Matt Holt

Don't trust the CDC while RFK Jr. is in charge The HHS secretary, a notorious anti-vaxxer, is now posting his crank views on CDC's website

I can't stay quiet about what RFK jr is doing to the CDC and FDA:
stevensalzberg.substack.com/p/dont-trust...

At the start of the year, did anyone predict k-pop as a featured part of the macys thanksgiving day parade?

And this is the simplest entry point for getting the direct BASEPAIR scoring given *sequences* as opposed to variants:
docs.rs/aardvark-bio...

There are likely ways we can make the previous two entry points more simple like this one, if needed.

This is the more general entry point that will "solve" a region for both GT and BASEPAIR scoring:

docs.rs/aardvark-bio...

Sorry, the docs are a bit of a mess and could use some love when I get time.

That entry point will get you the GT-based scoring (exact match) for a set of variants. There are some examples in the unit tests that can function as simple examples: docs.rs/aardvark-bio...

crates.io: Rust Package Registry

If you're looking to use some of aardvark's functionality in your own code, we've made aardvark available on crates.io for easier access under the `aardvark-bio` name:

crates.io/crates/aardv...

Gotta say, it’s a hard time to be a historian of medicine whose focus was pre-antiseptic / pre-vaccine era.

Of course, big shout out to our beta testers who helped shape the changes in this release! Let me know if there are other additions you'd like to see in the future.

Release StarPhase v2.0.0 · PacificBiosciences/pb-StarPhase Changes Database construction (pbstarphase build) has been updated to support sub-allele definitions from PharmVar Variants and alleles are now annotated as either being "core" or "sub" types By ...

We have released StarPhase v2.0! The key addition is support for PGx sub-allele definitions for genes from PharmVar. While we were in there, we made some other QoL upgrades as part of v2. Let us know what you think!

Full release notes: github.com/PacificBiosc...

GitHub - PacificBiosciences/aardvark: A tool for sniffing out the differences in vari-Ants A tool for sniffing out the differences in vari-Ants - PacificBiosciences/aardvark

Aardvark?

github.com/PacificBiosc...

World first: Radboudumc pioneers new genetic test in clinical practice - New test is faster, more efficient, and provides more diagnoses for rare diseases 17 November 2025

Long-read genome sequencing is new first-tier generic test in diagnostics of rare diseases

So satisfying to see a long journey end in best-possible diagnostic test for patients with rare diseases @radboudumc.bsky.social.

www.radboudumc.nl/en/news-item...

(1/n)

Over Lansing, MI!

I just try to avoid major deviations from norms, even if those deviations are *technically* in spec. There’s usually no reward, just a high risk of a bunch of user issues/complaints distracting from the fun parts of what we do.

This sounds like the kind of thing that would break a lot of parsers, I guess the current VCF spec doesn’t work for some reason?

What we know, final edition of the night:
[Now in 3 parts]

—Prop 50 wins
—VA Dems flip Gov, LG, AG
—Dems gain leg seats in VA, NJ, & MS
—Dems defend NJ-Gov
—Dems win NJ+VA trifectas
—Mamdani wins
—PA Dems win state supreme court
—ME anti-mail voting measure loses
—GA Dems flip 2 statewide offices

Poshanka!

TotK is the obvious extension. If you like Mario Odyssey, DK Bananza is somewhat similar to both (and kid friendly if that matters). It’s hard to find a game with adventure/story/cinematics + open world + puzzles/crafting, which is part of why BotW was so awesome!

Looking at code from 12+ months ago always feels like the uncanny valley of code self-review. There's evidence of my coding fingerprint, and I *know* I wrote the code, but it's not quite how I would do it today.

Editorial_Board Editorial Team Editor-in-Chief Xun Xu, PhD; BGI Research, Shenzhen, China Executive Editor Hongling Zhou; GigaScience Press, BGI Shenzhen, China Edito

About half the GigaScience editorial board (incl me) just resigned (academic.oup.com/gigascience/... is not yet updated). I resigned because it is very unclear what is happening and why - see @scedmunds.bsky.social blog post gigasciencejournal.com/blog/and-its..., for eg

Hurricane Melissa is the THIRD Category 5 storm of 2025, tying the record set by the legendary 2005 season.

And get this, 80% of this season's hurricanes have reached Category 4 or 5 strength. That's the highest percentage in Atlantic history.

Advancing human health with HiFi long-read sequencing YouTube video by PacBio

Want a rare look inside @pacbio.bsky.social facility and hear how customers use HiFi for HLA typing and PGx? We made a 6-min documentary this summer. Check it out! www.youtube.com/watch?si=nXb...

Release Aardvark v0.9.0 · PacificBiosciences/aardvark Changes Adds the optional RECORD_BP comparison type to all summary files. Review our methods for details on this metric. This metric is enabled with --enable-record-basepair-metrics. The GT and BA...

Our first major update for Aardvark since the pre-print is now available. We added an optional "record basepair" score type which may better match historical tandem repeat metrics, and also made some of the less-used metrics optional as well.

Full release notes here: github.com/PacificBiosc...

It’s challenging as well, the difference in AI slop and human sloppiness is hard to distinguish. I didn’t want to name the preprint because it could just be poor writing and inattention to detail, hard to say.

I think I just found my first AI generated preprint on bioRxiv. Unclear methodology, invalid citations, and dead links. Are these supposed to get reported somewhere?

Second "No Kings Day" protests likely the largest single-day political demonstration since 1970, with 4.2-7.6 million participants Here are the initial results from our crowdsourced crowd-counting estimates

Good evening. We estimate that between 4.2 and 7.6 million people turned out for the No Kings Day demonstrations held around the country on Saturday. This makes Oct 18 very likely the biggest single-day U.S. protest event since 1970. www.gelliottmorris.com/p/second-no-...

I should have stayed an extra day after #ASHG25

Our third #ASHG25 CoLab begins in one hour at 10:15 am in Theater 1!

Hear from #PacBio and @epicypher.bsky.social on Fiber-seq epigenomics for integrated chromatin, genome, and methylome insights, plus Revio workflow updates and big announcements on what’s next for #Revio and #Vega in 2026 👀.

I’ll be presenting a poster on Mitorsaw for #PacBio HiFi mitochondrial analysis today! Come see me this afternoon at #ASHG25 poster #4050 to chat about that or other topics!

Eric Green receiving the ASHG Leadership Award. Talks about being the first institute or center director to lose his leadership role. Said that he failed to doge the bullet. #ASHG25

ASHG Plenary Session starting with the awards ceremony honoring Eric Green with the Leadership Award of @geneticssociety.bsky.social reflecting on his career in human genetics & genomics leading the Human Genome Project & the NHGRI and the leadership principles he has learned throughout #ASHG25