Donat Wulf
@donat.bsky.social
fascinated by gene regulatory networks. Postdoc at UC Berkeley #R #python
https://scholar.google.com/citations?user=sgykqjgAAAAJ&hl=de
https://scholar.google.com/citations?user=sgykqjgAAAAJ&hl=de
Reposted by Donat Wulf
PlantCV v4: Image analysis software for high-throughput plant phenotyping https://www.biorxiv.org/content/10.1101/2025.11.19.689271v1
November 20, 2025 at 5:04 PM
PlantCV v4: Image analysis software for high-throughput plant phenotyping https://www.biorxiv.org/content/10.1101/2025.11.19.689271v1
Reposted by Donat Wulf
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/plcell/artic...
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
academic.oup.com
October 29, 2025 at 6:59 AM
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/plcell/artic...
Reposted by Donat Wulf
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/pub/ubadah/p...
Beware giving this site your unpublished data
Users noticed the website had fake testimonials and a domain name registered seemingly overnight.
open.substack.com
October 23, 2025 at 2:07 PM
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/pub/ubadah/p...
Reposted by Donat Wulf
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 🧪 🧶🧬 🌾 🌍
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...
www.biorxiv.org/content/10.1...
October 12, 2025 at 9:26 PM
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 🧪 🧶🧬 🌾 🌍
Reposted by Donat Wulf
Thrilled 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...
www.nature.com/articles/s41...
TEtrimmer: a tool to automate the manual curation of transposable elements - Nature Communications
Transposons are repetitive DNA sequences that are hard to identify and map accurately. TEtrimmer automates key manual steps, enabling faster and more reliable annotation of transposable elements in any genome.
www.nature.com
September 25, 2025 at 12:32 PM
Thrilled 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...
www.nature.com/articles/s41...
Reposted by Donat Wulf
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...
jamanetwork.com/journals/jam...
September 23, 2025 at 3:46 PM
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...
jamanetwork.com/journals/jam...
Reposted by Donat Wulf
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
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
F1000Research Article: Sustainable data analysis with Snakemake.
Read the latest article version by Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Peter C. van Dyken, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Filipe G. Vi...
f1000research.com
September 23, 2025 at 10:18 AM
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
We have updated the presented features and the design patterns.
#sciworkflows #reproducibility
Reposted by Donat Wulf
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
September 17, 2025 at 8:00 PM
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
Reposted by Donat Wulf
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.
Filter, tag, annotate, sort, and flexibly convert to CSV/TSV, JSON, JSONL, YAML and FHIR via a unified syntax.
Vembrane
vembrane.github.io
September 18, 2025 at 6:53 PM
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.
Filter, tag, annotate, sort, and flexibly convert to CSV/TSV, JSON, JSONL, YAML and FHIR via a unified syntax.
Reposted by Donat Wulf
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/newsletter/4...
Stephen Long
emails.illinois.edu
September 13, 2025 at 9:59 AM
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/newsletter/4...
Reposted by Donat Wulf
NEWS & VIEWS: Conserved language of plant gene regulation (Neeta Lohani) doi.org/10.1093/plph... #PlantScience
Conserved language of plant gene regulation
Imagine your cell as a smart home where genes are like appliances that need to be turned on or off at the right times. This regulation is mediated by trans
doi.org
September 12, 2025 at 7:51 PM
NEWS & VIEWS: Conserved language of plant gene regulation (Neeta Lohani) doi.org/10.1093/plph... #PlantScience
Reposted by Donat Wulf
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!
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...
blast.ncbi.nlm.nih.gov/doc/blast-ne...
2025 BLAST NEWS — BlastNews 0.1.1 documentation
blast.ncbi.nlm.nih.gov
September 6, 2025 at 5:03 AM
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!
Plus, gzipped fastas for makeblastdb! Finally!
Reposted by Donat Wulf
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.
Application instruction and link: careers.msu.edu/jobs/researc...
Please email me if you have any questions.
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...
careers.msu.edu
September 4, 2025 at 2:00 PM
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.
Application instruction and link: careers.msu.edu/jobs/researc...
Please email me if you have any questions.
Reposted by Donat Wulf
Our department (Berkeley PMB) is hiring an asst. prof. in Plant Resilience to Climate Change! aprecruit.berkeley.edu/JPF05049
Assistant Professor - Plant Resilience to Climate Change - Department of Plant and Microbial Biology
University of California, Berkeley is hiring. Apply now!
aprecruit.berkeley.edu
September 2, 2025 at 9:52 PM
Our department (Berkeley PMB) is hiring an asst. prof. in Plant Resilience to Climate Change! aprecruit.berkeley.edu/JPF05049
Reposted by Donat Wulf
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...
www.nature.com/nplants/volu...
August 20, 2025 at 11:18 AM
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...
www.nature.com/nplants/volu...
Reposted by Donat Wulf
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!
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!
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...
nph.onlinelibrary.wiley.com
August 19, 2025 at 1:17 PM
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!
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 Wulf
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
July 1, 2025 at 7:28 PM
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
Reposted by Donat Wulf
June 2, 2025 at 9:55 PM
Reposted by Donat Wulf
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
May 13, 2025 at 5:58 PM
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
Reposted by Donat Wulf
A tRNA-gRNA multiplexing system for CRISPR genome editing in Marchantia polymorpha. https://www.biorxiv.org/content/10.1101/2025.04.18.649274v1
April 21, 2025 at 3:02 AM
A tRNA-gRNA multiplexing system for CRISPR genome editing in Marchantia polymorpha. https://www.biorxiv.org/content/10.1101/2025.04.18.649274v1
Reposted by Donat Wulf
polars-bio - fast, scalable and out-of-core operations on large genomic interval datasets www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/biodatageeks...
March 26, 2025 at 9:37 AM
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.
💻 🍃 Comparative analysis of #GRN identifies conserved regulators in seed plants
by Donat Wulf, Andrea Bräutigam
https://buff.ly/46BDLY5 #GRN #PlantScience 🧪
by Donat Wulf, Andrea Bräutigam
https://buff.ly/46BDLY5 #GRN #PlantScience 🧪
buff.ly
February 5, 2025 at 10:21 PM
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.
Reposted by Donat Wulf
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...
www.nature.com/articles/s41...
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...
www.nature.com
January 22, 2025 at 10:34 PM
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...
www.nature.com/articles/s41...
Reposted by Donat Wulf
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
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....
onlinelibrary.wiley.com/doi/full/10....
January 14, 2025 at 8:11 PM
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
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
Reposted by Donat Wulf
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)
January 8, 2025 at 3:30 PM
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)