Andrea Dallapè
@daddea.bsky.social
cryoEM enthusiast, cryoET enthusiast soon.
Last months as Research Assistant in WilsonLab, University of Hamburg, SPA cryoEM & ribosomes. Love Heterogeneity Analysis and continuous movements.
Water diviner, always!
Last months as Research Assistant in WilsonLab, University of Hamburg, SPA cryoEM & ribosomes. Love Heterogeneity Analysis and continuous movements.
Water diviner, always!
Reposted by Andrea Dallapè
#MD blind predictions of water/ions around Tetrahymena ribozyme #RNA matched cryo-EM data better than our baselines! Congrats #CASP16 + @rachael-kretsch.bsky.social + 23 brave groups. Still a ways to go — time for #DeepLearning of water? Community paper: doi.org/10.1002/prot...
November 11, 2025 at 12:53 AM
#MD blind predictions of water/ions around Tetrahymena ribozyme #RNA matched cryo-EM data better than our baselines! Congrats #CASP16 + @rachael-kretsch.bsky.social + 23 brave groups. Still a ways to go — time for #DeepLearning of water? Community paper: doi.org/10.1002/prot...
Reposted by Andrea Dallapè
New paper alert! Scientists in Clemens Plaschka’s lab at the IMP and @juliusbrennecke.bsky.social's lab at
@imbavienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: bit.ly/4nHcvys
@imbavienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: bit.ly/4nHcvys
November 6, 2025 at 4:04 PM
New paper alert! Scientists in Clemens Plaschka’s lab at the IMP and @juliusbrennecke.bsky.social's lab at
@imbavienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: bit.ly/4nHcvys
@imbavienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: bit.ly/4nHcvys
Reposted by Andrea Dallapè
Hey #TeamTomo …would you like to try some 🍦ICECREAM!? Our @unibas.ch colleagues over at the @ivandokmanic.bsky.social lab have developed a stunningly effective tool to de-noise and de-wedge your tomograms. The contrast and details will give you brain freeze! 🍨❄️🤯
Please try, we need feedback 🧪🧶🧬🔬
Please try, we need feedback 🧪🧶🧬🔬
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 5:57 PM
Hey #TeamTomo …would you like to try some 🍦ICECREAM!? Our @unibas.ch colleagues over at the @ivandokmanic.bsky.social lab have developed a stunningly effective tool to de-noise and de-wedge your tomograms. The contrast and details will give you brain freeze! 🍨❄️🤯
Please try, we need feedback 🧪🧶🧬🔬
Please try, we need feedback 🧪🧶🧬🔬
Reposted by Andrea Dallapè
As ever, beautiful #cryoEM work from the lab of Hong Zhou with field-defining insights using #cryoET:
“Kiss-shrink-run” unifies mechanisms for synaptic vesicle exocytosis and hyperfast recycling | Science
www.science.org/doi/10.1126/...
“Kiss-shrink-run” unifies mechanisms for synaptic vesicle exocytosis and hyperfast recycling | Science
www.science.org/doi/10.1126/...
“Kiss-shrink-run” unifies mechanisms for synaptic vesicle exocytosis and hyperfast recycling
Synaptic vesicle (SV) exocytosis underpins neuronal communication, yet its nanoscale dynamics remain poorly understood owing to limitations in visualizing rapid events in situ. Here, we used optogenet...
www.science.org
October 16, 2025 at 10:34 PM
As ever, beautiful #cryoEM work from the lab of Hong Zhou with field-defining insights using #cryoET:
“Kiss-shrink-run” unifies mechanisms for synaptic vesicle exocytosis and hyperfast recycling | Science
www.science.org/doi/10.1126/...
“Kiss-shrink-run” unifies mechanisms for synaptic vesicle exocytosis and hyperfast recycling | Science
www.science.org/doi/10.1126/...
Just some 3D classification 🤩 WOW.
Congratulations
Congratulations
Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️
www.biorxiv.org/content/10.1...
#teamtomo
www.biorxiv.org/content/10.1...
#teamtomo
October 16, 2025 at 2:26 AM
Just some 3D classification 🤩 WOW.
Congratulations
Congratulations
Reposted by Andrea Dallapè
Very excited that my final postdoctoral work is now online in Cell @cellpress.bsky.social.
www.sciencedirect.com/science/arti...
Using 16 (!) cryo-EM structures, we uncovered how the three proteins coronin, cofilin and AIP1 work together to rapidly disassemble actin filaments.
www.sciencedirect.com/science/arti...
Using 16 (!) cryo-EM structures, we uncovered how the three proteins coronin, cofilin and AIP1 work together to rapidly disassemble actin filaments.
October 13, 2025 at 9:04 AM
Very excited that my final postdoctoral work is now online in Cell @cellpress.bsky.social.
www.sciencedirect.com/science/arti...
Using 16 (!) cryo-EM structures, we uncovered how the three proteins coronin, cofilin and AIP1 work together to rapidly disassemble actin filaments.
www.sciencedirect.com/science/arti...
Using 16 (!) cryo-EM structures, we uncovered how the three proteins coronin, cofilin and AIP1 work together to rapidly disassemble actin filaments.
Reposted by Andrea Dallapè
Awesome re-analysis of the Franklin / Crick / Watson story. Explains how Franklin produced (with considerable skill) the *pictures* that made the penny drop for slow-on-the-uptake Watson. Sadly, paywalled.
www.cambridge.org/core/journal...
www.cambridge.org/core/journal...
Reassessing Discovery: Rosalind Franklin, Scientific Visualization, and the Structure of DNA | Philosophy of Science | Cambridge Core
Reassessing Discovery: Rosalind Franklin, Scientific Visualization, and the Structure of DNA - Volume 79 Issue 1
www.cambridge.org
October 11, 2025 at 7:43 PM
Awesome re-analysis of the Franklin / Crick / Watson story. Explains how Franklin produced (with considerable skill) the *pictures* that made the penny drop for slow-on-the-uptake Watson. Sadly, paywalled.
www.cambridge.org/core/journal...
www.cambridge.org/core/journal...
Wait uh, what?? 🤩
Ballistic Microscopy (BaM) www.biorxiv.org/content/10.1101/2025.10.07.681030v1 #cryoem
October 10, 2025 at 12:56 AM
Wait uh, what?? 🤩
Reposted by Andrea Dallapè
This year’s #NobelPrize in Physiology or Medicine has been awarded to three scientists for discovering how the immune system distinguishes friend from foe. https://scim.ag/3Wt5rdi
Medicine Nobel goes to three researchers who identified immune system’s security guards
Mary Brunkow, Fred Ramsdell, and Shimon Sakaguchi discovered regulatory T cells that prevent autoimmune disease
scim.ag
October 6, 2025 at 1:45 PM
This year’s #NobelPrize in Physiology or Medicine has been awarded to three scientists for discovering how the immune system distinguishes friend from foe. https://scim.ag/3Wt5rdi
Reposted by Andrea Dallapè
Check out our new preprint on an integrated pipeline combining in situ #cryo-ET with MALDI #MSImaging for single-cell identification and classification from previously analysed EM-grids.
Link: www.biorxiv.org/content/10.1...
Link: www.biorxiv.org/content/10.1...
September 19, 2025 at 6:07 PM
Check out our new preprint on an integrated pipeline combining in situ #cryo-ET with MALDI #MSImaging for single-cell identification and classification from previously analysed EM-grids.
Link: www.biorxiv.org/content/10.1...
Link: www.biorxiv.org/content/10.1...
Reposted by Andrea Dallapè
Helical Reconstruction of Amyloids in cryoSPARC?
We present guidelines, limitations & future perspectives for processing amyloids in cryoSPARC @structurabio.bsky.social.
Great collaboration of the Kelly Lab and @landerlab.bsky.social #cryoEM #amyloid www.biorxiv.org/content/10.1...
We present guidelines, limitations & future perspectives for processing amyloids in cryoSPARC @structurabio.bsky.social.
Great collaboration of the Kelly Lab and @landerlab.bsky.social #cryoEM #amyloid www.biorxiv.org/content/10.1...
October 5, 2025 at 4:16 AM
Helical Reconstruction of Amyloids in cryoSPARC?
We present guidelines, limitations & future perspectives for processing amyloids in cryoSPARC @structurabio.bsky.social.
Great collaboration of the Kelly Lab and @landerlab.bsky.social #cryoEM #amyloid www.biorxiv.org/content/10.1...
We present guidelines, limitations & future perspectives for processing amyloids in cryoSPARC @structurabio.bsky.social.
Great collaboration of the Kelly Lab and @landerlab.bsky.social #cryoEM #amyloid www.biorxiv.org/content/10.1...
Reposted by Andrea Dallapè
Muyuan Chen has turned structural biology into an immersive experience with his new video game Meowtabolism, now available on Steam.
Try the demo here: store.steampowered.com/app/4045010/...
Give Muyuan feedback: steamcommunity.com/app/4045010
#ScienceGaming #StructuralBiology #CryoEM #STEMOutreach
Try the demo here: store.steampowered.com/app/4045010/...
Give Muyuan feedback: steamcommunity.com/app/4045010
#ScienceGaming #StructuralBiology #CryoEM #STEMOutreach
October 4, 2025 at 1:34 PM
Muyuan Chen has turned structural biology into an immersive experience with his new video game Meowtabolism, now available on Steam.
Try the demo here: store.steampowered.com/app/4045010/...
Give Muyuan feedback: steamcommunity.com/app/4045010
#ScienceGaming #StructuralBiology #CryoEM #STEMOutreach
Try the demo here: store.steampowered.com/app/4045010/...
Give Muyuan feedback: steamcommunity.com/app/4045010
#ScienceGaming #StructuralBiology #CryoEM #STEMOutreach
Reposted by Andrea Dallapè
Historically, viruses were thought to primarily use host cell's translational machinery. New work from @harvardcellbio.bsky.social faculty Amy Lee reveals that a giant DNA virus encodes its own IF4F initiation complex, suggesting an unexpected evolutionary innovation. www.biorxiv.org/content/10.1...
Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life
In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA virus...
www.biorxiv.org
October 2, 2025 at 6:10 PM
Historically, viruses were thought to primarily use host cell's translational machinery. New work from @harvardcellbio.bsky.social faculty Amy Lee reveals that a giant DNA virus encodes its own IF4F initiation complex, suggesting an unexpected evolutionary innovation. www.biorxiv.org/content/10.1...
Reposted by Andrea Dallapè
Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
September 26, 2025 at 2:28 AM
Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
Reposted by Andrea Dallapè
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 6:00 PM
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/🧵
Reposted by Andrea Dallapè
Huntingtin binds and bundles F-actin!
Thrilled to team up with the Humbert (Sorbonne Université) and Song (KAIST) labs on this discovery.
We had a blast doing cryo-ET on this unexpected complex — and now so many new questions lie ahead!
#TeamTomo #CryoET #HTT #actin
doi.org/10.1126/scia...
Thrilled to team up with the Humbert (Sorbonne Université) and Song (KAIST) labs on this discovery.
We had a blast doing cryo-ET on this unexpected complex — and now so many new questions lie ahead!
#TeamTomo #CryoET #HTT #actin
doi.org/10.1126/scia...
September 25, 2025 at 3:01 PM
Huntingtin binds and bundles F-actin!
Thrilled to team up with the Humbert (Sorbonne Université) and Song (KAIST) labs on this discovery.
We had a blast doing cryo-ET on this unexpected complex — and now so many new questions lie ahead!
#TeamTomo #CryoET #HTT #actin
doi.org/10.1126/scia...
Thrilled to team up with the Humbert (Sorbonne Université) and Song (KAIST) labs on this discovery.
We had a blast doing cryo-ET on this unexpected complex — and now so many new questions lie ahead!
#TeamTomo #CryoET #HTT #actin
doi.org/10.1126/scia...
Reposted by Andrea Dallapè
Ever wondered how to position organelles in bacteria? Wonder no more!
Happy to have contributed to this fantastic story from @cellforganized.bsky.social' lab.
The avenues this opens in the synthetic biology space are enormous!
Movie: Carboxysomes positioned in E. coli!
Preprint: shorturl.at/D6xVg
Happy to have contributed to this fantastic story from @cellforganized.bsky.social' lab.
The avenues this opens in the synthetic biology space are enormous!
Movie: Carboxysomes positioned in E. coli!
Preprint: shorturl.at/D6xVg
September 23, 2025 at 3:31 PM
Ever wondered how to position organelles in bacteria? Wonder no more!
Happy to have contributed to this fantastic story from @cellforganized.bsky.social' lab.
The avenues this opens in the synthetic biology space are enormous!
Movie: Carboxysomes positioned in E. coli!
Preprint: shorturl.at/D6xVg
Happy to have contributed to this fantastic story from @cellforganized.bsky.social' lab.
The avenues this opens in the synthetic biology space are enormous!
Movie: Carboxysomes positioned in E. coli!
Preprint: shorturl.at/D6xVg
Reposted by Andrea Dallapè
A molecular-resolution look into the near-native architecture of the spinach chloroplast🌱. This one was a long time in the oven, but we're happy to finally share our "version of record". What long-standing debates did we settle? Check back for a short thread🧵 on Monday. #TeamTomo #PlantScience 🧪🧶🧬🔬🌾
🌱 Using ‘compelling’ methods, including #CryoET, researchers mapped spinach thylakoid membranes at single-molecule precision, revealing how photosynthetic complexes are organised and settling long-standing debates on chloroplast architecture.
buff.ly/j3TSIkn
buff.ly/j3TSIkn
September 20, 2025 at 7:24 PM
A molecular-resolution look into the near-native architecture of the spinach chloroplast🌱. This one was a long time in the oven, but we're happy to finally share our "version of record". What long-standing debates did we settle? Check back for a short thread🧵 on Monday. #TeamTomo #PlantScience 🧪🧶🧬🔬🌾
Reposted by Andrea Dallapè
Structural dynamics of mitochondrial ATP synthase in Chlamydomonas reinhardtii revealed by in situ CryoET https://www.biorxiv.org/content/10.1101/2025.09.10.674987v1
September 16, 2025 at 4:30 PM
Structural dynamics of mitochondrial ATP synthase in Chlamydomonas reinhardtii revealed by in situ CryoET https://www.biorxiv.org/content/10.1101/2025.09.10.674987v1
Impressive! Congratulations!
Happy to share a new preprint from the Clarke & Vallese (@fravallese.bsky.social) labs reporting #cryoem structures of two RBC stomatin complexes – with AQP1 & UT-B - continuing the SPFH theme from our recent vault preprint! This was a fun one and has been cooking for a while - read on for more! ⬇️
August 30, 2025 at 3:18 PM
Impressive! Congratulations!
Reposted by Andrea Dallapè
New Title Alert: AITom- an open-source platform for AI driven cellular electron cryo-tomography analysis.
Learn more here: buff.ly/LLGhjvY
#SBGrid #SBGridSoftware #StructuralBiology
Learn more here: buff.ly/LLGhjvY
#SBGrid #SBGridSoftware #StructuralBiology
Research
Xu Lab of Computational Biology
buff.ly
August 12, 2025 at 4:03 PM
New Title Alert: AITom- an open-source platform for AI driven cellular electron cryo-tomography analysis.
Learn more here: buff.ly/LLGhjvY
#SBGrid #SBGridSoftware #StructuralBiology
Learn more here: buff.ly/LLGhjvY
#SBGrid #SBGridSoftware #StructuralBiology
Reposted by Andrea Dallapè
We found a new #ecological factor in #microbial mats: the #bacterial contractile injection system. Using #cryoET, #metagenomics, & quantitative #immunoTEM, we studied this feature directly in natural populations of bacterial #cells.
Check out 🧐 our new preprint 📜:
www.biorxiv.org/content/10.1...
Congrats🎉 to @vasilgaisin.bsky.social and Corina Hadjicharalambous, who studied contractile injection systems directly in hot spring♨️ bacterial mats🦠
#microsky #teamtomo #Chloroflexota
www.biorxiv.org/content/10.1...
Congrats🎉 to @vasilgaisin.bsky.social and Corina Hadjicharalambous, who studied contractile injection systems directly in hot spring♨️ bacterial mats🦠
#microsky #teamtomo #Chloroflexota
August 12, 2025 at 11:50 AM
We found a new #ecological factor in #microbial mats: the #bacterial contractile injection system. Using #cryoET, #metagenomics, & quantitative #immunoTEM, we studied this feature directly in natural populations of bacterial #cells.
Lovely.
So many US states I never heard of before, I definitely have to study an US map much better
So many US states I never heard of before, I definitely have to study an US map much better
My goto is to ask LLMs how many states have R in their name. They always fail. GPT 5 included Indiana, Illinois, and Texas in its list. It then asked me if I wanted an alphabetical highlighted map. Sure, why not.
August 8, 2025 at 6:34 AM
Lovely.
So many US states I never heard of before, I definitely have to study an US map much better
So many US states I never heard of before, I definitely have to study an US map much better
Reposted by Andrea Dallapè
Not my area at all, but how cool are these cryoEM structures of purely RNA-based assemblies!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 6, 2025 at 10:42 PM
Not my area at all, but how cool are these cryoEM structures of purely RNA-based assemblies!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Andrea Dallapè
Here is the correct link: www.biorxiv.org/content/10.1...
Cryo-EM structures of Egl-BicD-RNA complexes reveal how diverse mRNAs are selected for subcellular localization
Localization of mRNAs is a widespread mechanism for controlling where proteins operate in cells and underpins many fundamental processes, from embryonic patterning to synaptic plasticity. This spatial...
www.biorxiv.org
August 5, 2025 at 11:18 AM
Here is the correct link: www.biorxiv.org/content/10.1...