iiinova — where your digital self keeps evolving

Reposted by Donat Wulf

bioRxiv Plant Bio @biorxiv-plants.bsky.social · 24/09/2026

A comprehensive Arabidopsis transcription factor binding atlas reveals pervasive positional and syntactic organization of their DNA binding www.biorxiv.org/content/10.64898/20…

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bioRxivpreprint @biorxivpreprint.bsky.social · 23/09/2026

Transcription factors read a second regulatory code in chromatin www.biorxiv.org/content/10.64898/20…

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Nature Plants @natplants.nature.com · 08/09/2026

New Brief Communication: "Cell-based CRISPRa screen identifies a papillae-specific receptor kinase mediating broad-spectrum fungal resistance in rice" rdcu.be/ZZFv8dTuRi8a A RK that positively regulates fungal resistance via silicon-mediated physical & biochemical defences. #PlantScience

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Stowers Institute @stowersinstitute.bsky.social · 08/09/2026

The Stowers Institute partnered with Google DeepMind on AlphaGenome Atlas, a new AI-powered resource mapping predictions for 9+ billion possible single-letter DNA changes. 🧬 Stowers’ @juliazeitlinger.bsky.social Ph.D., helped guide its development and demonstrate its potential. bit.ly/4r4Bn6C

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KWS Group @kwsgroup.bsky.social · 27/07/2026

Job opportunity! 🌱 At KWS Einbeck (Germany), we have an exciting opening for a Group Lead for Molecular Trait Analysis & Genomics. 👉 Read more & apply online: jobs.kws.com/job/Einbeck-...

jobs.kws.com

Group Lead (m/f/d) for Molecular Trait Analysis and Genomics

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Joris Sprakel @jorissprakel.bsky.social · 25/07/2026

How do transcription factors bind DNA strongly, and in a switch like manner, while remaining sequence specific? Our new paper on a canonical plant TF suggests the answer is a previously underappreciated assembly state: transcription factor nanoclusters. www.science.org/doi/10.1126/...

science.org

Nanoclustering of a plant transcription factor enables strong yet specific DNA binding

Transcription factor nanoclusters balance the DNA binding trade-off between weakly binding oligomers and nonspecific condensates.

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Reposted by Donat Wulf

Alejandro Montenegro @aemonten.bsky.social · 26/05/2026

"(...) plasmids are chromatinized in an organized, sequence-dependent manner and adopt a heterogeneous and incomplete chromatin architecture relative to nuclear-encoded chromatin fibers" www.cell.com/molecular-ce...

cell.com

Chromatin architectures underlying plasmid-based assays for regulatory variant effects

Mallory et al. develop plasmid Fiber-seq to map chromatin architecture along individual transfected plasmids at near-nucleotide resolution, which reveals that plasmids adopt heterogeneous chromatin pa...

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Reposted by Donat Wulf

Darius Kosmützky @dariuskos.bsky.social · 31/03/2026

🚨 New Preprint! 🚨 For my PhD, I investigated an over 20-year-old mystery in photosynthesis: What does the highly conserved but enigmatic protein cytochrome c6A actually do? We found: c6A helps algae stayin' alive in the "DISCO". 🪩 See the thread below & read the preprint: doi.org/10.64898/202...

Algae in the DISCO! (AI generated image before it was cringy to do that)

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Kaisa Kajala @kaisakajala.bsky.social · 26/03/2026

I am excited to announce that we have two open positions on our recently funded MYBstery M-WEAVE (NWO-DFG) project! 1) Postdoc in my team at Utrecht University (NL). www.uu.nl/en/organisat... 2) PhD in the team of @lauraragni.bsky.social at University of Freiburg (DE). (See thread)

Ad banner: germinating plant, Utrecht University, VACANCY: Postdoc position in Experimental & Computational Plant Biology

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Carolin Delker @carolindelker.bsky.social · 17/03/2026

Very nice talk from Sanja Zenker (Bielefeld university) on the dissection of specificities in transriptional Regulation!

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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 02/03/2026

Pangenomes, really? Most early “pangenomes” = oligogenomes (oligo, Gr., few). More recent “pangenomes” generally = poligenomes (polis, Gr., many). True pangenomes (pas, Gr., every/all) would be rare indeed. 🙏🏼 @zbao.bsky.social for pointing out his review. www.nature.com/articles/s41...

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Jürgen Knauer @juergenknauer.bsky.social · 24/02/2026

🚨Two fully funded PhD opportunities in Australia! Improving C4 photosynthesis in vegetation models. Supervised by Dani Way (ANU, Canberra) and myself (UTS, Sydney). 1. Lab- and field-based project at ANU – see flyer below 2. Modelling project at UTS – www.findaphd.com/phds/project...

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Rüdiger Simon @simonrdg.bsky.social · 18/02/2026

CEPLAS starts a number of new projects, and we are looking for 12 Postdocs ❗ CEPLAS projects are always highly collaborative, that means postdocs working with us will always closely interact with several CEPLAS research groups. Find all postdoc openings here: www.ceplas.eu/en/training-...

ceplas.eu

CEPLAS: Call 2026

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Reposted by Donat Wulf

Félix de Carpentier @fdecarpentier.bsky.social · 15/02/2026

I'm super happy to share my new preprint reporting a study in collaboration with the Seebeck (Basel) and Sasso (Leipzig) labs: www.biorxiv.org/content/10.6... We discovered that ovothiol A, a thiohistidine, is a major antioxidant in the green alga Chlamydomonas. (1/4)

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Etienne Bacher @etiennebacher.bsky.social · 12/02/2026

#rstats tidypolars 0.17.0 is available! tidypolars provides the tidyverse syntax while using polars for better perf. In this release: - support new functions from dplyr 1.2.0 (filter_out, when_any...) - pivot_wider with lazyframe - bug fixes and more News: tidypolars.etiennebacher.com/news/

tidypolars.etiennebacher.com

Changelog

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Reposted by Donat Wulf

Ronan @omalley-regulome.bsky.social · 10/02/2026

New preprint! The same TFs can drive distinct regulatory programs depending on where they bind.  TSS → rapid stress responses  Intronic & upstream → cell-type programs  Enhancer-like CRMs → embryo/meristem programs  Coding-sequence binding → repression www.biorxiv.org/content/10.6...

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Reposted by Donat Wulf

Laurie Belcher @lauriebelch.bsky.social · 29/01/2026

Calling all OrthoFinder users! We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny. GLADE runs directly on OrthoFinder results. www.biorxiv.org/content/10.6... github.com/lauriebelch/... (1/10)

biorxiv.org

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Reposted by Donat Wulf

CEPLAS - Cluster of Excellence on Plant Sciences @ceplas.bsky.social · 09/12/2025

‼️Please RT: The CEPLAS Graduate School call for 2026 is now open! Detailed info on our website: bit.ly/4q19JWk @hhu.de @unicologne.bsky.social @mpipz.bsky.social @fz-juelich.de @leibnizipk.bsky.social @plantsciencedbg.bsky.social

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Reposted by Donat Wulf

bioRxiv Plant Bio @biorxiv-plants.bsky.social · 20/11/2025

PlantCV v4: Image analysis software for high-throughput plant phenotyping www.biorxiv.org/content/10.1101/202…

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Reposted by Donat Wulf

Rory Craig @rorycraig.bsky.social · 29/10/2025

Excited to introduce Auxenochlorella as a new algal reference organism for fundamental plant science and bioengineering. A paper in two parts: a genetic toolkit for site-specific genomic manipulation, paired with the most unusual genome I’ve ever worked on academic.oup.com/plcell/artic...

academic.oup.com

Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella

Auxenochlorella, green algae shaped by evolutionary forces acting on vegetative diploids, are amenable to discovery research and bioengineering via efficie

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Reposted by Donat Wulf

Ubadah Sabbagh @ubadahsabbagh.com · 23/10/2025

PSA: Many of you may have noticed a website floating around called formatmypaper(dot)com. People rightly noted something was fishy. I dig into what happened here: open.substack.com/pub/ubadah/p...

open.substack.com

Beware giving this site your unpublished data

Users noticed the website had fake testimonials and a domain name registered seemingly overnight.

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Reposted by Donat Wulf

Ben Engel @cellarchlab.com · 12/10/2025

The KEY🔑 to regulating Rubisco phase separation in the Chlamydomonas algal pyrenoid. Beautiful work by Shan He, @mjonikas.bsky.social, and friends. #PhaseSeparation #CO2 #PlantScience 🧪 🧶🧬 🌾 🌍

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Reposted by Donat Wulf

Mark Peifer (He, him) @peiferlabunc.bsky.social · 23/09/2025

As scientists and educators, we can help our students and their families wrestle with complex issues. I just send this message to my Genetics class, and the relevant link to the study jamanetwork.com/journals/jam...

BIOL 220 Autism has known causes and tylenol use is not one of them

Dear Students

One thing we as biologists can do is help our friends and families navigate complex biomedical issues. As we'll discuss later this term, autism is a complex set of different disorders lumped under a single label. 30 years ago its causes were unknown, but as we'll see, remarkable advances in human genetics have given us key insights. We also know, based on experiment, what does NOT cause autism. Large epidemiological studies have been done to test proposed causes. Here is an gold standard example: "Acetaminophen use during pregnancy was not associated with children’s risk of autism, ADHD, or intellectual disability in sibling control analysis."

https://jamanetwork.com/journals/jama/fullarticle/2817406

Links to an external site.

We're now at the point where people with very responsible jobs are spreading lies about disease causation. It's our job to counter with facts.

Mark Peifer

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Reposted by Donat Wulf

Sebastian Soyk @sebastiansoyk.bsky.social · 17/09/2025

Our department of Plant Molecular Biology at the University of Lausanne @unil.bsky.social is recruiting a Tenure-Track Assistant Professor in the field of Plant-Organism Interactions 🌱🐛🦠🍄! Application before November 30, 2025. See the official job ad for more details: tinyurl.com/mtxdcz6p

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Reposted by Donat Wulf

Johannes Köster @johanneskoester.bsky.social · 18/09/2025

Our tool #vembrane has a new homepage, providing a high level summary of all the things you can do with it to transform VCF/BCF files via simple Python expressions: vembrane.github.io Filter, tag, annotate, sort, and flexibly convert to CSV/TSV, JSON, JSONL, YAML and FHIR via a unified syntax.

vembrane.github.io

Vembrane

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Sebastian Schornack @dromius.bsky.social · 13/09/2025

Saddened to hear about the passing of Steve Long. His work had a profound impact on plant science. A true loss to the scientific community. @ripeproject.bsky.social emails.illinois.edu/newsletter/4...

emails.illinois.edu

Stephen Long

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Reposted by Donat Wulf

Philipp Bayer @philippbayer.bsky.social · 06/09/2025

It's actually amazing how long I've been waiting for this. No more guessing which column has the querycovperc! Plus, gzipped fastas for makeblastdb! Finally!

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Reposted by Donat Wulf

Chenxin Li, PhD @chenxinli2.bsky.social · 04/09/2025

MSU is great place to do plant science research. My lab will be a great place to develop new expertise in genomics and plant molecular biology. Application instruction and link: careers.msu.edu/jobs/researc... Please email me if you have any questions.

careers.msu.edu

Research Associate-Fixed Term - East Lansing, Michigan, United States

Position Summary The Li lab in the Department of Plant Biology is recruiting a postdoctoral research associate to work on project(s) in plant molecular biology, biochemistry, and/or genomics. The idea...

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Reposted by Donat Wulf

Nature Plants @natplants.nature.com · 20/08/2025

The August issue is now fully online, with a beautiful cover that might be a nostalgia trigger for some of us (young people can find an explanation in the Editorial): www.nature.com/nplants/volu...

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Reposted by Donat Wulf

Karolina Heyduk @kheyduk.bsky.social · 19/08/2025

Our "Joshua tree is CAM" paper is finally out: nph.onlinelibrary.wiley.com/doi/10.1111/... Data collection started back in 2021, when we saw weird results in some RNAseq that made me stop and wonder if Joshua trees, long thought to be C3, were actually...CAM!

nph.onlinelibrary.wiley.com

Cryptic CAM photosynthesis in Joshua tree (Yucca brevifolia, Y. jaegeriana)

Joshua trees are long-lived perennial monocots native to the Mojave Desert in North America. Composed of two species, Yucca brevifolia and Y. jaegeriana (Asparagaceae), Joshua trees are imperiled by...

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Reposted by Donat Wulf

The Plant Cell @theplantcell.bsky.social · 01/07/2025

Small DNA elements can act as both insulators and silencers in plants (Tobias Jores , Nicholas A Mueth , Jackson Tonnies , Si Nian Char , et al) doi.org/10.1093/plce... #PlantScience

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Reposted by Donat Wulf

PlantEvolution 🌱🌾 @plantevolution.bsky.social · 02/06/2025

Beautiful tribute to Joanne Chory on @scifri.bsky.social! www.sciencefriday.com/segments/be-...

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Reposted by Donat Wulf

Plant Physiology @plantphys.bsky.social · 13/05/2025

Regulation of Crassulacean acid metabolism at the protein level in Kalanchoë laxiflora (Katharina Schiller , Saskia Janshoff , Sanja Zenker , Prisca Viehöver , James Hartwell , Jürgen Eirich , Iris Finkemeier , Andrea Bräutigam) doi.org/10.1093/plph... #PlantScience

doi.org

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Reposted by Donat Wulf

bioRxiv Plant Bio @biorxiv-plants.bsky.social · 21/04/2025

A tRNA-gRNA multiplexing system for CRISPR genome editing in Marchantia polymorpha. www.biorxiv.org/content/10.1101/202…

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Stephen Turner @stephenturner.us · 26/03/2025

polars-bio - fast, scalable and out-of-core operations on large genomic interval datasets www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/biodatageeks...

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Donat Wulf @donat.bsky.social · 05/02/2025

For all new people to bluesky. Here is the result of my PhD thesis where I compared the regulation of C3 and C4 photosynthesis in C3 and C4 grasses. Arabidopsis and Chlamydomonas were included as well.

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noam @prywes.bsky.social · 22/01/2025

Fun to see it out in print! I was really lucky to have an amazing team to work with on this. If this sort of work seems interesting to you or someone you know, please feel free to reach out (planning to staff a lab later this year). www.nature.com/articles/s41...

nature.com

A map of the rubisco biochemical landscape - Nature

A massively parallel assay developed to map the essential photosynthetic enzyme rubisco showed that non-trivial biochemical changes and improvements in CO2 affinity are possible, signposting further e...

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Stefan A. Rensing @rensingstefan.bsky.social · 14/01/2025

TAPscan v4, final verson available: dx.doi.org/10.1111/tpj.... Annotate TF families yourself or access web-UI online. Thanks to @petrollromy.bsky.social @shiltemann.bsky.social @jandevries.bsky.social @watertoland.bsky.social

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Tobias Jores @tobiasjores.bsky.social · 08/01/2025

1. #postdoc position (m/f/d, TV-L E13, 100%, 3 years) in plant synthetic biology to design and characterize inducible transgene expression cassettes. This is a collaborative project with @nicolabiologist.bsky.social (University of Cambridge) and Christine Queitsch (University of Washington)

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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 17/12/2024

The Chlamydomonas reinhardtii CLiP2 mutant collection expands genome coverage with high-confidence disrupting alleles www.biorxiv.org/content/10.1101/202…

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Donat Wulf @donat.bsky.social · 18/09/2024

Meeting up with Team Compbio at #BT2024DBG to celebrate the publication of one of my PhD projects: Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants academic.oup.com/insilicoplan... It was great to be back in Germany again!

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Reposted by Donat Wulf

in silico Plants @insilicoplants.bsky.social · 06/08/2024

NEW! Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants from @andreabraeutigam.bsky.social @donat.bsky.social #PlantScience #GRN #photosynthesis #MachineLearning buff.ly/46BDLY5

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Andrea Bräutigam @andreabraeutigam.bsky.social · 21/11/2023

And here is one of them. We model gene regulatory networks, compare them and analyze evolution of photosynthesis. By comparing multiple networks we find high confidence regulators for photosynthesis (or any pathway you care to study really); @donat.bsky.social again www.biorxiv.org/content/10.1...

biorxiv.org

Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Donat Wulf @donat.bsky.social · 21/11/2023

Our prepring about comparative gene regulatory network analysis is available on bioRxiv! We focused on the regulation of C4 and C3 photosynthesis and identified conserved regulators for other pathways too. www.biorxiv.org/content/10.1... #Bioinformatics #generegulation #photosyntheis #PlantScience

biorxiv.org

Comparative analysis of gene regulatory networks identifies conserved regulators in seed plants

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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Donat Wulf @donat.bsky.social · 31/10/2023

I should have added #PlantScience thanks @somssich.bsky.social for pointing that out. Still learning how stuff works here.

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