Donat Wulf
fascinated by gene regulatory networks. Postdoc at UC Berkeley #R #python
scholar.google.com/citations?user=sgyk…
- Reposted by Donat WulfCalling 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)
- Reposted by Donat Wulf‼️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
- Reposted by Donat WulfPlantCV v4: Image analysis software for high-throughput plant phenotyping biorxiv.org/content/10.1101/202…
- Reposted by Donat WulfExcited 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...
- Reposted by Donat WulfPSA: 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...
- Reposted by Donat WulfThe KEY🔑 to regulating Rubisco phase separation in the Chlamydomonas algal pyrenoid. Beautiful work by Shan He, @mjonikas.bsky.social, and friends. #PhaseSeparation #CO2 #PlantScience 🧪 🧶🧬 🌾 🌍
- Algal pyrenoids—condensates that mediate ~1/3 of Earth’s CO2 fixation—change size and number as cells divide. Our data suggest a simple control mechanism: a kinase that continuously ejects material from the condensate! ☀️🌍🔬💧 #Biophysics #Photosynthesis www.biorxiv.org/content/10.1...
- Reposted by Donat WulfThrilled to share that our TEtrimmer paper has just been published in Nature Communications! A big thank you to all collaborators — the article is now online ;) www.nature.com/articles/s41...
- Reposted by Donat WulfAs 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...
- Reposted by Donat WulfVersion 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
- Reposted by Donat WulfOur 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
- Reposted by Donat WulfOur 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.
- Reposted by Donat WulfSaddened 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...
- Reposted by Donat WulfNEWS & VIEWS: Conserved language of plant gene regulation (Neeta Lohani) doi.org/10.1093/plph... #PlantScience
- Reposted by Donat WulfIt'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!
- A BLAST update adding support for compressed files and csv output with headers is a Good Friday night surprise! blast.ncbi.nlm.nih.gov/doc/blast-ne...
- Reposted by Donat WulfMSU 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.
- Reposted by Donat WulfOur department (Berkeley PMB) is hiring an asst. prof. in Plant Resilience to Climate Change! aprecruit.berkeley.edu/JPF05049
- Reposted by Donat WulfThe 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...
- Reposted by Donat WulfOur "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!
- Reposted by Donat WulfSmall 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
- Reposted by Donat WulfBeautiful tribute to Joanne Chory on @scifri.bsky.social! www.sciencefriday.com/segments/be-...
- Reposted by Donat WulfRegulation 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
- Reposted by Donat Wulf[Not loaded yet]
- Reposted by Donat Wulfpolars-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.
- 💻 🍃 Comparative analysis of #GRN identifies conserved regulators in seed plants by Donat Wulf, Andrea Bräutigam buff.ly/46BDLY5 #GRN #PlantScience 🧪
- The arabidopsis gene regulatory network and the chlamydomonas gene regulatory network were validated in these preprints: Chlamydomonas: doi.org/10.1101/2023...
- And arabidopsis: doi.org/10.1101/2023... For my postdoc I will use these methods to investigate the regulation of biomineralization in diatoms.
- Reposted by Donat WulfFun 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...
- Reposted by Donat WulfTAPscan 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
- TAPscan v4: Annotation of 138 TF/TR families across 678 species, focus on plants. Of 18 new (sub)fmilies, nine were gained in the most recent common ancestor of the Streptophyta (comprising streptophyte algae and land plants), or within streptophyte algae. 1/2 onlinelibrary.wiley.com/doi/full/10....
- Reposted by Donat Wulf1. #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)
- Reposted by Donat WulfThe Chlamydomonas reinhardtii CLiP2 mutant collection expands genome coverage with high-confidence disrupting alleles biorxiv.org/content/10.1101/202…
- Reposted by Donat WulfMany 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!
- Reposted by Donat WulfNEW! 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
- Reposted by Donat WulfAnd 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.
