John Doench

Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines - Nature Methods The analysis presented in this Brief Communication shows that, despite their complexity, current deep learning models do not outperform linear baselines in predicting gene perturbation effects, thus e...

An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social

www.nature.com/articles/s41...

"Alignment to NCBI-nr showed top hits to proteins from several Streptococcus spp. (Streptococcus cristatus, S. pyogenes and Streptococcus sanguinis), but none exceeding a sequence identity of 86.3%. Taken together, these three natural Cas9s yielded a cumulative identity of 98.3% for OpenCRISPR-1"

CNBC: The EPA is moving to rescind this endangerment finding on carbon dioxide and greenhouses gases. Is that a danger to public health?

MAKARY: To be honest, I don't know enough about that issue

CNBC: You're in charge of our public health! Can you look into it for us?

For those interested in the latest in thinking about indirect cost reimbursement...

Here is a one-page summary of the FAIR model.

www.cogr.edu/sites/defaul...

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I don’t think anyone is prepared for what they just did w/ ICE.

This is not a simple budget increase. It is an explosion - making ICE bigger than the FBI, US Bureau of Prisons, DEA,& others combined.

It is setting up to make what’s happening now look like child’s play. And people are disappearing.

I really thought that the Republicans in the Senate were going to step up and do the right thing, because I was standing near an oil derrick when it exploded and an iron spike lodged in my skull so I can’t remember anything that happened before 6 minutes ago.

You live in a country where they are banning Shel Silverstein and Calvin & Hobbes

Thx for this thread!

2/ For the last five years, MAGA has been bathed in political violence.

Most importantly, MAGA's celebration of January 6th and Trump's decision to pardon ALL the Jan 6 rioters - including the most violent - became a clear endorsement of violence committed in his name.

Whoa! Hats off to ABC News reporter Matt Gutman for keeping his cool yesterday.

This LAPD officer needs to be relieved of duty if he can’t handle an alleged “touch” without snapping.

What an amazing job by that reporter!

Wanna end the war and stuff? Ya gotta sing loud!

I did not know this was the news I needed to hear. But it is.

Baby Is Healed With World’s First Personalized Gene-Editing Treatment The technique used on a 9½-month-old boy with a rare condition has the potential to help people with thousands of other uncommon genetic diseases.

Could also ask about promise of mRNA therapies (don't bother asking about vaccines per se) which saved this baby's life. Why are they yanking grants that develop this technology? www.nytimes.com/2025/05/15/h...

Uncertainty looms as MU School of Medicine rescinds offers amid proposed NIH cuts MU School of Medicine graduate programs rescinds offers to future students due to proposed cuts to National Institutes of Health’s budget

I'd ask about why HHS (NIH in particular) isn't spending the money Congress has appropriated. Impacts are real. For example, Missouri school of medicine isn't taking students this year b/c of budget uncertainty: www.columbiamissourian.com/news/higher_...

I will be damned if I allow a bunch of Confederate-waving January 6th apologists give the American people a lecture on flag waving.

There is ZERO reason to enter an argument about patriotism with people who still worship traitors to America 150+ years later.

They. Are. Breaking. The. Law.

The only place I can find "Kraft for Mayor" signs are on the lawns of mansions in Chestnut Hill... which is not in the city of Boston.

Durbin to Bhattacharya: "I can't understand it. I disagree w/ this admin on so many things. But this is the one that really gets to me personally. To think this nation would walk away from medical research. For God's sake...cancer, your budget requests a 38% cut to the National Cancer Institute"

DEAN: What's the tariff on bananas?

LUTNICK: Generally 10%

DEAN: Walmart has already increased the cost of bananas by 8%

LUTNICK: If you build in America, there is no tariff

DEAN: We cannot build bananas in America

I searched "Kraft Mayor" and this is what came up.

Good to know a search engine thinks a jar of mayonnaise is a better fit for mayor of my city than some nepo baby.

From the TEA Party to the Democratic Party Yup, I'm finally making the leap

"Right now, the Democratic Party is democracy’s lone defender and best hope."

socialcontractwithjoewalsh.substack.com/p/from-the-t...

“DOGE has installed geniuses with an engineering mindset and unbelievably talented people on computers. I actually asked Elon one time, what’s their primary thing? And they have a lot of primary things all having to do with being smart.”

He said that

If you put two NYT stories together you do get “man allegedly completely strung out on drugs uses the US government to kill 300,000 people”

THREAD 🧵

Internal State Department records show that months of warnings have become a reality: The Trump administration’s sudden withdrawal of foreign humanitarian aid has brought about death, violence and unrest. 1/

Homicide rates: NY 4.5, FL 7.2
Life expectancy: NY 79, FL 76.1
Uninsured rate: NY 4.8, FL 10.7

What's in that beverage cup? And does it have some Back to the Future logo on it? I don't know why I want to know that, I just do. Also, TIL that they made a musical out of Back to the Future.

Comprehensive post on what the New Yorker is getting wrong about Covid, HIV, and public policy:

Happy MEMORIAL DAY WEEKEND to all the HATERS and washed up LOSERS like Taylor Not-so-Swift and Bruce “not the boss of me” SpringBEAN who shouldn’t have been BORN in The USA! Thank you for your attention to this matter!!

YouTube video by Amanpour and Company Breakthrough Prize-Winning Biochemist on the Deadly Cost of Funding Cuts | Amanpour and Company

David Liu @harvard.edu beautifully articulates the criticality of basic science funding for developing revolutionary therapeutics like life-saving base editors 👏

youtu.be/8YhJM6zxYDw?...

Three things made the US a rich and powerful nation: the rule of law, its science & innovation system, and openness to foreign talent. Remarkable how Trump has taken a sledgehammer to all three. No enemy of this country could do more.