Jeff Vierstra
@jeffvierstra.bsky.social
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 (🇺🇸🇨🇱). http://vierstra.org
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...
November 8, 2025 at 12:53 AM
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...
Reposted by Jeff Vierstra
🥁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...
🗓️Register here for upcoming session and the entire series:
us06web.zoom.us/webinar/regi...
November 3, 2025 at 12:03 PM
🥁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...
🗓️Register here for upcoming session and the entire series:
us06web.zoom.us/webinar/regi...
Southern fjords of Chile on a boat.
October 29, 2025 at 11:17 AM
Southern fjords of Chile on a boat.
Reposted by Jeff Vierstra
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!
October 17, 2025 at 12:14 PM
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....
September 18, 2025 at 5:58 PM
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....
Reposted by Jeff Vierstra
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...
@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...
Faculty Recruitment
chemh.stanford.edu
September 17, 2025 at 5:54 PM
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...
@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.
We're super excited to announce the entire lineup for the Fall season of Fragile Nucleosome Seminars, starting on Sept 10th at 1200 EDT / 1600 UTC with @gracebower.bsky.social and @creminslab.bsky.social!
register here for the entire series: us06web.zoom.us/webinar/regi...
register here for the entire series: us06web.zoom.us/webinar/regi...
September 1, 2025 at 5:31 PM
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.
A 🧵: Last week, I wrote about Jeff Vierstra, who carries the gene for a devastating, rare form of ALS. The disease killed his mom and all three of her siblings, along with relatives dating back to the 1800s.
Then, in 2020, two of his sisters began showing symptoms.
Then, in 2020, two of his sisters began showing symptoms.
Did a drug prevent this man’s ALS?
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
August 30, 2025 at 7:03 AM
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.
August 29, 2025 at 8:32 PM
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.
August 20, 2025 at 11:22 PM
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.
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.
August 13, 2025 at 9:36 PM
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.
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).
August 13, 2025 at 3:43 AM
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).
Reposted by Jeff Vierstra
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
If you want to know how it went, see the following email that I just sent.
1/13
August 11, 2025 at 8:10 PM
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
If you want to know how it went, see the following email that I just sent.
1/13
Reposted by Jeff Vierstra
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...
www.statnews.com/2025/07/28/a...
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,
www.statnews.com
July 28, 2025 at 1:15 PM
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...
www.statnews.com/2025/07/28/a...
hotspot3: our chromatin accessibility peak caller is now a package – "pip install hotspot3" to try it out.
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/vierstralab/...
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
github.com
July 27, 2025 at 1:50 AM
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!
July 12, 2025 at 3:09 AM
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!
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/vierstralab/...
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
github.com
July 8, 2025 at 3:07 AM
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/vierstralab/...
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.
Excited our paper is out in Cell @cp-cell.bsky.social!
🧬⚡ DNA photo-crosslinking proteomics in living cells
🎯 Pinpoints protein-DNA interactions to single amino acids
🌎 Globally quantifies DNA binding for >1800 proteins at a timescale of minutes
🔗 www.cell.com/cell/fulltex...
🧵
🧬⚡ DNA photo-crosslinking proteomics in living cells
🎯 Pinpoints protein-DNA interactions to single amino acids
🌎 Globally quantifies DNA binding for >1800 proteins at a timescale of minutes
🔗 www.cell.com/cell/fulltex...
🧵
The human proteome with direct physical access to DNA
Zero-distance photo-crosslinking reveals direct protein-DNA interactions in living
cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale
of minutes with single-amino-aci...
www.cell.com
May 24, 2025 at 12:28 AM
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.
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...
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.
www.columbiadoctors.org
May 23, 2025 at 7:34 PM
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...
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!).
May 13, 2025 at 7:42 PM
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!).
Two genome scientists at the end of the world!
May 12, 2025 at 4:42 PM
Two genome scientists at the end of the world!
Reposted by Jeff Vierstra
There is still time to submit an abstract! The deadline is now extended to May 14.
Like regulatory genomics? Don’t miss this very fun meeting! May 7 is the deadline for early registration and abstract submission www.asbmb.org/meetings-eve...
Evolution and core processes in gene expression
June 26–29, 2025 | Kansas City, Mo.
www.asbmb.org
May 9, 2025 at 7:33 PM
There is still time to submit an abstract! The deadline is now extended to May 14.
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...
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...
www.nature.com
May 9, 2025 at 2:15 PM
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...
Reposted by Jeff Vierstra
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
April 8, 2025 at 1:52 PM
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