Emil Thomasen@EmilThomasen

Computational structural biology. Postdoc at Flatiron Institute.

 New York, NY
Joined March 2012
Emil Thomasen retweeted
Pilar Cossio@PilarCossio2
Sep 30
*Job alert*: Postdoc position at the Flatiron Institute to work on biophysical inference and cryo-EM. ❄️ 🔬Applications are welcome! apply.interfolio.com/193799
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Emil Thomasen retweeted
Pilar Cossio@PilarCossio2
Sep 4
Very excited to share my first blog post with @mhli41 @EmilThomasen 🎉 Can we capture an ensemble? Lessons learned from averages and single-molecule measurements in structural biology. @open_rss
Minhuan Li
@mhli41
Sep 4
New @open_rss blog (rs-station.github.io/2026/08…) on a question we’ve been thinking about a lot: what information about a molecular ensemble survives measurement and processing? @PilarCossio2 @EmilThomasen A fuzzy cryo-EM map is not itself an ensemble. But an averaged measurement is not limited to an average structure either. We use ensemble resolution to frame the better question: what differences between molecular distributions can the data actually distinguish?
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Emil Thomasen retweeted
Minhuan Li
@mhli41
Sep 4
New @open_rss blog (rs-station.github.io/2026/08…) on a question we’ve been thinking about a lot: what information about a molecular ensemble survives measurement and processing? @PilarCossio2 @EmilThomasen A fuzzy cryo-EM map is not itself an ensemble. But an averaged measurement is not limited to an average structure either. We use ensemble resolution to frame the better question: what differences between molecular distributions can the data actually distinguish?
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Paper on the role of disorder in peroxisome proliferator-activated receptors and the functional consequences of transient IDR–DBD interactions by Milena Lalic, Elisabeth Thomsen, Birthe Kragelund and many good colleagues (w simulations by Emil Thomasen) doi.org/10.1038/s41467-026-7…
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New preprint in which we built and simulated full-length models of α-Synuclein fibrils to reveal how the fuzzy coat mediates selective binding of peptides to amyloid fibrils Work led by Carlos Pintado-Grima in a nice collaboration with Salvador Ventura's lab
bioRxiv Bioinfo@biorxiv_bioinfo
Apr 21
Full-Length Molecular Models of Brain-Derived α-Synuclein Fibrils Reveal a Fuzzy-Coat-Mediated Mechanism for Selective Peptide Binding biorxiv.org/content/10.64898… #biorxiv_bioinfo
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Integrative structural biology by the sea The Jan 31st deadline for our FEBS advanced course on integrative structural biology is getting closer, so get your applications in for Lost In Integrative Vol. 2 probingbiomolecules2026.febs… network.febs.org/posts/integ…
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Emil Thomasen retweeted
Sonya@sonyahans
7 Nov 2025
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/ch…

CAHRA 2026: Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms

A community-wide data processing challenge for cryo-electron microscopy.

heterogeneity.notion.site
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Exciting news! I am grateful and thrilled to join the Section for Biomolecular Sciences #UCPH. We use single-molecule tools to study how pioneer factors interact with chromatin and promote cell reprogramming. Join our ERC-project PIONEER, now recruiting on all levels!⬇️
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Replying to @EmilThomasen
@EmilThomasen, @LindorffLarsen, @LabVanni and colleagues refine the MD simulations package Martini 3 to more accurately model multidomain proteins with flexible linkers and disordered regions. nature.com/articles/s41467-0…
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Our paper on rescaling protein-protein interactions in Martini 3 is now out Work led by @EmilThomasen & @SkaalumTorur and in collaboration w collaboration with @sriraksha616 & @asmolsim in @LabVanni doi.org/10.1038/s41467-024-5…
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I'm very happy to have defended my PhD thesis. I want to thank @CarloCamilloni, @ProteinMagnus, and @aelangkilde for a great discussion on integrative modelling in my defense, and thanks to @LindorffLarsen, SBiNLab, and our collaborators for making the PhD a great experience.
Kresten Lindorff-Larsen@LindorffLarsen
6 Nov 2023
Big congratulations to @EmilThomasen on successfully defending his PhD today 🎓 🎉 🍾 🍿 🥃 And thanks to opponents @CarloCamilloni, @ProteinMagnus & @aelangkilde for leading an excellent discussion on integrative modelling, coarse grained models, and the future of the field 🙏
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Emil Thomasen retweeted
Max Bonomi@BonomiMax
20 Oct 2023
Our EMMIVox approach for accurate model and ensemble refinement using #cryoEM maps and Bayesian inference is out in @biorxivpreprint Work led by Samuel Hoff @institutpasteur @DBSC_IP with contributions from @EmilThomasen and @LindorffLarsen biorxiv.org/content/10.1101/…

Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference

Converting cryo-electron microscopy (cryo-EM) data into high-quality structural models is a challenging problem of outstanding importance. Current refinement methods often generate unbalanced models...

biorxiv.org
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Very happy to share our preprint: Recalibration of protein interactions in Martini 3 led by @EmilThomasen & @SkaalumTorur on our end, and in a collaboration with @sriraksha616 & @asmolsim in @LabVanni. 1/10 doi.org/10.1101/2023.05.29.5…
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CALVADOS is on Colab. Run a coarse-grained simulation of your favourite IDR in 5–30 mins (depending on length of protein and simulation) using just sequence and conditions as input. colab.research.google.com/gi…
Kresten Lindorff-Larsen@LindorffLarsen
8 May 2023
Replying to @LindorffLarsen
If your favourite IDR is missing from the IDRome, you can generate your own ensemble using a Colab implementation of our CALVADOS model (or use the machine learning model we present in the paper to predict chain compaction from sequence). colab.research.google.com/gi…
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Happy to share our new paper on self-consistently determining the oligomeric states and conformational ensembles of SPOP using SAXS and MD simulations. Check out @LindorffLarsen's thread for a quick overview of the work.
Kresten Lindorff-Larsen@LindorffLarsen
9 Mar 2023
How do you analyse SAXS data of a system when it shows both conformational and compositional heterogeneity? For the answer, see work led by @EmilThomasen out in @eLife, where we determine conformational ensembles of the self-associating protein SPOP. 1/n doi.org/10.7554/eLife.84147
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PhD fellowship in structural bioinformatics available in the group in our #PRISM centre 🇩🇰 If you love proteins, know a bit of programming and like to do quantitative analyses based on protein structure and sequence, this might be for you. jobportal.ku.dk/phd/?show=15…
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Excited to present work by @EmilThomasen in a collaboration with Matt Cuneo & @TanjaMittag where we study the conformational and compositional heterogeneity of the self-associating E3 ligase adaptor protein SPOP in solution using SAXS and simulations. 1/n doi.org/10.1101/2022.10.08.5…
bioRxiv Biophysics@biorxiv_biophys
9 Oct 2022
Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations biorxiv.org/cgi/content/shor… #biorxiv_biophys
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I am looking for a PhD student and a postdoc to join my lab @BIO_UCPH to work on developing polymers for native nanodiscs and transporters. 🧪❄️🔬 Read more and apply here: hautzen.com/openings
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I'm happy to share the final version of our work on improving the Martini 3 🍸 model for simulations of disordered 🍝 and multidomain 🧶 proteins This was a strong team effort 🇩🇰🇮🇹 by @EmilThomasen @FrancPesce Mette Roesgaard & @GiulioTesei 1/8 doi.org/10.1021/acs.jctc.1c0…
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There's a few spots left for our FEBS course in integrative structural modelling in Greece May 9–15, 2022. Deadline for applications March 25. probingbiomolecules2022.febs…
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