Jeff Vierstra

Just wrapped up writing about what I have learned studying the noncoding mammalian genome over the course of the last 17 years. Should be on bioRxiv mid next week!

Here's the ad for the Genome Sciences faculty positions ap.washington.edu/ahr/position...

GHT-SELEX shows that transcription factors are particular about which genomic loci they bind, and C2H2 zinc finger proteins engage different fingers at different sites. www.nature.com/articles/s41...

You dont need advanced ML models to see base-resolution transcription factor occupancy and element-wise cis-regulatory logic. Just turn to a 40yo technology and basic stats. Still waiting for a structural biologist to help with 3d-modeling of composite regulatory DNA elements from DNase I profiles.

The Encyclopedia of DNA Elements https://www.biorxiv.org/content/10.64898/2026.07.06.731365v1

Check out ths CBS news segment about me. I may be the first person in world to be recieving a preventive ASO therapy for inherited familial ALS and it appears to be working! Still things to be hopeful for despite the absolute dumpster fires occurring all over the world. youtu.be/1BdZb67w43s

Getting up-close and personal with the Patagonian fjords near the Beagle Channel.

SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation https://www.biorxiv.org/content/10.1101/2025.11.14.688492v1

Double full rainbow at the end of the world at Cape Horn, Chile 🇨🇱

With all the wild stuff going on in the States (and the world) I am going to escape reality for a while on a sailing trip to the end of the world around Cape Horn and the Beagle Channel (named after the HMS Beagle of Charles Darwin and Robert Fitzroy fame). Thinking this might be type 2 fun...

🥁This Wednesday , in #FragileNucleosome seminar, we are excited to host @hannahlong.bsky.social and @jeffvierstra.bsky.social to tell us about amazing work they are doing! 🗓️Register here for upcoming session and the entire series: us06web.zoom.us/webinar/regi...

Southern fjords of Chile on a boat.

It’s been a pleasure to organize the Rules of Protein-DNA Recognition meeting in Cancun. Spectacular talks and an amazing and supportive scientific community!

Great resource! I should mention (since it's not on the website) that all of the chromatin accessibility data (DNase I) was generated at the UW & Altius Institute over the course >15years. The proper references for these data are: www.nature.com/articles/nat... and www.nature.com/articles/s41....

Please apply to our tenure-track faculty position at @stanford-chemh.bsky.social! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely! chemh.stanford.edu/opportunitie...

Looks like a great couple of months of seminars! Come check out my talk on November 5th if you want to learn about our progress in mapping the nucleotide-resolved structure and function of cis-regulatory DNA elements across thousands of cell types and states.

Wild to see a thread about me. I think the broader topic (as Jason points out) is what does the future of preventive medicines look like for at risk gene carriers? I also hope this gives people some hope to those dealing with devastating and (previously) unactionable inherited genetic diseases.

Does one sample (or even 10) suffice to define core cell type regulatory elements? NO! Because of both biological and technical variability you need to profile many (typically >15). The additional peaks are enriched for trait associated variants, so you miss a lot of possibly important signal.

Look at this and tell me I am wrong : DNaseI footprinting data is unparalleled in genomics. ~700 high quality datasets for an upcoming ENCODE data drop.

For some reason I was re-reading the DEseq2 paper and was reminded of what a statistical masterpiece that method is. Every time I read the paper I seem to learn something new. Not too many papers achieve that bar (at least for me).

I listened to Bhattacharya on Steve Bannon's "War Room" podcast. If you want to know how it went, see the following email that I just sent. 1/13

Jeff Vierstra was likely doomed by his DNA. A radical experiment gave him a chance to rewrite his fate — before ALS symptoms ever began. www.statnews.com/2025/07/28/a...

hotspot3: our chromatin accessibility peak caller is now a package – "pip install hotspot3" to try it out.

You might know that my life mostly revolves around skiing. I am organizing a 25 day sail & ski trip to Antarctica in Dec. 2025 and have space for 1-2 more people. We leave from Ushuaia, AR on the Tierra del Fuego (early Dec.) DM me for details and pass this around if you know anyone interested!

A parting gift from Wouter. www.biorxiv.org/content/10.1...

This is cool and a blast from the past. Way back in grad school I spent like 10 months building a femtosecond laser to x-link TFs to DNA but could never get it to work.