There are few researchers for whom an entire field is so clearly distinct before and after their work. The gap between evolutionary biology "before Joe" and "after Joe" is just awesome. It is a measurably different enterprise, and the reach of his influence doesn't end at the phylogeny. Hats off!

Molecular mimicry of a pathogen virulence target by a plant immune receptor | Science www.science.org/doi/10.1126/...

I’m starting at Oregon State University this September as Herbarium Director and Assistant Professor in the Department of Botany and Plant Pathology. An absolute dream job and I am so grateful! Looking to grow the lab soon and will update here. In the meantime please don’t hesitate to reach out!

The two papers: www.science.org/doi/10.1126/... and www.science.org/doi/10.1126/...

Weisberg Lab PhD student Boluwatife Giwa presented her research on Botrytis genomics at the 2026 APS Pacific Division Meeting and was awarded the 1st place poster award and a travel award. Congrats!

Now out! We show that TEs can be horizontally transferred between fungal species via Starships. Once transferred, these TEs can become active, changing the genome organization and affecting the lifestyle of the recipient fungus. www.nature.com/articles/s41... @oggenfussursula.bsky.social #TEsky

Hi all. I am very excited that after 6 years I finally got my phylogenetic comparative methods book and online exercises online. Feel free to use and share. The book is here: nhcooper123.github.io/pcm-primer/. Note that it is not finished, we had to abandon it before the sunk costs fallacy broke us

Here is it! Super new science from us on horizontal gene transfer & bact defense systems! Liyana OW YONG discovered the first-of-its-kind defense factor AbjA that triggers 'abortive conjugation' as a defense mechanism, by targeting the T4SS! How neat?! #MicroSky 1/7 www.biorxiv.org/content/10.6...

Samples returned from the asteroid Ryugu contain all five canonical nucleobases (A, G, C, T, U). Their presence in Ryugu and Bennu supports the hypothesis that carbonaceous asteroids contributed to the prebiotic chemical inventory of early Earth. http://dlvr.it/TRWtVp ☄️

Final version of our last paper is out! www.nature.com/articles/s41...

Effector-triggered stomatal immunity prevents leaf invasion by bacterial pathogens https://www.biorxiv.org/content/10.64898/2026.03.09.710543v1

What this technology is going to do is not end higher education, but it is going to undo so much of the baseline work on accessibility by pushing overworked professors to take things back to offline modalities, in person timed exams, keeping tech out of the classroom, etc.

Koonin's lab in NIH is looking for postdocs. If you know someone who is interested, please spread the word. The details about the position are below: www.training.nih.gov/jobs/pdf-ecb...

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. 🧵

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

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...

USDA postdoctoral fellowships are open. If you’re interested in writing a postdoc fellowship with me in plant immunity, spatial defense, or vector-borne disease, please reach out. (US citizens, nationals, permanent residents only; PhD awarded Jan 2023–Jan 2027.) www.nifa.usda.gov/grants/progr...

www.pnas.org/doi/10.1073/... Excited to share that PNAS published our research article focused on "Why are Ralstonia goofy?"

This position is still open. The Weisberg lab is recruiting a postdoc or Ph.D. student to study horizontal gene transfer in plant-associated microbial communities. Please see the job ad for more information and feel free to contact me if you have any questions!

Lizards have evolved their own version of rock-paper-scissors. Here's my story on the genetics behind nature's games. Gift link: nyti.ms/493KGMI

After years of struggling with how to cryopreserve one of our endosymbiotic bacteria, we found something that worked! 🦠☃️ We crowd-sourced suggestions and then @ruthwright.bsky.social tried the most common ones (like 🥛...). Want to do the same? Here is how we did it: www.biorxiv.org/content/10.6...

Thrilled to have our paper out in @science.org. Cell division guides plant cell wall formation. Does the reverse hold? We show that bimodal pectin methylesterification, via PME5 mRNA nuclear sequestration, influences plant cell division and cell plate orientation. www.science.org/doi/10.1126/...

"Common principles of immune receptor channels..." #ThingsThatMakeYouGoHmm 🤔 www.nature.com/articles/s41...

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

How does the arms race between #bacterial defense systems and mobile genetic elements contribute to #microbiome community structure? Read below for an insightful exploration of this issue! It will not disappoint @plosbiology.org 🧪 #bacteria #immune #phage #ecology

I taught (and co-taught) a course on human population genetics from 2000-2024. Having retired, I'm now making all the course materials public: github.com/alanrogers/p... #popgen #evbio

New preprint: 🚀🧬 Starship in the genome of the lichen fungus Xanthoria. Discovery of giant transposons Starships challenged what we thought we knew about fungal genomes. But what about Starships in #lichen fungi? Let us present Tangerine! 🖥️ 🧪 🦠 🧫 #SymbioSky doi.org/10.1101/2025...

Cellular energy sensor SnRK1 suppresses salicylic acid–dependent and –independent defenses and bacterial resistance in Arabidopsis www.pnas.org/doi/abs/10.1...

🧬🛡️How are new immune mechanisms created? We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org. 👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors! doi.org/10.1073/pnas...

I tried an even harder example on Gemini Pro image generation and this is quite scary/amazing. I asked for a microscopy image of around 20 HeLa cells, GFP tagged 20% nuclear, 10% membrane, +1 nuclear staining, + overlap. Image below and prompt in the following post.

Our new collaborative work led by @taliamycota.bsky.social Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social and collaborators: @plantricia.bsky.social et al. tinyurl.com/5yx2wmz5 (1/n)

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/...

I’ve released a tool to sketch and edit phylogenetic trees! yawak.jp/PhyloWeaver/ Load a Newick file and intuitively add/remove/resize branches. Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.

gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats

Our manuscript comparing Nanopore vs. Illumina reads for population-level variant calling and genotyping is now out: journals.asm.org/doi/10.1128/... . This work was led by Andrea Schiffer and @arftrhmn.bsky.social.

How do GWAS and rare variant burden tests rank gene signals? In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck! 🧬🧪🧵 www.nature.com/articles/s41...

The 5th of 6 faculty positions in UNC Biology is posted. We're working with the @ncbg.bsky.social to fill a joint position as Director of the UNC Herbarium at @ncbg.bsky.social and as Associate Professor within the Department of Biology (BIOL). Please share 1/n unc.peopleadmin.com/postings/308...

Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils www.biorxiv.org/content/10.1... #jcampubs

@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/...

If you admix barcodes in your Illumina library, use Demulticoder: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes | Phytopathology® apsjournals.apsnet.org/doi/10.1094/...

A one-of-a-kind repeated natural experiment. Population Genomic Analysis of Two Independent Clonal Invasions of the Sudden Oak Death Pathogen into One Forest | Phytopathology® apsjournals.apsnet.org/doi/10.1094/...

New paper with my (amazing) friend and mentor @jrpenades.bsky.social Really looking forward to see what plasmid aficionados think of this one!! With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others www.cell.com/cell-reports...

Still a couple of formatting things that need fixing (this is a "pre-proof") but our genomes paper is now available online! www.sciencedirect.com/science/arti... Really happy to see it out there, I hope people find it useful/interesting!

job alert: UC Davis is looking to hire a 9 month tenure-track Assistant Professor of Mycology in the Department of Plant Pathology. More details below, for full consideration submit by 1 December 2025 recruit.ucdavis.edu/JPF07339

This is first paper from a new line of research in my lab, with more to come soon. If interested in PDPs I highly recommend this @baym.lol paper www.nature.com/articles/s41... and this classic from Matti Jalasvuori royalsocietypublishing.org/doi/10.1098/...

UNC Chapel Hill is hiring an Assistant Professor in Plant Molecular Biology. Per Jeff Dangl MPMI candidates are also highly desired in the search. unc.peopleadmin.com/postings/307...

Here’s published version of our manuscript using GWAS to investigate tailocin sensitivity in Pseudomonas syringae. TL:DR pretty clear LPS is tailocin receptor but also that P.syringae often completely swaps out its entire O antigen biosynth pathway w/ recombination academic.oup.com/g3journal/ad...

Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58 | Science Advances www.science.org/doi/10.1126/...

Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...