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johnny connolly @jcons.bsky.social · 10h

In a hilarious and unfortunate coincidence, two completely unrelated metagenomic methods, both sharing the name "PHLAME", were published this year:
www.sciencedirect.com/science/arti...
www.biorxiv.org/content/10.1...

Intraspecies associations from strain-rich metagenome samples

Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting…

www.sciencedirect.com

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Reposted by johnny connolly

thetranscendedman @atranscendedman.bsky.social · Sep 5

London researchers estimate COVID-19 vaccines cost $79B in 2020–21 but returned $4.8–$37.8T in health and economic benefits.

That is $60–$475 gained for every $1 invested, making them one of the best global investments ever.

www.medrxiv.org/content/10.1...

The global return-on-investment of COVID-19 vaccines in the first year of the vaccination programme

COVID-19 vaccines played a critical role in reducing global health burden during the COVID-19 pandemic, but their rapid development required extraordinary effort. This study aims to evaluate their glo...

www.medrxiv.org

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Nick Boyd @nboyd.bsky.social · Sep 2

Recently tested some de-novo minibinders against two targets (thanks Adaptyv!) designed using our open-source design library, `mosaic`; our best method got hit rates of 7/10 and 8/10 and affinities as low as single-digit nanomolar. Wrote up some thoughts here: blog.escalante.bio/minibinder-d...

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Anthony Edwards @edwardsanthonyb.bsky.social · Aug 27

Meteorologists now face a Trump ‘loyalty test’ when applying to National Weather Service jobs.

The essay questions — which have nothing to do with meteorology — are part of federal guidelines launched as part of the Trump administration’s efforts to recruit “patriotic Americans” to its workforce.

Meteorologists now face a Trump ‘loyalty test’ when applying to National Weather Service jobs

After firing hundreds of meteorologists, the National Weather Service announced it is filling vacant positions. Applicants are being asked to detail their support for Trump’s policies.

www.sfchronicle.com

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johnny connolly @jcons.bsky.social · Aug 28

This was the best case scenario. Unfortunately, we ended up with the Other Thing

johnny connolly @jcons.bsky.social · Nov 20

I think the best case scenario for the RFK HHS is that he focuses on food additives and chemicals the entire time

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THE CITY @thecity.nyc · Aug 21

Bob Clark, VP of marketing for Herr Foods, Inc., said the company was surprised to see it was mentioned in the press.

“While we can’t speak to the details of the story,” he said, “we can confirm that our Sour Cream & Onion flavor is money.”

www.thecity.nyc/2025/08/21/w...

The Chips Fall as Rivals Fry the Mayor

The jokes and jabs are flying as Eric Adams’ closest aides was slapped with new criminal charges the day after another of his longtime allies offered a reporter cash inside a potato chip bag.

www.thecity.nyc

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johnny connolly @jcons.bsky.social · Aug 19

I drafted for a fantasy league that's been going since high school last night. One of the younger guys (2-3 years below me) had to take a call in the middle. When he came back he said "Sorry, my paralegal is out today" I have never felt so old in my entire life

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johnny connolly @jcons.bsky.social · Aug 16

Trying to determine when industry will see the damage from lack of new research. I think probably starting in ~4-5 years?

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johnny connolly @jcons.bsky.social · Aug 11

maybe an area that recently went from 0 to a gajillion overnight does not meet OP's definition of stable

johnny connolly @jcons.bsky.social · Aug 11

HENRY (UK): year 8 of employment with major bank, turned down for mortgage

HENRY (USA): Yacht purchase tied up with paperwork

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ghost malone ergo propter malone @proptermalone.bsky.social · Aug 5

this work saved millions of lives in 2021, won the Nobel Prize in 2023, and is cancelled in 2025

Jen Bendery @jbendery.bsky.social · Aug 5

"The U.S. Department of Health and Human Services (HHS) today announced the beginning of a coordinated wind-down of its mRNA vaccine development activities...."

cc: Sen. Bill Cassidy

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johnny connolly @jcons.bsky.social · Jul 22

Looking for an apartment in SF has made me understand why people are so insane about housing there. You have to pay a gajillion dollars for a single room in a house and meanwhile there are no buildings above two stories

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johnny connolly @jcons.bsky.social · Jul 18

Hire Javier Sola

a man wearing a helmet and a yellow shirt that says lyonnaise on it

ALT: a man wearing a helmet and a yellow shirt that says lyonnaise on it

media.tenor.com

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johnny connolly @jcons.bsky.social · Jul 18

It was a great minute we had to enjoy the Jonas TT

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johnny connolly @jcons.bsky.social · Jul 18

It’s over

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johnny connolly @jcons.bsky.social · Jul 14

Hard to overstate how damaging this will be to science and universities broadly

Denis Wirtz @deniswirtz.bsky.social · Jul 14

Grant terminations have grabbed the headlines and have seen legal action, but even more damaging to the US research enterprise has been the massive decrease in number of research grants issued by federal agencies

NIH has seen a decrease of 57% in the number of awards & 63% in value compared to FY24

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Denis Wirtz @deniswirtz.bsky.social · Jul 14

Grant terminations have grabbed the headlines and have seen legal action, but even more damaging to the US research enterprise has been the massive decrease in number of research grants issued by federal agencies

NIH has seen a decrease of 57% in the number of awards & 63% in value compared to FY24

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johnny connolly @jcons.bsky.social · Jun 25

i don't think smith was ever mayor

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Jack A Gilbert @gilbertjacka.bsky.social · Jun 23

New Consensus Statement in Nature Microbiology!
Working with low-biomass microbiome samples? From deep subsurface rocks to human lungs, contamination is a major challenge. We offer field-to-data analysis guidelines to help keep your results clean.
📖 doi.org/10.1038/s415...

Guidelines for preventing and reporting contamination in low-biomass microbiome studies - Nature Microbiology

In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize contaminants.

doi.org

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Segata Lab @cibiocm.bsky.social · Jun 3

🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!

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

🧵⬇️

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Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer - Nature Medicine

An analysis of 18 metagenomic datasets of individuals with colorectal cancer, adenomas and healthy controls yields improved cancer prediction accuracy based solely on gut metagenomics, as well as the ...

www.nature.com

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Jeremy Berg @jeremymberg.bsky.social · May 12

Slow grant making continues. Here is a graph through May 1st.

2/n

A graph with clusters gray curves showing NIH grant making for fiscal years 2015-2024 with a red curve showing slower grant making in fiscal year 2025.

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Rich Abdill @richabdill.com · May 9

"This cross-sectional study of the oral microbiome in US adults showed that a few genera were universally present and a different set of genera explained a high percentage of oral microbiome diversity across the population."

Oral Microbiome Profile of the US Population

This cross-sectional study examines the demographic, socioeconomic, behavioral, anthropometric, metabolic, and clinical characteristics of the oral microbiome of US adults.

jamanetwork.com

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johnny connolly @jcons.bsky.social · May 6

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Karen James @kejames.bsky.social · May 4

The “brain drain” will be a primarily domestic phenomenon, w/ STEM-trained people moving into non-STEM occupations.

There are not remotely enough STEM jobs abroad for our *millions* scientists, and even if there were, moving is hard, expensive & dependent on multiple intersecting privileges.

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Helen Branswell 🇨🇦 @helenbranswell.bsky.social · May 4

There are a lot of questions being asked about the awarding of a $500M grant to an #NIH team to develop a new (old) vaccine platform that could be used for a "universal" #flu vaccine. www.statnews.com/2025/05/03/n...

Scientists question NIH project’s use of 20th century technology to make a universal flu vaccine

$500 million NIH program to make vaccines against pathogens that can trigger pandemics uses approach pioneered in last century

www.statnews.com

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