Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

Reminder: a large (2.5M+) sibling control study found "no evidence of increased risk of autism, ADHD, or intellectual disability associated with acetaminophen use". Precisely the kind of data that requires serious consideration before declaring mission accomplished. jamanetwork.com/journals/jam...

Now hiring a computational postdoc (evolutionary genomics, molecular evolution) in my lab at Emory University. If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch. faculty-emory.icims.com/jobs/151181/...

PIWI clade Argonautes are essential for transposon silencing. Without them, animals are sterile due to massive transposon activity. But how does piRNA-guided target interaction translate into silencing? PhD student Júlia Portell Montserrat has an intriguing answer www.cell.com/molecular-ce...

Three new kids on the block. ARMADA, BRIGADE, and TALON. Impressive how multiple labs all come together to contribute to discovery. Great collaboration with Simon, Chase, and Eugene. From the very talented Ryan Bell, together with Thomas Gaudin and our own Yi Wu. www.biorxiv.org/content/10.1...

YprA is a helicase popping up in multiple defense systems. In our new preprint (led by Ryan Bell), we investigate YprA clades and describe new defense systems. Importantly, ARMADA II synergizes with Druantia III; and Zorya II, Druantia III, and ARMADA II often travel together on various MGEs.

Sanasar has been digging into how bacterial defense systems shift under different phage attack modes – from long-term infections by similar phages to constantly changing phage assaults. Glad to be part of that story, out today

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

www.biorxiv.org/content/10.1... #phagesky #phage

An inspiring read! academic.oup.com/genetics/adv... A beautiful historical perspective on Ester Lederberg's legacy from @ccwendling.bsky.social & @zacharybailey.bsky.social

New paper alert! We suggest caution in the analyses of viral auxiliary metabolic genes and propose a new overarching term - 'auxiliary viral genes' (AVGs) to describe different types of such genes. @simrouxvirus.bsky.social #phagesky #Microsky www.nature.com/articles/s41...

Preprint: We discovered phage proteins that sequester diverse immune signaling molecules, including cUMP, cCMP, and N7-cADPR The first viral sponges to inhibit Pycsar and type IV Thoeris Congrats to talented leading author Romi Hadary! Read her thread to learn more about our findings

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

It was a great pleasure to contribute to this work by Jemma Fendley, @mmolari.bsky.social, and Boris Shraiman on pan-genomes, linkage, and recombination in phage genomes. We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org. [1/6] www.biorxiv.org/content/10.1...

RFdiffusion2 is now live! github.com/RosettaCommo... You can now design proteins, and in particular enzymes from just partially defined amino acid side chains, and without defining their sequence position or order!

A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti- #phage defense www.cell.com/molecular-ce... #bacteriophage #MicroSky

😮 Cool work from Sylvain Moineau #phage #phagesky www.nature.com/articles/s41...

Really cool link between tRNA copy number and bacterial cell wall 🦠 #rnasky #microsky academic.oup.com/nar/article/...

Preprint: “Structural modeling reveals viral proteins that manipulate host immune signaling” Using AI-guided structural modeling, we find new families of viral proteins that sequester or cleave host immune signaling molecules Congrats Nitzan Tal! www.biorxiv.org/content/10.1...

When I was offered the position of Director of NIGMS in 2003, I had a range of experiences as an applicant, a grantee, and a study section member (and chair), but actually knew relatively little about how NIH operated. 1/n

Happy to be part of this fascinating project studying why some mutant mtDNA in baker's yeast outcompete wt mtDNA journals.plos.org/plosgenetics...

New preprint: Modeling protein expression with explicit tRNA dynamics. We find that there's an optimum level of codon usage bias that maximizes expression. We also find charged rare tRNAs get fully depleted in late-stage bacteriophage T7 infection. www.biorxiv.org/content/10.1...

Happy to be part of this effort to understand evolution of gene order in prokaryotic genomes. For different groups of closely related genomes (ATGCs) genome rearrangement to gene flux ratio in order of 0.1 pointing to the tremendous role of gene gain/loss www.pnas.org/doi/10.1073/...

Breaking news: Staff at the National Institutes of Health have issued a declaration calling on their director to depoliticize the agency and reverse spending cuts.

www.nature.com/articles/s41... Herring forgot how to migrate

We're thrilled to share the published version of our DRT9 story, online today @nature.com! Congratulations to all authors! www.nature.com/articles/s41...

Cool work by Sanasar investigating how bacteria-phage dynamics affect the distribution of antiphage defense systems in the genome www.biorxiv.org/content/10.1...

New manuscript out in @asm.org MRA! We develop a new R package called methylMapR to characterize the prokaryotic functional methylome from long read PacBio data. journals.asm.org/eprint/SNT8I... Check it out and do give the package a try! github.com/therealtotod...

Excited to share our latest from my postdoc at @mskcancercenter.bsky.social in the Sfeir Lab, in collaboration with the Simon Powell Lab! We uncovered a novel genome repair mechanism in human cells: RNA-templated DNA double-strand break repair (RT-DSBR). (1/5)

New paper @isme-microbes.bsky.social : Among a sample of 1044 vibrio phages, we found 17 new Schizotequatrovirus with large genomes (>250kb), a broad host range, and yet a low frequency in our samples (?!). #MicroSky #PhageSky

Really excited to share this story from Jake in the lab! We have found bacterial protein toxins that can enter Gram positive bacterial cells without the need for a receptor resulting in broad spectrum antibacterial activity.

Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released! (Most credit to Minh Bui and @roblanfear.bsky.social and their labs) ecoevorxiv.org/repository/v...

Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social: rdcu.be/eg4OA 1/

Almost all grant-review meetings under Trump 2.0 remain suspended at the US National Institutes of Health (NIH), preventing the world’s largest public funder of biomedical research from spending much of its US$47 billion annual budget. https://go.nature.com/4gM6oW4

this website from the House Democrats on the Science, Space, and Technology Committee is surveying the impact of the Administration’s mass firings of federal employees from science agencies—share with friends you know have been affected

An absolute must-read from @katherinejwu.com on the rapid destruction of American science: www.theatlantic.com/health/archi...

Our best wishes go out to all the amazing NIH people who were removed. We see your service and your good work. We will do whatever we can to fight. Take care of yourself and then when you’re ready, jump back in the fray. 💕 1/

Musk? Trump? Who Exactly Is Running the Federal Government? www.nytimes.com/2025/02/05/o...

The NYT asked me to write an op-ed on Musk and the Treasury and then took a pass. I hope it will still get read.

This is a threat to take seriously. "One of the United States’ leading funders of science and engineering research is planning to lay off between a quarter and a half of its staff in the next two months, a top National Science Foundation official said Tuesday." www.politico.com/news/2025/02...

Yes, I am mad. This is a start, more to come. Longer format to engage with what's happening & provide context to those in/out of science about what's at stake for science and society. substack.com/inbox/post/1...

We interrupt your regularly-scheduled chaos to bring you some cool microbiome science. 🦠 🖥️ 🧬 "Longitudinal phage–bacteria dynamics in the early life gut microbiome" now out in Nature Microbiology. We wanted a way to measure bacteria and phage in metagenomes 1/ www.nature.com/articles/s41...

Happy to see our paper out @ Nat Comm We discovered a bacterial NLR-like pattern recognition receptor that can sense 3 different viral proteins as a signature for infection. This explains its broad defense against different phage families Congrats Nathalie Béchon! www.nature.com/articles/s41...

Should've done this a long time ago, but here's my first post on #Bluesky. Check out my postdoc paper on a bacterial ubiquitin-like defense system that we recently published! www.nature.com/articles/s41...

To celebrate all these new arrivals on BlueSky, did you see this recent preprint on the role of amyloïd in anti-phage defense? Molecular characterization of amyloid as signal transduction in E. coli phage defense, with super cool links wt fungi controlled cell death! www.biorxiv.org/content/10.1...

A collection of researchers working on bacterial defense and offense systems, including secretion systems, immunity mechanisms, bacterial warfare, and microbial arms races. Please share and let me know if you'd like to be added (or removed) from the list.