Brian Plosky

For decades, human genome editing has been limited to small, localized modifications.

Today, in a new paper published in @science.org , researchers from Arc's Hsu lab show that bridge recombinase technology is capable of large-scale genomic rearrangements in human cells.

In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design.

Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.

New work from Arc's @pauldatlinger.bsky.social of our Genome Engineering Technology Center. Congrats!

Many of the most complex and useful functions in biology emerge at the scale of whole genomes.

Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵

In a new preprint from @brianhie.bsky.social's lab, the team reports the first generative design of viable bacteriophage genomes.

Leveraging Evo 1 & Evo 2, they generated whole genome sequences, resulting in 16 viable phages with distinct genomic architectures.

"It is a big loss for Nature Methods and its audience. I think your role there in the past decade has transformed and re-defined the imaging related landscape for the entire community." 😭 These notes make me sentimental, but they also show me that doing this job well matters. #editorgoals

Vaccines are safe and effective. RFK Jr. isn’t.

Image of Toronto

JOB ALERT 🚨 We are hiring TWO principal investigators in cell, molecular, systems, or chemical biology in Toronto, Canada at @sinaihealth.bsky.social. We provide a generous startup, fully funded salary and academic appointment at U of Toronto.

www.nature.com/naturecareer...

Please repost!

Behind the Data of the Virtual Cell Challenge | Arc Institute To enable meaningful model comparison in the Virtual Cell Challenge, we needed more than just a new Perturb-seq dataset; we needed a high-quality and high-fidelity benchmark. This required us to make ...

In this blog post from Arc scientists, learn about some of the decisions that went into the dataset and three-metric evaluation framework developed for the first Virtual Cell Challenge.
arcinstitute.org/news/behind-...

I don’t know who needs this right now, but I really enjoy browsing “Paper Skygest”, a feed of posts on academic papers *from people you follow*. I think it’s what a lot of us are actually here for

I have an idea… journals.plos.org/plosbiology/...

Doing the right thing In this editorial, Brian Plosky makes a distinction between retracting papers because of honest errors of interpretation and other types of retractions.

It would be nice if there was a distinction between retraction for misconduct versus major errors. That’s one reason I wrote this: www.cell.com/molecular-ce...

Google Colab

To help competitors get started, our team created a Colab notebook that guides participants through training and running inference on an ML model. For this example we started with STATE, the recently released model from Arc: colab.research.google.com/drive/1QKOtY...

Over 2,000 people have registered for the Virtual Cell Challenge to create an AI model that can generalize for unseen perturbations. Hundreds of competitors have been submitting results from their models and the race, as you can see from the leaderboard, is heating up:

The Arc Institute Investigator Retreat is off to a great start! Huge thanks to Dave Burke and @brianhie.bsky.social for for sharing their computational research, and to Isha Jain, Will Allen, Faranak Fattahi, and Alex Pollen for diving into cell biology and neuroscience.

Our 2nd Investigator Retreat wrapped up with talks from Core Investigators Christoph Thaiss and Felix Horns, our incoming Science Fellow Maya Arce, and some of our Innovation Investigators and Ignite Awardees. We look forward to seeing how the connections made this week turn into new collaborations.

Academia may be a prestige economy but it wasn’t some choice of scientific leadership- we do it to ourselves, every day. Leadership rarely makes tenure criteria too down - it’s a committee of peers that sets it up for institutions. Leadership doesn’t sit on study sections - it’s peers doing it!

NIH Plans to Cap Publisher Fees, Dilute “Scientific Elite” Director of the National Institutes of Health says that capping research journals’ open-access fees will help rein in the $19 billion academic publishing industry and bolster scientific debate.

NIH Director say journals "bully scientists into paying large fees".

No. Academia is a prestige economy in which scientific leadership chose to make journals the currency & Gold OA was deemed 'the way'. Publishers just cashed in; you don't have to pay $10K

www.insidehighered.com/news/governm...

I think I made a difference! Anoxia was accepted in today’s @nytimes.com spelling bee!

Somewhat disappointing that bluesky has not been a major source of traffic to our Challenge. Seems like a struggle (at least for me) to get decent engagement here. LinkedIn is much better for me. X is still doing well for others

Check out the challenge and our initial model (released earlier this week):

Challenge Website: virtualcellchallenge.org
State model blog post: arcinstitute.org/news/virtual...

Virtual Cell Challenge: Toward a Turing test for the virtual cell Virtual cells are an emerging frontier at the intersection of artificial intelligence and biology. A key goal of these cell state models is predicting cellular responses to perturbations. The Virtual ...

We hope this will catalyze progress towards even better models - like how CASP brought us to protein folding models like AlphaFold and RoseTTAFold. You can read about the Challenge in @cellpress.bsky.social

Commentary in Cell: www.cell.com/cell/fulltex...

What an exciting week at @arcinstitute.org We started off with the release of State, our perturbation prediction (virtual cell) model, and today, we are kicking off the Virtual Cell Challenge

Introducing Arc Institute’s first virtual cell model: STATE

A White Nationalist Wrote a Law School Paper Promoting Racist Views. It Won Him an Award.

I’m sure the Trump Administration will be canceling all grants to the University of Florida because of their failure to combat anti-Semitism. Any day now.

www.nytimes.com/2025/06/21/u...

This was a tough one!

A White Nationalist Wrote a Law School Paper Promoting Racist Views. It Won Him an Award.

Why is the current admin okay with this at University of Florida? It seems far worse than anything Harvard did. Of course, we know it is just pretext…
www.nytimes.com/2025/06/21/u...

Please RT ! 5️⃣ days left to register. Gordon Conference “Histone and DNA modifications” Tuscany 🇮🇹 20.-25. July 25 🗓️ Regulation of genome function by histone and nucleic acid modifications. Great speaker lineup !!! >25 talks will be chosen from abstracts. Submit yours ➡️ shorturl.at/hBjyT

Barbara McClintock portrait

🧬🌽 Happy Transposon Day! 🌽🧬

Today we celebrate the birthday of Barbara McClintock - scientist extraordinaire and discoverer of jumping genes. Still the only woman to have an unshared Nobel Prize in the biomedical sciences #TransposonDay2025

Maybe some more oxygen to the brain is needed before they include this word…