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Dan Browne

@drbfx.bsky.social
69 followers 262 following 8 posts

Space cowboy riding a massive rock across the galaxy, wrangling genomes and herding data. PhD in Biochemistry @TAMUBCBP. Working @LanzaTech. GitHub: github.com/dbrowneup LinkedIn: linkedin.com/in/drbrowne

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Reposted by Dan Browne
bioRxivpreprint @biorxivpreprint.bsky.social · 21/07/2026
Scalable single-cell isoform profiling with sequencing-by-expansion www.biorxiv.org/content/10.64898/20…
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Nature @nature.com · 21/07/2026
Nature research paper: People use fast and flat simulation to reason about new games go.nature.com/4vxhiGA
go.nature.com
People use fast and flat simulation to reason about new games - Nature
Large-scale behavioural studies show that people approach a new game systematically and adaptively rationally. A cognitive model called the ‘Intuitive Gamer’ offers insights into this process and may inform the design of more flexible AI systems.
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Karl Bode @karlbode.com · 21/07/2026
if your software runs amok I maintain that the problem is you
thebureauinvestigates.com
Claude disobeyed Anthropic CEO in simulations
In testing, Claude went against boss’s orders and helped an employee blow the whistle about a safety concern
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Dan Browne @drbfx.bsky.social · 21/07/2026
What if a company figures out how to make money doing mCDR? Profit is to a company as Gibbs free energy is to a chemical reaction. Negative free energy means a reaction is spontaneous. Profit means a company can grow and do more.
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Zamin Iqbal @zaminiqbal.bsky.social · 20/07/2026
Significant update to the AllTheBacteria paper, including discovering new antimicrobial peptides and testing in vitro and vivo. This has grown into a fantastic collaboration!
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Dan Browne @drbfx.bsky.social · 21/07/2026
Do you have a link to the preprint or a PDF version that is publicly available? Sucks not to have University library access anymore. So much good stuff stuck behind paywalls.
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Aude Bernheim @audeber.bsky.social · 21/07/2026
Out @cp-cellhostmicrobe.bsky.social, natural products meet bacterial immunity! We used genomics to identify lanthivirins: a family of >2,000 lanthipeptide BGCs that protect Actinobacteria against phages. Led by @hshomar.bsky.social & @mariegllm.bsky.social www.sciencedirect.com/science/arti...
sciencedirect.com
A family of lanthipeptides with anti-phage function
Bacteria produce natural products to adapt to their environments, with phage interactions as major ecological and evolutionary drivers. While some nat…
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Reposted by Dan Browne
Cameron Thrash @jcamthrash.bsky.social · 28/04/2026
Quantifying phage-host dynamics using droplet microfluidics www.nature.com/articles/s41... #jcampubs
nature.com
Quantifying phage-host dynamics using droplet microfluidics - Nature Communications
Bacteriophages are key tools in molecular biology and promising agents against antibiotic-resistant bacteria. Here, the authors present a high-throughput droplet microfluidics platform that co-encapsu...
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Reposted by Dan Browne
Nature @nature.com · 28/04/2026
This researcher created a fictional illness, and fake studies funded by the Professor Sideshow Bob Foundation and University of the Fellowship of the Ring and the Galactic Triad. LLMs warned people the illness was real. go.nature.com/4cQabS5
go.nature.com
Scientists invented a fake disease. AI told people it was real
Nature - Bixonimania doesn’t exist except in a clutch of obviously bogus academic papers. So why did AI chatbots warn people about this fictional illness?
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Reposted by Dan Browne
Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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💪🏽🤟🏼💪🏿🫶🏽 L Ramalho 🍉 @ramalho.org · 24/04/2026
www.thatprivacyguy.com/blog/anthrop...
thatprivacyguy.com
Anthropic secretly installs spyware when you install Claude Desktop — That Privacy Guy!
Anthropic's Claude Desktop silently installs a Native Messaging bridge into seven Chromium browsers, including browsers Anthropic's own documentation says it does not support, and browsers the user ha...
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Reposted by Dan Browne
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 25/04/2026
GenNA: Conditional generation of nucleotide sequences guided by natural-language annotations www.biorxiv.org/content/10.64898/20…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 25/04/2026
PanVariants: Best Practice for Pangenome-based Variant Calling Pipeline and Framework www.biorxiv.org/content/10.64898/20…
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bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 25/04/2026
PhAGE Enables One-Step Genome Integration of Large DNA Fragments in Escherichia coli www.biorxiv.org/content/10.64898/20…
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bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 10/04/2026
Physical theory of epigenetic memory and its biological implications www.biorxiv.org/content/10.64898/20…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 10/04/2026
A computational model for quantifying instability of tandem repeats across the genome www.biorxiv.org/content/10.64898/20…
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Sam Horsfield @samuelhorsfield.bsky.social · 30/03/2026
ggCaller v1.5.0 is out! We've removed the integrated clustering to enable users to benefit from new Panaroo features. Now, ggCaller generates GFFs that can be used with any clustering method. But for fans of an integrated ggCaller pangenome workflow read on... github.com/bacpop/ggCal...
github.com
GitHub - bacpop/ggCaller: Bifrost graph gene caller.
Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.
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Reposted by Dan Browne
Stephen Turner @stephenturner.us · 05/03/2026
Genome modelling and design across all domains of life with Evo 2 www.nature.com/articles/s41...
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Reposted by Dan Browne
EMBO @embo.org · 05/03/2026
What happens when single-author science papers become rare? 🧪 An EMBO Reports Science & Society article explores whether solo publications are being edged out by collaborative #research, and what that means​ for #creativity in #science: link.springer.com/article/10.1038/s…
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Keith Robison @omicsomics.bsky.social · 05/03/2026
Ultima Genomics Solaris 2.0: Greater Version, Smaller Beads, Lose A Box 🧬💻 #AGBTGM26 omicsomics.blogspot.com/2026/03/ulti...
omicsomics.blogspot.com
Ultima Genomics Solaris 2.0: Greater Version, Smaller Beads, Lose A Box
Ultima Genomics announced the 2.0 version of their Solaris chemistry at AGBT.  Perhaps the biggest splash here is that Solaris 2.0 relies on...
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Reposted by Dan Browne
Stu West @stuwest.bsky.social · 04/03/2026
New paper showing that bacteria with more genes for cooperation can live in a broader range of habitats and that genes for cooperation are more more likely to be in the accessory genome www.pnas.org/doi/10.1073/... @lauriebelch.bsky.social
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Tim Straub @timothystraub.com · 05/03/2026
Cool mouse model showing how the gut microbiome is so personalized! A healthy microbiome is NOT one size fits all. Bugs and host are likely co-adapting as we age.
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Reposted by Dan Browne
Stephen Turner @stephenturner.us · 05/03/2026
Large-scale online deanonymization with LLMs arxiv.org/abs/2602.16800
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Reposted by Dan Browne
Rubin Lab @therubinlab.bsky.social · 12/02/2026
Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠 We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵
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Piotr Lukasik @sympiotr.bsky.social · 11/02/2026
Our new paper in @natcomms.nature.com is now online-early! We describe independent evolution of bacterial genomes of only ~50–52 kb — the smallest known outside cellular organelles — revealing striking convergence toward minimal gene sets. 🔗 doi.org/10.1038/s414...
The visualization of two bacterial genomes, of 50 and 52kb, representing independent instances of extreme genomic reduction in ancient heritable endosymbionts of planthoppers.
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Robert Aboukhalil @robert.bio · 12/02/2026
We just released a video from our visit to @plasmidsaurus.bsky.social, where we spoke with Mark Budde and team: www.youtube.com/watch?v=nS2o... Highlights include: ✅ 3D printed magnetic bead contraptions ✅ When sequencing more is easier than sequencing less ✅ Bread machine analogies
youtube.com
The "Why Not?" Era of Sequencing Has Begun
YouTube video by OMGenomics
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Reposted by Dan Browne
Barry Butler Photography @barrybutler9.bsky.social · 18/01/2026
Sunrise on Sunday. Today in Chicago.
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Barry Butler Photography @barrybutler9.bsky.social · 09/01/2026
The Morning Lights. Twilight before sunrise in Chicago on Thursday.
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Ming Tommy Tang @tommytang.bsky.social · 28/12/2025
Free deep learning book with ipython notebooks udlbook.github.io/udlbook/
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Reposted by Dan Browne
bioRxivpreprint @biorxivpreprint.bsky.social · 27/12/2025
The geometry of cooperation: decoding microbial interactions www.biorxiv.org/content/10.64898/20…
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Keith Robison @omicsomics.bsky.social · 15/12/2025
I had fun being interviewed on this podcast www.legible.bio/p/ep-2-evolu...
legible.bio
Ep 2: Evolution of Biotech with Keith Robison
Lab automation, small molecules, life at Gingko Bioworks, and more
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Reposted by Dan Browne
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 15/12/2025
CompBio and MIRaS : A Multi-omic Analysis Platform Built on a Memory-Based Intelligence Engine www.biorxiv.org/content/10.64898/20…
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Stephen Turner @stephenturner.us · 09/12/2025
hf claude code skills allow you to fine-tune an LLM in natural language. E.g.: "Fine-tune Qwen3-0.6B on the dataset open-r1/codeforces-cots" and it'll validate datasets, choose GPU types, kick off HF Jobs, monitor progress, and publish checkpoints/models huggingface.co/blog/hf-skil...
huggingface.co
We Got Claude to Fine-Tune an Open Source LLM
We’re on a journey to advance and democratize artificial intelligence through open source and open science.
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Megan Dennis @mydennis.bsky.social · 08/12/2025
Excited to share our final accepted version of the CiFi method out today: www.nature.com/articles/s41...
nature.com
CiFi: accurate long-read chromosome conformation capture with low-input requirements - Nature Communications
Hi-C methods for studying 3D genome structure typically require millions of cells and struggle with repetitive regions. Here, authors develop CiFi, combining 3C with PacBio HiFi sequencing, enabling c...
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Chris Mancuso @mancusosci.bsky.social · 08/12/2025
The #1 organism used to make biocement has never been engineered... until now! Excited to share our work on Sporosarcina pasteurii! Esp. since it's the first project I've contributed to here at Cultivarium :) www.biorxiv.org/content/10.6...
biorxiv.org
A genetic platform for a biocementation bacterium
Sporosarcina pasteurii is the most widely studied bacterium for microbially-induced calcium carbonate precipitation (MICP), a process of intense interest for materials and construction applications. D...
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Reposted by Dan Browne
Simon Roux @simrouxvirus.bsky.social · 09/12/2025
🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and @titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ? doi.org/10.1093/narg...
doi.org
Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations
Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru
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Daan Speth @daanspeth.bsky.social · 21/11/2025
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social doi.org/10.1093/bioa... The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives. More information on globdb.org 1/5 🖥️🧬🦠
doi.org
GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
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Cameron Thrash @jcamthrash.bsky.social · 20/11/2025
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes academic.oup.com/nar/advance-... #jcampubs
academic.oup.com
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob
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Nature @nature.com · 10/11/2025
Getting Rosalind Franklin’s story right is crucial, because she has become a role model for women going into science www.nature.com/articles/d41...
nature.com
What Rosalind Franklin truly contributed to the discovery of DNA’s structure
Franklin was no victim in how the DNA double helix was solved. An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player.
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Antonio Camargo @apcamargo.bsky.social · 06/11/2025
🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8) www.biorxiv.org/content/10.1...
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bioRxivpreprint @biorxivpreprint.bsky.social · 06/11/2025
Tracking community change via network coherence www.biorxiv.org/content/10.1101/202…
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Keith Robison @omicsomics.bsky.social · 05/11/2025
Nineteen - musings on shrinking the number of amino acids in a proteome 🧬🖥️ omicsomics.blogspot.com/2025/11/nine...
omicsomics.blogspot.com
Nineteen
If I had been more atop things, I would have written this just under a week ago, on the nineteenth anniversary of my starting to write in th...
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Barry Butler Photography @barrybutler9.bsky.social · 05/11/2025
Wednesday's WOW! This morning's spectacular panorama sunrise over Chicago.
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James McInerney @jomcinerney.bsky.social · 30/10/2025
I've often wondered about what we should call organisms whose similarity might be due to acquired genetic material. It got a little complicated, but I made a stab at it here Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
academic.oup.com
Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes
Abstract. The classification of living systems presents significant challenges due to the prevalence of gene transfer between genomes. Traditional taxonomi
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Jeremy Baskin @jeremybaskin.bsky.social · 30/10/2025
Check out this chemoproteomics tour de force from @stephanhacker2.bsky.social and colleagues — want to know which electrophiles label which amino acid residues proteome-wide? Finally, a comprehensive comparative study with a ton of insights on old and new warheads and optimized workflows. Bravo!
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Landon Getz @landongetz.bsky.social · 30/10/2025
Excited to share: DNA glycosylases are diverse antiviral effectors. They recognize phage base modifications and initiate genome destruction. A structure‑guided approach made the scope of this discovery possible! 🧪 #phagesky doi.org/10.1101/2025... #phage #microbiology
doi.org
Antiviral Defence is a Conserved Function of Diverse DNA Glycosylases
Bacteria are frequently attacked by viruses, known as phages, and rely on diverse defence systems like restriction endonucleases and CRISPR-Cas to survive. While phages can evade these defences by cov...
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Barry Butler Photography @barrybutler9.bsky.social · 31/10/2025
Ready For Rugby? The pitch is all set as of this morning at Chicago's Soldier Field for the Ireland versus New Zealand match on Saturday.
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Barry Butler Photography @barrybutler9.bsky.social · 27/10/2025
Monday's final light in the West Town area of Chicago at day's end.
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Pedro Beltrao @pedrobeltrao.bsky.social · 28/10/2025
Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...
github.com
GitHub - aqlaboratory/openfold-3: OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3
OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3 - aqlaboratory/openfold-3
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 27/10/2025
1/2 Want to become up to date with pangenomes and genome graphs and their history? Check out this fantastic review by @zbao.bsky.social! Complexity welcome: Pangenome graphs for comprehensive population genomics #pangenomes #plantscience #genomegraphs www.cambridge.org/core/journal...
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