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holtjma.bsky.social
Matt Holt
@holtjma.bsky.social
890 followers 150 following 240 posts
Staff scientist at @PacBio; formerly @hudsonalpha; avid gamer; opinions are my own
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holtjma.bsky.social
Matt Holt @holtjma.bsky.social · Nov 19
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...
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 ...
github.com
Reposted by Matt Holt
needhibhalla.bsky.social
“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.”
January 26, 2026 at 3:26 PM
Reposted by Matt Holt
erictopol.bsky.social
Point blank.
10-shots.
Execution.
A US citizen, a VA ICU Nurse.
Then lying.
Blocking a real investigation.
January 26, 2026 at 1:00 AM
Reposted by Matt Holt
barackobama.bsky.social
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.
January 25, 2026 at 5:39 PM
Reposted by Matt Holt
sifill.bsky.social
I cannot imagine the devastation this family is experiencing today. This statement is powerful and must be read.
January 25, 2026 at 1:52 AM
Reposted by Matt Holt
petebuttigieg.bsky.social
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.
January 24, 2026 at 9:08 PM
Reposted by Matt Holt
jonathanmladd.com
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.
January 22, 2026 at 2:17 PM
Reposted by Matt Holt
goldwagnathan.bsky.social
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.
reichlinmelnick.bsky.social Aaron Reichlin-Melnick @reichlinmelnick.bsky.social · 5d
Senator Gallego weighs in as well. Note that at the start of 2025 he was considered a *moderate* on immigration and co-sponsored the Laken Riley Act. Him and many other Dems have been increasingly horrified at what ICE is doing and shifted away from a "more enforcement" focus.
Ruben Gallego @RubenGallego Yeah I am not voting to give whatever ICE has become more tax payer money. It’s no longer an immigration enforcement arm of the US government. Quote The Associated Press @AP · 1h BREAKING: Immigration officers are asserting sweeping power to enter homes without a judge’s warrant, a memo obtained by AP says. 5:50 PM · Jan 21, 2026 · 476 Views
January 21, 2026 at 11:09 PM
Reposted by Matt Holt
xkcd.com
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...
How long would you survive with no DNA?
YouTube video by xkcd's What If?
www.youtube.com
January 21, 2026 at 8:27 PM
holtjma.bsky.social
We just released a fairly substantial update to HiPhase that enables (beta) support for RNA (isoseq) datasets. There are some incidental improvements to WGS phasing as well!

Full release notes here: github.com/PacificBiosc...
January 20, 2026 at 8:33 PM
Reposted by Matt Holt
ahoischen.bsky.social
1,000 PacBio genomes in a prospectively designed clinical utility study.
This was the biggest and most important study that made us go live in diagnostics.

Long-read genomes as a genetic first tier test across many rare diseases!
www.medrxiv.org/content/10.6...
Clinical long-read genome sequencing for rare disease diagnostics
Background Diagnostic evaluation of rare genetic disorders continues to rely on multiple test modalities, despite the increasing use of short-read exome or genome sequencing as first-tier tests. Long-...
www.medrxiv.org
January 19, 2026 at 8:30 AM
Reposted by Matt Holt
bencollins.bsky.social
Block instantly.
January 17, 2026 at 12:13 AM
holtjma.bsky.social
Finally found time to play expedition 33… what an absolutely phenomenal experience! (Just ended act 2 for those who have played)
January 16, 2026 at 4:37 AM
Reposted by Matt Holt
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
HLi Lab - Vacancies
Openings
hlilab.github.io
January 14, 2026 at 3:44 PM
Reposted by Matt Holt
mrvollger.bsky.social
I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt:
employment.utah.edu/salt-lake-ci...
Jobs | University of Utah
Founded in 1850, The University of Utah is the flagship institution of higher learning in Utah, and offers over 100 undergraduate and more than 90 graduate degree programs to over 30,000 students. Uni...
employment.utah.edu
January 12, 2026 at 9:04 PM
Reposted by Matt Holt
reichlinmelnick.bsky.social
NEW: Data released by ICE shows that virtually the entire growth of detention in the last few months has been among people with no criminal record at all - no prior convictions (no matter how minor) and no pending criminal charges.
Chart showing "Detention Population, Among Those Arrested in the interior, by Criminal Record, May 2019 through January 27, 2026. There are three lines on the graph: prior conviction, pending criminal charges, and no criminal record. from 2019 through January 2025, "prior conviction" is by far the highest, followed by pending charges much lower down and "no criminal record" the lowest. During the Biden admin, very few people arrested by ICE in the interior and detained had no criminal record. Beginning in January 2025, all three lines jump, but the highest spike is among those with no criminal records. By September, that has become the single largest. Since that point, there are now thousands more people in detention with no criminal record than people with prior convictions.
January 9, 2026 at 12:55 AM
holtjma.bsky.social
I feel like no matter how many times I build a tool with multi-threading, I will always build it sub-optimally the first time...

(bonus: it's often the first *few* times 🫠)
January 6, 2026 at 11:09 PM
Reposted by Matt Holt
mehdirhasan.bsky.social
A reminder - before Trump, MAGA, Musk and Fox rewrote history - that this is what the entire country agreed had happened five years ago today:
January 6, 2026 at 12:40 PM
Reposted by Matt Holt
nycsouthpaw.bsky.social
That is a lot of news to wake up to.
January 3, 2026 at 12:37 PM
Reposted by Matt Holt
maia.computer
we reproduce asexually, releasing clouds of spores at certain points in our lifecycles, like some species of fungi
December 28, 2025 at 10:58 PM
Reposted by Matt Holt
xkcd.com
Funny Numbers

xkcd.com/3184/
Comic. [Banner: Mathematical Society: 2025 Meeting.] PERSON 1 with bun: Any other new developments from the year to cover before we wrap? PERSON 2: Oh, the teens picked a new funny number. PERSON 3 with short hair: Aww, I’m glad to hear they’re still doing that. PERSON 4 with ponytail: I’ll add it to the list. [List: 23 (skidoo!; 42; 69; 420; 1,337; 58,008; [circled]: 67]
December 26, 2025 at 10:44 PM
Reposted by Matt Holt
holtjma.bsky.social
There's an opening in our CompBio group at #PacBio. Apply below if you're interested in method / tool development for long-read sequencing applications! #Bioinformatics

pacbio.wd12.myworkdayjobs.com/PacBio-/job/...
December 12, 2025 at 6:40 PM
Reposted by Matt Holt
jsantoyo.bsky.social
CiFi: accurate long-read chromosome conformation capture with low-input requirements. #HiFi #LongRead #Sequencing @natcomms.nature.com 🧪🧬 🖥️
www.nature.com/articles/s41...
December 16, 2025 at 11:30 AM
holtjma.bsky.social
There's an opening in our CompBio group at #PacBio. Apply below if you're interested in method / tool development for long-read sequencing applications! #Bioinformatics

pacbio.wd12.myworkdayjobs.com/PacBio-/job/...
December 12, 2025 at 6:40 PM
Reposted by Matt Holt
stevensalzberg.bsky.social
I can't stay quiet about what RFK jr is doing to the CDC and FDA:
stevensalzberg.substack.com/p/dont-trust...
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
stevensalzberg.substack.com
November 29, 2025 at 7:51 PM
holtjma.bsky.social
At the start of the year, did anyone predict k-pop as a featured part of the macys thanksgiving day parade?
November 27, 2025 at 10:22 PM