We are excited to release the BAT!🦇🚨 We've used this phylogenetic analysis pipeline in our lab for years, and grad Ben Sheppard now presents a Github release and preprint. I run BAT analyses almost daily. It makes exploring gene families routine, customizable, and fun🧵

From bioRxiv: Common genomic selection benchmarks may overstate breeding gains, prompting calls for more realistic evaluation methods in crop improvement. (Daniel E Runcie) ▶️ www.biorxiv.org/content/10.6... #PLantScience #PlantBreeding

Excited to share new work from us in the @spicybotrytis.bsky.social lab on Botrytis-legume co-transcriptomics. Similar disease phenotypes between your hosts could be masking a ton of underlying transcriptional plasticity 🌱💥 academic.oup.com/g3journal/ad...

Interesting tidbit of pangenome variation. Showing something works in one individual each in two distantly related species doesn’t mean it is highly conserved across all individuals or even most species in between those two.

Only took a couple of months but the brothers are besties now.

Gotta love all the canvas jokes when students out there are wondering if they will be allowed to graduate. Yes it’s a $&$& show but damn, this is a $&$& show that could mess up students majorly. Solve the immediate crisis then go after the long term problem.

In todays my brain is shot from 10,000 words after editing 30 writing assignments. Broad integrative research for a lab isn't the wise path. Wiser is a focused contributor to integrative research. Easy categorization facilitates understanding, or comfort therein, of the lab.

You gotta love the arguments that science (side note NIH is not a synonym for science) has lost the track on risky research and how do we reform science. But this never discusses the required reformation of politics/society discussions as risky science is the easiest to attack as a waste of money.

🌱 From The Plant Cell: Identifying an aberrant RNA trigger reveals why some engineered genes shut down, guiding design of more stable traits in crops. (Richard Michelmore , Blake C Meyers) ▶️ academic.oup.com/plcell/artic... #PlantScience #PlantBiology

congrats to José Alonso for this prestigious accomplishment and great honor supported by your colleagues! @alonsostepanovalab.bsky.social cals.ncsu.edu/news/nc-stat...

Over the moon for @jrossibarra.bsky.social ! A great scientist, colleague, and friend. Still terrible puns though.

Hiring at IPB Halle! Department Head & Director – Chemistry of Natural Products and Bioactives. Exceptional position with outstanding support & research environment. Apply now by April 24, 2026!-> berufungsportal.uni-halle.de #NaturalProductChemistry #AcademicJobs #IPB #PlantScience

Hey #MPMI crowd, we are having trouble finding co-proteome papers looking into the host and pathogen proteome at the same time. I know they must exist but can’t find them. Any suggestions?

Another paper hot off the press! We profiled protein abundance, acetylation, and phosphorylation in rice infected with Magnaporthe oryzae. Awesome work led by @pri-auler.bsky.social. It was great hosting her in my lab for a year long post-doc internship!!! onlinelibrary.wiley.com/doi/10.1111/...

It is that time of the year when the @ipbhalle.bsky.social puts together an excellent lineup for speakers for our Plant Biochemistry Symposium. This time the symposium reflects Steffen Abel’s scientific interests as we celebrate his time at the IPB

The NSF BIO Plant Biology Act (H.R.7949) would strengthen investments in plant and microbial research—helping drive innovation and protect U.S. agriculture. Learn why it matters and how to take action 👉 buff.ly/xRu6Eqz #PlantScience #SciencePolicy

The brothers get along. The little one is 10 months and the big one is six years.

In the argument about AI, fundamentals and enabling creativity in education, I keep thinking back to art museums. What has always stunned me about impressionists and cubists is not how they created entirely new styles. It is their early works showing how phenomenal their fundamental skills were.

We are hiring! We’re excited to recruit a postdoc to our lab at UC Davis to work on plant immune engineering and single-cell analyses of plant pathogen interactions. Apply by June 1. Please repost. www.coakerlab.org/postdoctoral...

Gitta is an excellent scientist and mentor 🤩

Three Botrytis/Eudicot papers accepted. A reevaluation point on a question about generalism started with @katherinedenby.bsky.social 's sabbatical 24 years ago. Continued by a broad team of undergrads to post-docs including @annajomu.bsky.social @ccaseys.bsky.social and more not on bsky.

I have a feeling a lot of scientists need a intro genetics refresher.

One can easily predict 75-90% of the genes for a known specialized metabolite pathway in a new species with just phylogeny and co-expression. No machine learning needed. And no synteny needed. The problem is the edge cases of brand new genes that don’t coexpress. The Achilles of machine learning.

Full version available now of our new pennycress paper at @newphyt.bsky.social - great working with @stairwaytokevin.bsky.social, @spicybotrytis.bsky.social, @jotlovell.bsky.social, et al. Come for the pretty pictures, stay for the cool science! nph.onlinelibrary.wiley.com/doi/epdf/10....

Was not Andrew. IIRC, was Herman Höfte representing the Versailles groups and it wasn't on the schedule at Arabidopsis 1993 in Columbus OH. The talk was given on an overhead projector via transparencies. Bechtold et al 1993 was the sea change. This meeting was off the hook . 1/n

Community resource: Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome Bird, et al. nph.onlinelibrary.wiley.com/doi/10.1111/... #PlantScience

It was a total delight to work with this team and be involved with this project! And we found such cool results!

Passed puppies.

Out now in @newphyt.bsky.social with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social & more! Our high-quality pennycress pangenome is a striking example of genome architecture shaping different kinds of genomic variation, including some surprising centromeric movement

We also used this as an opportunity to look at the evolution of immunity gene clusters (NLRs) at a higher level across species and show that the well-documented turnover of these genes is juxtaposed against positional conservation across species. The clusters are the same but the players change

Dad, What is for rainy day breakfast?

It is kind of interesting how AI pushes in Biology and other areas largely ignore information content theory or statistical ideas of independence.

The annual rodent patrol service in exchange for nesting platform payment is back. We are still having discussions on snakes.

Thoughts on this theoretical. Create an artificial standard with no evidential support and is technically impossible to exclude a large body of work that directly implicates the novelty of a related body of work.

So jazzed for my colleague @gittacoaker.bsky.social for being elected as an AAAS Fellow! She's an outstanding scientist, leader, mentor, and colleague

The baby is trying to be an equine influencer with his photo shoots.

My major conclusion from plant pangenomes papers is that there is a ton of gene loss at all levels of the phylogenies. This leads to the smaller conclusion that proving horizontal gene transfer versus unusual gene retention in the face of massive losses will be a major problem.

What if a super successful fungal plant pathogen has little evidence of structural variation, horizontal gene transfer or their ilk? It’s just a nice Mendelian meiosis and inheritance, etc. does that make it the odd one?

In random asides to ignore: The GO term glucosinolate (terpene, etc) is a generic grouping that does not group by mechanism, regulation or function. It mainly groups by a chemical moiety within a diverse set of compounds. So better to not make mechanistic, regulatory or functional ideas from it.

What if our assumption that regulatory networks are highly conserved is wrong? And every accession, individual, subspecies, etc does things very differently using the same tools?

By studying how a switch on the wall works, how much do we learn about how a light bulb creates light? In todays issue of random thoughts while cleaning horse stalls.

Things are so weird that I am seeing the same people that once said “glucosinolates are so limited that nothing about them has any generalizable insight and shouldn’t be funded”, now say “glucosinolates are so well studied we should use the info to train AI to predict other systems”.

Anyone else think it is possible for a paper to be too mechanistic?

Anyone know of the word for things like fitness, flowering, growth, quantitative disease resistance, etc. that are actually not singular things but instead grouping terms that encompass diverse mechanisms and phenomena, misleading that they are a singular entity?

We really need to come up with a way to better name genes across species. Using the Arabidopsis name, e.g. MYC2, in something like Cymbidium is basically never true as there are so few true 1:1 orthologues across plants.

Check out our new preprint by @octaviarmn.bsky.social and @liobarueger.bsky.social in collaboration with @meikeburow.bsky.social - we investigate the spatial effect of glucosinolates on root microbiomes in Arabidopsis and Camelina! www.biorxiv.org/cgi/content/... lots of cool stuff!

Have you ever wondered 🤔... Does phenotypic variance respond to environmental perturbation? Does it have a genetic basis? Are mean and variance regulating loci exposed to different selection pressures? These and more questions are explored in our new preprint 🔥 www.biorxiv.org/content/10.6...

Did you know that most knockouts in Arabidopsis actually do have phenotypes and aren't some redundancy situation? All you have to do is measure in multiple tissues in multiple environments and then the phenotypes show up. Redundancy was an assumption never tested.

Any inklings if ChatGPT is being used by prospective students to assess which faculty are best at a given university? Wondering if integrated scientists are punished by ChatGPT algorithms as those algorithms likely direct focus to specialists in defined field rather than generalists across fields.

Happy valentines a couple of days early.