Jeff Vierstra

Investigator @ Altius Institute for Biomedical Sciences. High-resolution mapping of chromatin structure & function. Back to back clinical trial champion.

[Jeff Vierstra @jeffvierstra]

Look for this over the next couple of weeks on bioRxiv!

[Jeff Vierstra @jeffvierstra]

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!

[Jeff Vierstra @jeffvierstra]

These data correspond to >1,000 individuals and we performed phased genotyping and allelic imbalance analysis with regulatory genomes (millions of SNVs). We have also uniformly processed and integrated >10,000 publicly available ATAC-seq datasets.

[Jeff Vierstra @jeffvierstra]

Please try it out and give us feedback.

[Jeff Vierstra @jeffvierstra]

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.

https://t.co/4tMH82yeG0

[Jeff Vierstra @jeffvierstra]

We have applied this to ~4000 DNase I and >10,000 ATAC-seq (publicly available on SRA) datasets (to be released very soon), and it seems to pass the "taste-test" as we call it. Maybe sometime in the future we will write this up -- though don't hold your breath 😂.

[Jeff Vierstra @jeffvierstra]

https://t.co/tZQhvkIKtn

[Jeff Vierstra @jeffvierstra]

CBS did a segment on an experimental therapy in which I am one of the first individuals to receive prophylactically for genetic ALS.

[Columbia Medicine @ColumbiaMed]

A story of hope: Jeff Vierstra, living with an ultra-rare form of ALS, is thriving on an experimental therapy under the care of Columbia neurologist Dr. Neil Shneider. Through his research and work with the n-Lorem Foundation, patients with ultra-rare ALS mutations can access personalized therapies that may extend survival via the Silence ALS program. https://t.co/R5wskUsaIJ

[Jeff Vierstra @jeffvierstra]

We have also seen scRNA-seq artifacts like this is the split-pool/combinatorial indexing methods that really mess up interpretation.

[Anshul Kundaje @anshulkundaje]

Could AI agents have found this kind of artifact? And if so why have they not found such issues so far? Has anyone tried "Find cryptic issues in this data from a new platform". Will it find novel artifacts like this one? Folks developing new assays & platforms should try this.

[Jason Ukman @JasonUkman]

Did a drug prevent this man’s ALS? Via @Jasonmmast
https://t.co/nVwdJk7Bz0

[STAT @statnews]

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, he wiggled it around in Vierstra’s… https://t.co/6WmESoBISe

[Jeff Vierstra @jeffvierstra]

FYI I am the second patient. You can read more about my family here:

https://t.co/FFCtj1CNg7

[Columbia Medicine @ColumbiaMed]

Two ALS patients experienced a remarkable response to the experimental therapy ulefnersen (formerly jacifusen), developed by #ColumbiaMed neurologist Dr. Neil Shneider in collaboration with Ionis Pharmaceuticals — offering renewed hope for others affected by the disease.

🔗 https://t.co/QKlIO14dnc