You might be wondering why we haven't updated outbreak.info for months. Well, the reason is that GISAID cut our access in January - as they did others. Without telling us. After a ♾️ back and forth, that is now permanent. More on that soon - and why GISAID should not be trusted with critical data.

I am so proud to work at this place, and prouder still of my friends and colleagues featured in this peace. We are “ground zero” for the assault on science and objective reality now underway. www.nytimes.com/2025/05/21/u...

I'm very grateful to @harvard.edu for taking a stand today for academic independence. In solidarity and appreciation, I just made a donation. For those who are able to, I hope you consider it too... They need to know that they have community support www.washingtonpost.com/education/20...

Would love to hear an affirmative & persuasive theory from Republicans of how the US can maintain leadership on research, technology & development in a way that does not operate through universities Because right now I do not see it!

I’m a biomedical researcher who lost his wife to cancer. Finding cures is personal to me. What’s happening at the NIH is devastating. Here’s my editorial in my hometown newspaper. www.vindy.com/opinion/edit...

I had two grant proposals up for review in the NIH Bacterial Virulence (BV) study section. It was canceled without notice this morning. Without those grants, my lab must close within a year. And so the purge of scientific research in the US continues 🤬 #MicroSky 🦠🧫🧪🧬🔬

The Philadelphia Eagles won the Super Bowl. The Birds are funded by direct costs and indirect costs. Direct costs are players’ salaries. Indirect costs are everything else. Coaches, trainers, workout equipment, footballs, uniforms. Eagles could not have won the superbowl without indirect costs.

NIH indirects case update: Hearing ongoing now, and I'll try to live tweet some notable exchanges. Prior to more detailed arguments, Judge Kelley starts off with a few point questions to both sides: (I'm paraphrasing here)

I just covered this for @thetransmitter.bsky.social — will keep following! www.thetransmitter.org/funding/fede...

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

also this same org has this super useful infographic, breaking down the difference between direct and indirect (also called Facilities and Administration) costs and what F&A costs can and cannot be used for at a research university or institute

Here's a quantitative illustration of what's happening with NIH funding.

Here’s Sally Rockey (then deputy director of the office of extramural research) describing indirect costs as career NIH staff do youtu.be/1XvVibv2opQ?...

This is a list of blockbuster drugs in 2024. Guess how many can trace their origins to NIH funded research? All of them.

There are legit criticisms of IDCs and how they are negotiated, but cutting infrastructural and administrative support to 1/4-1/6 of what it was overnight is a devastating assault on universities and US biomedical research.

A Primer on Indirect Cost Rates

American science and medicine has been thrown into chaos and uncertainty over the past week. Here are some stories to get up to speed. 1/12

I think some people hear “grants” and think that without them, scientists and government workers just have less stuff to play with at work. But grants fund salaries for students, academics, researchers, and people who work in all areas of public service. “Pausing” grants means people don’t eat.

Just adding two data points. Consortium kickoff meeting for tomorrow was cancelled this morning, but the SRO for a virtual study section Feb 6 says the meeting is still on (for now)

Anyone else hearing that NIH IC’s Advisory Council meetings are being cancelled?

This summer, a prominent colleague said he believed that male scientists were the subject of discrimination, and later suggested that DEI discussions were not welcome or appropriate topics for scientific meetings. Other colleagues and I wrote this long-overdue response medium.com/@andrewsu/di...

Here's how you discover a potent new drug vs Covid with 212 scientists/47 organizations/15 countries working together Open-science, patent free, high-throughput structural biology based design, A.I. www.science.org/doi/10.1126/...

Both the graduate internship program internship.uoregon.edu and the LAUNCH event www.instagram.com/p/CzXXwFWJlsM/ seem pretty great, worth checking out! 🧬🖥️

Interested in applying for the Knight Campus Graduate Internship Program Bioinformatics & Genomics track? Apply for LAUNCH: oregon.qualtrics.com/jfe/form/SV_... This is an immersive program where students from historically marginalized groups in STEM can explore the field of bioinformatics.

Please encourage any psych, cog, and/or neuroscience undergrads wanting an intensive, immersive, supportive, and *paid* summer research experience to apply! WashU’s ENDURE program is world class, and my lab would be delighted to support a mentored research project 🙂 endure.wustl.edu/apply/

Pretty sure I missed in (reform Jewish) Sunday school where nauseating attacks on civilians were to be countered with nauseating attacks on even more civilians, esp children. There does seem to be growing disapproval of this response, including from high places, but I can’t believe it’s not more.

Flu shot + COVID shot -- same arm or opposite?

A guide to BlueSky for Scientists * Common questions * Links to resources * An explanation of feeds * A directory of science feeds Please share with scientists on BlueSky! Written by me and @markrubin.bsky.social 🧪 #stats #PsychSciSky #neuroscience

“When I see people watching the horrible tragedy that is happening here as if it were a Super Bowl of victimhood, in which you support one team and really don’t care about the other, empathy becomes very, very selective. You see only some pain. You don’t want to see other pain.”

Scripps Research is hiring in all departments this year www.scripps.edu/faculty/facu... Selfishly, I'd love to see more applicants in all areas of bioinformatics and computational biology!

agree

In the context of the NSF Prototype Open Knowledge Graph (Proto-OKN) new.nsf.gov/tip/updates/..., I'm recruiting a person with expertise in open science / open data generally, and interest or experience with Wikidata specifically. Postdoc or staff scientist level. Contact me!

When every person in the country is a finger-twitch away from becoming a mass murderer, frequent massacres are inevitable. It’s just a law of large numbers. Is someone angry enough to kill today? The answer will always, inescapably, be yes. The easier the killing, the more victims will die.

This 2019 Science Advances paper lives rent-free in my head, and I think it's the social science paper that I mention the most in everyday conversation with my peers or elders... #youths #olds #science www.science.org/doi/10.1126/...

Folks from Stanford HAI have introduced a transparency index for LLMs. We need more of this type of work. #machinelearning #LLMs hai.stanford.edu/news/introdu...

At my institution, we have seen attrition of so many female faculty members. Since there are always other legitimate reasons, our administration seems not to acknowledge the trend. Hopefully this study will provide hard data to show we should be looking at our institutional climate

1/ New paper! “Gender and retention patterns among U.S. faculty” w/ N Laberge KH Wapman @samzhang AC Morgan M Galesic BK Fosdick @danlarremore @aaronclauset: www.science.org/doi/10.1126/... A systematic study of gendered rates & reasons for faculty attrition in US academia 🧵

Social media embraced and destroyed news. Particularly local news. And now they are abandoning it. I hope we can reinvest in local news using models like the @sltrib.com to regrow the Fourth Estate.

I really like the new NIH grant review criteria. Wish they'd enacted this long ago. nexus.od.nih.gov/all/2023/10/...

Looking forward to this seminar later today 12PM PT / 3PM ET by Zhiyong Lu "Large Language Models for Biomedicine: from PubMed Search to Clinical Trial Matching" uclahs.zoom.us/j/92250165188

Good reading on the human foundation underneath all the shiny AI www.wired.com/story/millio...

My lab website is long overdue for an overhaul. Definitely want to go with a static site generator. github.com/greenelab/la... from @casey.greenelab.com's lab seems like the obvious choice. Any other notable options to consider?

“The more uncomfortable truth is that academic science has never been a trade that selects for or supports the best scientific minds in the world.” https://www.scientificamerican.com/article/nobel-prize-debate-misses-the-mark-on-the-real-culprits-ignoring-scientific-merit/

huh, guess that was a noob sort of things to do to add hashtags...

Not sure what is worthy of a first post. How about noting that my lab is hiring! Looking for folks anywhere along the plane connecting biology & chemistry, computer science, software engineering, and statistics. Particularly those with an interest in building #bioinformatics infrastructure! #jobs