Version 3 of the Snakemake rolling paper is now pulbished on @f1000publishing.bsky.social: f1000research.com/articles/10-... We have updated the presented features and the design patterns. #sciworkflows #reproducibility

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

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.

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...

NEWS & VIEWS: Conserved language of plant gene regulation (Neeta Lohani) doi.org/10.1093/plph... #PlantScience

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!

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.

Our department (Berkeley PMB) is hiring an asst. prof. in Plant Resilience to Climate Change! aprecruit.berkeley.edu/JPF05049

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...

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!

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

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

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

A tRNA-gRNA multiplexing system for CRISPR genome editing in Marchantia polymorpha. https://www.biorxiv.org/content/10.1101/2025.04.18.649274v1

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

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.

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...

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

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)

The Chlamydomonas reinhardtii CLiP2 mutant collection expands genome coverage with high-confidence disrupting alleles https://www.biorxiv.org/content/10.1101/2024.12.16.626622v1

Many transcription factor families have evolutionarily conserved binding motifs in plants https://www.biorxiv.org/content/10.1101/2024.10.31.621407v1

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!

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

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...

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

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

Very happy that our Chlamydomonas manuscript is out. We used RNA-seq and DAP-seq to investigate several CLiP insertion mutants predicted by gene regulatory network inference.

We keep writing stories up - @donat.bsky.social is the lead author on our work on transcriptional networks in #chlamydomonas which control #photoacclimation. www.biorxiv.org/content/10.1...