marek mutwil 🇺🇦

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

[marek mutwil 🇺🇦 @LabMutwil]

1/ How conserved are plant stress responses across 1 billion years of evolution? We built a cross-kingdom stress atlas spanning 36 species, from green algae to angiosperms, across 9 stresses. 13.6M DEG calls from 3,200+ manually curated experiments. 🧵https://t.co/2aZ46FjKYw

[marek mutwil 🇺🇦 @LabMutwil]

20 years of plant biology in one chart. We asked: which techniques rose, which faded (source, Plant Cell)?
RNA-seq: 0.3% → 34% (≈100×). CRISPR: 0 → 21%. Northern blot, microarray, RT-PCR: collapsed. Western, qPCR, confocal: still everywhere.
#PlantBiology

[marek mutwil 🇺🇦 @LabMutwil]

Currently, the analysis is limited to open access corresponding authors from Plant Cell (for now)

[marek mutwil 🇺🇦 @LabMutwil]

Few days ago we shipped RPG — every Plant Cell paper as a Q→M→F graph. 150,000 nodes, 2,600 papers.

Today: the people who connect those papers.

A new expert similarity network at https://t.co/ndaFZyEQp7 🌱 1/6

[marek mutwil 🇺🇦 @LabMutwil]

Why this matters beyond plant biology: science happens at intersections. Between people, between fields, between methods that shouldn't have been combined until someone did.

Making those intersections visible is the goal.
Try it free: https://t.co/ndaFZyEQp7
Built by @MutwilLab

[marek mutwil 🇺🇦 @LabMutwil]

@Eric_T_Thurman I agree (in principle), but the amount of information available (which is also being generated at an accelerating pace) makes this unpractical.

[marek mutwil 🇺🇦 @LabMutwil]

Reading a scientific paper takes hours. No PI, no student, can keep up. And keyword search finds words, not ideas.

So we built a Research Process Graph: a new way to read the literature.

https://t.co/ndaFZyEQp7 🌱 1/7

[marek mutwil 🇺🇦 @LabMutwil]

@AramModrek Not to my knowledge, but it should be eminently transferrable :)

[marek mutwil 🇺🇦 @LabMutwil]

It is said that science and art are related, and @AnneOsbourn1 definitely takes it to the next level.

[Anne Osbourn @AnneOsbourn1]

Check out Rockall by Anne Osbourn by Story Machine on @Kickstarter https://t.co/hjUvTFCy14

[marek mutwil 🇺🇦 @LabMutwil]

Plant biology is just the start. The approach generalizes to any scientific field.

Try it free: https://t.co/ndaFZyEQp7

Built by the @MutwilLab at the University of Copenhagen. Feedback welcome at https://t.co/ULPoB9yR78 as this is early.

[marek mutwil 🇺🇦 @LabMutwil]

Why this matters beyond plant biology:

Science is structured knowledge stored as unstructured prose. RPG turns the research process itself into a queryable database. Ask the literature directly -> get grounded, paper-linked answers in seconds instead of weeks.

[marek mutwil 🇺🇦 @LabMutwil]

Assembled by Jooa Moon and @eugenekoh_ROS

[marek mutwil 🇺🇦 @LabMutwil]

🚨PEO v0.2 is out. The Plant Gene Expression Omnibus now spans 147 plant species (up from 100), with 62M sample expression annotations and 6.3M annotated genes — free to browse across the green tree of life.

https://t.co/IX8Wiz5gAr #PlantBiology #Bioinformatics #PlantScience