HPRC2: A human pangenome reference with near-complete coverage of common genetic variation https://www.biorxiv.org/content/10.64898/2026.07.21.739710v1

Since I only get a couple weeks to peer-review papers, what's happening to *my* papers for the several months they're in review at the journal?

🔥 Does switching to a pangenome reference actually improve your association study? We tested it, and the answer is yes, measurably. Our preprint is online now: "Pangenome-based human genome analysis improves trait association and genomic prediction": doi.org/10.64898/202...

Pangenome-based human genome analysis improves trait association and genomic prediction

The Human Pangenome Reference Consortium has generated 462 open-access reference genomes and a variation graph that represents differences among them, providing a substrate for pangenome-based analysi...

doi.org

Congratulations to Prof Richard Durbin, winner of the 2026 Genetics Society Medal! His pioneering work in computational genomics has transformed how we analyse and understand genome sequences.

Growing neurons from stem cells—in high school! 🧠 A Genomics Institute platform uses cloud-connected microscopes so students design real stem cell experiments remotely. New study shows it measurably boosts STEM identity, especially for Hispanic & first-gen students. news.ucsc.edu/2026/0...

This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...

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.

npr.org

“The message, very clearly, they’re sending is, do not speak out on behalf of Chinese postdocs. If you do, you’re going to pay a penalty...It seems pretty obvious that this is an attempt by the current administration to silence people that question their activities." — Roger Innes, IU AAUP member

A Professor Defended a Postdoc Who Was Deported. Now His Lab Has Been Suddenly Locked Down.

Work at an Indiana University biology lab was halted amid federal scrutiny, affecting dozens of researchers. “The damage is significant and mounting,” the department chair told The Chronicle.

chronicle.com

#dna #captcha

We got "Help me write" in our #UCSC Google Docs and I really can't deal with its little text prompt flashing in and out at the cursor position whenever I stop typing in order to think. I told to our IT that it meaningfully interferes with my ability to write in Google Docs and they can't fix it.

Jordan@jordanpfot.bsky.social · 3mo ago

What the hell www.newyorker.com/culture/prog...

earthrise in santa cruz

I feel like this all the time when trying to generate code with Claude Code. I end up spending lots of time reviewing what are supposedly *my own* pull requests for terrible ideas. I want to be reading code written by people *better at it than I am*, and I'm definitely not.

John FitzGiraffe Kennedy@jgiraffekennedy.bsky.social · 4mo ago

Here, the engineer becomes a full‑time auditor of an unending flow of machine‑generated nonsense. It is extremely expensive cognitively, even if the code is decent. Reading code is more difficult than writing it, and rewriting code is more frustrating than writing it. (7)

Very happy to see both vg and Sequence Tube Map being used for Sorghum pangenomics! www.nature.com/articles/s41...

Joint Genome Institute@jgi.doe.gov · 4mo ago

"We wanted to build a resource that demonstrates DNA sequence diversity, gene repertoire, and the phenotypic diversity across this plant in one accessible resource." — John Lovell, JGI Plant Program More: https://jgi.doe.gov/user-science/science-stories/sorghum-pangenome-opens-more-doors-discovery

Today, March 31st, is International Trans Day of Visibility. In an era of immense difficulty for the community, it can be hard to remember that Trans Day of Visibility is as much about positivity as it is about awareness and resistance.

Ever receive a BAM aligned to “GRCh38” and realize that could mean several different references? We just released ref-solver, a tool that identifies the reference genome behind BAM/CRAM/FASTA files by comparing sequence dictionaries to known builds. 🔗 whatsmygenome.fulcrumgenomics.com Read more 👇

it has been [0] days since I've tried to emulate 64-bit atomic operations using 32-bit atomic ops in a system with relaxed memory ordering

Bit different from our usual work A PhD applying metagenomics to identify microbial plastic degradation and metabolism, fully funded studentship (UK students only). www.findaphd.com/phds/project...

A metagenomics approach to discover novel plastic degrading microbial pathways at University of Birmingham on FindAPhD.com

PhD Project - A metagenomics approach to discover novel plastic degrading microbial pathways at University of Birmingham, listed on FindAPhD.com

findaphd.com

Our latest vg release introduces GBZ v2 with better compression for sequences. I originally assumed that the total sequence length in a pangenome graph would be similar to the size of the genome. This does not hold in the full HPRC graphs due to unaligned centromeres.

Looking for a postdoc to build my new lab at TGen (Phoenix, AZ) focused on pangenome methods for cancer and complex disease. Full stack — from pangenome assembly and compression to association studies and somatic variant discovery. Reach out if interested! guarracinolab.github.io#join

Guarracino Lab | Pangenome Research

We develop methods to build and analyze pangenomes, with applications in cancer and complex disease. Translational Genomics Research Institute, Phoenix, AZ.

guarracinolab.github.io

Native Bio has made the @nytimes.com for the second time. The #IDsov movement is a tidal wave....and a solution for these difficult times. “We are at a fork in the road. Do not choose hate & do not choose unsustainability.” ~ 21st Century Maxim, Author Unknown www.nytimes.com/2026/02/05/s...

He Built a Server to Protect Indigenous Health Data

nytimes.com

This was such a fun project. Adam's thread on it is a great summary!

Adam Phillippy@aphillippy.bsky.social · 6mo ago

Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]

Excellent piece about why race is not a biological category and how medical education needs to respond. www.bmj.com/content/392/...

Race is not a biological category: challenging this misconception will help tackle racism in healthcare

Healthcare professionals must reject flawed racial generalisations, writes Jasmeen Kanwal Institutional racism in healthcare has received increased coverage in recent years, including in The BMJ ’s ...

bmj.com

Apply ASAP to be a "Genomics Senior Systems Architect" AKA Linux Herder at @ucscgenomics.bsky.social ! The first test is convincing www.ucsc.edu/careers/ to show you #job number 82880.

Are #redhat #quay.io Docker container builds down for anyone else? Mine are failing with no logs, and then my trigger gets "automatically disabled due to successive internal errors".

You find yourself in the middle of a fastq file. You see + and @ all over the place. How do you find the start of the current record?

Did anybody ever actually write up the "Heng Effect" (where adding variants to your pangenome graph can *reduce* its usefulness for samples unlikely to contain those variants)? Or is it just deep vg lore known only in our lab?

Kiddo age 5: daddy you don't work, you just sit at the computer Kiddo age 12: dad you just write grants

SMBE2026 Symposium 21 | From genomic graphs to evolutionary insights: standardising pangenomes for population inference 📨 Abstract submission smbe2026.org/abstracts 📋 Programme details smbe2026.org/programme #SMBE2026

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods

Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

nature.com

I am just hearing that Rust contains a type `Infallible`. Its description, "The error type for errors that can never happen.", sounds like the tagline for someone's next startup. doc.rust-lang.org/std/convert/...

Rust Language@rust-lang.org · 8mo ago

Rust 1.92.0 has been released! 🌈 🦀 This version adds RwLockWriteGuard::downgrade(), adds Location::file_as_c_str(), improves diagnostic and validation for various attributes, no longer warns for unused Result<(), Infallible>, and more! Check out the announcement: blog.rust-lang.org/2025/12/11/R...

This double helix is not double helixing correctly.

Institute for Genome Sciences@genomescience.bsky.social · 8mo ago

Come work with us at the Institute for Genome Sciences @medschool.umaryland.edu in #Baltimore! We're hiring an Assistant/Associate Professor of #Genomics & #Bioinformatics, #PhD, #MD, or both #Computational #Biology Learn more/Apply: bit.ly/GenoBioinfo