Marcel Dickmanns | 🌿❄️🔬

Excited to finally share this work also in written form! 🎉 Huge thanks to all co-authors and collaborators — this really was a team effort, and I’m very grateful for all the ideas, discussions, and hard work that went into it. Thanks everyone! #TeamTomo #cryoET #autophagy

It makes me sad to see a paper in a fancy journal that I didn't see on bioRxiv before 😢

Gorgeous paper and a plea for open data.
⬇️ See thread ⬇️

Why Most Published Research Findings Are False Published research findings are sometimes refuted by subsequent evidence, says Ioannidis, with ensuing confusion and disappointment.

"Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true."
dx.plos.org/10.1371/jour...

I might stay for some honest soul-baring.

Wonder whats wrong with this place. Do we need more emojis, more "thrilled to announce" and "happy to share", and "congratulations🥳" as super pesonal one-click option?
(pls no!)

They are marks of authenticity now.

Word trying to correct "Thank you for catching..." to "thank you for making this mistake".

Microsoft spell check trying to sabotage reviewer replies again 🙄

Final version is out! Our large-scale cryo-ET dataset 🔬 of Chlamydomonas reinhardtii 🦠 is now published in @cp-molcell.bsky.social

Huge collaborative effort! So glad to see the community already using it to develop new resources & tools.

Check it out here: shorturl.at/z4i4c
#CryoEM #CryoET

All of the above, often minus FP OE. On top, I find it helpful to consider the broader functional context. What interactors are known? Relevant sequence motifs present? Domain annotations? What are orthologs in other species doing? etc.

*proto

Experimental evidence for enzymatic cell wall dissolution in a microbial protoplast feeder (Orciraptor agilis, Viridiraptoridae) - BMC Biology Background Several protists have evolved the ability to perforate the cell walls of algae and fungi to specifically feed on their cell contents. These phagotrophic “protoplast feeders” represent an in...

Entire cytoplasts even. Curious to see what happens where both plasma membranes meet.

Different species' but the images in here are amazing too: link.springer.com/article/10.1...

Image of cell junction puncta from https://www.molbiolcell.org/doi/full/10.1091/mbc.E23-03-0077

To build the body plan of an animal, cells must adhere to one another via cell-cell junctions. We now know these assemble as punctate protein complexes containing thousands of proteins, but how this occurs remains mysterious. 1/n 🧪
www.molbiolcell.org/doi/full/10....

Hey Mark, pretty cool thanks for the thread. Any idea what the Cno nuclear localization is about - randomly passing in and out or does it have nuclear function?

Jan 2024 apparently.
www.embo.org/press-releas...

🥳 Our new paper on C2CD3 is out in @plosbiology.org
With the labs of @cellarchlab.com , @chgenoud.bsky.social , and @stearnslab.bsky.social , we revealed the mammalian centriole Distal Ring architecture by combining #UExM and in situ #CryoET.
Big congrats to @ebertiaux.bsky.social and all involved.

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.