Sign in

Matt Holt

@holtjma.bsky.social
914 followers 159 following 270 posts

Staff scientist at @PacBio; formerly @hudsonalpha; avid gamer; opinions are my own

PostsRepliesMedia
Reposted by Matt Holt
Jocelyne Bruand @jocelyne8.bsky.social · 15/09/2026
Our Isocall paper is out on bioRxiv www.biorxiv.org/content/10.6...! 🎉 Isocall enables scalable joint isoform calling on PacBio data, allowing for the characterization of isoform diversity across cohort-scale data. (1/7)
174
Reposted by Matt Holt
Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 28/08/2026
I am delighted to announce that The Department of Human Genetics at the University of Utah is continuing a multi-year recruiting initiative for multiple tenure-track faculty positions at the rank of Assistant Professor. Please share and consider applying! utah.peopleadmin.com/postings/208...
183102
Reposted by Matt Holt
Alex Spahn 🌋🌪️☄️ @spahn711.bsky.social · 28/08/2026
A quick edit of tonight's beautiful lunar #eclipse.
A close-up photo of the full Moon during a 96% lunar eclipse. The top of the Moon is bright white, but most of the rest is orange to red in color.
243154542
Matt Holt @holtjma.bsky.social · 27/08/2026
Our article introducing Aardvark for variant benchmarking is now published in Genome Biology! “Aardvark: sifting through differences in a mound of variants” DOI: doi.org/10.1186/s130... GitHub: github.com/PacificBiosc... Follow along for some highlights… 1/N
doi.org
Client Challenge
12210
Reposted by Matt Holt
Ryan Hall, Y’all @rhyall.bsky.social · 25/08/2026
Thursday night, 96% of the Moon will disappear into Earth’s shadow. Most of the U.S. will be able to see it. One of the coolest sky events of the year.
03920
Reposted by Matt Holt
Mayor Zohran Kwame Mamdani @mayor.nyc.gov · 18/08/2026
I'm listening, I'm learning. Safety first, NYC.
852345344422
Matt Holt @holtjma.bsky.social · 17/08/2026
Happy “GitHub is borked” day to those who celebrate!
010
Matt Holt @holtjma.bsky.social · 13/08/2026
Finally got around to beating Expedition 33… I was not emotionally prepared for the incredible journey of that game! 10/10, no notes
030
Matt Holt @holtjma.bsky.social · 11/08/2026
I'm always excited to see HiFi and our tools applied to PGx diplotyping and discovery! "Characterization of NAT2 Using Long-Read Sequencing: Allele, Diplotype, and Phenotype Call Accuracy Compared to Other Testing Strategies": ascpt.onlinelibrary.wiley.com/doi/10.1002/...
ascpt.onlinelibrary.wiley.com
Characterization of <fi>NAT2</fi> Using Long‐Read Sequencing: Allele, Diplotype, and Phenotype Call Accuracy Compared to Other Testing Strategies
The NAT2 pharmacogene is essential in drug metabolism, particularly for aromatic amines and hydrazines. Genetic variations in NAT2 categorize individuals as rapid, intermediate, or poor metabolizers ...
010
Reposted by Matt Holt
Dr. Lucky Tran @luckytran.com · 10/08/2026
Important: Trump’s executive order is NOT legislation. Though the executive order promotes more misinformation about vaccines, nothing has changed about the availability of childhood vaccines. For evidence-based guidance, please follow and share American Academy of Pediatrics recommendations.
AAP Recommended Immunization Schedule
3023021315
Reposted by Matt Holt
Nils Homer @nilshomer.com · 08/08/2026
When running benchmarks on shared tenancy systems (e.g. AWS), it's hard to compare cpu/wall times over time, even with many replicates.  have seen performance differences up to 20% just based on fighting others for access to the memory sub-system.
121
Reposted by Matt Holt
Eric Topol @erictopol.bsky.social · 06/08/2026
Against all odds, with an HHS that has defunded mRNA research programs, the FDA just approved the first mRNA flu vaccine
452763583
Reposted by Matt Holt
Justice Of Toren One Var @jyn.dev · 05/08/2026
i'm really proud of this policy. it's not perfect, but i think it's close to the best that was possible given all the constraints. i'm excited that this will make things easier for mods and reviewers, and hopeful that it will spark change in Rust's governance. blog.rust-lang.org/inside-rust/...
blog.rust-lang.org
rust-lang/rust is adopting an LLM policy | Inside Rust Blog
Want to follow along with Rust development? Curious how you might get involved? Take a look!
1016724
Reposted by Matt Holt
Aaron Sojourner @aaronsojourner.org · 25/07/2026
Admirable clarity @science.org
The Trump administration hates academic science funding, full stop. They hate where that money goes, and they hate who it goes to. They want to keep all that money for themselves, to hand out to favored cronies who can help them get elected and to steer yet more money and more power back into their hands.

That’s it. That’s the story
4974912713
Reposted by Matt Holt
Stephen Turner @stephenturner.us · 18/07/2026
How it started 👇... how it's going: blog.stephenturner.us/p/ai-dry-jul... Reflections on trying to go a month without AI. I made it two weeks (sort of).
blog.stephenturner.us
AI Dry July: Aborted
Reflections on trying to go a month without AI. I made it two weeks (sort of). 5.2k words, 23 minutes reading time.
0122
Reposted by Matt Holt
Randall Munroe @xkcd.com · 16/07/2026
Time Change xkcd.com/3272/
3-panel comic. (1) PERSON 1 behind podium on stage: We all hate springing forward. But we love falling back. (2) [Audience pictured listening] PERSON 1: Therefore, we are abolishing the *spring* time change *only*. We’ll gain an hour every year, but never lose one. (3) PERSON OFF-PANEL: Won’t that cause the clocks to spiral out of sync with the sun? PERSON 1 holding up a fist: *Then we will meet the chaos clear-eyed and well-rested!*
543738711
Reposted by Matt Holt
Adam Ameur @adameur.bsky.social · 03/07/2026
For those interested in PacBio's SPRQ-Nx chemistry and reusable SMRT Cells: in the Genome of Sweden project, we moved from 2 to 3 acquisitions per SMRT Cell in June. The results are impressive—we’re now approaching 400 Gb HiFi yield from a single SMRT Cell!
094
Reposted by Matt Holt
Alex Hoischen @ahoischen.bsky.social · 26/06/2026
Excited to share our ‘perspective’ on significant impact long-read sequencing technologies, genome assemblies and better (AI-assisted) interpretation-tools will bring to our field of medical genetics – as we are entering an era of “near-perfect genome sequencing”. www.nature.com/articles/s41...
nature.com
Near-perfect genome sequencing in medical genetics - Nature Genetics
This Perspective introduces near-perfect genome sequencing, which encompasses diploid genome assembly, pangenome references and artificial intelligence-driven variant interpretation, and proposes a ro...
163
Reposted by Matt Holt
Climate.us @climate.us · 23/06/2026
Climate.us is live. Built by members of the team behind Climate.gov, this new independent nonprofit website keeps trusted climate information easy to find, easy to use, and harder to erase. #ClimateForUs #ClimateUS
601548978
Reposted by Matt Holt
Nils Homer @nilshomer.com · 21/06/2026
Rust and python bindings for minibwa are available on crates.io and pypi.org: github.com/fg-labs/mini...
github.com
GitHub - fg-labs/minibwa-bindings: Rust and Python bindings for minibwa — Heng Li's lightweight bwa
Rust and Python bindings for minibwa — Heng Li's lightweight bwa - fg-labs/minibwa-bindings
1112
Reposted by Matt Holt
Fulcrum Genomics @fulcrumgenomics.com · 17/06/2026
@tfenne.bsky.social has a new post on tuning up bioinformatics’ old plumbing: HTSJDK, jlibdeflate, chelae, mako, GLIMPSE, verifyBamID, bwa-mem3, and the low-level tools behind everyday workflows. Improve the infrastructure. Validate the behavior. Let the gains compound. Blog post 👇
Bioinformatics runs on a hidden layer of shared infrastructure. samtools, GATK, Picard, htsjdk, Snakemake, Nextflow, and the libraries beneath them carry a huge share of day-to-day work. Most of it stays out of sight, like city plumbing.
271
Reposted by Matt Holt
PacBio @pacbio.bsky.social · 16/06/2026
One of the first preprints using the #PacBio Vega benchtop HiFi sequencer is now available. The study demonstrates accurate detection of mitochondrial heteroplasmy down to 1% using a single full-length mtDNA amplicon and applies the workflow to Parkinson's disease research. 🔗 bit.ly/4a4rP4c
031
Reposted by Matt Holt
Heng Li @lh3lh3.bsky.social · 16/06/2026
Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357
1193109
Reposted by Matt Holt
Rob Patro @robp.bsky.social · 14/06/2026
salmon 2.0 (the rust re-write) is now live! It's also the version you get if you install via bioconda. This is a from-scratch rewrite in rust, and the base for future development. I'll post a more detailed thread tomorrow, but you can read the docs here combine-lab.github.io/salmon/
combine-lab.github.io
salmon
Fast, accurate transcript quantification from RNA-seq reads.
25316
Reposted by Matt Holt
Adam Ameur @adameur.bsky.social · 14/06/2026
These are beta test results of PacBio's reusable SMRT-cells, run on human blood DNA from the "Genome of Sweden" project. Results have been really impressive so far, with an average >250Gb per SMRT-cell over 2 acquisitions. We are now about to expand to 3 acquisitions
0114
Reposted by Matt Holt
Deborah Moine @deborahmoine.bsky.social · 12/06/2026
Excited to be heading to #ESHG2026 😃 If you're attending, feel free to stop by the #PacBio booth (420) and say hello. I'd be happy to chat about #PureTarget, HiFi sequencing, and targeted sequencing applications. If you're not attending ESHG, you can still catch this webinar on demand below.
032
Reposted by Matt Holt
Johannes Köster @johanneskoester.bsky.social · 12/06/2026
#rustbio 4.0 has been released. It harmonizes the error handling, improves the API, makes gap-open/extend behavior in pairwise alignment more intuitive and in-line with the literature, improves GFF parsing, and allows incremental building of the rank-select datastructure. github.com/rust-bio/rus...
github.com
Release v4.0.0 · rust-bio/rust-bio
4.0.0 (2026-06-12) ⚠ BREAKING CHANGES Replace anyhow with typed thiserror errors (#674) Change Phase conversion methods to use TryFrom for better error handling (#625) for pairwise alignment, only...
0197
Reposted by Matt Holt
PacBio @pacbio.bsky.social · 07/06/2026
Every bib represents a name, a loved one, or the entire rare-disease community. At the PacBio 5K on June 27, we carry them across the finish line together. 👟 Join us in Del Mar, San Diego and make your steps count. Sign up today: bit.ly/4mh0yQV #SeqItForward5K
031
Reposted by Matt Holt
Alex Hoischen @ahoischen.bsky.social · 04/06/2026
Congrats to all co-authors from out HiFi-Solves EMEA consortium! www.pacb.com/hifi-solves/ This study was driven particularly by the great @bartvds.bsky.social; with important contributions from Hanno Jörn Bolz Johannes Zschocke Malte Spielmann and their teams.
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
253
Reposted by Matt Holt
The American Journal of Human Genetics @ajhgnews.bsky.social · 04/06/2026
🧬New from @ahoischen.bsky.social & co! 📄HiFi sequencing accurately identifies clinically relevant variants in paralogous genes
cell.com
HiFi sequencing accurately identifies clinically relevant variants in paralogous genes
Long-read HiFi genome sequencing combined with Paraphase enables comprehensive detection of all clinically relevant variant types in paralogous genes. It resolves “dark” regions while enabling haploty...
164
Matt Holt @holtjma.bsky.social · 02/06/2026
Following up on the major functional release of MethBat v1, we have had some more time to further optimize the tool and add some convenient features in v1.1. Run-time is *substantially* faster, especially if you're only looking for 5mC pileups! Update notes here: github.com/PacificBiosc...
020
Reposted by Matt Holt
Heng Li @lh3lh3.bsky.social · 30/05/2026
Jeremy Wang developed rammap, a minimap2 rewrite in Rust. It achieves comparable or better performance than minimap2 and produces identical output to minimap2. During rewrite, Jeremy found two long-existing bugs in minimap2 which are fixed in v2.31. www.biorxiv.org/content/10.6...
biorxiv.org
310944
Reposted by Matt Holt
Katie Mack @astrokatie.com · 29/05/2026
It’s truly astonishing to see how comprehensively the US government is tearing down every part of the system that has made it up until now a world-leading power in science, research, and technological development. The entire world will suffer from this wanton destruction.
23980482825
Matt Holt @holtjma.bsky.social · 27/05/2026
We released an update for HiPhase today that has a large impact on wall clock time required for some samples, with negligible differences in accuracy and block lengths. Full release here: github.com/PacificBiosc...
github.com
Release HiPhase v1.7.0 · PacificBiosciences/HiPhase
Changes Added a limit to the WFA edit distance that scales with the length of the mapping. This reduces run-time in regions with short mapped fragments and high edit distance relative to the refer...
000
Reposted by Matt Holt
Seth Stadick @ducktapeprogrammer.bsky.social · 27/05/2026
In case you don't follow it already, reminder that this exists! scientificcomputing.rs/monthly/
scientificcomputing.rs
Scientific Computing in Rust
the Scientific Computing in Rust annual workshop and monthly newsletter.
052
Reposted by Matt Holt
Andrew Gallant @burntsushi.net · 26/05/2026
I've added an AI policy to ripgrep that was shamelessly copied from uv's policy. I plan to add this to the rest of my projects, but if anyone wants to offer feedback on wording, now would be a good time! github.com/BurntSushi/r...
github.com
611416
Reposted by Matt Holt
PacBio @pacbio.bsky.social · 26/05/2026
SPRQ-Nx chemistry is now shipping worldwide, bringing sub-$300 HiFi genomes to the Revio platform! This global rollout cuts sequencing costs by 30%, making it easier than ever to scale high-throughput workflows Full press release here: bit.ly/49HwmcL #SPRQNx #PacBio #HiFisequencing #Revio
0147
Reposted by Matt Holt
NPR @npr.org · 25/05/2026
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
n.pr
Researchers say the Trump administration is finding new ways to punish science
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
17416196
Matt Holt @holtjma.bsky.social · 19/05/2026
We had a *major* update to MethBat v1 today in preparation for SPRQ-Nx release. This included a `pileup` sub-command for 5mC, 5hmC, and 6mA and extension of the existing functionality to support the additional base mods. Full notes here: github.com/PacificBiosc...
110
Reposted by Matt Holt
👻madeline bOoOoOoOodent👻 @oldenoughtosay.com · 17/05/2026
I’m sorry but if you aren’t sure of a citation, whether what it means or that it exists… why are you citing it. why are you referring to something you haven’t read or don’t understand? that defeats the entire bloody point
561972339
Reposted by Matt Holt
Pathoplexus @pathoplexus.org · 09/05/2026
1/ 🚀 Pathoplexus now supports the Andes variant of Hantavirus (ANDV). ANDV is the variant identified in the recent MV Hondius cases, & the Hantavirus variant previously identified as having occasional human-to-human transmission. pathoplexus.org/andv #hantavirus #hondius
18339
Matt Holt @holtjma.bsky.social · 04/05/2026
The immediate action by so many states to make gerrymandering worse reveals just how awful of a ruling the SC made. Minorities will suffer most because of this.
000
Reposted by Matt Holt
Carl T. Bergstrom @carlbergstrom.com · 28/04/2026
More details on the firing of the National Science Board. The NSF now has no director, deputy director, or board. They have issued almost no new awards in 2026. The plan appears to be to completely destroyed the agency. The details are horrifying and have Russ Vought written all over them.
insidehighered.com
Board Ouster Raises Further Concerns About NSF’s Future
The White House axed all members of the board overseeing the National Science Foundation Friday, leaving the agency with no board, director or deputy director. It finally provided a reason Monday afte...
6821751331
Reposted by Matt Holt
PacBio @pacbio.bsky.social · 21/04/2026
Happening now at #AACR26! Visit #PacBio Poster 5510 to see Zev Kronenberg present a new way to hunt for microsatellite instability in long-read data. See how the "Owl" tool is advancing bioinformatics workflows for MSI detection. 📍 Section 4, Board 15 ⏰ Until 5 PM
073
Matt Holt @holtjma.bsky.social · 17/04/2026
“Bioinformatics would be a more enjoyable field if more tools were written in Rust.” Shout it from the rooftops
1122
Reposted by Matt Holt
Ragnar {Groot Koerkamp} @curiouscoding.nl · 14/04/2026
Jeez... 6 in a day... this is gonna be so bad for the ecosystem long term. Even if none of these gains any traction, the name squatting and confusion/bloat that others will have to deal with just to figure out which crates are/are not serious is a pain.
crates.io screenshot showin 6 crates, most of which *-rs, all created 2 days ago
3122
Reposted by Matt Holt
Emily J @emexastris.bsky.social · 11/04/2026
Gifs and insults aside, science in general - including space science - is *incredibly* international. This is something we can do because we do it together.
3829111
Reposted by Matt Holt
A. Marmot 🌱 @aminus.bsky.social · 11/04/2026
congratulations to the astronauts who made it around the Moon and back *in spite* of having to use Microsoft Outlook in space
3450101
Reposted by Matt Holt
Dan Immergluck @danimmergluck.bsky.social · 08/04/2026
Brutal.
A WHOLE CIVILIZATION
WILL DIE TONIGHT
My son needs lunch, and I have to put his backpack together, but a whole civilization will die tonight, so I'm wondering if they've closed their schools.
Like, a snow day, maybe, except instead of snow it's
"keep your children home so if you die, you die together" — instead of "well open back up once the plows have cleared" it's
"we don't know if we'll be here tomorrow, hold your babies tight."
It's just "talk" I'm told, which I've been told before.
"It's how the president makes his deals." But I've never heard anyone talk about other human beings this way, and I'm not certain I can look my son in the eyes if we all agree to stomach it one more time.
A civilization will die tonight, but as I zip up his backpack and kiss him off to school I think: if this is what we call leadership then I'm not entirely sure ours isn't already dead.
@michaelfdubois
Mukad A QuBoy
@michacifdubois
393944018
Matt Holt @holtjma.bsky.social · 08/04/2026
There is something implicitly funny about asking Cursor to write a skill that constrains it. "Hey buddy, you're going off the rails here. I need you to make up some rules for yourself so I don't have to keep rejecting your changes."
020