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johnny connolly

@jcons.bsky.social
1.1K followers 297 following 1.5K posts

microbial ecology, metagenomics, science policy and funding. Ph.D. in systems & computational biology (2024)

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johnny connolly @jcons.bsky.social · 01/10/2026
ntm the New Deal
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johnny connolly @jcons.bsky.social · 29/09/2026
I can think of at least one place to use Sonnet 5.5!
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johnny connolly @jcons.bsky.social · 29/09/2026
Manuscript here: latch.bio/metagenomics...
latch.bio
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johnny connolly @jcons.bsky.social · 29/09/2026
We created 100 evaluation problems, spanning different hosts, tasks and contexts, to assess the performance of the latest models. No model was able to correctly complete more than 60% of the evaluations (including GPT Astra, which scored < 50%!) benchmarks.bio/metagenomics
benchmarks.bio
benchmarks.bio — Agentic benchmarks on messy, real-world biological data
Current agentic AI benchmark results across omics, therapeutics, and biosecurity tasks built from messy, real-world biological data.
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johnny connolly @jcons.bsky.social · 29/09/2026
As the use of metagenomics methods continues to expand, it is inevitable that researchers will attempt to use frontier AI for analysis. It is therefore critical that we have some kind of assessment of agent capabilities. I give you: MetagenomicsBench #MicroSky 🧪 🧬🖥️ blog.latch.bio/p/c55a6336-7...
blog.latch.bio
LatchBio
Intelligence Infrastructure for Biology. Click to read LatchBio, a Substack publication with tens of thousands of subscribers.
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johnny connolly @jcons.bsky.social · 29/09/2026
Not true on the only metric that matters:
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johnny connolly @jcons.bsky.social · 29/09/2026
White paper 🔜
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johnny connolly @jcons.bsky.social · 29/09/2026
Just did the unthinkable: got my thesis hardcopy off the shelf to look up a citation
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johnny connolly @jcons.bsky.social · 22/09/2026
“side hustlers”
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johnny connolly @jcons.bsky.social · 13/01/2026
I feel like woke up and found out someone shaved my head, give me my files back
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johnny connolly @jcons.bsky.social · 13/01/2026
my laptop died :( debating springing for data recovery, but I don't think I have anything irreplaceable enough to justify the cost
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johnny connolly @jcons.bsky.social · 18/12/2025
it all strikes me as very motte/bailey. "Microsatellites control number of digits" is falsifiable, but all this other stuff is just looney tunes
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johnny connolly @jcons.bsky.social · 17/12/2025
Didn't realize this was such a hot research area, honestly. About time!
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johnny connolly @jcons.bsky.social · 17/12/2025
Very interesting: people with aphantasia (like yours truly) display significantly less pupil constriction when told to imagine a bright light elifesciences.org/articles/72484
elifesciences.org
The pupillary light response as a physiological index of aphantasia, sensory and phenomenological imagery strength
Physiological evidence shows that the pupillary response to imagined light can be used to index the strength and vividness of an individual’s visual imagery and as a new tool for confirming aphantasia...
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johnny connolly @jcons.bsky.social · 04/12/2025
Nature Portfolio is just a plot by big Nature to sell more Nature
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johnny connolly @jcons.bsky.social · 02/12/2025
not a question but "I'm really into probiotics!"
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johnny connolly @jcons.bsky.social · 18/11/2025
Inexcusable. My heart breaks for the patients and researchers on the receiving end of this. 118 cancer trials and 97 ID trials canceled for petty political reasons arstechnica.com/health/2025/...
arstechnica.com
Trump admin axed 383 active clinical trials, dumping over 74K participants
It’s a “violation of foundational ethical principles of human participant research.”…
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derek guy @dieworkwear.bsky.social · 13/11/2025
we need a department of kerning
The Department of War's seal hangs on a wall. The kerning appears to be off.
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🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 21/10/2025
NEW method! eComp is a new, #evolution-informed #compression method🗜️ for multiple #sequence alignments (#MSAs)...that outperforms gzip! Unlike gzip's row-based compression, eComp implements a simple #column-based solution for compression, following how biological information is stored in MSAs
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johnny connolly @jcons.bsky.social · 28/10/2025
data science is my passion
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johnny connolly @jcons.bsky.social · 15/08/2024
The most mathematically rigorous microbiology papers I read pale in comparison to articles with titles like Composition of Snail Species on New Jersey Beaches (1965)
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johnny connolly @jcons.bsky.social · 15/08/2024
I find it very funny that people whose job it was to like, count trees in 1960s Wisconsin were well-versed in Information Theory
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johnny connolly @jcons.bsky.social · 16/10/2025
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...
sciencedirect.com
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…
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Jon Douglas @atranscendedman.bsky.social · 05/09/2025
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...
medrxiv.org
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...
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Anthony Edwards @edwardsanthonyb.bsky.social · 28/08/2025
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.
sfchronicle.com
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.
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johnny connolly @jcons.bsky.social · 28/08/2025
This was the best case scenario. Unfortunately, we ended up with the Other Thing
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The City Reporter @thecityreporter.nyc · 21/08/2025
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...
thecity.nyc
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.
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johnny connolly @jcons.bsky.social · 19/08/2025
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 · 17/08/2025
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 · 11/08/2025
maybe an area that recently went from 0 to a gajillion overnight does not meet OP's definition of stable
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johnny connolly @jcons.bsky.social · 11/08/2025
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 bones @proptermalone.bsky.social · 05/08/2025
this work saved millions of lives in 2021, won the Nobel Prize in 2023, and is cancelled in 2025
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johnny connolly @jcons.bsky.social · 22/07/2025
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 · 18/07/2025
Hire Javier Sola
media.tenor.com
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
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johnny connolly @jcons.bsky.social · 18/07/2025
It was a great minute we had to enjoy the Jonas TT
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johnny connolly @jcons.bsky.social · 18/07/2025
It’s over
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johnny connolly @jcons.bsky.social · 14/07/2025
Hard to overstate how damaging this will be to science and universities broadly
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Denis Wirtz @deniswirtz.bsky.social · 14/07/2025
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 · 25/06/2025
i don't think smith was ever mayor
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Jack A Gilbert @gilbertjacka.bsky.social · 23/06/2025
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...
doi.org
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.
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Segata Lab @cibiocm.bsky.social · 03/06/2025
🥁NEW publication from our lab: the largest meta-analysis of gut microbiome associations with CRC! www.nature.com/articles/s41... 🧵⬇️ 1/6
nature.com
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 ...
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Jeremy Berg @jeremymberg.bsky.social · 12/05/2025
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 · 09/05/2025
"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."
jamanetwork.com
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.
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johnny connolly @jcons.bsky.social · 06/05/2025
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Karen James @kejames.bsky.social · 04/05/2025
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 · 04/05/2025
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...
statnews.com
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
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Mike Boylan-Kolchin @mbkplus.bsky.social · 02/05/2025
NSF has two kinds of grants, standard (where all of the awarded $ is issued up front) and continuing (where the awarded $ is issued in yearly increments). It sounds like they're freezing any expenditures on awarded continuing grants and not making any new awards for now. Disastrous for US science. 🧪
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Scott Delaney @scott-delaney.bsky.social · 30/04/2025
NEW: We (mostly @noamross.net) launched a website to shine a brighter light on terminated NIH and NSF grants. grant-watch.us It links to our NIH & NSF trackers, grant info submission forms, and other info. We'll also add new analyses soon. Check it out and let us know what else you'd like to see.
grant-watch.us
Grant Watch
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John Lees @johnlees.bacpop.org · 30/04/2025
Our subclustering and transmission pipeline, PopPIPE has now been published: www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
Integrated population clustering and genomic epidemiology with PopPIPE
Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations and as an additional source of information when detecting possible transmission...
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