marek mutwil 🇺🇦

Aim: improve gene function predictions of the plant kingdom to produce more climate change-resilient and nutritious crops.

[marek mutwil 🇺🇦 @LabMutwil]

5.6M genes from 149 plants in one aligned map 🌱

Aligned with ESCAPE, a non-rigid method from our autoresearch loop. Flowering plants merge into one shared core, while ferns, lycophytes & mosses keep their own islands.

Compare ORBIT / THESEUS / ESCAPE: https://t.co/Fzb2g7gXba

[marek mutwil 🇺🇦 @LabMutwil]

@KamounLab 😂🤣

[marek mutwil 🇺🇦 @LabMutwil]

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 🇺🇦 @LabMutwil]

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.

[marek mutwil 🇺🇦 @LabMutwil]

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.

[Molecular Plant & Plant Communications @MPlantPCom]

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 |https://t.co/cdkH1md2M7| Submit: https://t.co/usbacOjgbF

[marek mutwil 🇺🇦 @LabMutwil]

@KamounLab @sangerinstitute You mean:

[marek mutwil 🇺🇦 @LabMutwil]

@KamounLab @delaconcepcionj We need to talk!

[marek mutwil 🇺🇦 @LabMutwil]

@UCPH_Research https://t.co/JiFBjgwRGc. degree is a must. Duration is 3 years for 2 year https://t.co/JiFBjgwRGc. or 1+3 years for 1 year https://t.co/JiFBjgwRGc. holders.

[marek mutwil 🇺🇦 @LabMutwil]

🌱 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: https://t.co/faBPcMVgSJ

[marek mutwil 🇺🇦 @LabMutwil]

@KamounLab tsk tsk

[marek mutwil 🇺🇦 @LabMutwil]

I am documenting the process publicly, including failed approaches, costs, reproducibility problems and tasks where human judgment remains essential.
Development notes: https://t.co/fcg9vt3pSX

[marek mutwil 🇺🇦 @LabMutwil]

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.
https://t.co/mnndyxBytD 1/5

[marek mutwil 🇺🇦 @LabMutwil]

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

[marek mutwil 🇺🇦 @LabMutwil]

@lpachter @Josephmrich Wonderful. Can it also submit reimbursement forms 😅

[marek mutwil 🇺🇦 @LabMutwil]

@szintri One could make even a bespoke version with claude code. We now live in an era where personalised software is so easy to do. I made a command center app just for myself, including short, medium, long time planners, email analysis and LLM-based replies, LLM-based project status...

[marek mutwil 🇺🇦 @LabMutwil]

@xuzhougeng Thanks. Not yet, this is still an early prototype. I think we will have something in 2027

[marek mutwil 🇺🇦 @LabMutwil]

🌱 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.

https://t.co/PRhoLXBs2o

#PlantScience #RNAseq #Bioinformatics