Brad Bowles 🧬🔬💻

Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.

Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉

www.nature.com/articles/s41...

We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!

🧵

bioRxiv bat signal going up. We have a big backlog of submissions. If any affiliates have time to do some screening, we (and all the authors) would be immensely grateful! 🙏

I was also under this misconception 🙋‍♂️ thanks for sharing this mini review!

Exploring R and Rust in Bioinformatics – Online Developer Forum, 28 July 2025 – Bioconductor community blog A blog for the Bioconductor community!

🚀 Reminder: Bioconductor Developer Forum is this Monday!

🧵 Topic: R & Rust in Bioinformatics
🗓️ July 28 | 🕚 11am EDT / 5pm CEST
🔗 Details + Zoom: blog.bioconductor.org/posts/2025-0...

#Bioconductor #RStats #RustLang #OpenSource

How I sleep every night living in the Pacific Northwest:

I am looking to connect with my plant bio assistant professor cohort. If you know someone (or if it’s you!) please let me know.

#PlantScience

Legend says the ancient Babylonians once tried to sequence and annotate God's own genome, and for their ambition and hubris they were forever cursed to have different annotation formats and standards so they could never do genomics with ease again.

Scientists, especially Seattle ones! One of my research scientists is heading to her PhD and we're looking to fill her spot, if not replace her. If you know someone looking to do cool and impactful translational research give them this:

uwhires.admin.washington.edu/ENG/Candidat...

Finn from adventure time making two characters kiss

90% of your work in a zebrafish lab is basically this:

As requested - A Starter Pack of PIs in Biology (or related fields) who are recruiting PHD STUDENTS! If you would like to be added, feel free to ask! go.bsky.app/Bf4DRFm

Anecdote re: science in the current era:

Had dinner last night with a herpetologist who had her NSF grant terminated (illegally, as far as I can tell). She's studying how pythons eat huge meals 1-2 times a yr, during which they greatly increase the size of their heart and other organs. 1/4

Much love for the UCSC genome browser team, it is a tool I use weekly and something I probably couldn’t live without 🫡

INDIANA JONES AND THE ILLEGALLY IMPOUNDED GRANT MONEY.

Hello! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @cp-cellreports.bsky.social, @mardakheh.bsky.social and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit!

tinyurl.com/ydn6e3ac

Zohran Mamdani's socialist promises: No reviewer requests for additional experiments.

#AcademicChatter

🖥️🧬I have a tool/lib that I want to make that I think will be useful. But, all of my students are busy with projects. While I have a plan & cycles to help, it will take way longer if I do it all myself. It needs to be written in Rust & be fast. If you’re interested in learning more, please ping me!

please share 🙌
Applications for a postdoctoral position in *Bioinformatics* in my lab are still open!
Come and work with us @armilabs.bsky.social @monashuniversity.bsky.social
at the beautiful
Melbourne 🇦🇺

Apply here careers.pageuppeople.com/513/cw/en/jo...
Inquiries: nir.eynon@monash.edu

So important! Please contact your Republican senators, especially Sen. Susan Collins (R-ME), Sen. Shelley Moore Capito (R-WV), Sen. Bill Cassidy (R-LA), Sen. Katie Britt (R-AL), and Sen. Dave McCormick (R-PA). 🙏 amplify!

Please share this widely and encourage students to apply! Many of our current graduate students were recruited through this program -- happy to answer any questions and connect with students
bsky.app/profile/stan...

Hey bioRxiv Affiliates - we have a backlog again. If any affiliates are around to screen, we'd be immensely grateful - more importantly the authors in the queue would be too!

1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬

www.science.org/doi/full/10....

cassidy deserves every ounce of anger and mockery. we also still need to work with him to limit the damage if possible

Did You Work on a Terminated NIH Grant? ProPublica Wants to Hear From You. The National Institutes of Health is canceling grants that are seen as conflicting with the Trump administration’s priorities. We want to hear from researchers who have been affected.

Did You Work on a Terminated NIH Grant? ProPublica Wants to Hear From You. www.propublica.org/getinvolved/...

If you're a designer/illustrator who works with scientists to make figures for publications, this might be interesting for you. 👇

🚨Pre-print alert! 🧬🖥️🧪
For the first time we looked at what happens in the blood transcriptome just after bariatric surgery. A lot happens and it happens fast!

So happy to push this “side project” to the finish line! A thread 👇🧵
1/13

As computational biologists, my lab understands that careful version naming is key.

My god. 6 MILLION acres of public lands in Oregon, including the vast majority of our national forests, will be sold in a fire sale if the MAGA budget passes.

Huge crowd in Seattle's Cal Anderson Park for the #NoKings rally. People standing from the Black Lives Matter street mural on Pine all the way to Denny. Bands, banners, and speeches from Congresswoman Jayapal, MLK Labor, and others.

A large crowd of protestors in Seattle

A large crowd of protestors marching in the street

Phenomenal turnout at the No Kings March here in Seattle!

FYI: The House Committee on Science, Space, and Technology, Democratic Staff, is trying to get more info on the impact of recent research grant terminations.

If your award has been canceled since Jan 20, you can fill out this survey: democrats-science.house.gov/grantcancela...