Marcel Dickmanns | 🌿❄️🔬

Totally! And they rate outputs from their own model family higher.
arxiv.org/abs/2508.06709

At this stage, automated text review should probably average across multiple models.

Where do I queue for squid takeover stickers?

Depends on the cell type and downstream processing but chemical lysis is gentle (detergent + enzymes). Probably cheaper than a pressure homogenizer short- to medium-term?

Talk titles for IDPSeminars on Dec 4th at noon central time. Alex Holehouse (Washington University in St. Louis): Sequence-to-ensemble with STARLING Birthe Kragelund (University of Copenhagen): Disordered protein complexes and the origins of life

We're back for our final seminar of 2025 with talks from @alexholehouse.bsky.social and Birthe Kragelund! 1 pm EST or 7 pm European time. If you're not already signed up, head on over to idpseminars.com to register!

Murnau Conference nailing the hot topic:

"The overarching theme of this edition will be “(Un)structural biology: in situ, in vitro, in silico”. Besides amazing cellular and 4D structural biology, we will have a session covering the topic of condensate structural biology."
🔗 murnauconference.de

CryoET of symbiotic cell-cell interfaces 🦑🦠
🔗 www.biorxiv.org/content/10.1...

Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...

AI model Helixer predicts eukaryotic genes ab initio, directly from a plain text FASTA file.

No RNA-seq.
No protein homology.
No repeats, hints, or curated evidence.

Raw genome → accurate gene models.
Deep learning + HMM, published in @natmethods.nature.com

www.nature.com/articles/s41...

Like PAGE ruler but 10 kDa blue instead of green. Otherwise scarily real looking!

(couple years later AF2 dropped and 'do we still need to crystallize small domains?' became a valid question)

As undergrad I had to purify and crystallize a new protein that kept aggregating no matter what. In distress fantasized about an algorithm to predict good buffer conditions & mutations.

This dataset + what’s in PDB already would be a decent start.

Next generation of 1001 Genomes Plus browser and data download Please indicate all features you would like to see in a browser that displays features of completely sequenced Arabidopsis thaliana genomes

We (Nordborg & Weigel labs) need input on the next generation of genome browsers & data download modes for the #Arabidopsis #1001GenomesPlus project. We have now a curated collection of over 500 long read genomes.

Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...

Why IDPs Are Poor Candidates for Homotypic LLPS

🧵👇A thread

Dewars are full to the rim with green stuff. But someone might..

Bar: 15 um.

Microtubule-based vacuum cleaner 👀

The logo of the conference symbolises a plant cell, plant leaves, plant cell's organelles, and a bug. It also offers the details of the 39th Conference Molecular Biology of Plants (#MBP2026) taking place from 16th to 19th March 2026 in Hennef, Germany

Registration is open to take part in the Molecular Biology of Plants (#MBP2026), which especially invites early career scientists to present their molecular #plantsci research www.pflanzen-molekularbiologie.de/en/conferenc...

Electrostatic changes enabled the diversification of an exocyst subunit via protein complex escape - Nature Plants The evolutionary diversification of an exocyst subunit was enabled by electrostatic shifts leading to its dissociation from the ancestral complex.

My main work as postdoc @plantophagy.bsky.social lab in @gmivienna.bsky.social is out in @natplants.nature.com 🌱🎉

We asked how can protein complexes diversify without compromising their function and explored this question using the plant #exocyst complex.

www.nature.com/articles/s41...

New OA Article: "In situ architecture of the nuclear pore complex of the higher plant Arabidopsis thaliana" rdcu.be/eNFiR

Advanced imaging techniques and computer modelling to create a detailed structural model of a nuclear pore complex from a seed plant.

www.plabipd.de/pubplant_cla...

and striped shirts

The argument is that "under review" is fine, but "under review at X" should not be a quality proxy. Also, if preprinted, you get a doi to put on the CV and ppl can actually read your work regardless of crazy review times.

Curious which parameters everyone uses to consider res pairs as potentially interacting. Thoughts?

My set for screening (AND):
Side chain heavy atom distance <= 4.2 Å
PAE <= 8 Å
Combined pLDDT >= 140
pDockQ > 0.3

+bird poo

Icecream: High-Fidelity Equivariant Cryo-Electron Tomography Cryo-electron tomography (cryo-ET) visualizes 3D cellular architecture in near-native states. Recent deep-learning methods (CryoCARE, IsoNet, DeepDeWedge, CryoLithe) improve denoising and artifact cor...

Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧

@delaconcepcionjc.bsky.social from @gmivienna.bsky.social (a @johninnescentre.bsky.social alumnus) delivered his 2026 Early Career Research Award Lecture on NLR engineering and his ongoing cryo-ET work! #BiochemEvent

Second, I’m slowly getting to be in the camp that proteins don’t have functions but instead have properties. What biology does with those properties is a somewhat different matter. So maybe we need to predict properties (kcat, Kd, etc) as well

Great read & perspective!

"We can't leave all the fun to the biologists; we should zoom out while they zoom in."

Very happy and proud to share the #Spirogyra genome: 50 Mbp small, lacking almost all plastid division proteins and many transcription factors. Kudos to all the many people involved in this multi year project!
@jandevries.bsky.social
@watertoland.bsky.social
www.biorxiv.org/content/10.1...

Lovely irony with the typo in the last one.

✨Excited that the main project of my PhD is now available as a pre-print on #bioRxiv

Here, we used #CryoET to visualise mitochondrial proteostatic stress and together with SPA #CryoEM shed light into the functional cycle of the Hsp60:10 chaperone system. #TeamTomo

🔗 www.biorxiv.org/content/10.1...