C. elegans is a real animal and we set out to understand how it comes to have its distinctive biogeography. Its ancestral center of diversity is in the higher elevation forests of Hawaii. Its closest relatives are spread across east Asia. Did they travel from Asia? [Preprint 🧵]

┏┓ ┃┃╱╲ In this ┃╱╱╲╲ house ╱╱╭╮╲╲ we pretend ▔▏┗┛▕▔ that hg38 ╱▔▔▔▔▔▔▔▔▔▔╲ does not exist ╱╱┏┳┓╭╮┏┳┓ ╲╲ ▔▏┗┻┛┃┃┗┻┛▕▔

For comparison, the two studies cited in today’s FDA press release included 8,856 and 996 children respectively.

I was unsurprised to see that the FDA announcement on leucovorin ... doesn't include a single peer-reviewed citation.

I think it is likely that Dr. Kuperwasser and Dr. El-Deiry will present misinformation about the SV40 promoter-enhancer in COVID19 vaccines tomorrow at ACIP. I strongly recommend that you read @gorskon.bsky.social’s excellent work on the topic before the fearmongering begins.

Is there something wrong with the HLA-II entries of the HLA Ligand Atlas? Looked up the model PRAME epitope A2/SLLQHLIGL and found it's mostly detected on HLA-II alleles -- which doesn't make sense of a teeny little 9mer. (it's also weird to see it so much on healthy samples)

We were wondering: Do protein language models learn epistatic signals during pretraining? Turns out, yes! Protein Language Models Capture Structural and Functional Epistasis in a Zero-Shot Setting www.biorxiv.org/content/10.1...

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

Open postdoc position in my former lab at @danafarber.bsky.social and @harvard.edu Medical School (CFCE). A working environment full of nice and smart people! careers.dana-farber.org/job/12169/po...

Was just refused a COVID booster at my local Walgreens despite this change in policy 🫠

Please take a moment to tell us how you use the Genome Browser: surveymars.com/q/mnb... Your feedback supports future improvements and our continued funding.

Since the article is paywalled, the study (Interagency Coordinating Committee on the Prevention of Underage Drinking draft report) is here: www.federalregister.gov/documents/20...

A proposed new rule would limit international students on F1 or J1 visas to stays in the US of no longer than 4 years. This effectively means that intl. students will no longer come to graduate school here (time to PhD is 5-6 years). You can comment here: www.federalregister.gov/documents/20...

RFK must go. Please contact your congresspeople about this. Ask them why RFK was allowed to unilaterally fire a senate appointee because she contacted senators – the appropriate oversight body – after the HHS secretary demanded that she break the law & betray Americans’ public health.

This is absolutely catastrophic for U.S. higher education, and for U.S. global leadership. Just the latest in a series of senseless acts of self-sabotage by a malevolent administration bent on making the United States weak and poor.

My bicycle was just stolen in Capitol Hill Seattle. Please keep an eye out for a small sized Salsa Vaya, green bicycle with a rear rack, steel fenders, dynamo hubs, 26” wheels. Parked at a bike rack at 15th and Pike. Saw my lock cut and thrown on the ground.

Anyone know what program & settings was used to make these figs? I assume it isn't pymol or chimera (pic from @asimovpress.bsky.social on the other site)

Academics being assigned another unpaid volunteer role:

My lab is going to be imminently looking for a computer scientist or a biologist with deep understanding of R to develop and give bioinformatic education to postdocs. This is perfect for someone who likes teaching. You'd need to be in the Pittsburgh area. Feel free to reach out with questions.

It’s also sickening to watch Silicon Valley market their mediocre AI product as “PhD’s in your pocket” when their pals in the White House are destroying the institutions that mint actual human PhD’s

RFK Jr. backs down all the time when he gets push back, so if anyone wants to call, here's the HHS number 1-877-696-6775. I'd also call your senators/reps as well.

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!

🚀 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...

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

🖥️🧬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: [email protected]

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....

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.

Phenomenal turnout at the No Kings March here in Seattle!