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
Jeff Vierstra
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Using only training data from >4,000 human reference DNase I datasets we can also predict mouse DNase I. Also, it's readily tunable with the enormous amount of publicly available ATAC-seq data deposited to SRA.
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.
I am well aware that one can find a sentence in the "Acknowledgments" section, but seems insufficient given that their whole project is only possible because of these resources.
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.
Look for this manuscript to be online within the next couple of weeks on bioRxiv! Also, if you want to try out the data let me know as we are testing a new data packaging format.
We have also created a data portal complete with a coding chatbot to access the raw and processed data (>4,000 reference DNase I and >10,000 ATAC-seq samples). Coming soon to bioRxiv!
Getting up-close and personal with the Patagonian fjords near the Beagle Channel.
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
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...
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
