different approach to read mapping? Our new preprint describes portello, a method which demonstrates the potential for such improvements. (1/5)

This looks really interesting

Were you aware that these are available for the community:
- an efficient fasta/q parser in Rust
- a quick rolling hash library
- a minimizer library
All in Rust 🦀

So SCOTUS, with its fabricated-out-of-thin-air immunity doctrine, has actually made American presidents less accountable than LITERAL royalty.

Personally, I have not had a ton of success on anything complex.

But, I *love* it for the painful work. Eg, the fact that it can blast out unit tests and documentation that are often more complete than my own is awesome and saves my energy for the engaging complex work!

ICE plans to spend $38.3 billion turning warehouses into detention centers ICE plans to spend $38.3 billion converting warehouses into detention centers, according to planning documents, more than the annual budgets of 22 states.

So now the US is spending the enormous sum of $38 billion to build concentration camps? ICE is calling them "detention centers" but we know what they really are. I cannot believe my country would do this. Everyone should speak out against it wapo.st/3OfarSk

"Moderna's CEO announced the company will no longer invest in new Phase 3 vaccine trials for infectious diseases: 'You cannot make a return on investment if you don't have access to the U.S. market. Vaccines for Epstein-Barr virus, herpes, and shingles have been shelved.” 9:12 AM Feb 12, 2026 604.8K Views

In terms of what cures are being lost:

- Epstein-Barr virus is perhaps the major trigger for multiple sclerosis
- herpes simplex virus causes cold sores, genital herpes, infections in babies, deadly meningitis
- shingles virus causes an intensely painful disease

Prasad overruled FDA staff to reject Moderna's flu vaccine application The rejection is the latest instance of Vinay Prasad overruling career FDA scientists to place vaccines under harsher scrutiny.

The flu and pneumonia kill over 45,000 people a year. Moderna developed a new mRNA flu vaccine for people 50 and older--who are most at risk. Prasad, unilaterally, against the recommendation of experts within the agency, denied Moderna's appplication. www.statnews.com/2026/02/11/m...

“Diplotypes were assigned using the pb-StarPhase algorithm, which was considered the gold standard for this study”

😎

✨ A new star allele was born! Excited to share our first in vivo pharmacokinetic recall study involving 114 participants from @ESTbiobank with previously uncharacterised variants in CYP2C19 and CYP2D6:
www.nature.com/articles/s41... #Pharmacogenomics @pharmvar.org @clinpgx.org

Please share this with your network: Postdoctoral position available in my group.

www.linkedin.com/jobs/view/43...

Comic. [Person talking to person with black hat.] PERSON 1: Historically, it refers to a ceremony to predict the weather using a rodent. But nowadays people often use it to mean “a time loop experienced by one person.” PERSON 2: …What. [caption] Easily our weirdest holiday.

Groundhog Day Meaning

xkcd.com/3202/

Screenshot of an X post by Omar Jimenez (@OmarJim…, 7h) stating that Minnesota Attorney General Keith Ellison says he doesn’t have the names of the agents who shot Alex Pretti, adding: “I’ve been a lawyer for 36 years. I’ve never seen anything like this before.” Below is a CNN video thumbnail showing a split screen: on the left, an older man in a black cap and glasses labeled “Brown | Business Owner,” and on the right, Keith Ellison in a suit. A CNN “LIVE” bug appears in the corner.

This is a cover up of a murder, led by our own federal government.

“We cannot pursue our mission to improve the health and well-being of all Americans while DHS agents are murdering, assaulting, and terrorizing people who call this country home…We believe ICE and CBP are a greater threat to the health of our nation than the lapse of HHS services.”

Point blank.
10-shots.
Execution.
A US citizen, a VA ICU Nurse.
Then lying.
Blocking a real investigation.

The killing of Alex Pretti is a heartbreaking tragedy. It should also be a wake-up call to every American, regardless of party, that many of our core values as a nation are increasingly under assault.

I cannot imagine the devastation this family is experiencing today. This statement is powerful and must be read.

Post from Pete Buttigieg that reads: If there was ever a moment for libertarians and conservatives to step up and join the rest of us, we’re in it. Americans have to unite and stop this descent from a freedom-loving nation into the kind of place where masked, militarized government agents are sent to politically noncompliant areas to roam the streets, terrorize civilians, and deploy violence with impunity.

It’s currently operating totally outside of our constitutional rules. Habeas corpus , due process of law, equal protection, freedom of speech, 4th amendment protections against search and seizure, are all not being enforced in any common sense or meaningful way.

I would argue that the case for dismantling ICE has, at this point, virtually nothing to do with larger questions of immigration enforcement and reform, it's just clearly incompatible with a free and democratic society to maintain a secret police force with sweeping and arbitrary authority.

YouTube video by xkcd's What If? How long would you survive with no DNA?

How long would you survive with no DNA?

What the latest What If? video in collaboration with
@minuteearth.bsky.social!

www.youtube.com/watch?v=s3oL...

As always, let us know if you encounter any issues or have suggestions on improving the tool!