We had a lovely celebration today at ISB, for Mary. Beyond the work and the prize, it is worth highlighting that Mary is always friendly, collected, thoughtful, and very humble. Such a delight to see her recognized!!

"Announcing the Biomedical Data Translator: Initial Public Release" pubmed.ncbi.nlm.nih.gov/40635371/ Translator is the knowledge-graph integration system we're developing to support hypothesis generation by scientists. Funded by NCATS. As I said in the past, best consortium ever. Awesome people. 🧪

Atul Butte died yesterday. The world lost a giant. A big bear of a man. With a huge smile. With love for everyone. With energy that could power a room. I loved everything about Atul. I loved how he was always happy. I loved how excited he was about science and helping people.

Interesting new study on emergence and disruption of cooperativity in a denitrifying microbial community, by postdoc in the lab Alex Carr (from his PhD work with Nitin Baliga). academic.oup.com/ismej/articl...

Breakthrough in search for HIV cure leaves researchers ‘overwhelmed’

This is superbly interesting. Quite clear evidence of theory of mind at work.

Youtube offered this to me today, likely because of my love for Hania Rani's music. Büşra Kayıkçı's music is delightful!

HAPPY 75th, NSF! We’re celebrating this milestone by highlighting some of NSF’s most transformative accomplishments—innovations that have shaped our world and continue to drive progress in health, technology, the environment, and beyond. Read on 🧵(1/11):

We are saddened to share the passing of Valerie Logan Hood, beloved wife of ISB Co-founder Dr. Lee Hood. Valerie’s dedication to K-12 education shaped ISB’s education programs & and her influence continues to be felt by students and educators in WA state and beyond. isbscience.org/news/philant...

Excellent message. Be kind to all!

🧪

Fascinating and important read indeed. I'm sure there are plenty of cultural differences on this topic, too.

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

Watch it all... www.youtube.com/watch?v=hyco...

Stand Up for Science. Seattle.

This is indeed a beautiful graphic!

I got laid off today, with the rest of 18F. 18F was an elite federal software shop. We made gov't websites work better, more efficiently for the American people. We saved taxpayers from getting screwed over by contractors. And were fired for it. We made this website to tell our story: 18f.org

Data request! Do you assess frailty index in your aging C57 mouse studies? @dantong-zhu.bsky.social is making new and improved clocks to predict age and lifespan based on frailty data & we aim to validate widely! Reach out if you want to collaborate 🐀👵⏰ Especially if you have female data + lifespan!

As a great darkness falls over the US it becomes more and more important to be the light. Know the bad, but stick to the good Everything changes #metta

🚀 We're Hiring: Contracts Specialist! 🚀 Join @isbscience.org's Legal & Innovation team (Seattle, Hybrid) to manage contracts, NDAs, & licensing for cutting-edge research. 🔹 2+ yrs contracts/paralegal experience required 📌 Apply at isbscience.bamboohr.com/careers/42 Boost or tag a great candidate!

Another explainer, for those who prefer video animations. Please amplify, particularly to non-scientists. 🧪

not paying indirect costs for research is like only paying the players in the Super Bowl. can't have a Super Bowl without coaches, referees, security, janitors, announcers, stadium staff, and a stadium - and you can't have research without supporting people and facilities

A visual for the more visually oriented! What overhead/indirect costs actually pay for. 🧪

Great explainer for those not familiar with what indirect costs actually mean and do, in scientific research. 🧪

🚨 We're Hiring! @isbscience.org is looking for a Health & Safety Specialist to lead lab services operations & oversee health & safety programs in a dynamic research environment. Join us & make an impact! Apply here: isbscience.bamboohr.com/careers/41?s... #Hiring #HealthAndSafety #LabJobs

Reproducibility of 🧪 scientific results strongly depends on data access. Centralizing content in gov-managed/mandated systems seemed to be the way to go, but now it is clearly a risky model. What are your strategies for preserving access to the crucial data you need to do and share your research?

Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings https://www.biorxiv.org/content/10.1101/2025.01.23.634511v1

We are heartbroken by the passing of Ginny Ruffner, a beloved artist and passionate advocate for ISB. Her art inspired us, her advocacy lifted us, and her legacy will live on. Read more: www.seattletimes.com/entertainmen.... Donations can be made to SOLA (Support Old Lady Artists): solaseattle.org.

Your self identity is valid. Negativity from voices of fear mongering & hate will never change your courage & authenticity. You are supported, respected & cared about by a community that loves you. Never forget that. I am so glad you are here. 🫶🏼🏳️‍⚧️🫂

One could nitpick about meaning of 'freezing': If I cool water to 27 F, it doesn't actually freeze at 27 F, it does so at 32 F. It will already be frozen by the time it reaches 27 F. But the AI demonstrates its lack of understanding by explicitly stating that the water will still be liquid at 27 F.

How can single-cell transcriptomics profile phage infection in individual microbial cells? Check out our preprint with Anika Gupta, Norma Morella, Dmitry Sutormin & other authors, in collaboration with Georg Seelig (UW) and Neel Dey (Fred Hutch). www.biorxiv.org/content/10.1...

Check out the first publication from the Kane lab @isbscience.org! RNAseq analysis of sex differences in aging across tissues - spoiler alert - there are lots of them! bsd.biomedcentral.com/articles/10.... Congratulations and thans to @dantong-zhu.bsky.social, @judywbio.bsky.social & other authors.

In our latest preprint, led by Master's student Gechlang Tang, we put forth a modest proposal: why not just use host-derived reads as a normalization factor for estimating absolute bacterial biomass in stool metagenomes? 🦠💩📈 @isbscience.org www.biorxiv.org/content/10.1...

This makes a lot of sense.

Yet another awesome video by Jess of the Shire, this time about the #music on Middle Earth (including that of the Ainur, technically before Arda). All around #Tolkien goodness. I'll only quibble with the choice of caption on the videos, frequently not the main point. www.youtube.com/watch?v=EQl9...

Saw this soon after getting off the bus. Made me wonder, again, at the Spanish expression "solo como un hongo"... literally "lonely like a mushroom". #fungifriends

Today's cutest forest find. Guessing a chip cherry (Leratiomyces ceres). #fungifriends

letting go means this - holding with an open hand still water, flowing #haiku #dhamma #dharma

glint on forest path windstorm debris all around stern owl greets the night #fungifriends #haiku

Read ISB's news release here: isbscience.org/news/2024/11...

This website worked incredibly well for my NSF COA doc prep.

When applying to NSF for funding, each senior personnel has to provide a “Collaborators and Other Affiliations” (COA) form, which can be quite onerous. A couple of years ago I created a tool bit.ly/NSF_COA for automating this, and recently hardened it. I hope it is of use, and feedback is welcome! 🧪

Preprint is out! We created and integrated knowledge graphs from underlying data, including EHRs, multiomics, and registries on clinical trials and drug approvals. Query via smartAPI. Part of the larger effort for NCATS Biomedical Data Translator, which is BTW the most awesome consortium ever!

This seems to be the earliest mention of Hania Rani on bluesky. Her music is extraordinary, both technically and emotionally. I particularly love "Buka" in youtu.be/sp3B97N67Cw?... - but the entire concert is amazing. 🎧

A Cortinarius and a Russula. You really don't want to eat these... even though that's exactly what the tree behind them is about to do. (From a delightful mushroom hunting outing with friends, this last Saturday.) #fungifriends

A preprint of the work we did this Summer with the awesome Skye. Always a pleasure to mentor such amazing interns!

Inspired by @drsueishaq.bsky.social I got heirloom broccoli seeds, and they've started sprouting. Always exciting to see seeds doing their awesome thing. :)

Frightening if true: data from long-lived sea sponges suggests starting point of impacts from industrial revolution have been calibrated incorrectly. Based on new data, we surpassed 1.5°C of warming a decade ago. Only 1 study so far, but would explain scale of current #climate chaos 🧪 #AmWriting