Shaun Mahony
Studying gene regulation and transcription factor binding with machine learning. Assoc Prof at Penn State. 🇮🇪
- Reposted by Shaun MahonyIn #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
- Reposted by Shaun MahonyI'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...
- Reposted by Shaun MahonyA 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.
- Reposted by Shaun MahonyHeads 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
- 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?
- 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...
- 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...
- 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 are highly dynamic during Plasmodium blood stage development; almost two thirds of the genome changes chromatin state during the IDC.
- 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.
- 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...
- 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).
- 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).
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View full threadOne 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.
- Reposted by Shaun MahonyLooks like my book is available for pre-order: a.co/d/cTKIwBN #EpigeneticsBook
- Reposted by Shaun Mahony@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
- Reposted by Shaun Mahony"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...
- Reposted by Shaun MahonyThe #RegSys @iscb-regsys.bsky.social track is gonna be outstanding again this year with a great selection of talks and keynotes @verapancaldi.bsky.social, Mafalda Dias, Roser Vento-Tormo, and @lucapinello.bsky.social ! www.iscb.org/ismbeccb2025...
- Reposted by Shaun MahonyPaper alert! I am really pleased to share the final version of the work led by Irène Amblard in the team on a regulatory switch controlling Cdx2 expression during posterior body development! #regulatorylogic #devbio @mrc-lms.bsky.social @imperialmed.bsky.social
- Reposted by Shaun MahonyThis a really exciting leap forward for genomic sequence to activity gene regulation models. It is a genuine improvement over pretty much all SOTA models spanning a wide range of regulatory, transcriptional and post-transcriptional processes. 1/
- Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
- This has been a wild story to follow. Someone is leading a campaign of pure harassment against @devoevomed.bsky.social 1/ bsky.app/profile/devo...
- First it was anonymous stories on junk news sites suggesting his own scientific work was fraudulent (bsky.app/profile/devo...). Then they claimed copyright over his own images to get him banned from twitter (bsky.app/profile/devo...). And now it's lawsuit threats. 2/
- Why? Everything started after he had the audacity to suggest that Colossal Bio's transgenic grey wolf with 14 mutated genes is not, in fact, a de-extinct dire wolf. 3/ substack.com/inbox/post/1...
- I really hope this colossally backfires on whoever's responsible. Hopefully the Streisand effect is still in full force and this gets picked up by the press. (btw, you know who else tried to silence critics with lawsuit threats? Theranos)
- Reposted by Shaun Mahony@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
- Reposted by Shaun MahonyMuch more important things going on in the world, but wanted to share this new work on parent-of-origin effects & “non-canonical” genomic imprinting in developmental plasticity of honey bees, out now in Genome Biology 🧪🧬🔄 link.springer.com/article/10.1...
- Reposted by Shaun MahonyA very special first post on Bluesky: I’m excited to share that I’ll be starting my lab at Penn State this coming January in the Dept of Biochemistry & Molecular Biology! I’ll be hiring at all levels soon. Check out updates, thoughts, and positions on the lab account: @hanna-lab.bsky.social
- Reposted by Shaun MahonyFree in-person registration is open for #MLCB2025! Sept 10-11 at @nygenome.org and online at youtube.com/@mlcbconf. Paper/abstract deadline is June 1, more deets including our fantastic invited speaker lineup at mlcb.org! Please RP.
- Reposted by Shaun Mahony🧬 Just out in Bioinformatics Advances: "Perspective on recent developments and challenges in regulatory and systems genomics" Find the full paper here: doi.org/10.1093/bioadv/vbaf106
- Reposted by Shaun MahonyOur New perspective explores breakthroughs & challenges in regulatory & systems genomics: from cis-regulatory code & 3D chromatin to spatial omics & AI models. 🔗 doi.org/10.1093/bioa... #Genomics #Bioinformatics #RegulatoryGenomics
- Reposted by Shaun Mahonyai.stanford.edu/postdoctoral... Postdoc candidates with strong expertise in AI for bio should apply for this new Stanford SAIL fellowship. We encourage applicants who would like to work with multiple SAIL faculty (we are part of SAIL as well). Come join us
- Reposted by Shaun Mahonyour work on the molecular differences between transcription factor isoforms is out now in Molecular Cell! key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity many are "negative regulators" & misexpressed in cancer www.sciencedirect.com/science/arti...
- Reposted by Shaun MahonyWhy AI won’t replace scientists capable of making disruptive conceptual breakthroughs - they pose questions that challenge, rather than align with, the training data set thomwolf.io/blog/scienti...
- Reposted by Shaun Mahony@austintwang.bsky.social is a fantastic grad student in the lab who will be completing his PhD in the Fall & is looking for research position in AI for bio in industry. www.austintwang.com 1/
- Reposted by Shaun MahonyBy crushing cancer research, what are Elon & Trump making more efficient? Their NIH funding cuts are illegal—so instead, they're suffocating the grant approval process for cancer researchers with so much red tape that labs & clinical trials will be forced to shut down.
- Reposted by Shaun Mahony🎆Next #FragileNucleosome meeting is less than a week away! We are delighted to host @manucazottes.bsky.social, @robertadolling1.bsky.social & @leandrosboukas.bsky.social ! We will discuss evolution of XIST regulatory network, cancer epigenetics, and MDEMs! 🗓️ us06web.zoom.us/webinar/regi...
- Reposted by Shaun Mahony🚨PA colleagues: "Senator Fetterman wants to hear from you about how the federal funding freeze is affecting Pennsylvania." "If your project has been impacted, please fill out our constituent impact form:" forms.office.com/g/mFv2JAPxpC Get out your Other Support and share that info!
- NIGMS MIRA explicitly asks for the following in investigator biosketches: “Include descriptions of significant service to the scientific community that are beyond normal mentoring and committee duties expected at the PD's/PI's institution.” They can’t then punish a PI based on the type of service
- Might even be a 1A issue, since the punishment would be based on an act of speech and not based on the work to be funded
- Reposted by Shaun MahonyAnother school curtails admissions, even offers already made. This is on #Trump, #Musk and #Vought. Time to fight back. www.thedp.com/article/2025...
- Reposted by Shaun MahonyThe University of Pittsburgh confirmed Friday that there would be no new Ph.D. offers of admission while Pitt works to understand how reduced federal aid could impact the institution.
- Reposted by Shaun MahonyAlmost all grant-review meetings under Trump 2.0 remain suspended at the US National Institutes of Health (NIH), preventing the world’s largest public funder of biomedical research from spending much of its US$47 billion annual budget. go.nature.com/4gM6oW4
- It looks like 8/8 study sections that were scheduled to begin today have been cancelled: www.csr.nih.gov/RevPanelsAnd...
- Are other outlets covering this? It's effectively another freeze on NIH funding. By my count, 3/8 study sections were cancelled today, 4/8 are cancelled tomorrow. Will only get worse as we hit those that were not posted before 1/20 @zey.bsky.social ? www.thetransmitter.org/funding/fede...
- Are other outlets covering this? It's effectively another freeze on NIH funding. By my count, 3/8 study sections were cancelled today, 4/8 are cancelled tomorrow. Will only get worse as we hit those that were not posted before 1/20 @zey.bsky.social ? www.thetransmitter.org/funding/fede...
