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

A solution to the indexing dilemma in large pangenomes, by Parsa Eskandar from UCSC: Lossless Pangenome Indexing Using Tag Arrays", offering a practical indexing layer to develop scalable aligners and downstream graph-based tools www.biorxiv.org/content/10.1... #wabi25

I'll be speaking in this webinar (go.roche.com/sbx-d) on September 10, where I'll share our benchmarks and observations for Roche's SBX sequencing instrument, as well as models developed by our team for SBX data.

Starting of day 2 on a high note with Christina Boucher's keynote "Recursive Parsing and Grammar Compression in the Era of Pangenomics"! #WABI2025

Is more genomic data always better? Not necessarily, the benefits may eventually plateau. Keynote talk by @benlangmead.bsky.social in #WABI2025 link.springer.com/article/10.1... FORGe: prioritizing variants for graph genomes

Pangenome-guided sequence assembly via binary optimisation www.biorxiv.org/content/10.1... "a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex regions without bias towards a single reference...a new tool kmer2node for aligning reads onto pangenome graphs

#WABI25 HAS KICKED OFF! @benlangmead.bsky.social is givening the opening keynote now wabiconf.github.io/2025/talks/t...

UC Santa Cruz has some experts on cyborg philosophy

Oh man; I wish I’d been aware of this earlier! IMO, this is one of the most important topics touching academic research in the computationally-adjacent sciences (read as, basically all science).

There was a workshop on 25 years of the FM-index and the CSA after SEA. I would have liked to attend, but I had other commitments. The invited speakers were Giovanni Manzini and Roberto Grossi, as the other purpose of the workshop was to present them Festschrifts for their 60th birthdays. 1/6

Unfortunately, this tip tends to be a part of the hidden curriculum, even though it is exactly the lesson someone should take from every peer review.

Scientists! @skypeascientist.bsky.social matches scientists with classrooms, libraries, & more for virtual Q&As! It's easy and fun! We are looking for 750 more volunteers by 8/15 If you're down to chat with 1-5 classrooms this semester, sign up here www.skypeascientist.com/sign-up.html

Little writeup on the speed of fasta parsers, at last. Basically: both needletail and paraseq are process input linearly, and thus have a limit around 4 GB/s. By giving each thread its own slice of the input file, we're limited by RAM bandwidth instead :) curiouscoding.nl/posts/fasta-...

The Platinum Pedigree: a long-read benchmark for genetic variants. #HumanGenome #ReferenceGenome #PlatinumPedigree #LongReads #Benchmarking #GeneticVariants @natmethods.nature.com 🧬 🖥️ www.nature.com/articles/s41...

🚨New preprint out! 🧬Short reads can now decode centromeres. 🌍We reveal population-scale centromere haplogroups and their links to disease. biorxiv.org/content/10.1... (1/n)

A field in which only the top 5% of participants are able to practice is not a field that can continue to exist.

Sharing our lab logo that @ethankocak.com made years ago. The drum is an Inupiaq style drum, part of the storytelling/scicomm we stress in the lab. We study population variation in the stickleback gut microbiome, captured nicely in the design. I get compliments all the time!

Join HPRC at ASHG 2025 for a workshop on the Human Pangenome: data, tools & workflows. 📅 Oct 14 10AM–12PM | Learn how to access, analyze & work with the pangenome. Details: www.ashg.org/product/ashg...

I'm happy to share our latest manuscript "Impediments to countering racist pseudoscience", coauthored with @gillianrbrown1.bsky.social @kztwyman.bsky.social & Marcus Feldman.

A bonebed in Arizona provides researchers with a glimpse of life in equatorial late Triassic Pangaea. The assemblage includes the earliest documented occurrences of turtles and pterosaurs. In PNAS: www.pnas.org/doi/10.1073/...

We open our second day at #Hitseq @hitseq.bsky.social with our last key note speaker Tobias Marschall and his insightful talk about the human pangenome and the challenges for structural variation analysis. His work has focused on tackling current limitations such as sample size and remaining gaps

Two papers in today's issue of @nature.com ‬: 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.

🚨 We're hiring! NCMBM @ncmbm.bsky.social is looking for 2 new group leaders to join our vibrant research community. Ready to build your own group with strong support and a solid startup package? Interested and attending #ISMBECCB2025? Let’s connect! 🔗 www.jobbnorge.no/en/available...

Congratulations @benlangmead.bsky.social!

💻 Just released a new tutorial: How to write a Bash script, featuring an IDE and a command-line running directly in your browser. No setup required. sandbox.bio/tutorials/ba...

📣 JOB ALERT: We are looking for a Senior Software Engineer to join our pathogen genomics team! Be a part of creating and maintaining tools that public health officials are using to track the spread of dangerous pathogens 🦠 Apply here: careerspub.universityofcalifornia.edu/psc/ucsc/EMP...

Previous studies of extrachromosomal circular DNA #eccDNA in #plants are based on short-read seq. @vanderschuren-lab.bsky.social uses long-read seq to obtain a map of full-length eccDNAs from #Arabidopsis, identifying their genomic origins & epigenetic regulation @plosbiology.org 🧪 plos.io/44Mq3RI

Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen... Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!

Random paper title generator is here! {A} {fast,faster,improved} {{algorithm,algorithms} for} {approximate string,pattern} {matching,searching} {using {SIMD,AVX2,AVX512}}

🚨 For everyone who uses All of Us Workbench 🚨 Apparently, if the creator of a workspace no longer has access, *the entire workspace gets deleted*. Ask me how I know this. 🫠 It doesn't matter who the owners are. Make sure to back up all your work in a workspace with a PI as a creator!

Toil 9.0.0 is out now! You can publish Dockstore workflow metrics back to @dockstore.org out of the box! github.com/DataBiospher...

My colleague asked me to circulate this job posting for Professor / Associate Professor in Computational Biology / Genomics at the University of Tokyo (P.S. I'm not affiliated): www.k.u-tokyo.ac.jp/en/informati...

We finished this edition with a delightful keynote by Jean Monlong who guided us through his journey about finding SVs in pangenomes #JOBIM2025 👏🏻

We turn 25 today! July 7th marks the 25th anniversary of the human genome going online and the start of the UCSC Genome Browser. Then vs. now, we have 165k monthly visitors, and our codebase is over three million lines of code. See our news for more: bit.ly/genomeBrowser...