📣 New preprint from us at phagefoundry.org 📣 A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort www.biorxiv.org/content/10.1...

We developed and evaluated a method to learn python chemical structure classifiers using LLMs. These can give classifications+explanations at runtime. With @jannahastings.bsky.social @justaddcoffee.bsky.social Noel O'Boyle, Daniel Korn, Adnan Malik jcheminf.biomedcentral.com/articles/10....

Hiding in plain sight - how close are we to mapping ALL 🧬enhancers🧬 in the genome? Our new paper by Mannion et al. takes a systematic look at "hidden enhancers" and why they remain so hard to find. With @mosterwalder.bsky.social, @jlopezrios.bsky.social & many more www.nature.com/articles/s41...

Very exciting to see the research from @cziscience.bsky.social on the rBio distilling a black box foundation model (in this case a "virtual cell" perturbation model) into a smaller reasoner LLM. And it uses ontologies as part of RL! chanzuckerberg.com/blog/rbio-re...

The Alliance webinar for August is this Thursday (Aug 21, noon EDT), on Ontologies and the Alliance, presented by Chris Mungall. You can preregister for the zoom link here forms.gle/GzMnmwK23SzP...; please preregister by midnight EDT Wednesday Aug 20.

This is terrible news, not just for fly research, Drosophila is a key model organism that helps us understand shared biological pathways and the systems that underpin many human diseases 💔💔💔

FlyBase needs your help! We ask that European labs continue to contribute to Cambridge, UK FlyBase, whereas US and other non-European labs can contribute to US FlyBase. For more information and how to donate: wiki.flybase.org/wiki/FlyBase...

@cmungall.bsky.social‬ tackles complex #knowledgeManagement challenges in the life sciences with well-honed collaborative methods and AI-augmented computational tooling, streamlining #ontology creation and #knowledgeGraph building. knowledgegraphinsights.com/chris-mungall/

Exceptional Contributions to Biocuration - Lifetime Achievement Award winner: Ruth Lovering Ruth has contributed extensively to the curation of key resources such as HGNC, Gene Ontology (GO), and IMEx, and has been instrumental in developing curation standards. Ruth is a past chair of the ISB EC.

Exceptional Contributions to Biocuration - Advanced Career Award winner: Kimberly Van Auken Kimberly's career reflects expertise, sustained innovation, & dedicated service to community. She's contributed to many projects, including WormBase, the Gene Ontology, & the Alliance of Genome Resources.

Exceptional Contributions to Biocuration - Early Career Award winner: Tiago Lubiano. Tiago's a passionate and motivated scientist interested in linked open data, ontologies, the semantic web, and their application in modeling cells and cell types. He is active in many curation projects & with ISB.

@severaltimes.bsky.social talking about the BioPortal MCP at #BOSC2025 / #BOKR2025 #ISMBECCB2025

Nice Chris is raising the topic of AI-assisted coding. There are huge advantages of Agentic AI applications here, but there are also risks (watch this space for more on this topic) #ISMBECCB2025 #BOSC2025

Just as Chris launched into the topic of knowledge censorship, the AI transcription and the slides stopped working. Coincidence?? 🤔 #BOSC2025

A full room during @cmungall.bsky.social's #BOSC2025 / #BOKR2025 keynote talk at #ISMBECCB2025

Looking forward to seeing many of you this week at ISMB, and talking to you about our work on agentic AI and knowledge bases! Doubly honored to be selected for this joint session, the open-bio community has been a huge influence on how I approach ontologies and knowledge base development.

Wow, AlphaGenome is a huge deal, 1mb context windows, and prediction of a variety of features, with cell and tissue specificity! Read @anshulkundaje.bsky.social's excellent thread for the details. I want to additionally highlight one additional thing for my structured data nerd friends...

I know there's no bottom, but this is really fucking chilling.

Interesting AI read. 15-23% of uncultivated microbes may engage in symbiotic relationships. www.biorxiv.org/content/10.1...

This is a must-read piece by @math-rachel.bsky.social about AI evaluation, and how the system of reward and apportioning credit in AI research is broken rachel.fast.ai/posts/2025-0.... TL;DR -- we need deep fact checkers!

Flybase lost all of the NIH support overnight - it is a disaster for the community. Please consider donating. I just did! www.philanthropy.cam.ac.uk/give-to-camb...

This guy, @albertburneko.bsky.social, is a genius. Please read his brilliant article on Elon Musk's deranged and morally repugnant Mars colonisation schtick. defector.com/neither-elon...

The Network State ideology hinges on something called "jurisdictional arbitrage." That's when you evade the rules of one place or territory by outsourcing your needs or dirty deeds to another territory. El Salvador has become a Network State for Concentration Camps. Expect more moves like this.

Mr. Abrego Garcia was illegally abducted by the Trump Admin and, by their own admission, wrongly deported to El Salvador. He shouldn’t have to spend another second away from his family. I'm flying to El Salvador tomorrow morning to check on his condition and discuss his return.

If President Trump can wrongly deport a Maryland father to a prison in El Salvador and then defy a 9-0 Supreme Court order to facilitate bringing him home, who’s next? This threatens the rights and freedoms of everyone in the United States.

Dr. Richard Youle was fired today. He is an eminent scientist who has done important work on brain diseases like dementia and Parkinson’s. Musk and Trump are stopping NIH research into cures, for diseases from cancer to Alzheimer’s. Americans did not vote for this.

The first of many big defeats for Elon Musk. He is delusional, unstable, and weak. He is overplaying his hand. If we fight, we win. He will go down as one of the most despised men in history. It is up to us. Time to turn the tide. Gift link: www.nytimes.com/2025/04/01/u...

Innocent people — undesirables, political dissidents — are being sent to camps here and abroad. A scapegoated minority is being persecuted, made an example of. Wrongthink is being stricken from government institutions and civil society. There is no more "if" authoritarianism arrives. It's here.

Tonight an unbelievable **34,000 people** gathered for our Denver rally to take on billionaires and win our country back. This was the largest political gathering in Denver since Obama in 2008. Also bigger than the 2024 DNC. And the largest ever rally in Bernie’s career (and obviously, mine too).

NIH spending more than pays for itself. It generates about $2.5 for every $1 spent. In terms of research productivity, NIH funding dwarfs the rest of the world. The only long-term potential rival is China. Politicizing the NIH's scientific processes will hand China a huge strategic advantage.

Yet another extremely stupid and destructive move appears to be underway. Those people who advised me to calm down, that everything was actually going to work out fine, know what they can go do with themselves. kffhealthnews.org/news/article...

Scientists Say NIH Officials Told Them To Scrub mRNA References on Grants kffhealthnews.org/news/article...

New preprint! We worked with @msftresearch.bsky.social and @broadinstitute.org to see whether large language models (LLMs) can be useful to variant scientists in deciding whether genetic variants seen in a patient are responsible for their disease. tl;dr yes they can: www.biorxiv.org/content/10.1...

In one more slice from the idiotic time we live in, NCIT is obsoleting terms not because they are incorrect but to comply with an executive order. If the EO doesn't match reality, apparently we change reality? #biocuration evsexplore.semantics.cancer.gov/evsexplore/c...

Columbia grad student with a green card and a pregnant US citizen wife, abducted by ICE because of his political organizing, and now his lawyers can't find him. Hey, @schumer.senate.gov. This is your constituent. Bring him back home.

Delighted and proud to speak on Friday at the Berkeley #StandUpForScience march. 📢🔭🧑‍🔬🥼🔬🧪📡🛰️🌎 Science and education are under attack, but standing together we can resist ✊ Huge thanks to the organizing team for the opportunity to speak! www.standup4scienceberkeley.com

Before I start, let me thank the brave folks within NIH who have shared information, hints, and other materials that have helped me sort this out. I don’t know most of your names and, even if I did, no one would ever hear them from me. So here is what appears to be going on… 1/n

82% of human protein-coding genes now have robust, consistent functional annotations, thanks to the combined efforts of biocurators across the GO consortium, Model Organism Databases, SwissProt/UniProtKB, all based on explicit evolutionary modeling via PANTHER families!

DOGE is about to receive full access to IRS taxpayer data. On its own, that’s horrific. But it gets worse. The guy with access reposted content by Nick Fuentes (who advocates killing Jews) & says he was inspired to join DOGE by Ron Unz (an antisemitic Holocaust denier). This is beyond dangerous.

Thanks to all of the NIHers and their friends who reached out to me. I am still here (DM me or Signal jeremymberg.78) I still have a very incomplete picture but based on what I have been told, the damage to NIH and to many wonderful people who work(ed) there is/was impossible for me to imagine 1/n

On January 6th, 1995, my (now ex) wife and I boarded a flight from Heathrow to JFK on a one way ticket. We had two suitcases and about $900 in cash - this was everything we owned and we were moving to the US. We thought it was maybe for 2-3 years. I had visited the US once, for a conference, and

The parallels with private equity takeovers seem so obvious: strip mine the country of all its long-term capacity for resilience and growth (research, education) in exchange for short term gain (tax cuts).

Even worse incompetence: they accidentally fired, then apparently today un-fired, hundreds of the people who manage America's nuclear weapons.

um...okay

Doing the unthinkable: The deep cuts to the #CDC's workforce today are expected to decimate the Epidemic Intelligence Service, a program that has trained public health rapid responders for decades. Envy of the world. Poof! www.statnews.com/2025/02/14/t...

Happy Valentines Day, Bluesky! Enjoy this comparative heart anatomy thread, which I rescued from the other site

Every year Elon Musk's companies receive nearly 1/3 as much in government contracts as he just slashed from annual NIH budgets. I assume DOGE will be investigating in 3-2-

Seventy-one-year-old woman dies after being sent home from USAID funded hospital. Others die after hospitals close in refugee camps www.telegraph.co.uk/global-healt...