I’m so pleased to be named a AAAS Fellow! I remember opening the original email thinking wow, which of my awesome faculty won this nice thing (a perk of being chair is getting emails like that) but it was me! www.washington.edu/news/2026/03...
We've launched a department Trainee Emergency Fund, to help support EVERYONE BELONGING IN SCIENCE by meeting urgent financial needs of students and postdocs. Every gift will be matched, up to $1,000, by Nels Elde. Click to see a message from Aaron Quinlan and to donate!
www.givecampus.com/s/w46xg1
Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs. Led by Yan Gao.
Another terminal based tool to interactively monitor all running #Snakemake workflows is #snkmt: github.com/cademirch/sn....
Brent Pedersen, Mitchell Vollger and I have "posted" our preprint of the manuscript describing bedder, a complement to the functionality of bedtools. The "preprint server" we have chosen is google docs because it was rejected by biorxiv.
docs.google.com/document/d/1...
404 for me. Any chance you are ready to share broadly?
It’s 5 years late but I had some time to update and finally write a little about rustybam. Its unique features really center on liftover operations that preserve the underlying alignment which can be composed in a surprising number of useful ways.
New lab photo for the first time in too many years. I am so proud of this team's curiosity, camaraderie, and collabative energy.
It’s an issue but a similar policy at Princeton ruined my undergraduate experience. My cohort quickly established the top ~20% of performers and then for the next three years studied exclusively within the that group to protect their grades. Ruining the opportunity to learn from your best peers.
AlphaGenome is out in @nature.com today along with model weights! 🧬
📄 Paper: www.nature.com/articles/s41...
💻 Weights: github.com/google-deepm...
Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc
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]
Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.
First authors: @saracarioscia.bsky.social & @aabiddanda.github.io
I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt:
employment.utah.edu/salt-lake-ci...
Mapping single-cell diploid chromatin fiber architectures using DAF-seq - @uwgenome.bsky.social @uwdeptmedicine.bsky.social go.nature.com/4rFTAHy
We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
The effects of genetic variants primarily occur in differentiated cells meaning we need to access these cell types to measure variant effects for most disease genes. We developed saturation genome editing in stem cells (iPSC-SGE) to enable phenotyping in diverse genetic and cell contexts at scale!
Happy to share work spearheaded by former grad student Colin Shew testing shared duplicated cis regulatory elements (CREs) using an MPRA. While we find some high effect CREs, collectively paralog differences represent modest effects accounting for observed gene expression divergence.
@mollyschumer.bsky.social if the data is pre SPQR chemistry I would recommend fibertools. If it’s new data then you can use Jasmine from Pacbio, Andrew and I spent a fair amount of time looking at the Jasmine results and they look good. And it will all still work with downstream fibertools commands
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.
@uwmedicine.bsky.social what is this? Trying to get your patients and employees with insurance to pay for full medical bills during check in before billing insurance… Disappointing and wrong.
Ben Langmead promoted to full professor. Computer science.
Congratulations to @benlangmead.bsky.social on his promotion to full professor! 🎉 Prof. Langmead is recognized across the computational and life sciences fields for his innovative methods helping to transform how biomedical researchers and other life scientists access and use DNA sequencing data. 🧬
Thrilled that our study on human gene duplications and brain evolution is out! It was a true labor of love, with special shout-outs to my co-first author @jmuribescr.bsky.social and my PhD mentor @mydennis.bsky.social. Huge thanks as well to @aidaandres.bsky.social for all the popgen wisdom!
Check out our latest work co-led by @dcsoto.bsky.social and @jmuribescr.bsky.social identifying hundreds of human duplicated gene families using the new T2T-CHM13 assembly, with a focus on those potentially contributing to brain evolution 🧪: authors.elsevier.com/a/1lTQtL7PXu...
How it started vs. How it's going #Tenured
Grateful to all those who've been a part of this journey so far. But the fun is just getting started 💪
Curious to find out just what this privilege of tenure can enable. Let's see how we can put it to the test. Feel free to share ideas 😉
#AcademicSky
Some personal news: amid everything going on, I’ve been promoted to Professor. I am so deeply grateful to all of the past and present members of the lab, who allowed me to be a part of their journey. I am so honored to call all of you my colleagues.
Today, my NIH colleagues and I did something scary but really important. We spoke up about egregious harms we are seeing happen to research participants and public health through thoughtless and politicized policies at NIH. 🧵1/3
apnews.com/article/nih-...
You may be excited, @mrvollger.bsky.social, but we are even more so! I can't wait to be your colleague!
