johnny connolly @jcons.bsky.social · 29/09/2026I can think of at least one place to use Sonnet 5.5! 000
johnny connolly @jcons.bsky.social · 29/09/2026Manuscript here: latch.bio/metagenomics...latch.bio 000
johnny connolly @jcons.bsky.social · 29/09/2026We 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/metagenomicsbenchmarks.biobenchmarks.bio — Agentic benchmarks on messy, real-world biological dataCurrent agentic AI benchmark results across omics, therapeutics, and biosecurity tasks built from messy, real-world biological data. 110
johnny connolly @jcons.bsky.social · 29/09/2026As 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.bioLatchBioIntelligence Infrastructure for Biology. Click to read LatchBio, a Substack publication with tens of thousands of subscribers. 162
johnny connolly @jcons.bsky.social · 29/09/2026Just did the unthinkable: got my thesis hardcopy off the shelf to look up a citation 100
johnny connolly @jcons.bsky.social · 13/01/2026I feel like woke up and found out someone shaved my head, give me my files back 020
johnny connolly @jcons.bsky.social · 13/01/2026my laptop died :( debating springing for data recovery, but I don't think I have anything irreplaceable enough to justify the cost 120
johnny connolly @jcons.bsky.social · 18/12/2025it all strikes me as very motte/bailey. "Microsatellites control number of digits" is falsifiable, but all this other stuff is just looney tunes 000
johnny connolly @jcons.bsky.social · 17/12/2025Didn't realize this was such a hot research area, honestly. About time! 000
johnny connolly @jcons.bsky.social · 17/12/2025Very interesting: people with aphantasia (like yours truly) display significantly less pupil constriction when told to imagine a bright light elifesciences.org/articles/72484elifesciences.orgThe pupillary light response as a physiological index of aphantasia, sensory and phenomenological imagery strengthPhysiological 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... 130
johnny connolly @jcons.bsky.social · 04/12/2025Nature Portfolio is just a plot by big Nature to sell more Nature 030
johnny connolly @jcons.bsky.social · 18/11/2025Inexcusable. 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.comTrump admin axed 383 active clinical trials, dumping over 74K participantsIt’s a “violation of foundational ethical principles of human participant research.”… 0208
Reposted by johnny connollyderek guy @dieworkwear.bsky.social · 13/11/2025we need a department of kerning 3798568801
Reposted by johnny connolly🧬Jacob L Steenwyk @jlsteenwyk.bsky.social · 21/10/2025NEW 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 3199
Reposted by johnny connollyjohnny connolly @jcons.bsky.social · 15/08/2024The most mathematically rigorous microbiology papers I read pale in comparison to articles with titles like Composition of Snail Species on New Jersey Beaches (1965) 131
Reposted by johnny connollyjohnny connolly @jcons.bsky.social · 15/08/2024I find it very funny that people whose job it was to like, count trees in 1960s Wisconsin were well-versed in Information Theory 121
johnny connolly @jcons.bsky.social · 16/10/2025In 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.comIntraspecies associations from strain-rich metagenome samplesGenetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting… 040
Reposted by johnny connollyJon Douglas @atranscendedman.bsky.social · 05/09/2025London 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.orgThe global return-on-investment of COVID-19 vaccines in the first year of the vaccination programmeCOVID-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... 78644
Reposted by johnny connollyAnthony Edwards @edwardsanthonyb.bsky.social · 28/08/2025Meteorologists 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.comMeteorologists now face a Trump ‘loyalty test’ when applying to National Weather Service jobsAfter 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. 13177100
johnny connolly @jcons.bsky.social · 28/08/2025This was the best case scenario. Unfortunately, we ended up with the Other Thing 0152
Reposted by johnny connollyThe City Reporter @thecityreporter.nyc · 21/08/2025Bob 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.nycThe Chips Fall as Rivals Fry the MayorThe 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. 503241572
johnny connolly @jcons.bsky.social · 19/08/2025I 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 021
johnny connolly @jcons.bsky.social · 17/08/2025Trying to determine when industry will see the damage from lack of new research. I think probably starting in ~4-5 years? 0102
johnny connolly @jcons.bsky.social · 11/08/2025maybe an area that recently went from 0 to a gajillion overnight does not meet OP's definition of stable 000
johnny connolly @jcons.bsky.social · 11/08/2025HENRY (UK): year 8 of employment with major bank, turned down for mortgage HENRY (USA): Yacht purchase tied up with paperwork 050
Reposted by johnny connollyghost malone ergo propter bones @proptermalone.bsky.social · 05/08/2025this work saved millions of lives in 2021, won the Nobel Prize in 2023, and is cancelled in 2025 16973922977
johnny connolly @jcons.bsky.social · 22/07/2025Looking 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 030
johnny connolly @jcons.bsky.social · 18/07/2025Hire Javier Solamedia.tenor.coma man wearing a helmet and a yellow shirt that says lyonnaise on itALT: a man wearing a helmet and a yellow shirt that says lyonnaise on it 151
johnny connolly @jcons.bsky.social · 18/07/2025It was a great minute we had to enjoy the Jonas TT 010
johnny connolly @jcons.bsky.social · 14/07/2025Hard to overstate how damaging this will be to science and universities broadly 050
Reposted by johnny connollyDenis Wirtz @deniswirtz.bsky.social · 14/07/2025Grant 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 3159102
Reposted by johnny connollyJack A Gilbert @gilbertjacka.bsky.social · 23/06/2025New 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.orgGuidelines for preventing and reporting contamination in low-biomass microbiome studies - Nature MicrobiologyIn this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize contaminants. 04722
Reposted by johnny connollySegata 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... 🧵⬇️ 1/6nature.comPooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer - Nature MedicineAn 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 ... 34222
Reposted by johnny connollyJeremy Berg @jeremymberg.bsky.social · 12/05/2025Slow grant making continues. Here is a graph through May 1st. 2/n 1143
Reposted by johnny connollyRich 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.comOral Microbiome Profile of the US PopulationThis cross-sectional study examines the demographic, socioeconomic, behavioral, anthropometric, metabolic, and clinical characteristics of the oral microbiome of US adults. 051
Reposted by johnny connollyKaren James @kejames.bsky.social · 04/05/2025The “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. 321226260
Reposted by johnny connollyHelen Branswell 🇨🇦 @helenbranswell.bsky.social · 04/05/2025There 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.comScientists 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 58723
Reposted by johnny connollyMike Boylan-Kolchin @mbkplus.bsky.social · 02/05/2025NSF 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. 🧪 317866
Reposted by johnny connollyScott Delaney @scott-delaney.bsky.social · 30/04/2025NEW: 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.usGrant Watch 6291183
Reposted by johnny connollyJohn Lees @johnlees.bacpop.org · 30/04/2025Our subclustering and transmission pipeline, PopPIPE has now been published: www.microbiologyresearch.org/content/jour...microbiologyresearch.orgIntegrated population clustering and genomic epidemiology with PopPIPEGenetic 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... 243