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Erik Thiede

@erikhthiede.bsky.social
278 followers 242 following 107 posts

Asst. Professor of Chemistry at Cornell University. Interests: Bio, Chem, ML, Statistical Estimation, Electron Microscopy, Good code.

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Reposted by Erik Thiede
pilarcossio.bsky.social @pilarcossio.bsky.social · 10/02/2026
#BPS2026 The T&C subgroup is hosting a fun event on Saturday evening, Feb 21st 🎉 Open bar for 2 hours + food! Tickets are selling fast, so sign up soon: www.biophysics.org/2026meeting/...
biophysics.org
BPS2026 Annual Meeting Subgroup Dinners| Biophysical Society
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Structural Biology @actacrystd.iucr.org · 04/02/2026
M​ichael J. O'Brien et al.: CryoJAX: a cryo-electron microscopy image-simulation library in JAX #CryoEM #ImageSimulation #AutomaticDifferentiation @harvard@unewhaven@Cornell...#IUCr journals.iucr.org/paper?S2059798326…
journals.iucr.org
CryoJAX: a cryo-electron microscopy image-simulation library in JAX
The authors have developed cryoJAX, a cryo-EM image-simulation library for developing data-analysis techniques across cryo-EM modalities. CryoJAX is built on JAX, an emerging scientific computing framework in Python well suited for cryo-EM data analysis.
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Sjors Scheres @sjorsscheres.bsky.social · 10/12/2025
Postdoc opportunity with Michel Goedert and myself to work on #cryoEM/#cryoET structures of #amyloids. Feel free to email me with any questions you might have. mrc.tal.net/vx/mobile-0/...
mrc.tal.net
Postdoctoral Scientist - Neurobiology - Dr Michel Goedert - LMB 2752 - Medical Research Council
Location: Cambridge. Vacancy: Postdoctoral Scientist - Neurobiology - Dr Michel Goedert - LMB 2752. Closing Date: 04/01/2026, 23:55
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Erik Thiede @erikhthiede.bsky.social · 05/12/2025
Bit belated, but our article on error analysis for MSMs is in JCTC! pubs.acs.org/doi/abs/10.1...
pubs.acs.org
Error Breakdown and Sensitivity Analysis of Dynamical Quantities in Markov State Models
Markov state models (MSMs) are widely employed to analyze the kinetics of complex systems. But despite their effectiveness in many applications, MSMs are prone to systematic or statistical errors, oft...
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Erik Thiede @erikhthiede.bsky.social · 02/12/2025
I'm giving a talk at One World Cryo EM (cryoem.world) tomorrow at 11:00am EST. Topic is 'Deconstructing Algorithms for “Discrete” Heterogeneity in Cryo-EM'. Sign up for their mailing list to tune in!
cryoem.world
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Erik Thiede @erikhthiede.bsky.social · 18/11/2025
www.thecrimson.com/article/2025... ...and what's more, absolutely none of this happens in a vacuum. There's much I love about academia, but one thing I absolutely hate is the way it permits professors to abuse the power they have over their mentees. We have systemic issues we need to face.
thecrimson.com
As Summers Sought Clandestine Relationship With Woman He Called a Mentee, Epstein Was His ‘Wing Man’ | News | The Harvard Crimson
When former Harvard President Lawrence H. Summers was pursuing a romantic relationship with a woman he described as a mentee, he turned to a longtime associate for guidance: convicted sex offender Jef...
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Erik Thiede @erikhthiede.bsky.social · 22/09/2025
We are hiring for a postdoc to work on the intersection of molecular simulation, machine learning, and cryo-EM! Please find the job posting here. thiedelab.github.io/docs/postdoc...
thiedelab.github.io
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Jeremy Baskin @jeremybaskin.bsky.social · 25/08/2025
Faculty opening in Cornell Chemistry at the Assistant Professor level in the area of chemical biology, broadly defined! academicjobsonline.org/ajo/jobs/30338 #chemjobs
academicjobsonline.org
Cornell University, Chemistry and Chemical Biology
Job #AJO30338, WDR-00054776 Assistant Professor - Chemistry and Chemical Biology, Cornell University (Ithaca, NY), Chemistry and Chemical Biology, Cornell University, Ithaca, New York, US
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Erik Thiede @erikhthiede.bsky.social · 26/08/2025
Back from our first group conference trip to ACS Fall. Was great to not only see new science, but also excellent watch the very excellent presentations from Josh (Rhodes), Diego, and Jeffrey, as well as the great reception Josh (Almonte)'s poster received!
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Erik Thiede @erikhthiede.bsky.social · 17/07/2025
Excellent read for anyone trying to understand what is up with all the AI hype nowadays.
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Erik Thiede @erikhthiede.bsky.social · 16/07/2025
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Erik Thiede @erikhthiede.bsky.social · 29/05/2025
Posting a job ad on behalf of Mat Sikora, who is doing some fascinating work on cryo-EM for glycans. He's looking both for PhDs and postdocs. science.phd.uj.edu.pl/join/biomedi...
science.phd.uj.edu.pl
Szkoła Doktorska Nauk Ścisłych i Przyrodniczych - Uniwersytet Jagielloński
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Erik Thiede @erikhthiede.bsky.social · 26/05/2025
Happy to see our first collaboration with the Yang group come through!
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James Fraser @fraserlab.com · 20/05/2025
We are looking to hire (yes, even in this economy!) a jr. specialist to train in protein prep/structural biology related to our AVOID-ome work as part of openadmet.org. A great position for someone who is looking to be a tech for a few years before grad or med school. aprecruit.ucsf.edu/JPF05424
aprecruit.ucsf.edu
Junior/Assistant/Associate/Full Specialist Positions Available
University of California, San Francisco is hiring. Apply now!
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Sam Blau @samblau.bsky.social · 14/05/2025
The Open Molecules 2025 dataset is out! With >100M gold-standard ωB97M-V/def2-TZVPD calcs of biomolecules, electrolytes, metal complexes, and small molecules, OMol is by far the largest, most diverse, and highest quality molecular DFT dataset for training MLIPs ever made 1/N
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Kim Weeden @weedenkim.bsky.social · 07/05/2025
One of grants frozen at Cornell: $6.7M (4 yrs) to develop heart pumps for babies born w/ heart defects. It took decades of work to get to point of prepping device for in-human clinical trials. No private company could do this. The cruelty of the Trump administration is heartbreaking. So to speak.
news.cornell.edu
Research at risk: Life-saving heart pumps for babies | Cornell Chronicle
After receiving a stop-work order from the federal government, the future of a device to help children with heart defects is uncertain.
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Erik Thiede @erikhthiede.bsky.social · 16/04/2025
Agreed: Universities are far too quick to ignore the words of the actual people in power, e.g. J.D. Vance saying, "Professors are the enemy" and "[Orban's seizure of universities is] the closest that conservatives have ever gotten to successfully dealing with leftwing domination of universities"
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Erik Thiede @erikhthiede.bsky.social · 01/04/2025
It is with great pleasure that I announce that the Thiede lab has solved the problem of interpretability in AI for Chemistry with our new neural network architecture: the Variational Alanine Encoder (VAE).
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Erik Thiede @erikhthiede.bsky.social · 01/04/2025
Wishing all the trans scientists out there who are continuing to do amazing work in adverse conditions a good trans day of visibility!
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Reposted by Erik Thiede
Coach Finstock @coachfinstock.bsky.social · 16/03/2025
I think it has more to do with you might get locked up for absolutely no reason at all and then flown to El Salvador to die in prison even though a judge said you should be released
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Erik Thiede @erikhthiede.bsky.social · 17/03/2025
Our (SMBP + SMBP alumns) man doing us proud.
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Erik Thiede @erikhthiede.bsky.social · 11/01/2025
How I've been generating nice equations in google slides:
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Erik Thiede @erikhthiede.bsky.social · 29/12/2024
On Hanukkah, Jews participate in many ancient rituals such as helping their parents transfer files between computers.
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Erik Thiede @erikhthiede.bsky.social · 25/12/2024
Y'all better have been getting those finger exercises in because those dreidels ain't gonna spin themselves.
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Erik Thiede @erikhthiede.bsky.social · 20/12/2024
First little piece of funding for our new project direction joint with the Yang group: characterizing electrochemical situations with ML + in-situ EM. Congratulations to Yao for the successful proposal! news.cornell.edu/stories/2024...
news.cornell.edu
2030 Project Fast Grant awards support energy systems of the future | Cornell Chronicle
Researchers from five colleges have received awards to support work on sustainable energy systems.
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Erik Thiede @erikhthiede.bsky.social · 18/12/2024
An excellent point, and something that we run afoul of in far too many of our algorithms that boil down to "generalization of PCA / CCA in some conformational space".
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Martin Vögele @martinvoegele.bsky.social · 16/12/2024
It is obvious that the PDB is biased towards proteins that scientists are more interested in. Similarly, its structures appear to be biased towards more interesting regions of proteins. This preprint finds that ligand binding sites tend to be more carefully modeled than the rest of the structure.
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Martin Bauer @martinmbauer.bsky.social · 12/12/2024
Googles claim that their result "lends credence to the notion that quantum computation occurs in many parallel universes" is nonsense, because their results are perfectly well explained by quantum mechanics independent of how you interpret it. 4/5
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Erik Thiede @erikhthiede.bsky.social · 12/12/2024
ESM3 structure predictions for multimers seem to be broken: In our (preliminary) experiments, it seems to always predict chain breaks around one amino acid in length.
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Erik Thiede @erikhthiede.bsky.social · 10/12/2024
Spent the last day of class yesterday telling my students that orbitals don't actually exist and real electrons exist in indescribable many-electron wavefunctions. For my next trick I'm telling all my nephews and nieces that Santa isn't real.
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Reposted by Erik Thiede
Zheng Shi @zs-biophys.bsky.social · 06/12/2024
Looking into condensates at ~1 nm resolution! www.biorxiv.org/content/10.1...
biorxiv.org
Quantitative Spatial Analysis of Chromatin Biomolecular Condensates using Cryo-Electron Tomography
Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficul...
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Reposted by Erik Thiede
Diego del Alamo @delalamo.xyz · 05/12/2024
Been a while since I read a paper like this: • "What [DiffDock] appears to be doing cannot be considered" docking • "Results are ... contaminated with near neighbors to test cases" • "Results for DiffDock were artifactual" • "Results for other methods were incorrectly done" arxiv.org/abs/2412.02889
arxiv.org
Deep-Learning Based Docking Methods: Fair Comparisons to Conventional Docking Workflows
The diffusion learning method, DiffDock, for docking small-molecule ligands into protein binding sites was recently introduced. Results included comparisons to more conventional docking approaches, wi...
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Erik Thiede @erikhthiede.bsky.social · 05/12/2024
Ray of light coming from the heavens.
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Erik Thiede @erikhthiede.bsky.social · 04/12/2024
Interesting article on the limitations of Alphafold2. Thanks Diego!
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Erik Thiede @erikhthiede.bsky.social · 02/12/2024
Steps to add a collaborator to a Github repo: 1. Enter Github PW on Laptop 2. Receive 2FA code to be entered on Github App 3. Enter PW into Github App 4. Enter different 2FA code from authenticator app 5. Re-request 2FA code for laptap. 6. Enter new code into phone app. 7. Add the user. Oy.
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Erik Thiede @erikhthiede.bsky.social · 28/11/2024
What are people's favorite non-diffusion generative models for protein structure? I'm 2-3 years behind in the literature and want to get caught up.
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Reposted by Erik Thiede
James Stevenson @allaboutchemist.bsky.social · 27/11/2024
Fascinating thread here: apparently, caffeine and ibuprofen both have binding affinity to their target proteins so weak that they might get tossed out of a typical drug discovery project!
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Erik Thiede @erikhthiede.bsky.social · 26/11/2024
Something that's come up in a few conversations and I think is underappreciated: the X-ray / cryo-EM structures you download from the PDB are average structures, but not *typical* structures: very few proteins in your sample actually look like that.
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MSKEducation @mskeducation.bsky.social · 25/11/2024
Checkout the latest work by our #MSKPostdoc @sukritsingh92.bsky.social
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Erik Thiede @erikhthiede.bsky.social · 24/11/2024
1.5 years in, and going from postdoc to assistant prof has been a bit of a let-down. I get far fewer opportunities to say, "If my calculations are correct."
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Erik Thiede @erikhthiede.bsky.social · 23/11/2024
Question for cryo-EM people on Bluesky. How would you describe the difference between discrete and continuous heterogeneity? Curious about people's perspectives / definitions / hot takes, not looking for one "right answer."
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Ishan Khatri @ishan.khatri.io · 10/11/2024
Continuing yesterdays rant about ML research code, I am back with another plea. Can we stop passing dictionaries around everywhere? Dictionaries are not self-documenting because I have to RUN the code in order to see what keys/values are in it. Dataclasses are almost always better. Use them pls 🙏
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