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Jeff Vierstra

@jeffvierstra.bsky.social
403 followers 400 following 140 posts

Senior Investigator @ Altius Institute for Biomedical Sciences. Research: High-resolution mapping of chromatin structure & function. Fun: Mountain shenanigans and skiing turns all year. Seattle, USA/Patagonia Chilena (🇺🇸🇨🇱). vierstra.org

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Reposted by Jeff Vierstra
Nature Methods @natmethods.nature.com · 06/08/2026
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...
nature.com
GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors - Nature Methods
GHT-SELEX—high-throughput SELEX with fragmented genomic DNA—shows that transcription factors can be rather particular about which genomic loci they bind, and that C2H2 zinc finger proteins often engag...
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Jeff Vierstra @jeffvierstra.bsky.social · 16/07/2026
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.
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Reposted by Jeff Vierstra
bioRxiv Genomics @biorxiv-genomic.bsky.social · 09/07/2026
The Encyclopedia of DNA Elements www.biorxiv.org/content/10.64898/20…
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Jeff Vierstra @jeffvierstra.bsky.social · 16/04/2026
We are finally putting the final touches on an operationally complete mapping of regulatory DNA via DNase I in both human (>4,000 samples) and mouse. To interact with the samples we created this neat browser interface complete with a chatbot!
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Jeff Vierstra @jeffvierstra.bsky.social · 04/04/2026
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
youtu.be
Experimental treatments brings hope to ALS patients
YouTube video by CBS Mornings
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Jeff Vierstra @jeffvierstra.bsky.social · 10/03/2026
Exciting results! We developed a single, generalizable ML model that can predict chromatin accessibility across any arbitrary cell type using a sample intrinsic and portable embedding. Notably works on samples generated over a 15 yr time interval with different technologies & methodologies.
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Jeff Vierstra @jeffvierstra.bsky.social · 30/01/2026
Surprised (but also not that surprised) that the AlphaGenome paper didn't officially cite any of the primary data used for training their model (see Fig. 1, thousands of datasets made with tremendous time and effort over >15yrs). What's up with that @nature.com ? www.nature.com/articles/s41...
nature.com
Advancing regulatory variant effect prediction with AlphaGenome - Nature
AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...
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Jeff Vierstra @jeffvierstra.bsky.social · 27/11/2025
Getting up-close and personal with the Patagonian fjords near the Beagle Channel.
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Reposted by Jeff Vierstra
bioRxiv Genomics @biorxiv-genomic.bsky.social · 16/11/2025
SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation www.biorxiv.org/content/10.1101/202…
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Jeff Vierstra @jeffvierstra.bsky.social · 12/11/2025
Double full rainbow at the end of the world at Cape Horn, Chile 🇨🇱
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Jeff Vierstra @jeffvierstra.bsky.social · 08/11/2025
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...
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Reposted by Jeff Vierstra
FragileNucleosome @fnucleosome.bsky.social · 03/11/2025
🥁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...
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Jeff Vierstra @jeffvierstra.bsky.social · 29/10/2025
Southern fjords of Chile on a boat.
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Reposted by Jeff Vierstra
Juan Fuxman Bass @fuxmanlab.bsky.social · 17/10/2025
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!
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Jeff Vierstra @jeffvierstra.bsky.social · 18/09/2025
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....
nature.com
The accessible chromatin landscape of the human genome - Nature
An extensive map of human DNase I hypersensitive sites, markers of regulatory DNA, in 125 diverse cell and tissue types is described; integration of this information with other ENCODE-generated data s...
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Reposted by Jeff Vierstra
Polly Fordyce @pollyfordyce.bsky.social · 17/09/2025
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...
chemh.stanford.edu
Faculty Recruitment
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Jeff Vierstra @jeffvierstra.bsky.social · 01/09/2025
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.
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Jeff Vierstra @jeffvierstra.bsky.social · 30/08/2025
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.
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Jeff Vierstra @jeffvierstra.bsky.social · 29/08/2025
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.
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Jeff Vierstra @jeffvierstra.bsky.social · 21/08/2025
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.
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Jeff Vierstra @jeffvierstra.bsky.social · 13/08/2025
Activity determining nucleotides on the BCL11A +58 enhancer according to a ML model built purely on DNase I data from thousands of cell types (this is just prediction for erythroid cells). Not bad w.r.t. functional data. The GATA1 site is the therapeutic target of Casgevy for SCD and B-thal.
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Jeff Vierstra @jeffvierstra.bsky.social · 13/08/2025
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).
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Reposted by Jeff Vierstra
Jeremy Berg @jeremymberg.bsky.social · 11/08/2025
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
Dear Dr. Bhattacharya:

I have listened to your performance on the “War Room” podcast with Steve Bannon. The segment begins with a discussion of Secretary Kennedy’s recent cancellation of $500M worth of contracts related to mRNA vaccines.

You say “You can’t have a platform where such a large percentage of the population distrusts the platform as we use it for vaccines and expect it to work.”  Later, you make comments that might explain why a large segment of the percentage distrusts this platform. For example, you say that the vaccine was not protective against contracting COVID and cite your own case on COVID after being vaccinated. However, you fail to cite the evidence for the clinical trials that led to the Emergency Use Authorization.
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Reposted by Jeff Vierstra
STAT @statnews.com · 28/07/2025
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...
statnews.com
Did a drug prevent this man’s ALS?
For over an hour, Jeff Vierstra lay still in Columbia University’s ALS clinic, as a doctor poked him ankle-to-throat with an electric needle. Sometimes,
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Jeff Vierstra @jeffvierstra.bsky.social · 27/07/2025
hotspot3: our chromatin accessibility peak caller is now a package – "pip install hotspot3" to try it out.
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Jeff Vierstra @jeffvierstra.bsky.social · 12/07/2025
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!
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Jeff Vierstra @jeffvierstra.bsky.social · 08/07/2025
We have created a new DNase I- & ATAC-seq peak caller that uses an adaptive background model that controls for copy number variation & aneuploidy. It performs a per-nucleotide test (+FDR correction) and is very fast. Please try it out and give us feedback! github.com/vierstralab/...
github.com
GitHub - vierstralab/hotspot3: A chromatin accessibility peak caller with an adaptive background model
A chromatin accessibility peak caller with an adaptive background model - vierstralab/hotspot3
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Jeff Vierstra @jeffvierstra.bsky.social · 02/07/2025
A parting gift from Wouter. www.biorxiv.org/content/10.1...
biorxiv.org
Epilogos: information-theoretic navigation of multi-tissue functional genomic annotations
Functional genomics data, such as chromatin state maps, provide critical insights into biological processes, but are hard to navigate and interpret. We present Epilogos to address this challenge by of...
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Jeff Vierstra @jeffvierstra.bsky.social · 24/05/2025
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.
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Jeff Vierstra @jeffvierstra.bsky.social · 23/05/2025
This is a wild post for me to make because I havent shared this with many people. Today, the Lancet published the results of a trial for a novel ASO therapy for FUS-ALS which me and my siblings participated(-ing). You can read about my experience here: www.columbiadoctors.org/news/jeffs-s...
columbiadoctors.org
Jeff’s Story: Defying a Family History of ALS through a New Drug Trial
After losing several family members to a rare, inherited form of ALS, Jeff remains symptom-free thanks to a groundbreaking clinical trial at Columbia.
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Jeff Vierstra @jeffvierstra.bsky.social · 13/05/2025
PSA: We just finished processing nearly all public ATAC-seq datasets from SRA (about 22,000 datasets). (Not?) Surprisingly, we had to throw-out nearly ~50% because they were low-quality (low signal-to-noise, duplicate rate, etc.). Check quality before analysis (TSS-enrichment is not sufficient!).
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Jeff Vierstra @jeffvierstra.bsky.social · 12/05/2025
Two genome scientists at the end of the world!
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Reposted by Jeff Vierstra
Julia Zeitlinger @juliazeitlinger.bsky.social · 09/05/2025
There is still time to submit an abstract! The deadline is now extended to May 14.
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Jeff Vierstra @jeffvierstra.bsky.social · 09/05/2025
Finally published! We developed an epigenomics to therapeutics screening approach that identifies naturally occurring elements that can titrate expression of transgenes at various levels including single elements stronger than the B-globin LCR. www.nature.com/articles/s41...
nature.com
Large-scale discovery of potent, compact and erythroid specific enhancers for gene therapy vectors - Nature Communications
This study presents a large-scale enhancer screening approach to optimize gene therapy vectors. A compact, potent, erythroid-specific enhancer used in a therapeutic vector, improved viral titers, tran...
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Reposted by Jeff Vierstra
Valentina Baderna @valentinabaderna.bsky.social · 08/04/2025
Happy to share the latest story from @arnaudkr.bsky.social's lab @embl.org! With @guidobarzaghi.bsky.social, we used Single Molecule Footprinting to quantify how often chromatin is accessible at enhancers after TF and chromatin environment changes! Check our preprint bit.ly/3XQMFxN + thread ⬇️ 1/11
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Jeff Vierstra @jeffvierstra.bsky.social · 24/03/2025
Amazing game. The penalty shot -- WOW! www.youtube.com/watch?v=XC7B...
youtube.com
Wisconsin vs. Ohio State: 2025 Women's Frozen Four hockey title highlights
YouTube video by NCAA Championships
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Jeff Vierstra @jeffvierstra.bsky.social · 05/03/2025
Not surprising that Evo2 (despite pre-print claims) can't even beat ~15yo approach for non-coding variant classification. How does a gimish of bacterial and metazoan genomes WITHOUT annotation going to learn this? Best to use functional data (i.e., ours -- DNase I data from 1000s of cell types).
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Jeff Vierstra @jeffvierstra.bsky.social · 04/03/2025
Go to Chile! Awesome conference + the most beautiful landscapes in the world (sorry NZ!).
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Jeff Vierstra @jeffvierstra.bsky.social · 20/02/2025
Hmm. I wonder if they will change what constitutes allowable indirect and direct expeditures. Will individual labs be able to negotiate lab space (i.e., rent)?
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Reposted by Jeff Vierstra
Judith Kribelbauer @jk-swietek.bsky.social · 12/02/2025
Looking for a Postdoc position in #Genomics at the interface of computational and molecular biology? -> The Rube lab at UC Merced is recruiting. I highly recommend you reach out! aprecruit.ucmerced.edu/JPF01874
aprecruit.ucmerced.edu
Postdoctoral Scholar in Genomics
University of California, Merced is hiring. Apply now!
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Jeff Vierstra @jeffvierstra.bsky.social · 08/02/2025
This is actually good IMHO. The indirect costs dont go to researchers! 30-40% of the indirect costs go to subsidize university building depreciation and the bloated administrative state. If you dig into the budget of various universities, the true operation budget is like 15% anyhow.
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Reposted by Jeff Vierstra
Noonan Lab @noonanlab.bsky.social · 30/01/2025
Out today in Cell: a comprehensive map of Human Accelerated Region gene targets in human and chimpanzee neural stem cells. Thread: authors.elsevier.com/a/1kWzdL7PXu... www.cell.com/cell/fulltex...
cell.com
Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment
Human accelerated regions (HARs) have been implicated in human brain evolution with limited understanding of the biological processes they alter. This study reports that HARs influenced brain evolutio...
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Reposted by Jeff Vierstra
Bart Deplancke @bartdeplancke.bsky.social · 10/01/2025
Fantastic opportunity: 🚀 Calling early-career scientists! Apply for the 2025 ELISIR Scholar at EPFL. From outstanding PhD straight to group leader. Join an interdisciplinary research community to conduct independent research in any area of #lifesciences in Lausanne, CH 👉 go.epfl.ch/ELISIR
go.epfl.ch
EPFL Life Sciences Early Independent Research Scholar (ELISIR)
From exceptional PhD directly to independent group leader
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Jeff Vierstra @jeffvierstra.bsky.social · 25/01/2025
I just read the recent "Multiscale footprints reveal..." paper. (www.nature.com/articles/s41...). The claim by authors (below) is based on ONLY 2 regions (amongst 100k) in 5 cell types. They don't provide genome-wide footprint calls, so how can they make these claims?! i.e., where's the evidence?
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Jeff Vierstra @jeffvierstra.bsky.social · 24/01/2025
There has been a couple of manuscripts released regarding transcription factor footprinting - or digital genomic footprinting (DGF) as we call it. I would like to put some of the claims, results and conclusions in context, since I have worked and published on this for ~15 years. 1/n
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Jeff Vierstra @jeffvierstra.bsky.social · 24/01/2025
Just de-activated my Twitter/X account. Same feeling of relief when I did this ~10 years ago on the facepile app.
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Jeff Vierstra @jeffvierstra.bsky.social · 17/01/2025
Going back to my hometown (Madison, WI) in January reminds me of why I live in the PNW now. Good thing I still own fleece lined pants!
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Jeff Vierstra @jeffvierstra.bsky.social · 17/01/2025
A manuscript from my group finally got accepted -- had a long review process and the authors moved on nearly 2 years ago. Still proud of this work, where we show how one can translate epigenetic mapping efforts into useful tools for therapeutics. www.biorxiv.org/content/10.1...
biorxiv.org
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors
Regulation of gene expression during cell development and differentiation is chiefly orchestrated by distal noncoding regulatory elements that precisely modulate cell selective gene activity. Gene the...
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