Dan Browne

Evolution of genotypic and phenotypic diversity in multispecies biofilms - npj Biofilms and Microbiomes npj Biofilms and Microbiomes - Evolution of genotypic and phenotypic diversity in multispecies biofilms

En route to the GRC for Microbial Population Biology, my conference home for 30🤯 years.

In this spirit, gladly sharing this new paper led by Henriette Roder who visited us a few years back, featuring an innovative new biofilm passage + microscopy system

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

A flyby of Earth from the International Space Station.

Credits: NASA

Sorry guys, I can't come out to play, I have to read the new paper by Gene Meyers, Richard Durbin and Chenxi Zhou!

Very excited to see the long-read #microbiome profiling feature included in this tool! I'll be taking a look at #PacBio HiFi performance in the near future.

Plasmids, prophages, and defense systems are depleted from plant microbiota genomes - Genome Biology Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. He...

Our new paper is online in Genome Biology:
"Plasmids, prophages, and defense systems are depleted from plant microbiota genomes"
genomebiology.biomedcentral.com/articles/10....

Synthetic biology could enable new types of programmable therapeutics. Our new preprint introduces synthetic protein circuits that selectively trigger cell death in Ras-mutant cancer cells, with interesting advantages compared to existing approaches.
www.biorxiv.org/content/10.1...

StarBASE-GP: Biologically-Guided Automated Machine Learning for Genotype-to-Phenotype Association Analysis We present the Star-Based Automated Single-locus and Epistasis analysis tool - Genetic Programming (StarBASE-GP), an automated framework for discovering meaningful genetic variants associated with phe...

StarBASE-GP: Biologically-Guided Automated Machine Learning for Genotype-to-Phenotype Association Analysis arxiv.org/abs/2505.22746 #bioinformatics #genetics

Happy to be part of this exciting work. A must-read for enhancer aficionados: A massive effort has gone into generating genome-wide STARRseq in hPSCs and conducting functional validation assays. Congratulations to all authors, Stefan and Ufuk, for leading this project 🎉.

Abstract submission extended to 1 July – Submit your work now!

Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...

Congress moves to loosen toxic air pollution rules The House and Senate both voted to loosen regulations on air pollutants like dioxin and mercury, which are associated with higher cancer risk.

Because they want to kill us, Congress voted to overturn a Clean Air Act regulation limiting toxic emissions from industrial facilities like refineries, chemical plants, and steel mills. This marks the first Congressional rollback of the landmark environmental law's protections since its creation.

It's *just* z<-z^2+c iterated, probably nothing to think about there

Autocycler: long-read consensus assembly for bacterial genomes Motivation Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using T...

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention).
www.biorxiv.org/content/10.1...
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Release DeepVariant 1.9.0 · google/deepvariant DeepVariant: In this version we have updated our training scheme for the HG002 sample with the newly released HG002-T2T truth set which improves accuracy against that truth set. Our labeling metho...

Release of DeepVariant and DeepSomatic v1.9

DV: Now train on HG002 T2T-Q100. Error reduction of 12% for Illumina and 30% for PacBio on this truth set. 25% faster. DeepTrio is 5x faster (20h -> 4h).

DS: New models FFPE_TUMOR_ONLY for {WGS, WES}. Much improved WGS models.

github.com/google/deepv...

The Trojans would've been stupid to reject the gift of the large wooden horse from Odysseus and the Greeks.

AmrProfiler: a comprehensive tool for identifying antimicrobial resistance genes and mutations across species Abstract. Antimicrobial resistance (AMR) remains a critical challenge in public health and research. AmrProfiler is a comprehensive tool with three special

Oh snap... just when we completed deploying our new AMR pipeline into our production pipeline for the ATCC Genome Portal - this AmaHzing paper comes out!

academic.oup.com/nar/advance-...

Brave Genius by Sean B. Carroll: 9780307952349 | PenguinRandomHouse.com: Books The never-before-told account of the intersection of some of the most insightful minds of the 20th century, and a fascinating look at how war, resistance, and friendship can catalyze genius.  ...

One of my favorite history of science books: "Brave Genius"

It's about Jacques Monod, discoverer of the lac operon, who risked everything to fight fascism/Nazis as a part of the French Resistance, along with his buddy Albert Camus.

Be like Jacques.

www.penguinrandomhouse.com/books/213596...

The dark matter of bacterial genomic surveillance—antimicrobial resistance plasmid transmissions in the hospital setting | Journal of Clinical Microbiology Antimicrobial resistance (AMR) poses a significant threat to human health. Most AMR determinants are encoded extra-chromosomally on plasmids. Although current infection control strategies primarily fo...

Switching to #PacBio #longread #WGS (lrWGS) improved detection of antimicrobial resistance (AMR) plasmid transmission in healthcare. lrWGS + real-time tools uncover hidden genomic elements, boosting #AMR surveillance and deep characterization.

🔗 Read the study: bit.ly/43tnXGT

Native nucleosomes intrinsically encode genome organization principles www.nature.com/articles/s41...
▶️Condensed purified native mononucleosomes with polyamines
▶️Nucleosomes from A compartments have low condensability and those from B compartments have high condensability

Release v4.9.0 · sourmash-bio/sourmash This release adds two significant feature sets to sourmash, without introducing any breaking changes. First, sourmash now fully supports fast, low-memory disk-based inverted indexes based on RocksD...

sourmash v4.9.0 is now available! Two big additions: fast, low-memory, on-disk inverted indexing with RocksDB; and skip-mers! See the release notes for more info.

Excerpt from the discussed article.

Life's survival depends on geothermal fields not only in the astrobiology models, but also in telluric environments here and now. Exciting pattern from older article:
www.pnas.org/doi/pdf/10.1...
🧪 ⚒️ #Geology #Paleobio #EvoBio

Deep origin of eukaryotes outside Heimdallarchaeia within Asgardarchaeota - Nature Ancestral reconstruction together with molecular dating of the last Asgard archaea and eukaryote common ancestor suggest that eukaryotes arose from the fusion of a H2-consuming archaeal host and a H2-...

Deep origin of eukaryotes outside Heimdallarchaeia within Asgardarchaeota www.nature.com/articles/s41...

Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information - Nature Communications Microbial maximum growth rates vary widely across species, and their measurement is challenging, especially for uncultivated organisms. Here, Xu, Zakem &amp; Weissman present Phydon, a framework for g...

Our newest on using genomic and phylogenetic information to predict microbial maximum growth rates www.nature.com/articles/s41... with @liangxu.bsky.social

Startup helps farmers grow plant-based feed and fertilizer using wastewater Fyto, founded by former MIT Tata Center translational research director Jason Prapas, has built an automated system for harvesting the aquatic plant Lemna, or duckweed, on dairy farms, for use as…

Turning wastewater into feed and fertilizer? This duckweed tech seems like a win-win if it can scale. Like so many food & agriculture innovations, this has its roots (though tiny & floating) in research that NSF and USDA have long funded.

Unraveling the tempo and mode of horizontal gene transfer in bacteria Research on horizontal gene transfer (HGT) has surged over the past two decades, revealing its critical role in accelerating evolutionary rates, facil…

www.sciencedirect.com/science/arti...

Nearly missed my bus stop reading this fascinating review :)

PurplePalozza. This morning on the Magnificent Mile in Chicago.

My painting LOST COAST

Roses are red — but their ancestors were yellow Nature - A genomic analysis of 84 species in the genus Rosa traces the evolutionary history of the beloved flower.

What colour were the first roses?

A large genomic analysis indicates that they were probably yellow

https://go.nature.com/4cHKhzO

minimap2 adds support for short read spliced RNA-seq alignment! lh3.github.io/2025/04/18/s...

Update on measles in the US, cases and deaths, in context of vaccine introduction