iiinova — where your digital self keeps evolving

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Seychelle Vos @voslab.org · 09/02/2026

🧪🧬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...

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Genetics Society of America @genetics-gsa.bsky.social · 13/01/2026

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

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ralucagordan.bsky.social @ralucagordan.bsky.social · 03/10/2025

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...

cell.com

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.

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Elizabeth Wood, PhD @lizbwood.bsky.social · 22/09/2025

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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James Bonfield @jbonfield.bsky.social · 15/09/2025

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 · 12/09/2025

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 · 07/09/2025

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...

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Shaun Mahony @shaunmahony.bsky.social · 23/08/2025

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...

biorxiv.org

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...

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John Greally @greally.bsky.social · 18/08/2025

Looks like my book is available for pre-order: a.co/d/cTKIwBN #EpigeneticsBook

a.co

Amazon.com

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Anshul Kundaje @anshulkundaje.bsky.social · 19/08/2025

@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

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Anthony Mathelier @amathelier.bsky.social · 21/07/2025

The #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...

iscb.org

RegSys

ISCB - International Society for Computational Biology

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Vicki Metzis @vmetzis.bsky.social · 27/06/2025

Paper 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

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Anshul Kundaje @anshulkundaje.bsky.social · 25/06/2025

This 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/

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Shaun Mahony @shaunmahony.bsky.social · 24/06/2025

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...

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Anshul Kundaje @anshulkundaje.bsky.social · 19/06/2025

@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/

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Sean Bresnahan @seantbres.bsky.social · 18/06/2025

Much 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...

link.springer.com

Intragenomic conflict associated with extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera) - Genome Biology

Background Caste determination of honey bees (Apis mellifera) exemplifies developmental plasticity, where differences in larval diet result in identical genotypes yielding either long-lived, reproduct...

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Michael Hanna @mike-hanna.bsky.social · 28/05/2025

A 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

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David A Knowles @davidaknowles.bsky.social · 15/05/2025

Free 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.

youtube.com

Machine Learning in Computational Biology

Youtube channel for the Machine Learning in Computational Biology conference: https://mlcb.github.io/

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Bioinformatics Advances @bioinfoadv.bsky.social · 14/05/2025

🧬 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

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Anshul Kundaje @anshulkundaje.bsky.social · 18/04/2025

ai.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

ai.stanford.edu

SAIL Postdoctoral Fellows – Stanford Artificial Intelligence Laboratory

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Kaia Mattioli @kaiamattioli.bsky.social · 26/03/2025

our 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...

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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 22/03/2025

Why 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...

thomwolf.io

🔭 The Einstein AI model

I shared a controversial take the other day at an event and I decided to write it down in a longer format: I’m afraid AI won't give us a compressed 21st century.

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Anshul Kundaje @anshulkundaje.bsky.social · 05/03/2025

@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/

austintwang.com

Austin T. Wang

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Senator Patty Murray @murray.senate.gov · 24/02/2025

By 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.

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FragileNucleosome @fnucleosome.bsky.social · 22/02/2025

🎆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...

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Vaughn Cooper @vscooper.micropopbio.org · 22/02/2025

🚨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!

forms.office.com

Microsoft Forms

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Shaun Mahony @shaunmahony.bsky.social · 22/02/2025

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

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Nature @nature.com · 20/02/2025

Almost 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

go.nature.com

Revealed: NIH research grants still frozen despite lawsuits challenging Trump order

The Trump administration is exploiting a loophole to keep a funding freeze in place, leaving researchers in limbo.

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Shaun Mahony @shaunmahony.bsky.social · 19/02/2025

It looks like 8/8 study sections that were scheduled to begin today have been cancelled: www.csr.nih.gov/RevPanelsAnd...

csr.nih.gov

Review Dates

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Shaun Mahony @shaunmahony.bsky.social · 19/02/2025

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...

thetransmitter.org

Federal Register hold makes ‘end run’ around court pause on NIH funding freeze

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Michael Meers @mpmeers.bsky.social · 18/02/2025

We think about this Q a lot--as noted above, we used CUT&RUN fragment size to infer that some nuc binding probably occurs, but our thought is that these events are likely transient so won't be efficiently captured via a re-ChIP-style method. FWIW C&R shows ~20% nuc-sized frags for FOXA1 ⬇️

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John Pearson @jmxpearson.bsky.social · 18/12/2024

And I’ll point out that in the case of success stories like Bell Labs or many tech research shops, the advances did not come from big vision but anarchic autonomy, researchers told, “Do whatever you want.” The breakthroughs were rarely in anticipated directions. 8/n

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New York Times Opinion @nytopinion.nytimes.com · 14/02/2025

JD Vance has expressed a “deep hostility to the entire academic enterprise, not just the so-called woke parts,” writes @michellegoldberg.bsky.social. "He wasn’t talking about making more room for right-wing ideas in universities or even dreaming of taking them over. He wanted to destroy it all."

nytimes.com

Opinion | Trump Wants to Destroy All Academia, Not Just the Woke Parts

The administration’s war on universities defies rational self-interest.

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Jeremy Berg @jeremymberg.bsky.social · 13/02/2025

Bluetorial: The rationale for the “NIH” indirect cost “plan” is based on misunderstood (unintentional or intentional) accounting and math The value of real government transparency

media.tenor.com

a cartoon of homer simpson holding a card

ALT: a cartoon of homer simpson holding a card

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Solid Evidence @solidevidence.bsky.social · 12/02/2025

Here's a quantitative illustration of what's happening with NIH funding.

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a grassland chase 🌾🌾🌾🌾 @chasesolidago.bsky.social · 12/02/2025

Things that Ted Cruz thinks is woke: Taking middle school kids on a field trip to see the eclipse www.nsf.gov/awardsearch/...

nsf.gov

NSF Award Search: Award # 2327186 - REAL Field Trip Model for the 2024 Total Solar Eclipses Lock

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Shaun Mahony @shaunmahony.bsky.social · 11/02/2025

Greenland famously acquired its name as a marketing tool to get viking settlers to move there. I'm fine with the new name if it encourages certain people to move there too

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Shaun Mahony @shaunmahony.bsky.social · 11/02/2025

What's the indirect rate at SpaceX? Tough to answer, since they're not reqd to publicize indirect rates like universities. BUT, the cost of a Falcon9 launch is $100M for US gov't and $67M for a private company. So the ADDITIONAL overhead that SpaceX charges for working with the US gov't is 50%.

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Bita Moghaddam @bita137.bsky.social · 11/02/2025

Many in biotech/private sector are boasting about their ways of funding and doing science But they are staffed with PhDs and postdocs we train in our NIH and NSF funded labs in universities With university labs lacking funds to train, the private sector will be profoundly harmed

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Shaun Mahony @shaunmahony.bsky.social · 11/02/2025

"Every $100 million in investment leads to 78 patents and $598 million in further research, according to N.I.H. calculations" Or $100 million will get the taxpayer one Falcon 9 launch with SpaceX www.nytimes.com/2025/02/11/o...

nytimes.com

Opinion | The Pharmaceutical Industry Heads Into Elon Musk’s Wood Chipper (Gift Article)

Who needs N.I.H. grants? A lot of red-state universities, for one.

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Shaun Mahony @shaunmahony.bsky.social · 11/02/2025

Did you all know that SpaceX charges the US Gov't $100M per Falcon 9 launch, even though the rocket costs them as low as $15M? But Elon would have you believe that cancer researchers at non-profit universities are the ones milking the system.

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Shaun Mahony @shaunmahony.bsky.social · 10/02/2025

We should talk more about where the US gov't gets huge value for taxpayer money. Take NIH study section: they get 25-30 expert PhD consultants to each spend 40-50 hours scrutinizing grant apps (incl 2 solid days of group discussion) and they pay them ~half of DC minimum hourly wage. And no coffee

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Joshua Sharp @joshuasharp.bsky.social · 08/02/2025

It certainly is NOT just a higher ed issue. My company exists today because of the NIH SBIR program. At a 15% indirect rate, that money won't support the research it supposedly funds. My company would not have existed, and would not be supporting drug discovery and development worldwide today.

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