“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

#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.

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.

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

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...

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

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...

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

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

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

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/...

This double helix is not double helixing correctly.

One day I will ... write out this database (in a graph orientated, Json compatible data format with Rust bindings). The one graph to rule them all (though @benedictpaten.bsky.social's Cactus graph is pretty darn close to the graph to rule them all from the genomics side)

I found a paper in the wild today where I couldn't click through to the cited references, because the DOIs for them appeared to have been sampled from a large language model instead of actually looked up, producing plausible-looking but wrong links.

SAVE THE DATE! Stoked to organize the 2026 Santa Cruz Developmental Biology Meeting with @rashmi-priya.bsky.social, @lowelab.bsky.social, and Shelbi Russell. Come learn about Biomedicine, Biomechanics, and the Biosphere, August 24-28, 2026. Registration dates, etc., coming soon! Please RT

Now available: vg 1.70.0 release, code name "Zebedassi," with a new "vg describe" tool for inspecting files. 🧪🧬🖥️ github.com/vgteam/vg/re...

Julie Ahringer from @gurdoninstitute.bsky.social @geneticscam.bsky.social @cam.ac.uk gives talk on decoding genome regulation during development. Exploring how chromatin accessibility changes throughout development enable single cells to become multicellular organisms.

@thinks.lol @khmiga.bsky.social Look you're famous

I think about this post every day 🧪

Haonan Wu gives a talk on "A k-mer-based estimator of the substitution rate between repetitive sequences" www.biorxiv.org/content/10.1... This work tackles the issue of Mash which ignores repeats in the genome, providing better distance estimation #GI2025

If you're interested in using pangenome graphs for comparative genomics, check out my webinar, part of EMBL-EBI's "Concepts, methods, and resources in pangenomics" series, available on-demand: www.ebi.ac.uk/training/eve...

If you're looking for a faculty position at the intersection of ecology and computing (both broadly defined), please apply to this joint search between the CEE Department and the College of Computing at MIT: cee.mit.edu/people/share...

Support diversity and excellence in STEM by giving to our Research Mentoring Internship (RMI) this Giving Day 🎁 Federal cuts to DEI grants have made your gifts VITAL to keeping this program alive. Please support student mentorship today: www.givecampus.com/schools/Univ...

It's Giving Day!!! You can help support 🎗pediatric cancer research AND a "degree-defining experience" for undergraduates by: 💸 Donating to Treehouse Childhood Cancer Initiative 🗣 Sharing this post to spread the word! 🔗 🎁 bit.ly/give2treehouse

The year is 2025. C++ modules still don't just work.

Going through @samuelhorsfield.bsky.social presentation on pangenome graphs in comparative genomics, courtesy of @training.ebi.embl.org. Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk! 💻🧬🦠🧫

“Bonferonni correction”, an invaluable method in #statistics, refers to the act of repeatedly correcting misspellings of the word Bonferroni at multiple places in a draft manuscript. #science #academia

🪰 folks! I spoke to the Transmitter about FlyBase. As noted at flybase.org, bridge $ ran out and many staff were laid off. Good news is stopgap contributions will keep core FlyBase operations active. But community support remains essential. Please donate @FlyBase and share! 1/2 tinyurl.com/FlyBase

UCSC's Brooks Lab tool FLAIR is helping to rewrite the story of cancer research—pushing precision medicine closer to truly individualized care. Learn how: santacruzworks.org/n...

Going through #pangenome lecture from @camillemrcht.bsky.social I missed yesterday. It looks like I get a shoutout on a slide! 🥳 Fantastic presentation, love the conceptual connection between traditional natural history collections and the modern bioinfo repos 🧬💻 www.ebi.ac.uk/training/eve...

I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

With a major influx of new people on here, guess it's time to re-share and update my starter pack of researchers working on scientific racism. If you know of any scientists, historians, journalists, or anyone else working this beat that aren't already included, please let me know so I can add them!

For those interested in #Indigenous #Genomics and #ASHG25 in Boston, here are some interested posters/talks/events coming out of the Tsosie Lab, @nativebio.bsky.social, and @d4itdr.bsky.social. For those looking for Friday plans, attend our Ancillary Event, debuting a #Tribal #data repository!

The T2T zebra finch genome has hatched! 🐣 🧬 @vertebrategenomes.bsky.social

🦒Long read giraffe is out!🦒 Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2

Also note: for comparison speed, 1-bit hashes beat everything else (top-right red line here). Because each bit is an independent sample, the entropy is very high. (Whereas comparing 8-bit sketches loses some information, because if two 8-bit values differ in the first bit, the other 7 are unused.)