Work I co-led with @jnoms.bsky.social is now online at @cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity. www.sciencedirect.com/science/arti...

Protein domains have no single definition, so why stick to one segmentation? 🧩 Instead of forcing structures into rigid classifications, we built AFragmenter. It uses AlphaFold PAE networks for a tuneable approach to domain parsing. You control the granularity. 👇 🔗 doi.org/10.1093/bioi...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

Happy to be part of this tremendous effort lead by @fnobrega.bsky.social to build a community-driven collection of Klebsiella strains & phages. Keep an eye on the Felixviridae, these phages are wild and seem to swap huge genome segments with ease 👀🧬

I've done a lot of work in Python this fall, and it hasn't endeared me to the language at all. Why does stuff have to be so complicated when you're doing it in Python? blog.genesmindsmachines.com/p/python-is-...

Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n) www.biorxiv.org/content/10.1...

Gluing a bulky host protein onto an immune surveillance complex is a wild mechanism of viral immune evasion! @natmicrobiol.nature.com #phagesky #phage #microsky www.nature.com/articles/s41...

Two days left to apply for a PhD or postdoc position in my lab!

Here is the full letter: collections.nlm.nih.gov/catalog/nlm:...

Last year it was discovered that a single bacterial NLR-like protein can recognize multiple, structurally unrelated phage proteins (Béchon et al, Kibby et al) Now, a new study shows the same for a plant NLR. Another example how principles of immunity remain conserved from bacteria to eukaryotes

New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester) #phagesky#microsky www.biorxiv.org/content/10.1...

@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎 www.pnas.org/doi/10.1073/...

Are you interested in studying RNA phages? We are looking for a PhD student and a postdoc to join the lab! For more information and how to apply, see below 👇 Please RT!

BREAKING: Friday night massacre underway at CDC. Doznes of "disease detectives," high-level scientists, entire Washington staff and editors of the MMWR (Morbidity and Mortality Weekly Report) have all been RIFed and received the following notice:

Thoughtful and well-informed op-ed from @ianlmorgan.bsky.social Definitely worth a read! www.the-scientist.com/nih-leadersh... 1/2

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/