Sonya

Super excited to have this preprint lead by @jayrshenoy out for people to see! Exciting work!

AlphaFold-based models like Boltz-2 and BioEmu train on atomic conformational structures in order to predict protein dynamics. But is it possible to train these models directly on cryo-EM map ensembles, harnessing conformational data that is typically not deposited in the PDB? Introducing CryoSampler: a new approach for fine-tuning Boltz-2 with raw supervision on cryo-EM map ensembles. 1/6🧵

Super proud of @PolymathicAI 's new foundation model on biomolecules! 🚀 It was probably the most challenging datasets 💪 we have gathered so far (which we are making public!) and realizing biology is super hard even when you work with the best domain scientists @PilarCossio2 @sonyahans @JonesyLab & @OlgaTroyanskaya Hats off to the team led by @SiavashGolkar J.Kovalic @irina_espejo , @samsledzieski & @mhli41 !

Postdoc job opening! This is a unique opportunity to work at the intersection of computation of experiment between us at the Flatiron and a time-resolved cryo-EM lab at the Crick: crick.wd3.myworkdayjobs.com/External/job/L… Deadline May 6.

Celebrating #BiophysicsWeek T&C partnered with Phase Space Invaders podcast: Robert Best @sonyahans @XuhuiHuangChem and host @MiWieczor Episode 32: Driving the Future of Biophysics: What’s Next in Theory and Computation? buzzsprout.com/2313153/episod…

If you're not on the multi-thousand-person cryo-EM listservs... we (EZ lab @PrincetonCS, @FlatironInst, #CCPEM) just announced a new #heterogeneity challenge for cryo-EM! #CAHRA2025 Webinar this Fri Nov 14 at 12p ET. Datasets and more info here: heterogeneity.notion.site/challenge We've been preparing this challenge for over a year 🥵 (designing the heterogeneity, collecting data, validating results and metrics). Super excited to finally share it with the community! There are three mystery❓❔❓ datasets! Some fun facts about each: 1) comp-het: an experimental dataset containing a mixture of mystery❔complexes 2) conf-het: we're asking folks to submit *atomic models* instead of density maps for the first time ❗️❕ 3) pose-entanglement: a simple dataset to test how much the pose distribution influences conformation estimation 🐎 Huge shoutout to the members of my group driving this work @FeathersRyan and Robert Heeter, @sonyahans + @PilarCossio2's groups @FlatironInst, and Joel Greer from Tom Burnley's group at #CCPEM. Calling both methods developers and users to participate! Check out our website for more details!

@IrinaBezsonova @buildmodels This is so cool! Love that you do this! Have you done a TRP channel?

This October I’m drawing 1 molecule a day inspired by proteins in pdb @buildmodels #Inktober2025 Day 23/31 Prompt FIREFLY Pdb: 2D1R Luciferase: firefly enzyme catalyzes a light-producing reaction that makes fireflies glow. Next: ROWDY Suggestions?

Announcing cryo-EM heterogeneity challenge #2, now dubbed the 2025 Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms (CAHRA)! Join us for a webinar next Friday (Nov 14th) to learn more. Datasets already posted here: heterogeneity.notion.site/challenge

Last week, #FlatironCCM and #FlatironCCB held a Computational Cryo-EM Workshop that focused on methods for 3D heterogeneity analysis including deep learning and statistical techniques in cryo-EM. #science #biology #math

Check out our latest preprint for the first community #cryoEM heterogeneity challenge 🎆🎇 @sonyahans @miroastore + method developers and participants!

That's a wrap! The results of the first #cryoEM heterogeneity challenge are up on biorxiv! biorxiv.org/content/10.110…

Interested in pursuing graduate studies in Biophysics at U-M? We're inviting prospective students to explore our program hands-on! We're now accepting applications for the Biophysics Graduate Preview Program on October 23-24, 2025.📅 Learn more & apply: lsa.umich.edu/biophysics/gra…

Come work with us on advancing science using LLMs! Exciting times ahead 🧑‍🔬🤖

📣 Calling all Rising Stars in Biological Engineering. Nominate someone or self nominate: forms.gle/EszC1AvRFpfN1G…

@IsraelF96135088 Thanks @IsraelF96135088 . Building on lots of other people's work here, and still a work in progress, but excited to publicize more broadly that we are working on this!

I like this stuff a lot! @sonyahans 👏

Registration is now open for our Benzon Symposium on "Protein structure prediction and design" Meeting will take place in Copenhagen 🇩🇰 on Sept. 1–4, 2025, and will feature an amazing list of speakers Get your application in before March 31st!

We are hiring a Flatiron Research Fellow in the Structural Molecular Biophysics team! Experience with cryoEM and/or membrane protein simulations are a plus! Happy to chat in person with anyone at #bps2025 ! apply.interfolio.com/160227

Excited for #bps2025! Check out what SMBp has been up to at these talks and posters! (Also follow me at the other place.) @miroastore @samsledzieski @a_anand_ojha

We're looking for Research Engineers to work at the intersection of LLMs and impactful scientific problems! Applications close next Tuesday 18th. Link to job ad in thread.