Investigator @ Altius Institute for Biomedical Sciences. High-resolution mapping of chromatin structure & function. Back to back clinical trial champion.
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!
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.
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
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 π.
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
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.
For over an hour, Jeff Vierstra lay still in Columbia Universityβs ALS clinic, as a doctor poked him ankle-to-throat with an electric needle. Sometimes, he wiggled it around in Vierstraβsβ¦ https://t.co/6WmESoBISe
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 β offering renewed hope for others affected by the disease.
π https://t.co/QKlIO14dnc