Shaun Mahony

Salt?

Chihuahua or Muffin? Last year, a bizarre picture quiz took the internet by storm as Karen Zack’s images of Animals vs. Food spread virally. Given the recent…

Or for vision ML intro: Chihuahua or muffin

blog.cloudsight.ai/chihuahua-or...

Datasaurus dozen?

en.wikipedia.org/wiki/Datasau...

The human coder would have been been tasked with validating the code could be held responsible for any mistakes. If we don’t teach coding to students, who will be responsible for validating?

I know they can be very helpful for coding, but I have also seen LLMs make egregious and hard to detect mistakes in code and analysis. When you posed the question about whether it would be any different if you hired a coder to do this - I think the answer is yes, and it’s a matter of responsibility

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.

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...

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

I thought arXiv accepted preprints?

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

Trustees increase Penn State president’s total pay by $1M. See the terms The package also included a contract extension for Bendapudi.

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?

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

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

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

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

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.

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

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

Chromatin states defined during the P. falciparum IDC

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.

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...

Figure showing that K562 CTCF ChIP-exo data provides consistent results between 1 and 5 sonication cycles, while data quality fades out from that point onwards.

One example: we found a range of sonication settings that provide similar results (at least for CTCF in K562). I kinda expected to see different cohorts of sites in differentially accessible chromatin being "released" by different sonication settings, but we see no evidence for that.

The manuscript contains practical advice on protocol aspects such as crosslinking conditions and develops a newly library construction workflow to take advantage of newer kits and techniques.

Side-by-side comparison of K562 CTCF ChIP-exo data from three protocols: MO-ChIP-exo, ChIP-exo v5.0 and ChIP-exo v1.1. MO-ChIP-exo is shown to have higher FRiP scores and higher peak counts.

MO-ChIP-exo offers improved signal-to-noise compared with other versions of the protocol (as measured by Fraction of Reads in Peaks - FRiP scores).

Overview of the existing ChIP-exo protocol alongside the new MO-ChIP-exo protocol. The figure highlights protocol steps that we investigated in our manuscript.

Daniela systematically investigated most steps in the protocol. Boxes with green highlights here are steps that were investigated and modified in our new mammalian-optimized ChIP-exo protocol (MO-ChIP-exo).

Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells By combining chromatin immunoprecipitation (ChIP) with an exonuclease digestion of protein-bound DNA fragments, ChIP-exo characterizes genome-wide protein-DNA interactions at near base-pair resolution...

New preprint from the lab: Dr. Daniela James led an effort to improve the ChIP-exo protocol for high-res protein-DNA interactions. Particularly focused on optimizing for use in mammalian cells and making the protocol compatible with newer Illumina sequencers.
www.biorxiv.org/content/10.1...

Is this your new plan for public funding of USPS?

Looks like my book is available for pre-order:

a.co/d/cTKIwBN

#EpigeneticsBook

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease.

Details below
careersearch.stanford.edu/jobs/computa...

Plz RT

Beyond AlphaFold: how AI is decoding the grammar of the genome Scientists are seeking to decipher the role of non-coding DNA in the human genome, helped by a suite of artificial-intelligence tools.

"I want to vibe code the genome"

—the illustrious @casey.greenelab.com

as quoted by @jperkel.bsky.social @nature.com 🧬🖥️ #MLSky www.nature.com/articles/d41...

I think State College is swarmed with them this year. I’ve saw tons of the nymphs earlier this summer and am starting to see lots of adults