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.

GFF was originally conceived of as an interchange format for chaining together gene subfeatures (splice sites, promoters, exons, etc) predicted by various specialized tools (HMMs, decision trees, neural nets, SVMs); rather like GENSCAN, but with the idea you could mix & match subfeature predictors

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)

IMO it’s weird and probably irresponsible to teach bioinformatics without some nod to the group dynamics that shaped (otherwise inexplicable) things like the GFF file format or the Gene Ontology. Not to mention why tools back then had names like BLAST and FASTA,but now are named after cuddly animals

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.)

Here are the results in terms of the number of projects. The number of funded projects in FY2025 is 4014 fewer than the number for FY2024. 2/3

I have eaten the precisionFDATruth Challenge v2 dataset that was in the NIST Public Data Repository and which you were probably going to cite in your paper Forgive me it takes 2.85 minutes to load vendor.js

Is the #precisionFDA Truth Challenge v2 dataset in NIST's Public Data Repository under doi.org/10.18434/mds... meant to be mysteriously missing?

"We present exciting and novel new findings on the topic of the gel I'm about to run, with confirmatory experiments I'll run next Tuesday..."

for some reason i thought being a professor would involve more mentoring and research and less filling out disclosures concerning whether plants and seeds were used in my computational study

More youtube videos coming soon to www.youtube.com/BenLangmead! New recording setup. I've got a couple videos in the editing phase and hope to keep up a rhythm of 1 new video per week.

Now published in GigaScience with minor improvements: academic.oup.com/gigascience/... * Download: zenodo.org/records/1490... * More info: github.com/lh3/panmask

A scalable indexing framework for pangenome graphs enables efficient, lossless, and haplotype-aware queries. Tested on HPRC graphs, it preserves accuracy while improving scalability. Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...

#Snakemake 9.10 has been released. The major change is that it now supports scheduling plugins. By that your scheduling algorithm research becomes immediately usable with thousands of workflows by thousands of users. snakemake.github.io

UC launches #SpeakUp4Science campaign as critical research faces unprecedented federal threats https://bit.ly/3USNFj5

GBZ-base has been a side project for me for a couple of years. It's basically a GBZ graph stored in SQLite instead of a custom file format. You can convert a GBZ graph to GBZ-base quickly and then extract subgraphs around nodes / reference positions on a laptop. 1/n

If your @orcid.org number ends with an `X` that means you are officially Cool, right? orcid.org/0000-0001-58...

A cell type is defined as the minimal unit to make a developmental biologist mad about a conversation

This means Servo might be feasible to use for a Sequence Tube Map desktop wrapper, I think.

I'm essentially unable to log into any websites run by Editorial Manager. I have 20 something different logins saved, with different usernames and passwords, for different journals. My password manager is useless, and I am at the point where every login requires a PW reset.

Finally printed and submitted my thesis :) You may call me Dr. now 🎓 curiouscoding.nl/thesis.pdf

job control wizardzines.com/comics/job-c... (from The Secret Rules of the Terminal, which is out now!)

Last talk of the day (before posters) "Lossless Pangenome Indexing Using Tag Arrays" presented by Parsa Eskandar! #WABI25