Marcel Dickmanns | 🌿❄️🔬
@madic.bsky.social
Shooting electrons, ions and photons (mainly) at plants to study cell-cell communication @mpibiochem.bsky.social & @hhu.de
Pinned
New preprint: In situ Architecture of #Plasmodesmata.
Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.
🔗 doi.org/10.1101/2025...
🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM
Using #cryoET, #AlphaFold & proteomics, we uncover the native organization of plant intercellular nanopores.
🔗 doi.org/10.1101/2025...
🧪🧵1/n
#teamtomo #PlantScience #Physcomitrium #Arabidopsis #cryoEM
Reposted by Marcel Dickmanns | 🌿❄️🔬
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...
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...
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...
www.nature.com
November 26, 2025 at 6:00 AM
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...
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...
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.
This dataset + what’s in PDB already would be a decent start.
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
November 25, 2025 at 6:24 PM
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.
This dataset + what’s in PDB already would be a decent start.
Reposted by Marcel Dickmanns | 🌿❄️🔬
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...
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
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
docs.google.com
November 24, 2025 at 2:49 PM
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...
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Reposted by Marcel Dickmanns | 🌿❄️🔬
Why IDPs Are Poor Candidates for Homotypic LLPS
🧵👇A thread
🧵👇A thread
November 20, 2025 at 6:32 PM
Why IDPs Are Poor Candidates for Homotypic LLPS
🧵👇A thread
🧵👇A thread
Microtubule-based vacuum cleaner 👀
Cellular structure self-organizes through an interplay between internal mechanisms and external cues. The single-celled suctorian P. collini builds a trap structure to capture large prey using microtubule feeding tentacles, creating feedback between cell morphology and prey availability.
November 19, 2025 at 3:35 PM
Microtubule-based vacuum cleaner 👀
Reposted by Marcel Dickmanns | 🌿❄️🔬
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...
October 31, 2025 at 2:33 PM
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...
Reposted by Marcel Dickmanns | 🌿❄️🔬
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...
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...
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.
www.nature.com
October 31, 2025 at 1:57 PM
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...
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...
Reposted by Marcel Dickmanns | 🌿❄️🔬
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.
Advanced imaging techniques and computer modelling to create a detailed structural model of a nuclear pore complex from a seed plant.
October 31, 2025 at 12:55 PM
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.
Advanced imaging techniques and computer modelling to create a detailed structural model of a nuclear pore complex from a seed plant.
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
My set for screening (AND):
Side chain heavy atom distance <= 4.2 Å
PAE <= 8 Å
Combined pLDDT >= 140
pDockQ > 0.3
I love AlphaFold—but please include PAE (Predicted Aligned Error) plots for every “interaction.” Pretty PDBs ≠ proof. If the PAE doesn’t show an interface, it ain’t one. Show the plots. Structural biology's reputation is on the line.
October 25, 2025 at 10:17 AM
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
My set for screening (AND):
Side chain heavy atom distance <= 4.2 Å
PAE <= 8 Å
Combined pLDDT >= 140
pDockQ > 0.3
Reposted by Marcel Dickmanns | 🌿❄️🔬
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🍧
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...
www.biorxiv.org
October 23, 2025 at 11:13 AM
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🍧
Reposted by Marcel Dickmanns | 🌿❄️🔬
@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
October 22, 2025 at 9:21 AM
@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
Reposted by Marcel Dickmanns | 🌿❄️🔬
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
October 15, 2025 at 2:58 PM
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."
"We can't leave all the fun to the biologists; we should zoom out while they zoom in."
I wrote a blog post about the future of structural bioinformatics.
Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs?
Let me know what you think.
jgreener64.github.io/posts/struct...
Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs?
Let me know what you think.
jgreener64.github.io/posts/struct...
Where next for structural bioinformatics?
jgreener64.github.io
October 17, 2025 at 5:19 AM
Great read & perspective!
"We can't leave all the fun to the biologists; we should zoom out while they zoom in."
"We can't leave all the fun to the biologists; we should zoom out while they zoom in."
Reposted by Marcel Dickmanns | 🌿❄️🔬
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...
@jandevries.bsky.social
@watertoland.bsky.social
www.biorxiv.org/content/10.1...
October 11, 2025 at 9:20 AM
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...
@jandevries.bsky.social
@watertoland.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Marcel Dickmanns | 🌿❄️🔬
✨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...
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...
October 8, 2025 at 3:59 PM
✨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...
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...
Reposted by Marcel Dickmanns | 🌿❄️🔬
New blog post. In which I analyze the new HHMI announcement and what it means for the science publishing ecosystem openrxiv.org/preprint-man...
Preprint mandates gather momentum - openRxiv
By Richard Sever, PhD. Chief Science & Strategy Officer, openRxiv Preprints speed up science by enabling researchers to disseminate reports of new findings immediately. They also represent a simple wa...
openrxiv.org
October 6, 2025 at 6:53 PM
New blog post. In which I analyze the new HHMI announcement and what it means for the science publishing ecosystem openrxiv.org/preprint-man...
You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly.
This saves some clicking around. Neat!
This saves some clicking around. Neat!
October 7, 2025 at 2:54 PM
You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly.
This saves some clicking around. Neat!
This saves some clicking around. Neat!
123 new genomes you say?
Time to update some sequence alignments 🥲
Time to update some sequence alignments 🥲
Here's 123 new bryophyte genomes for you!
Apparently, bryophytes time and again include microbial genes in their genomic repertoire, and occupy a langer gene space than vascular plants.
www.nature.com/articles/s41...
Apparently, bryophytes time and again include microbial genes in their genomic repertoire, and occupy a langer gene space than vascular plants.
www.nature.com/articles/s41...
Bryophytes hold a larger gene family space than vascular plants - Nature Genetics
A super-pangenome analysis incorporating 123 newly sequenced bryophyte genomes reveals that bryophytes exhibit a larger number of unique and lineage-specific gene families than vascular plants.
www.nature.com
September 25, 2025 at 10:53 PM
123 new genomes you say?
Time to update some sequence alignments 🥲
Time to update some sequence alignments 🥲
Thylakoids, the prettiest membrane structures in planty cryoET, in full glory:
Time for a thread!🧵 How different is the molecular organization of thylakoids in “higher” plants🌱? To find out, we teamed up with @profmattjohnson.bsky.social to dive into spinach chloroplasts with #CryoET ❄️🔬. Curious? ..Read on!
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵
September 25, 2025 at 10:48 PM
Thylakoids, the prettiest membrane structures in planty cryoET, in full glory:
Reposted by Marcel Dickmanns | 🌿❄️🔬
I am excited to share our new preprint on the CAGE complex, a mysterious hollow protein complex that I first saw years ago while surveying Tetrahymena ciliary lysate www.biorxiv.org/content/10.1... #cilia #protistsonsky 🧬🧪
September 23, 2025 at 5:08 PM
I am excited to share our new preprint on the CAGE complex, a mysterious hollow protein complex that I first saw years ago while surveying Tetrahymena ciliary lysate www.biorxiv.org/content/10.1... #cilia #protistsonsky 🧬🧪
Reposted by Marcel Dickmanns | 🌿❄️🔬
Correlative MS Imaging for cellular identification and analysis of in situ cryo-ET https://www.biorxiv.org/content/10.1101/2025.09.16.676641v1
September 19, 2025 at 2:49 AM
Correlative MS Imaging for cellular identification and analysis of in situ cryo-ET https://www.biorxiv.org/content/10.1101/2025.09.16.676641v1
Reposted by Marcel Dickmanns | 🌿❄️🔬
La-Proteina from NVidia to do co-design of fully atomistic protein structures (sequence + side-chains + backbone) for up to 800 residues is now open source with permissive licensing
🖥️ github.com/NVIDIA-Digit...
🗎 arxiv.org/abs/2507.09466
🖥️ github.com/NVIDIA-Digit...
🗎 arxiv.org/abs/2507.09466
September 11, 2025 at 8:23 AM
La-Proteina from NVidia to do co-design of fully atomistic protein structures (sequence + side-chains + backbone) for up to 800 residues is now open source with permissive licensing
🖥️ github.com/NVIDIA-Digit...
🗎 arxiv.org/abs/2507.09466
🖥️ github.com/NVIDIA-Digit...
🗎 arxiv.org/abs/2507.09466
Reposted by Marcel Dickmanns | 🌿❄️🔬
Trouble imaging actin in ExM? Meet HAK-Actin, a probe for U-ExM, cryo-ExM & iU-ExM. Enables post-expansion labeling for max signal. www.biorxiv.org/content/10.1...
Soon at @spirochrome.com
Led by O.Mercey and @lreymond.bsky.social, in collab with @dudinlab.bsky.social and @marinelap.bsky.social
Soon at @spirochrome.com
Led by O.Mercey and @lreymond.bsky.social, in collab with @dudinlab.bsky.social and @marinelap.bsky.social
August 28, 2025 at 7:03 AM
Trouble imaging actin in ExM? Meet HAK-Actin, a probe for U-ExM, cryo-ExM & iU-ExM. Enables post-expansion labeling for max signal. www.biorxiv.org/content/10.1...
Soon at @spirochrome.com
Led by O.Mercey and @lreymond.bsky.social, in collab with @dudinlab.bsky.social and @marinelap.bsky.social
Soon at @spirochrome.com
Led by O.Mercey and @lreymond.bsky.social, in collab with @dudinlab.bsky.social and @marinelap.bsky.social
H2B-mRFPruby, scale bar: 20µm
#live-imaging
#live-imaging
Scientists present an advanced new technique for live-imaging regenerating limbs, shown here on a sand flea.
buff.ly/WsOrSlR
buff.ly/WsOrSlR
August 25, 2025 at 3:00 PM
H2B-mRFPruby, scale bar: 20µm
#live-imaging
#live-imaging
Reposted by Marcel Dickmanns | 🌿❄️🔬
Our latest on brassinosteroid signaling: Ligand binding spectrum, specificity & selectivity of all BR receptors in Arabidopsis. By @albertocaregnato.bsky.social , @hmchen93.bsky.social and our great chemistry collaborators Mirek Kvasnica, Jana Oklestkova and Mirek Strnad.
August 9, 2025 at 9:01 PM
Our latest on brassinosteroid signaling: Ligand binding spectrum, specificity & selectivity of all BR receptors in Arabidopsis. By @albertocaregnato.bsky.social , @hmchen93.bsky.social and our great chemistry collaborators Mirek Kvasnica, Jana Oklestkova and Mirek Strnad.