Studying gene regulation and transcription factor binding with machine learning. Assoc Prof at Penn State. 🇮🇪
Shaun Mahony
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🧪🧬New preprint We present cryo-EM structures of reconstituted CTCF–nucleosome complexes, showing CTCF dimerization drives nucleosome oligomerization into defined higher-order assemblies. Disrupting CTCF–CTCF interfaces in mESCs reduces looping and impairs differentiation. tinyurl.com/CTCF-nucleos...
In #G3journal, @shaunmahony.bsky.social introduces a mammalian-optimized ChIP-exo (MO-ChIP-exo) protocol that builds upon previous ChIP-exo protocols with systematic optimization of crosslinking, harvesting, and library construction. buff.ly/KfvejKQ
I'm very pleased to announce the official publication of our lab's paper "DNA mutagenesis driven by transcription factor competition with mismatch repair" in today's issue of Cell! www.cell.com/cell/abstrac...
A fundamental lesson of modern AI is that scale is essential: training bigger models on bigger datasets unlocks new capabilities. A fundamental lesson of AI engineering is that scaling up isn't trivial: it is not just a matter of spending more money and resources.
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Penn State's closing seven Commonwealth campuses and laying off up to 500 employees, but it can afford an extra $1M/year for the President's pay? www.centredaily.com/news/local/e...
Within 24hrs, our board of trustees closed the local NPR station because transferring to new owners would have cost too much ($17M over 5 yrs) AND they increased the President's pay (total >$20M over next 7 yrs). How does this further PSU's land grant mission to extend knowledge to the public?
