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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 · 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
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
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
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 · 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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post malone ergo propter malone @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 · 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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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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johnny connolly @jcons.bsky.social · 30/04/2025
I assumed someone had done this already- could be pretty cool for microbial ecology/defined community work www.nature.com/articles/s42...
nature.com
Machine learning prediction of enzyme optimum pH - Nature Machine Intelligence
Accurately predicting the optimal pH level for enzyme activity is challenging due to the complex relationship between enzyme structure and function. Gado and colleagues show that a language model can ...
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skelly @iid.bsky.social · 30/04/2025
Journalists need to stop letting non-experts say unchallenged how "great" LLMs are for researchers and scientists and actually talk to a few. The public has the conception that this tool is in use by mathematicians and scientists using it to craft theories, when it is totally useless for this
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johnny connolly @jcons.bsky.social · 29/04/2025
NIH announces Human Instrumentality Project www.nih.gov/news-events/...
nih.gov
NIH to prioritize human-based research technologies
New initiative aims to reduce use of animals in NIH-funded research.
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johnny connolly @jcons.bsky.social · 29/04/2025
www.nature.com/articles/s41...
nature.com
Brief antibiotic use drives human gut bacteria towards low-cost resistance - Nature
Brief ciprofloxacin exposure in humans drives antibiotic resistance evolution in gut bacteria through selective sweeps, particularly involving DNA gyrase mutations, which persist long after exposure a...
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Nature Reviews Microbiology @natrevmicro.nature.com · 17/04/2025
ICYMI: New online! The global resistance problem and the clinical antibacterial pipeline
nature.com
The global resistance problem and the clinical antibacterial pipeline
Nature Reviews Microbiology, Published online: 10 April 2025; doi:10.1038/s41579-025-01169-8In this Review, Theuretzbacher explores current clinical antibacterial agents in clinical development, incorporating global health considerations and the need for effective, accessible therapies worldwide.
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johnny connolly @jcons.bsky.social · 23/04/2025
Now over a month since this beauty made it into print! journals.asm.org/doi/full/10....
Colorful graph depicting F. nucleatum pangenome
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Liz Ortiz de Ora @ortizdeora.bsky.social · 18/04/2025
I am thrilled to share the first manuscript from the Wiles lab! We present "Phollow", an in vivo phage-tagging approach that enables direct observation of phage outbreaks with single-virion resolution by live imaging. Here some highlights 👇 www.nature.com/articles/s41...
nature.com
Phollow reveals in situ phage transmission dynamics in the zebrafish gut microbiome at single-virion resolution
Nature Microbiology - ‘Phollow’ is a live imaging-based fluorescence tagging approach that can track phage replication and spread in situ with single-virion resolution.
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johnny connolly @jcons.bsky.social · 23/04/2025
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Maya Sen @mayasen.bsky.social · 18/04/2025
Ok so yeah, this has quickly become the #1 misunderstanding about the canceled grants the grants are not “subsidies” or “entitlements” to Harvard or Princeton or whatever they aren’t going into universities’ endowments they are competitive contracts won by these universities to do research
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johnny connolly @jcons.bsky.social · 17/04/2025
This is just unbelievable
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Sean Gibbons 🦠💩 @gibbological.bsky.social · 11/04/2025
In a review led by @gilbertjacka.bsky.social in @natmedicine.bsky.social we highlight the state of clinical translation in microbiome research. We have gone from basic discoveries to FDA-approved therapies in <20 years, on par with the pace of mRNA vaccine development. www.nature.com/articles/s41...
The timeline shows clinical development and regulatory milestones for VOWST, a microbial product used to treat rCDI.
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johnny connolly @jcons.bsky.social · 10/04/2025
WHAT www.nytimes.com/2025/04/09/b...
nytimes.com
Thomas Pynchon to Publish a New Novel This Fall
Featuring a Depression-era private eye, “Shadow Ticket” will be the 87-year-old writer’s first book since 2013.
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Josh Marshall @joshtpm.bsky.social · 07/04/2025
This is a big deal. Spread the word. But it’s tiny compared to the totality of what’s happening at NIH. Cure Research for all cancers, Alzheimer’s, everything is being gutted. Intentionally. It’s all getting burned to the ground but the news isn’t getting out. The new cures won’t be there for you.
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