Should patients be told when they’re part of an outbreak in a hospital? Does pathogen genomics change that? I first started this paper in 2020 in my bioethics class, and happy to share it peer reviewed, published now! www.cambridge.org/core/journal...

This is extremely cool and makes scientific sense. Anti-retrotransposon editing as precursor to mechanism for antibody diversification

Cell - a Cell Press journal@cp-cell.bsky.social · 2d ago

Now online! Co-option of retrotransposons promotes antibody diversification

Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

2. If you've seen this before, a single brain metastasis with an unknown primary, we want your instinct. Assume we haven't heard of what you're about to suggest. 3. Introductions. Doctors, researchers, labs, clinical trials, anyone working on cancer of unknown primary.

Exciting collaboration with @annabiosys.bsky.social's lab just went online. @isbscience.org metaSPLiT: a fast, efficient, and relatively low-cost method for single-cell transcriptomics in the human gut microbiome. 👇

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 5d ago

Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics https://www.biorxiv.org/content/10.64898/2026.07.30.741866v1

The manuscript describing SimPhyNI is now published! www.microbiologyresearch.org/content/jour... A few updates since last post, including some method tweaks that improve performance and speed. Also even easier to run. Try it for your microbial GWAS or epistasis needs!

High-precision binary trait association on phylogenetic trees

Traditional methods for identifying associations between genomic features and traits, or between pairs of genomic traits, struggle when applied to bacterial genomes. While several microbial genome-wid...

microbiologyresearch.org

Tami Lieberman@contaminatedsci.bsky.social · 7mo ago

Proud to announce SimPhyNI, a new tool for bacterial GWAS with higher precision and scalability than existing tools. Try it out and let us know what you think!!

Beautiful work (Petrungaro, Bollenbach lab) on evo trajectories toward abx resistance (E. coli). Goes beyond many other studies in its attention to the experimental setup (identical selective pressure across all lines). I strongly recommend reading the entire paper! www.nature.com/articles/s41...

Function-specific epistasis shapes evolutionary trajectories towards antibiotic resistance - Nature Communications

Antibiotic resistance can evolve through the combination of factors but the predictability of this is unclear. Here, the authors used high-throughput evolution experiments to reveal that antibiotic re...

nature.com

Out Now! A microbial PPARadigm for gut protection #MicroSky

A microbial PPARadigm for gut protection

Nature Microbiology, Published online: 30 July 2026; doi:10.1038/s41564-026-02423-2Two independent studies converge on the nuclear receptor PPARα as a key node in gut microbiome communication, highlighting it as a potential therapeutic target in intestinal diseases.

go.nature.com

But what Elena found is that in 8/10 HIV populations, haplotype lengths were basically exactly the same before, during and after the sweep. It seems like these sweeps are basically so soft that they’re not changing the linkage structure of the population??

Thread from @s-j-aitken.bsky.social explaining our new paper that finds strong epistatic interactions between germline genetic background and somatic driver mutations that set the course of cancer development.

Sarah Aitken@s-j-aitken.bsky.social · last wk.

🧬NEW PAPER🧬 To what extent is cancer development deterministic? Does the germline genome affect that predictability? Find out in our #StrainDifferences paper @nature.com "Genetic background sets the trajectory of experimental cancer evolution" www.nature.com/articles/s41... 🧵[1/14]

102 new Ebola cases and 45 deaths reported by DRC over past 24 hours. For context: Many Ebola outbreaks in the past have remained small. These numbers mean the DRC has reported more cases overnight than were reported IN TOTAL during each of about two dozen smaller Ebola outbreaks. 🧪

And here's a second NYU postdoc job ad, where I'm looking for a candidate that is interested in working on the gut-brain axis: apply.interfolio.com/189975 please share 🙏

Dear microbiome enthusiasts: I'm excited to be moving my lab to New York University this fall (& the NYU Institute for Engineering Health); with joint-appointment @isbscience.org I'm hiring a postdoc @ NYU to look at diet-driven evolution in the gut: apply.interfolio.com/189980 Please share! 🦠🤓

1/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 biorxiv.org/content/10.6...

Thrilled to be part of this new study, just out in PLOS Pathogens, describing how #HPV genomes change over time within individuals. Sambit Mishra of the Mirabello @lisamirabello.bsky.social group led this work, documenting years of within-host viral mutations in cervical samples from 351 women. 1/6

The Ebola outbreak in the DRC keeps growing at a shocking pace. We're already close to 2000 confirmed cases. Right now: 1926 confirmed cases (incl. 53 new cases in the last 24 hours) 702 of these have died insp.cd/sitrep-n058-...

What if I told you that your state rep can say they voted in favor of a bill, but you have no way of verifying that fact?

RNA can build. A short RNA self-assembles into a 60-subunit icosahedral cage like a viral capsid, but made entirely of RNA. The striking preprint also reveals a 57-nt RNA filament at ~2.7 Å. Congratulations, Lin Huang and colleagues! www.biorxiv.org/content/10.6...

1. A bit of evolutionary biology. I'm really intrigued by a new perspective piece from Steve Frank that explores connections between how natural selection creates systems that generalize and recent work in machine learning about the surprising capabilities of massively overparameterized systems.

Generalization as the great leap in evolvability: insights from machine learning

Abstract. Natural selection encodes learned information in the genome. Learned solutions may be tuned specifically to past challenges, failing in altered e

academic.oup.com

Our vices have pushed us farther from our founding virtue: the promise (often unmet) to move ever towards a 'more perfect union'. I'm ashamed of where we are. But this shame is what pulls us back to virtue, each successive generation. It is time to get to work, citizens. youtu.be/NBe5qbnkqoM?...

‘What To The Slave Is The Fourth Of July?’: Descendants Read Frederick Douglass' Speech | NPR

YouTube video by NPR

youtu.be

What do single bacterial cells do when they run out of carbon source? If you missed the preprint, check out the official publication: doi.org/10.1038/s443... If the total bacterial population on earth stays roughly constant, then there must on average be as much death as replication. 1/n

E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients - Molecular Systems Biology

Although in the wild bacteria likely spend most of their time deprived of nutrients and slowly starving to death, very little is known about how bacteria adapt their phenotype to starvation. Here we combine microfluidics with quantitative fluorescence microscopy of transcriptional reporters to comprehensively quantify growth and gene expression at the single-cell level in E. coli during carbon starvation. We find that all cells immediately stop growing upon loss of carbon source and that almost all remain alive for over 30 hours. Furthermore, entry into starvation triggers a dynamic expression program that is remarkably homogeneous across single cells, but highly variable across genes, causing dramatic remodeling of the proteome early in starvation. We further show that, as protein production and the rate of protein degradation both decay approximately exponentially, protein concentrations become essentially ‘frozen’ after the first 5 to 10 hours, setting phenotypes for several days of starvation. Finally, using experiments in which gene expression is inhibited for different periods, we show that protein production in the first 5 hours is crucial for protecting cells from stresses late in starvation.

doi.org

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

Leonard Leo is a lawyer, but he's never argued a case in court. He's never held elected office. But for years he rebuilt the American legal system, resulting in the Supreme Court's right-wing supermajority. (Published Oct. 2023)

We Don’t Talk About Leonard: The Man Behind the Right’s Supreme Court Supermajority

The inside story of how Leonard Leo built a machine that remade the American legal system — and what he plans to do next.

propublica.org

Last thing I did before vacation was submit a public comment on the destructive OMB proposal through @standupforscience.net and e-mail my reps again! Comments close July 13th

New preprint from our lab Statistical learning of bacterial growth in combinatorially constructed environments, led by brilliant PhD student Andrea Arrabal. www.biorxiv.org/content/10.6... We systematically study nutrient-nutrient interactions in bacterial growth under carbon-limiting conditions.

Looking forward to digging in! It seems totally reasonable to me that hgt/recombination based sweeps are 'harder' than snv based ones!

Peter Laurin@peterlaurin.bsky.social · last mo.

Super excited to share new work with my advisor @nanditagarud.bsky.social! We re-examine the rapidity of adaptation in the human gut microbiome and begin to characterize the adaptive architecture of selective sweeps spreading across human guts. www.biorxiv.org/content/10... 1/n:

As you might imagine, as someone who studies science and works on metrics, I have some thoughts on qed myself. I fully agree that the messaging can be described as tone-deaf and problematic. I don’t think it had to be. ripplingideas.org/2026/06/26/t...

The 1% club and the rocky road ahead for bioRxiv

The recent launch of qed’s “top 1%” preprint ranking has sparked controversy, with concerns about its arbitrary nature, potential harm to authors, and low-quality inclusions. Whil…

ripplingideas.org

Microbes that have the greatest genomic potential for secondary metabolism tend to be multicellular. Here, we show that signatures of ancestral BGC expansions within 3 bacterial phyla and 2 fungal lineages coincide with origins of complex multicellularity [1/12] 🧵 www.nature.com/articles/s41...

Complex multicellularity is linked with expanded specialized metabolite production in microorganisms - Nature Microbiology

The evolutionary emergence of complex multicellularity in bacteria and fungi, such as the ability for mycelial growth, is strongly associated with increased genomic carriage of biosynthetic machinery ...

nature.com

People always say "tell a story" but then don't explain how to do so! How is that helping? If we knew how to tell a story we wouldn't need the advice in the first place. 1/

Stephen Turner@stephenturner.us · last mo.

How to give a bad talk www.nature.com/articles/s41...

When I first saw the data that ultimately fueled these charts, my mind was blown. (See the note at the bottom of our story for detailed sourcing!) projects.propublica.org/why-carbon-c...