Aim: improve gene function predictions of the plant kingdom to produce more climate change-resilient and nutritious crops.
Denmark
Joined October 2014
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🌱 3 PhD positions for 2027 in computational plant biology & AI at @UCPH_Research!
Mutwil Lab seeks curious minds who question data and see the bigger picture. Prior coding experience optional; willingness to learn essential.
Details & initial enquiries: publish.obsidian.md/mutwilla…
1/4
Our CoNekT and PEO databases are being heavily scraped. From 7–15 October, CoNekT’s main site recorded 14.3 million requests. On 14 October, about 88% of 3.7 million requests matched two automated scraping patterns.
3/4
It could be competitors, AI data collectors or someone else. We cannot identify who is behind it. The impact is clear: during the worst period sampled, almost one in four requests to CoNekT failed, making the database harder for researchers to use.
4/4
We welcome reuse of CoNekT and PEO data. Large downloads need coordination so researchers can continue exploring genes and networks. Are other biology databases seeing similar scraping? #OpenScience #Bioinformatics
marek mutwil 🇺🇦 retweeted
Applied Plant Science : A sister journal to MP&PCom | #OpenAccess No APC for papers accepted by 31 Dec 2028 | 8 application-oriented areas: inclu. smart breeding, precision agriculture, medicinal plants, synthetic biology |sciencedirect.com/journal/ap…| Submit: editorialmanager.com/apsx
A personal project outside my usual computational biology work:
I have been building The Long Ascent, a turn-based deckbuilding game, to explore how far one person can take a complex project using current AI tools and a data-science mindset.
mutwil.github.io/ 1/5
One example from the evaluation process:
Eight external LLM agents played 44 fights using fixed seeds. Seven defeated the first boss.
This is an informal development experiment, not academic research or a measurement of human player difficulty. 4/5
I am documenting the process publicly, including failed approaches, costs, reproducibility problems and tasks where human judgment remains essential.
Development notes: patreon.com/LongAscend/posts…
🌱 Gene expression & co-expression across 630,000 RNA-seq samples from 10,700+ plant species — free, in your browser.
Search a gene → see where it's expressed on the UMAP → explore its co-expression network.
mutwil-plant-atlas-viewer.hf…
#PlantScience #RNAseq #Bioinformatics
I am pretty happy about how the new updated version of our Plant Atlas is working huggingface.co/spaces/mutwil… .
I selected trait 'Nodulating'. This compared gene expression in roots of nodulating vs. non-nodulating plants, and identified gene families such as nodulins and others.
1/RNA-seq accurately measures gene expression changes, right?
Wrong.
When a stress shuts down much of the transcriptome, standard analysis can report the OPPOSITE of what is happening. Our new paper fixes it, and saves money on the way. 🧵
8/It does what ERCC spike-ins and RUVg do, anchor the data to something constant. The difference: the reference is a whole living species pooled as tissue, so it goes through the full extraction and library prep, and it doubles as the multiplexing partner.
9/Cheaper, and quantitatively honest, stress transcriptomics. Great work led by Sabrina Tan and the team.
Paper: biorxiv.org/content/10.64898… Code + data: github.com/mutwil/multiplex-…
#PlantScience #RNAseq #Transcriptomics #Bioinformatics
