Ben Langmead

Here is the "effective payline" for each institute, estimated (by Claude) as the percentile where one can expect 80% probability of funding from a logistic regression fit. The effective payline has gone from a historic ~12% to 6% in 2025.

Very nice post, and this is very lovely work

National Institutes of Health faces leadership vacuum as director positions sit open More than half of the NIH's institutes and centers don’t have permanent directors, giving the Trump administration an unusual opportunity to reshape the agency. The latest departure came on Friday.

They won’t stop until the National Institutes of Health is a hollowed out RFK Jr. echo chamber and revenue generation machine for snake oil peddlers.

Trump official overruled FDA scientists to reject Moderna's flu shot FDA's top vaccine regulator, Vinay Prasad, is known for overruling scientists.

Moderna is at least the ninth company to have received a surprise rejection from Vinay Prasad and his team.

A Speech Every Democrat Should Watch Jon Ossoff lays out a message that can work for everyone in the party.

If you were online last weekend, you probably caught some clips from Jon Ossoff’s speech. It’s worth watching the whole thing because it’s an object lesson in how Democrats should communicate in the upcoming midterms. messagebox.substack.com/p/a-speech-e...

Prasad overruled FDA staff to reject Moderna's flu vaccine application The rejection is the latest instance of Vinay Prasad overruling career FDA scientists to place vaccines under harsher scrutiny.

The flu and pneumonia kill over 45,000 people a year. Moderna developed a new mRNA flu vaccine for people 50 and older--who are most at risk. Prasad, unilaterally, against the recommendation of experts within the agency, denied Moderna's appplication. www.statnews.com/2026/02/11/m...

Freeman Hrabowski III, the President Emeritus from the University of Maryland Baltimore County, giving a TED talk.

This is a powerful message from Freeman Hrabowski.

🧵

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The Biology of Genomes Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

Reminder that the abstract deadline for the Biology of Genomes meeting at CSHL is on Feb 13! We have a fantastic lineup of keynote speakers (Janet Kelso and Jonathan Pritchard) and session chairs. Submit your best science to this exciting and engaged meeting!
meetings.cshl.edu/meetings.asp...

Super thread, thank you Ragnar. I told my lab I would explain suffixient sets in a meeting this week and I'm going to start by just walking through your thread 🙏

Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]

New tool from @alexsweeten.bsky.social to find and classify all your satellites: "AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates"
📄 www.biorxiv.org/content/10.6...
📦 github.com/marbl/anianns

GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont

Announcing a new tool for "denoising" long-read amplicon sequences: savont.

Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.

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github.com/bluenote-157...

RFKJr's principal accomplishment as the nation's health guardian.

2025-26 CRA Outstanding Undergraduate Researcher Award Recipients Announced By Sheila Khan, Program Associate, CRA-E The Computing Research Association (CRA) congratulates the recipients of the 2025-26 CRA Outstanding Undergraduate Researcher Award. Faculty from institutio…

Congratulations to @hopkinsengineer.bsky.social undergrads Arda Uzunoğlu, Steven Tan, Suyu Ye, and Alvin Zhang on their Honorable Mentions for the Computing Research Association’s 2026 Outstanding Undergraduate Researcher Awards!

U.S. government has lost more than 10,000 STEM Ph.D.s since Trump took office A Science analysis reveals how many were fired, retired, or quit across 14 agencies

Wow. This is devastating.

www.science.org/content/arti...

A video of Alex Pretti reading out the final salute of an unnamed veteran he cared for until the end of his life in the ICU, posted to Facebook by his son.

Lies and Lawlessness The Camps, the Executions, and the Future

We have to see the logic of the killings as well as the killings themselves. The horror is a truth in itself. But it is also a sign of a political logic, one known from the totalitarian regimes of the twentieth century.
snyder.substack.com/p/lies-and-l...

RLBWT-Based LCP Computation in Compressed Space for Terabase-Scale Pangenome Analysis https://www.biorxiv.org/content/10.64898/2026.01.23.701410v1

The killing of Alex Pretti is a heartbreaking tragedy. It should also be a wake-up call to every American, regardless of party, that many of our core values as a nation are increasingly under assault.

Opinion | State Terror Has Arrived

A powerful piece by M. Gessen

I can't do it justice by excerpt

go read it (gift link)

www.nytimes.com/2026/01/24/o...

Post from Pete Buttigieg that reads: If there was ever a moment for libertarians and conservatives to step up and join the rest of us, we’re in it. Americans have to unite and stop this descent from a freedom-loving nation into the kind of place where masked, militarized government agents are sent to politically noncompliant areas to roam the streets, terrorize civilians, and deploy violence with impunity.

Judge warns Trump administration from changing plaintiffs immigration status in First Amendment case A federal judge ruled that the academics, who are party to a lawsuit alleging U.S. policy singles out noncitizens for detention or deportation over their pro-Palestinian activism on college campuses, ...

“Students and scholars shouldn’t have to live in fear that ICE agents could seize them from their homes merely for engaging in political expression. Today’s judgment makes emphatically clear that the administration’s campaign of intimidation must end.”

—Ramya Krishnan, @knightcolumbia.org

Optimizing sparse and skew hashing: faster k-mer dictionaries https://www.biorxiv.org/content/10.64898/2026.01.21.700884v1

Exclusive: key NIH review panels due to lose all members by the end of 2026 Thirteen of the agency’s advisory councils, which must review grant applications before funding is awarded, are on track to have no voting members.

If you / your lab / your institution rely on NIH funding, you need to read this and understand how this is one of many changes affecting you. www.nature.com/articles/d41...

Huge congratulations, Can! And well deserved.

DOGE Employees Shared Social Security Data, Court Filing Shows

Not only was DOGE illegally accessing your Social Security information, but it was also illegally offering to share it with third-party political groups working to overturn elections.

This is a deep betrayal of the public trust and must be fully investigated. www.nytimes.com/2026/01/20/u...

Common variation in meiosis genes shapes human recombination and aneuploidy - Nature Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...

Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.

First authors: @saracarioscia.bsky.social & @aabiddanda.github.io

What is the contribution made by universities to their research output?

It's complicated to compute, but an estimate by MIT suggests that for every dollar they obtain from the federal government, they co-invest one dollar.

More here: issues.org/federal-rese...

This line graph illustrates the percentage change in agency staff levels from the previous year for nine major U.S. federal scientific and health organizations between the fiscal years 2016 and 2025. The agencies tracked include the CDC, Department of Energy, EPA, FDA, NASA, NIH, NIST, NOAA, and NSF. For the majority of the timeline between 2016 and 2023, the agencies show relatively stable fluctuations, generally staying within a range of +5% to -5% change per year. However, there is a dramatic and uniform plummet starting in the 2024–25 period. Every agency depicted shows a sharp downward trajectory, with staffing losses ranging from approximately -15% to over -25%. The Environmental Protection Agency (EPA) shows the most significant decline, dropping to roughly -26%, while the National Institute of Standards and Technology (NIST) shows the least severe but still substantial drop at approximately -15%.

This is the most astonishing graph of what the Trump regime has done to US science. They have destroyed the federal science workforce across the board. The negative impacts on Americans will be felt for generations, and the US might never be the same again.

www.nature.com/immersive/d4...

Read the full transcript of Carney’s speech to World Economic Forum - National | Globalnews.ca Prime Minister Mark Carney gave a forceful speech in Davos, Switzerland, on the 'new world order' and how middle powers like Canada can benefit by working together.

The Carney speech is worth reading in full: globalnews.ca/news/1162087...