Major #Botany2026 FOMO, but the drive MA->OR starts this week. So, sharing from afar: I’m recruiting grad students for my new lab at OSU! Info: www.mckenzie-lab.org . We're going to have FUN with systematics, speciation genomics, methods, natural history, and more in North Am angiosperms. Reach out!

Just posted: a group paper describing major updates to my software pixy, for population genetic summary statistics. www.biorxiv.org/content/10.6... New since 2021: arbitrary ploidy, multiallelic sites, missingness-aware Watterson's θ and Tajima's D, Hudson's FST, multicore execution!

Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ

Diverse bacterial pattern recognition receptors sense the core phage proteome - Nature

Systematic analysis of prokaryotic STAND NTPases — relatives of animal and plant immune receptors — uncovers diverse antiviral sensors that detect most of the core structural and replicative proteins of bacteriophages.

go.nature.com

cnsplots: Publication-Ready Scientific Plots for Cell, Nature, and Science Journals github.com/faridrashidi... really cool work here from a postdoc at NIH.

GitHub - faridrashidi/cnsplots: 🎨 Toolkit for generating publication-quality plots for Cell, Nature and Science journals

🎨 Toolkit for generating publication-quality plots for Cell, Nature and Science journals - faridrashidi/cnsplots

github.com

We just published: Why you should sequence your plasmids (and how to do it for free) Through @GetGenome scientists in 100 countries can access free whole-plasmid sequencing —giving researchers the confidence to move their experiments forward. medium.com/p/why-you-sh...

Why you should sequence your plasmids (and how to do it for free)

Through GetGenome, scientists in 100 countries can access free whole-plasmid sequencing — removing barriers, improving quality control…

medium.com

Oregon State University's Department of Integrative Biology is currently hiring up to three tenure-track faculty members, with an emphasis on organismal biology. Note: Previous links are no longer active due to a change in our hiring system. oregonstate.wd501.myworkdayjobs.com/OSU_Careers_...

Assistant Professor

Department: Special Instructions to Applicants: To ensure full consideration, applications must be received by 10/1/26. Applications will continue to be accepted after the full consideration date, unt...

oregonstate.wd501.myworkdayjobs.com

Our paper out in Science today: The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell Congratulations @ostermanilya.bsky.social and co-authors!

Bacteria sense virus-induced genome degradation via methylated mononucleotides

Phages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...

science.org

Osterman Ilya@ostermanilya.bsky.social · 4w ago

Excited to share that our Metis story is now published in Science! 🎉 Bacteria can sense phage-induced degradation of their genome and activate immunity. Many thanks to everyone who contributed to this work. 📄 www.science.org/doi/10.1126/... More details in my earlier thread 🧵⬇️

#microsky New preprint from the lab! Widespread immune systems protect bacteria against conjugative plasmids www.biorxiv.org/content/10.6... Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab. 🧵⬇️

Widespread immune systems protect bacteria against conjugative plasmids

Conjugative plasmids are a class of mobile genetic elements capable of efficient transfer between bacterial cells. Although they can introduce beneficial traits such as antibiotic resistance to recipi...

biorxiv.org

We’re happy to introduce phageFACTor (Functional Annotation and Curation Tool) 👩‍💻Developed by Tanaïs Moreau, our most recent PhD candidate, and building on Phold, we were able to improve annotation of prophage genes by as much as 50% 🧬 You should check it out github.com/TMs-code/pha...

Mary-Dell Chilton died today. She should have won a Nobel for creating modern plant bioengineering. youtube.com/watch?v=AXc9677PvEA

Moments of Discovery: The Mary-Dell Chilton Story

YouTube video by National Inventors Hall of Fame - NIHF

youtube.com

So I'm finally thoroughly parsing through this preprint from @bjesseshapiro.bsky.social & Patrick Lypaczewski where they homebrewed targeted ONT library prep, and it's even more brilliant than at first glance. Plus they've been so generous in answering my questions. www.biorxiv.org/content/10.6...

🤯

Gc Rox@gcrox.bsky.social · last mo.

Are restriction/modification modules only used for host defense? @selmamhm.bsky.social shows an alternative use. "Restriction-modification systems are required for Neisseria gonorrhoeae pilin antigenic variation" www.pnas.org/doi/10.1073/pnas.2602688123 #Microd #Microsky. #Microbiology

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

Our paper on the YprA family of helicases and their roles in bacterial defence is now out! We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs www.sciencedirect.com/science/arti...

YprA-family helicases provide the missing link between diverse prokaryotic immune systems

Bacteria and archaea possess an enormous variety of antiviral immune systems that often share homologous proteins and domains. YprA-family helicases a…

sciencedirect.com

Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity @natmicrobiol.nature.com from Michael Laub & Abel Garcia-Pino www.nature.com/articles/s41...

Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity - Nature Microbiology

The activation of an antiphage defence system relies on host factors targeted by phages, a mechanism analogous to the way that eukaryotic innate immune systems detect pathogen-induced perturbations of...

nature.com

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!

The Royal Society@royalsociety.org · 2mo ago

Professor Joe Felsenstein FRS is elected a Fellow of the Royal Society. After initially working on population genetics theory of recombination, of migration, and of speciation, his main focus has been on phylogenetic inference. #RSFellows https://royalsociety.org/people/joseph-felsenstein-38106/

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

Molecular mimicry of a pathogen virulence target by a plant immune receptor

Plants and animals respond to pathogen attack by mounting innate immune responses that require intracellular nucleotide-binding leucine-rich repeat (NLR) proteins. These immune receptors detect pathog...

science.org

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/...

DefensePredictor: A machine learning model to discover prokaryotic immune systems

Antiphage defense systems protect bacteria from viral infection and have inspired important biotechnologies such as CRISPR-Cas9 while also revealing the evolutionary roots of eukaryotic innate immunit...

science.org

Nature@nature.com · 4mo ago

Bacteria have been fighting off viruses using a huge arsenal of molecular weaponry that scientists did not know about — until now. Researchers have identified proteins that could lead to virus-fighting drugs and technologies. go.nature.com/4dqQnXI

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

Transposable elements hitchhike on Starships across fungal genomes - Nature Communications

Large mobile genetic elements known as Starships act as vehicles for transferring transposable elements (TEs) between fungi. Here, Griem-Krey et al. show that these ‘hitchhiking’ TEs can drive rapid e...

nature.com

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...

Shu-Sin Chng@figlegend.bsky.social · last yr.

Extremely proud of newly minted PhD Dr Nur Liyana bte Ayub Ow Yong for her work in our lab! Some new science coming soon so stay tuned! 🎉🎉

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 ☄️

A complete set of canonical nucleobases in the carbonaceous asteroid (162173) Ryugu - Nature Astronomy

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

dlvr.it

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

Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation - Nature Microbiology

Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.

nature.com

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.

Ian Bogost@ibogost.com · 5mo ago

Is this bad

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. 🧵

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 6mo ago

Plasmids weaponize conjugation to eliminate non-permissive recipients https://www.biorxiv.org/content/10.64898/2026.02.10.705089v1