Brian Plosky

a sign that says we 're hiring in orange on a white background ALT: a sign that says we 're hiring in orange on a white background

Nature Methods is hiring! We are looking for candidates with expertise in genetics, genomics and/or molecular biology to join our editorial team in the US (NYC/Jersey City) or China (Shanghai/Beijing). Apply by December 12!

springernature.wd3.myworkdayjobs.com/SpringerNatu...

In Memoriam: Bert W. O'Malley, M.D. In Memoriam: Bert W. O'Malley, M.D....

A true legend.
www.bcm.edu/about-us/lea...

Work published today in @natbiotech.nature.com from Arc’s Luke Gilbert and Patrick Hsu labs presents a new way to insert large DNA sequences into the genome using engineered recombinases that don’t require DNA cutting or rely on the cell's repair machinery.

Coincidental juxtaposition of SNARE with the wrong kind of SNAP in my other feed:

Like the Monkey’s Paw—be careful what you wish for!

BINSEQ: A Family of High-Performance Binary Formats for Nucleotide Sequences Modern genomics produces billions of sequencing records per run, which are typically stored as gzip-compressed FASTQ files. While this format is widely used, it is not optimal for high-throughput proc...

I've updated the BINSEQ manuscript to stay up to date with changes since I originally put it out at the beginning of the year

Some notable changes:
1. Support for ambiguous bases with 4bit encoding
2. Support for sequence headers
3. Improved API

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

Welcome to our 9th Core Investigator and first physician-scientist, John Pluvinage. His team investigates the hidden overlap between autoimmunity and neurodegeneration, developing targeted treatments for mysterious neurological cases and common dementias.

Arc Core Investigator @genophoria.bsky.social will speak on a free, online panel with @tkaraletsos.bsky.social, @emmalundberg.bsky.social, and @ronalfa.bsky.social on Wed., Oct. 29, as part of GENbio's “The State of AI in Drug Discovery in 2025.” Register at: webinars.liebertpub.com/e/the-state-...

Maybe try @‘ing them? It might have worked for me bsky.app/profile/bria...

Just tried this out on a couple of preprints, and this seems legit! Only minor issue so far is the Word file for the plan not opening. Also, it seems that AI x Bio is not a fully supported domain yet. But nice that it prominently acknowledged that!

Hear how Arc, Ultima Genomics, and @10xgenomics.bsky.social are partnering to generate perturbation data at the scale needed to train virtual cell models on The Bio Report podcast with guests @genophoria.bsky.social, Gilad Almogy, and
Serge Saxonov: thebioreport.podbean.com/e/transformi...

Arc is looking for an outstanding early-career scientist to be our next Science Fellow. This program provides resources and freedom for those looking to transition into a principal investigator role immediately after doctoral training. Apply here: arcinstitute.org/programs/sea...

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...