Ricardo D. Righetto
@lifeonthewedge.bsky.social
Staff scientist @biozentrum.unibas.ch using algorithms to look at tiny stuff inside cells, or #cryoET if you prefer. Here I talk mostly about my research. Views my own. 🇧🇷 in 🇨🇭
Pinned
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
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 Ricardo D. Righetto
I am excited to share our new preprint on our structural and biochemical analyses of human methionine synthase (MTR). This was the hard work of Douglas Ferreira who carried out this research as a significant part of his PhD. #CryoEM www.biorxiv.org/content/10.1...
Structural insights into cobalamin loading and reactivation of human methionine synthase
Human methionine synthase (MTR) is an essential enzyme of one carbon metabolism. Consisting of a catalytic N-half and a cobalamin binding C-half, MTR utilises this intricate organometallic cofactor in...
www.biorxiv.org
November 11, 2025 at 12:48 PM
I am excited to share our new preprint on our structural and biochemical analyses of human methionine synthase (MTR). This was the hard work of Douglas Ferreira who carried out this research as a significant part of his PhD. #CryoEM www.biorxiv.org/content/10.1...
Reposted by Ricardo D. Righetto
Last week, the Dodonova lab published a fascinating paper on chromatin structures in Asgard archaea, microbes thought to be the closest relatives of complex life.
Asgard histones can wrap DNA into a “closed” form shared across archaea, and an “open” form similar to eukaryotic cells #sciart #blender
Asgard histones can wrap DNA into a “closed” form shared across archaea, and an “open” form similar to eukaryotic cells #sciart #blender
November 11, 2025 at 10:41 AM
Many Stentors were harmed in this study
(and it's great)
(and it's great)
Wound healing is a hallmark feature of all life, including single cells. In a new preprint, Ambika Nadkarni @biochembika.bsky.social investigates a new dimension in cellular wound healing: how cells recover AFTER the wound has been closed
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 11, 2025 at 9:36 PM
Many Stentors were harmed in this study
(and it's great)
(and it's great)
Reposted by Ricardo D. Righetto
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
November 7, 2025 at 10:44 AM
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Reposted by Ricardo D. Righetto
Our new preprint is out 🥳🥳🥳
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
November 3, 2025 at 12:26 PM
Our new preprint is out 🥳🥳🥳
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
This is pretty cool!
Undergrads @biozentrum.unibas.ch are learning RFdiffusion at our Structural Biology Block Course organized by @computingcaitie.bsky.social, Basile Wicky et al. 😉
www.nature.com/articles/s41...
Undergrads @biozentrum.unibas.ch are learning RFdiffusion at our Structural Biology Block Course organized by @computingcaitie.bsky.social, Basile Wicky et al. 😉
www.nature.com/articles/s41...
Atomically accurate de novo design of antibodies with RFdiffusion - Nature
The combination of computational design, laboratory-based screening and biophysical validation enables the de novo generation of variable heavy-chain antibody fragments and antibodies that precis...
www.nature.com
November 6, 2025 at 11:19 AM
This is pretty cool!
Undergrads @biozentrum.unibas.ch are learning RFdiffusion at our Structural Biology Block Course organized by @computingcaitie.bsky.social, Basile Wicky et al. 😉
www.nature.com/articles/s41...
Undergrads @biozentrum.unibas.ch are learning RFdiffusion at our Structural Biology Block Course organized by @computingcaitie.bsky.social, Basile Wicky et al. 😉
www.nature.com/articles/s41...
Reposted by Ricardo D. Righetto
Excited to share our latest @nature.com: How does naloxone (Narcan) stop an opioid overdose? We determined the first GDP-bound μ-opioid receptor–G protein structures and found naloxone traps a novel "latent” state, preventing GDP release and G protein activation.💊🧪 🧵👇 www.nature.com/articles/s41...
November 5, 2025 at 4:23 PM
Excited to share our latest @nature.com: How does naloxone (Narcan) stop an opioid overdose? We determined the first GDP-bound μ-opioid receptor–G protein structures and found naloxone traps a novel "latent” state, preventing GDP release and G protein activation.💊🧪 🧵👇 www.nature.com/articles/s41...
Reposted by Ricardo D. Righetto
Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
October 28, 2025 at 3:07 PM
Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
Reposted by Ricardo D. Righetto
Glushkova, Böhm, & Beck @maxplanck.de develop a publicly available computational method to measure the thickness of biological membranes in cryo-electron tomograms. Analysis of algae & human cells reveals systematic membrane thickness variations within & across organelles rupress.org/jcb/article/...
November 4, 2025 at 5:30 PM
Glushkova, Böhm, & Beck @maxplanck.de develop a publicly available computational method to measure the thickness of biological membranes in cryo-electron tomograms. Analysis of algae & human cells reveals systematic membrane thickness variations within & across organelles rupress.org/jcb/article/...
Always happy to see the #ChlamyDataset put to good use 😉
Just published! We share an open-source workflow to measure membrane thickness from tomograms, including a tutorial with 3D visualizations. We analyze thickness variations across organelles and reflect on where to define a membrane boundary. @becklab.bsky.social #teamtomo rupress.org/jcb/article/...
November 6, 2025 at 8:00 AM
Always happy to see the #ChlamyDataset put to good use 😉
I'm pleased to announce 🍦 Icecream 🍨 v0.3!
New features include:
* Training on multiple tomograms (same training time, with linear increase in RAM) 🚀
* Logging and plotting of the loss function 📉
* The --scale option is now called --eq-weight for clarity 😉
We'd love to hear your feedback! 🙏🏽
New features include:
* Training on multiple tomograms (same training time, with linear increase in RAM) 🚀
* Logging and plotting of the loss function 📉
* The --scale option is now called --eq-weight for clarity 😉
We'd love to hear your feedback! 🙏🏽
November 5, 2025 at 2:41 PM
I'm pleased to announce 🍦 Icecream 🍨 v0.3!
New features include:
* Training on multiple tomograms (same training time, with linear increase in RAM) 🚀
* Logging and plotting of the loss function 📉
* The --scale option is now called --eq-weight for clarity 😉
We'd love to hear your feedback! 🙏🏽
New features include:
* Training on multiple tomograms (same training time, with linear increase in RAM) 🚀
* Logging and plotting of the loss function 📉
* The --scale option is now called --eq-weight for clarity 😉
We'd love to hear your feedback! 🙏🏽
Reposted by Ricardo D. Righetto
imigração é um direito. fronteiras são inventadas. bichos migram, os seres humanos sempre mudaram de lugar.
I think this constant push for immigrants to feel & act ‘grateful’ is so insidious. Let’s change the narrative. Migration is a normal part of human behaviour, not a charity case. If you’re doing your best to do your best, you don’t need to do even more to be accepted. It’s your right to be accepted.
November 5, 2025 at 7:20 AM
imigração é um direito. fronteiras são inventadas. bichos migram, os seres humanos sempre mudaram de lugar.
Reposted by Ricardo D. Righetto
Remember when Aaron Swartz downloaded JSTOR archives that he had full legal rights to download and the FBI hounded him literally to death for it? Anyway,
NEW: Common Crawl, the massive archiver of the web, has gotten cozy with AI companies and is providing paywalled articles for training data. They’re also lying to publishers who have asked for material to be removed. “The robots are people too,” CC’s exec director told us when we asked about this.
The Nonprofit Feeding the Entire Internet to AI Companies
Common Crawl claims to provide a public benefit, but it lies to publishers about its activities.
www.theatlantic.com
November 4, 2025 at 2:06 PM
Remember when Aaron Swartz downloaded JSTOR archives that he had full legal rights to download and the FBI hounded him literally to death for it? Anyway,
Reposted by Ricardo D. Righetto
Neutralizing antibodies against Chikungunya virus and structural elucidation of their mechanism of action pubmed.ncbi.nlm.nih.gov/41184282/ #cryoem
November 4, 2025 at 10:15 AM
Neutralizing antibodies against Chikungunya virus and structural elucidation of their mechanism of action pubmed.ncbi.nlm.nih.gov/41184282/ #cryoem
Reposted by Ricardo D. Righetto
CryoWriter: A Robotic Solution for Improved Cryo-EM Grid Preparation https://www.biorxiv.org/content/10.1101/2025.11.01.686008v1
November 3, 2025 at 1:47 AM
CryoWriter: A Robotic Solution for Improved Cryo-EM Grid Preparation https://www.biorxiv.org/content/10.1101/2025.11.01.686008v1
Reposted by Ricardo D. Righetto
November 2, 2025 at 9:24 AM
Reposted by Ricardo D. Righetto
And it’s a double feature, as shown by @gautamdey.bsky.social ial & @floravincent.bsky.social for the sturdy #Diatoms! Also out today in @currentbiology.bsky.social 🌊
www.cell.com/current-biol...
www.cell.com/current-biol...
Diatom ultrastructural diversity across controlled and natural environments
Flori et al. establish high-resolution and generalizable immunofluorescence in cultured
and environmental diatoms, thanks to 4-fold cryo-expansion microscopy. This represents
a step-change for compara...
www.cell.com
October 31, 2025 at 2:42 PM
And it’s a double feature, as shown by @gautamdey.bsky.social ial & @floravincent.bsky.social for the sturdy #Diatoms! Also out today in @currentbiology.bsky.social 🌊
www.cell.com/current-biol...
www.cell.com/current-biol...
Reposted by Ricardo D. Righetto
🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
October 31, 2025 at 2:42 PM
🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
Reposted by Ricardo D. Righetto
This will be a long thread on yesterday police massacre in Rio.
In nothern Rio de Janeiro city, there is a couple of hills called Complexo da Penha. It's Comando Vermelho("Red Command", a drug gang), or CV, territory.
CV is the greatest gang in Rio, second in the whole Brazil.
+
In nothern Rio de Janeiro city, there is a couple of hills called Complexo da Penha. It's Comando Vermelho("Red Command", a drug gang), or CV, territory.
CV is the greatest gang in Rio, second in the whole Brazil.
+
🧵 Awful awful massacre in Brazil
Gente, é o maior massacre no Brasil desde o Araguaia. Entendo quem quer puxar pra Canudos ou Contestado ou etc, mas não podemos livrar a ditadura de 64 só porque ela escondia melhor seus corpos.
Morreram 41 guerrilheiros comunistas e mais de 1200 camponeses no Araguaia.
Morreram 41 guerrilheiros comunistas e mais de 1200 camponeses no Araguaia.
October 29, 2025 at 11:52 PM
This will be a long thread on yesterday police massacre in Rio.
In nothern Rio de Janeiro city, there is a couple of hills called Complexo da Penha. It's Comando Vermelho("Red Command", a drug gang), or CV, territory.
CV is the greatest gang in Rio, second in the whole Brazil.
+
In nothern Rio de Janeiro city, there is a couple of hills called Complexo da Penha. It's Comando Vermelho("Red Command", a drug gang), or CV, territory.
CV is the greatest gang in Rio, second in the whole Brazil.
+
Reposted by Ricardo D. Righetto
We are looking for a computational postdoc to work with us on new optimisation algorithms to make #RELION even better. Join our bubbly team at the @mrclmb.bsky.social in Cambridge, UK. 🤗 RTs appreciated.
mrc.tal.net/vx/appcentre...
mrc.tal.net/vx/appcentre...
Quick Check Needed
mrc.tal.net
October 29, 2025 at 9:17 AM
We are looking for a computational postdoc to work with us on new optimisation algorithms to make #RELION even better. Join our bubbly team at the @mrclmb.bsky.social in Cambridge, UK. 🤗 RTs appreciated.
mrc.tal.net/vx/appcentre...
mrc.tal.net/vx/appcentre...
Reposted by Ricardo D. Righetto
Congratulations to Yann Quilcaille, postdoc for #Climate Extremes at ETH Zurich, named to the #TIME 100 Climate 2025 list for exposing top carbon emitters driving extreme heat worldwide.
Yann Quilcaille: The 100 Most Influential Climate Leaders of 2025
Find out why Yann Quilcaille is on TIME's 2025 list of the 100 most influential leaders driving business climate action.
time.com
October 30, 2025 at 2:43 PM
E-mail, Discord, Slack, Zulip, WhatsApp, Signal 🫠
I guess the silver lining is I never, ever, have to use Teams?
I guess the silver lining is I never, ever, have to use Teams?
October 29, 2025 at 9:11 AM
E-mail, Discord, Slack, Zulip, WhatsApp, Signal 🫠
I guess the silver lining is I never, ever, have to use Teams?
I guess the silver lining is I never, ever, have to use Teams?
Reposted by Ricardo D. Righetto
Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE
Artificial Intelligence Driven protein Estimation (AIDE), enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods
doi.org/10.1093/bioi...
Artificial Intelligence Driven protein Estimation (AIDE), enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods
doi.org/10.1093/bioi...
October 29, 2025 at 7:45 AM
Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE
Artificial Intelligence Driven protein Estimation (AIDE), enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods
doi.org/10.1093/bioi...
Artificial Intelligence Driven protein Estimation (AIDE), enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods
doi.org/10.1093/bioi...
Reposted by Ricardo D. Righetto
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
Reposted by Ricardo D. Righetto
We’re back with the next DinoSphere Online Seminar!
Join us on Nov 4th, we're hosting:
Edmée Royen (ULiège) - Symbiodinium
Nicolas dos Santos Pacheco (Cambridge) - Perkinsids
📅 Tue, Nov 4 - 4 PM CET/3 PM GMT
💻 Zoom link: sites.google.com/view/dinosphere
Please spread the word!
#protistonsky
Join us on Nov 4th, we're hosting:
Edmée Royen (ULiège) - Symbiodinium
Nicolas dos Santos Pacheco (Cambridge) - Perkinsids
📅 Tue, Nov 4 - 4 PM CET/3 PM GMT
💻 Zoom link: sites.google.com/view/dinosphere
Please spread the word!
#protistonsky
October 28, 2025 at 3:29 PM
We’re back with the next DinoSphere Online Seminar!
Join us on Nov 4th, we're hosting:
Edmée Royen (ULiège) - Symbiodinium
Nicolas dos Santos Pacheco (Cambridge) - Perkinsids
📅 Tue, Nov 4 - 4 PM CET/3 PM GMT
💻 Zoom link: sites.google.com/view/dinosphere
Please spread the word!
#protistonsky
Join us on Nov 4th, we're hosting:
Edmée Royen (ULiège) - Symbiodinium
Nicolas dos Santos Pacheco (Cambridge) - Perkinsids
📅 Tue, Nov 4 - 4 PM CET/3 PM GMT
💻 Zoom link: sites.google.com/view/dinosphere
Please spread the word!
#protistonsky