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Miro Astore

@miroastore.bsky.social
457 followers 533 following 37 posts

Postdoc @rockefeller. Making cryoEM into a tool for RNA biophysics one molecule at a time.

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Miro Astore @miroastore.bsky.social · 27/04/2026
Responses to this work have been great. I want to specifically highlight the contributions of Robert Clark tinyurl.com/5dmm5yns. He started this project as an intern and made it into a rigorous study. He's starting to look for postdocs and I cant recommend him highly enough. Please reach out to him!
tinyurl.com
Have a look at my paper! I have had an amazing time working on this and I'm really proud of the outcome. I want to say thank you in particular to Miro Astore, Sonya Hanson and Pilar Cossio for the...
Have a look at my paper! I have had an amazing time working on this and I'm really proud of the outcome. I want to say thank you in particular to Miro Astore, Sonya Hanson and Pilar Cossio for the int...
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Miro Astore @miroastore.bsky.social · 24/04/2026
Everybody gave this their all so thank you for all your dedication robbieclark.bsky.social , Louis Smith, Ryan Szukalo , @mleighton.bsky.social , @sykhalid.bsky.social , Pablo Debenedetti, @pilarcossio.bsky.social and @sonyahanson.bsky.social. This wouldn't have happened without any of you!
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Miro Astore @miroastore.bsky.social · 24/04/2026
It's hard to express how much work went into this in a few tweets and how excited we all are by the results. Big things are still to come from CryoEM. This work has been a true team effort so thank you to all my coauthors and the scientific computing core at the Flatiron.
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Miro Astore @miroastore.bsky.social · 24/04/2026
We also developed a reweighting approach to reverse nearly all the effects of cooling. From the second law of thermodynamics, we found narrow constraints which allowed us to nearly completely recover the equilibrium ensemble from our cooled samples.
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Miro Astore @miroastore.bsky.social · 24/04/2026
Something interesting happened in the protein structure though. We found that after cooling, solvent exposed residues tended to exhibit greater changes than buried ones, and the whole protein compacted slightly. Whether this effects larger molecular systems remains to be seen.
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Miro Astore @miroastore.bsky.social · 24/04/2026
We cooled Trpcage at 7 rates, up to the slowest experimental rate where ice crystals form. We found that if a given state cannot exchange more than 5% of the total population to other states, its population is preserved after cooling. Further, no states were lost due to cooling.
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Miro Astore @miroastore.bsky.social · 24/04/2026
To our surprise, the rate at which we cooled the system had little influence on the solvent. By nearly every measure, the surrounding water acts like bulk no matter how quickly we cool it. This means that the glassy water in cryoEM samples acts like low density amorphous water.
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Miro Astore @miroastore.bsky.social · 24/04/2026
Our model system was the Trpcage protein which cold-unfolds. Meaning we know that the temperature we cooled toward has a different ensemble compared to the "hot" equilibrium we started from. By constructing an MSM with MD simulations, we could study the kinetic limits of cryoEM.
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Miro Astore @miroastore.bsky.social · 24/04/2026
CryoEM relies on rapid cooling to form vitreous ice. It's crucial that this happens faster than crystalline ice forms which takes 22 μs. By finding the "hot" ensemble of a molecule and then cooling it, we determined the effects of this cooling and found ways to reverse them.
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Miro Astore @miroastore.bsky.social · 24/04/2026
We just preprinted one of my favorite studies @FlatironInst . I was lucky to be part of an amazing team studying the effects of rapid cooling to preserve samples in cryoEM. Read on to learn about the limits of cryoEM for biophysics and how to overcome them www.biorxiv.org/content/10.6...
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Miro Astore @miroastore.bsky.social · 06/04/2026
How are competitive new grants looking ?
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Miro Astore @miroastore.bsky.social · 22/02/2026
Cannot recommend the talk by Louis Smith enough. It's been such an amazing project!
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Miro Astore @miroastore.bsky.social · 10/02/2026
Really neat math that I use a lot. Well done @pilarcossio.bsky.social, Wai Shing, Jeff and Adi!
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Michael O’Brien @m0bri3n.bsky.social · 06/02/2026
It’s been fun to put together and write up cryoJAX. Hooray for open-source cryo-EM software! Now it’s time to use it…
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Miro Astore @miroastore.bsky.social · 04/02/2026
github.com/michael-0bri...
github.com
GitHub - michael-0brien/cryojax: A cryo-electron microscopy image simulation library for building data analysis in JAX
A cryo-electron microscopy image simulation library for building data analysis in JAX - michael-0brien/cryojax
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Miro Astore @miroastore.bsky.social · 04/02/2026
Go use cryojax ! It's awesome! I can't wait to see what people do with it.
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Structural Biology @actacrystd.iucr.org · 20/01/2026
Alexandre G. Urzhumtsev: Quantifying distributions of cryo-EM projections #CryoEM #AngularDistributionOfViews #NonUniformDistribution ... #IUCr journals.iucr.org/paper?S2059798325…
journals.iucr.org
Quantifying distributions of cryo-EM projections
We propose a numerical measure to quantify the deviation of a distribution of cryo-EM 2D views from the uniform distribution. This approach allows the traditional two-dimensional projection diagrams to be complemented with quantitative characteristics and simple, easily generated curves that are straightforward to analyze.
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Miro Astore @miroastore.bsky.social · 31/12/2025
Thank you for writing it @fraserlab.com! It was super valuable and detailed.
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cryoEM papers @cryoempapers.bsky.social · 25/11/2025
The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge pubmed.ncbi.nlm.nih.gov/41280101/ #cryoEM
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cryoEM papers @cryoempapers.bsky.social · 20/11/2025
CryoLike: a Python package for cryo-electron microscopy image-to-structure likelihood calculations pubmed.ncbi.nlm.nih.gov/41258998/ #cryoEM
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Miro Astore @miroastore.bsky.social · 14/11/2025
Hello world! It's been a true joy to work on this with Michael. Both him and cryoJAX are things to keep an eye on. They're going to make amazing things happen in cryo and beyond.
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cryoEM papers @cryoempapers.bsky.social · 25/10/2025
CryoJAX - A Cryo-Electron Microscopy Image Simulation Library in JAX www.biorxiv.org/content/10.1101/2025.10.23.682564v1 #cryoEM
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Miro Astore @miroastore.bsky.social · 21/09/2025
Phew!
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Miro Astore @miroastore.bsky.social · 20/09/2025
The text of the order says it's a one time charge for new petitions, renewals and transfers. www.whitehouse.gov/presidential...
whitehouse.gov
Restriction on Entry of Certain Nonimmigrant Workers
BY THE PRESIDENT OF THE UNITED STATES OF AMERICA A PROCLAMATION The H-1B nonimmigrant visa program was created to bring temporary workers into the United
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Oli Clarke @olibclarke.bsky.social · 13/09/2025
This one is a bit of a departure from the usual and definitely a work in progress! We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below. Read on for details... 1/x
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Miro Astore @miroastore.bsky.social · 14/09/2025
I'm very excited to announce that I've just joined Steve_Bonilla's lab at @rockefelleruniv.bsky.social. With the help of @pilarcossio.bsky.social and colleagues at @flatironinstitute.org. I'll be developing cryoEM into a quantitative method to study RNA biophysics.
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Khaled_Selim Lab @selimlab.bsky.social · 24/07/2025
The results of the first #cryoEM heterogeneity challenge are up on biorxiv! www.biorxiv.org/content/10.1...
biorxiv.org
The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge
Despite the rise of single particle cryo-electron microscopy (cryo-EM) as a premier method for resolving macromolecular structures at atomic resolution, methods to address molecular heterogeneity in v...
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Miro Astore @miroastore.bsky.social · 24/07/2025
Link that works www.biorxiv.org/content/10.1...
biorxiv.org
The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge
Despite the rise of single particle cryo-electron microscopy (cryo-EM) as a premier method for resolving macromolecular structures at atomic resolution, methods to address molecular heterogeneity in v...
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Miro Astore @miroastore.bsky.social · 23/07/2025
Omg thank you. Oops www.biorxiv.org/content/10.1...
biorxiv.org
The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge
Despite the rise of single particle cryo-electron microscopy (cryo-EM) as a premier method for resolving macromolecular structures at atomic resolution, methods to address molecular heterogeneity in v...
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Miro Astore @miroastore.bsky.social · 23/07/2025
Omg thank you. Oops www.biorxiv.org/content/10.1...
biorxiv.org
The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge
Despite the rise of single particle cryo-electron microscopy (cryo-EM) as a premier method for resolving macromolecular structures at atomic resolution, methods to address molecular heterogeneity in v...
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Miro Astore @miroastore.bsky.social · 23/07/2025
You can also check out the analysis workflow and the datasets themselves if you'd like to learn more github.com/flatironinst... www.simonsfoundation.org/flatiron/cen...
github.com
GitHub - flatironinstitute/Cryo-EM-Heterogeneity-Challenge-1: The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge
The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge - flatironinstitute/Cryo-EM-Heterogeneity-Challenge-1
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Miro Astore @miroastore.bsky.social · 23/07/2025
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Miro Astore @miroastore.bsky.social · 23/07/2025
This has been so much work from my coauthors Geoff Woollard and David Silva-Sanchez, mentors @sonyahanson.bsky.social and @pilarcossio.bsky.social , Misha Kopylov at NYSBC, and all the participants who have continuously given us excellent feedback on the study and the manuscript. Thanks everybody!
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Miro Astore @miroastore.bsky.social · 23/07/2025
The last metric we used calculates the likelihood that a given ensemble of volumes is contained in a set of images. This one is really exciting because we don't need any ground truth to compare to. We see the same trends between the simulated and experimental datasets.
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Miro Astore @miroastore.bsky.social · 23/07/2025
The next is based on optimal transport. By calculating the differences between maps in a submission and the ground truth, we can calculate how close a submission is to the truth. We can also see how far from optimal participants estimated their populations.
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Miro Astore @miroastore.bsky.social · 23/07/2025
Now comes the real work. Comparing all this amazing data! We came up with three novel ways of comparing series of volumes. With the first we simply perform PCA on the voxel maps and compare their bases. Turns out to be a super useful way of comparing motions between submissions.
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Miro Astore @miroastore.bsky.social · 23/07/2025
We had amazing participation. Almost every method in the literature submitted to this challenge. We've chosen to keep the identity of the submissions anonymous (you'll see them in the manuscript denoted by icecream flavor hehe).
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Miro Astore @miroastore.bsky.social · 23/07/2025
We asked each participant to give us two things. 80 volume maps which they thought gave a good representation of the molecular states in the data. And relative populations between those molecular states.
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Miro Astore @miroastore.bsky.social · 23/07/2025
That's why we launched this challenge. We made two datasets, one experimental and one simulated. The simulated one was made with structures from molecular dynamics simulations. Here we hid a triple Gaussian for participants to discover. (Movie credit David Herreros).
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Miro Astore @miroastore.bsky.social · 23/07/2025
There has been an explosion of methods to determine molecular ensembles from single particle cryo-EM datasets. However, these methods all use totally different algorithms and it's currently unknown how to assess their accuracy without ground truth structures to compare with.
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Miro Astore @miroastore.bsky.social · 23/07/2025
That's a wrap! The results of the first #cryoEM heterogeneity challenge are up on biorxiv! biorxiv.org/content/10.110
biorxiv.org
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Miro Astore @miroastore.bsky.social · 30/03/2025
Super excited for this one! Great job guys.
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Lander Lab @landerlab.bsky.social · 19/03/2025
That’s a wrap on the 2025 Cold Spring Harbor CryoEM course! Huge thanks to the amazing students for your enthusiasm, the TAs for your dedication, and the invited lecturers for sharing your expertise. Keep pushing the boundaries of single particle EM - excited to see what you all accomplish next!
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Miro Astore @miroastore.bsky.social · 16/03/2025
Watch out world. I can pipette now.
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Lander Lab @landerlab.bsky.social · 16/03/2025
Saturday night and the lab is in full swing as the participants of the CSHL #CryoEM course prepare for the final competition - solve the structure of a mystery protein in less than 4 hours.
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Miro Astore @miroastore.bsky.social · 17/02/2025
Come work in a great place with great people. Loads of fun projects and ideas.
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 05/02/2025
Join leaders from CCDC, ICDD, ICSD, and RCSB PDB on February 12 to learn how data management impacts future research register.gotowebinar...
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Frank Noe @franknoe.bsky.social · 06/12/2024
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...
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YC Lin @yiechanglin.bsky.social · 19/11/2024
I made a MD starter pack! Dm or reply to be added ☺️☺️ go.bsky.app/QQjPjbL
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