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Shaun Mahony

@shaunmahony.bsky.social

1.5K followers 680 following 340 posts

Studying gene regulation and transcription factor binding with machine learning. Assoc Prof at Penn State. 🇮🇪

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Shaun Mahony @shaunmahony.bsky.social · Nov 14

Next, if you're looking for your daily hit of posts that focus on gene regulation, here's a relevant feed:
bsky.app/profile/shau...

The way the feed works is that it searches for posts containing #GeneReg or a set of keywords (see next post).

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Reposted by Shaun Mahony

ralucagordan.bsky.social @ralucagordan.bsky.social · 5d

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...

DNA mutagenesis driven by transcription factor competition with mismatch repair

Competition between transcription factors and mismatch repair machinery drives localized hypermutation at regulatory elements, with implications for cancer and genome evolution.

www.cell.com

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Shaun Mahony @shaunmahony.bsky.social · 11d

Tbh, I CAN’T understand why they limit to senior undergrads and 1st yr grad students. Reviewers are assessing a graduate research plan from students that either don’t know what program or what lab they are joining. And then NSF provides funding decisions too late to influence those decisions

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Shaun Mahony @shaunmahony.bsky.social · 12d

I thought arXiv accepted preprints?

Reposted by Shaun Mahony

Elizabeth Wood, PhD @lizbwood.bsky.social · 16d

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.

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Reposted by Shaun Mahony

James Bonfield @jbonfield.bsky.social · 23d

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

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Shaun Mahony @shaunmahony.bsky.social · 26d

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...

Trustees increase Penn State president’s total pay by $1M. See the terms

The package also included a contract extension for Bendapudi.

www.centredaily.com

Shaun Mahony @shaunmahony.bsky.social · 26d

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?

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Shaun Mahony @shaunmahony.bsky.social · 28d

Well yeah, but you said yourself above - an NoA is permission to get reimbursed for allowable expenses. If the NoA approves all funds and the end date is 4 years in the future, I don’t see where they can limit annual without a new NoA

Shaun Mahony @shaunmahony.bsky.social · 28d

I think it would be hard for them to implement any enforcement of annual spending levels when the NoA has all funds, right? Wouldn’t it require a new NoA that pulls back funds? I think the deviation would need to be extreme before they would do that

Shaun Mahony @shaunmahony.bsky.social · 28d

I’ve heard from those who have received NoAs with the full budget and the expiry set to the project end date. No limits in the NoAs as far as they reported and explicit guidance from POs that annual budgets are flexible

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Shaun Mahony @shaunmahony.bsky.social · 29d

I know of some MYF awards that have already been made. Claus is correct- all money is available up front to spend on any timeline

Shaun Mahony @shaunmahony.bsky.social · Sep 7

We also see varied associations between ApiAP2 transcription factor binding sites and chromatin states, suggesting a new way to categorize the activities of these TFs.

Shaun Mahony @shaunmahony.bsky.social · Sep 7

Chromatin states are highly dynamic during Plasmodium blood stage development; almost two thirds of the genome changes chromatin state during the IDC.

Plot showing the dynamic transitions between chromatin states across the Plasmodium IDC

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Shaun Mahony @shaunmahony.bsky.social · Sep 7

We found 11 chromatin states during the P. falciparum IDC, defined by combinations of chromatin accessibility and histone modifications. Some of these states comprise unusual combinations of histone marks and associations with regulatory activities that are not seen in higher eukaryotes.

Chromatin states defined during the P. falciparum IDC

Shaun Mahony @shaunmahony.bsky.social · Sep 7

New preprint from Alan Brown in our lab, who is co-advised by @llinaslab.bsky.social. In this study, Alan studied chromatin state dynamics during the asexual intraerythrocytic development cycle (IDC) of the human malaria parasite, Plasmodium falciparum.

www.biorxiv.org/content/10.1...