iiinova — where your digital self keeps evolving

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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026

ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...

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Pieter T. L. Beck @ptrbck.bsky.social · 15/09/2026

A longread on why Cofnas is doing pseudoscience, by yours truly. Many thanks to @forbetterscience.bsky.social for hosting the text!

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Charles C Roseman @evoroseman.bsky.social · 25/08/2026

RE: freedom of speech, academic freedom, and race science. In this (long) thread, I’m going to 1) establish my bona fides on academic freedom and race science, 2) show why academic freedom and freedom of speech are different and… 1/34

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Structura Biotechnology @structurabio.bsky.social · 17/08/2026

🚀 Preprint alert: cFAR and Relative Signal: Diagnosing Preferred Orientation in Single-Particle #CryoEM Explore how cFAR, tFAR, and Relative Signal provide complementary diagnostics for preferred orientation, tested across 14 #EMPIAR datasets and compared with established metrics 👉 bit.ly/4wBY1Ev

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Biohub @biohub.org · 11/06/2026

In a series of 3 papers and preprints, we’re thrilled to share with you the working laser phase plate. In collaboration with research led by Holger Müller at UC Berkeley, this is a huge innovation in imaging to make small and faint objects inside cells visible. bit.ly/4vK9LVn

Waves of laser light coming from four different directions and meeting in the middle brightly inside the cavity of the laser phase plate

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Pilhofer Lab 🦠❄️🔬 @pilhoferlab.bsky.social · 01/06/2026

🛠️💉It's time for engineering contractile injection systems! @chipericson.bsky.social & @davidschaumann.bsky.social introduce programmable CIS - PROCIS, combining tail length control, non-native cargo loading, and cell retargeting all in one system! www.biorxiv.org/content/10.6... 🧵 1/5

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Reese Richardson @reeserichardson.bsky.social · 28/05/2026

Thermo Fisher has now made public the company line, which is ?!??!?!??!?!?! you really gotta read it. cen.acs.org/research-int...

In a statement emailed to C&EN, Thermo Fisher Scientific chief communications offer Sandy Pound says, “We take antibody validation, specificity and accurate product documentation seriously, and we are committed to the transparent and ethical generation, analysis and presentation of scientific data. In the process of preparing antibody images for publication on our website, some images may have been adjusted to clarify for presentation purposes.”...In the company statement, Pound says that the company plans on “providing the original and adjusted versions of the relevant images, as well as ensuring that users are informed that antibody images may have been optimized for presentation on the website.” https://cen.acs.org/research-integrity/Sleuths-say-Thermo-Fisher-doctored/104/web/2026/05

https://cen.acs.org/research-integrity/Sleuths-say-Thermo-Fisher-doctored/104/web/2026/05

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Dimitry Tegunov @dtegunov.bsky.social · 03/05/2026

We're super excited to share MissAlignment: a new ML-based approach to reference-free tilt series alignment, spearheaded by @martenchaillet.bsky.social. We think it's going to make your cryo-ET life a lot better. Preprint: www.biorxiv.org/content/10.6... Code: github.com/warpem/miss-... 🧶 Thread:

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Brian Cook @bcryo.bsky.social · 23/03/2026

1) The Herzik lab is excited to announce our newest preprint in collaboration with the Grotjahn lab! We have developed a surfactant cocktail that seeks to overcome one of the more nefarious problems in #cryoEM, Air-water interface (AWI)-induced damage and preferred orientation (PO).

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Lucas Tafur @tafurlab.bsky.social · 13/02/2026

It took a while but it’s finally published! The GAP activity of SEAC (GATOR) is a metabolic switch that allows cells to quickly respond to changes in amino acid levels, both for inhibition and reactivation.

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Structura Biotechnology @structurabio.bsky.social · 27/01/2026

🚀 CryoSPARC v5.0 BETA is here! We’re excited to deploy another major #CryoSPARC release to help enable and accelerate #cryoEM data analysis. v5 has a redesigned underlying software system and many new features - highlights in thread! Full changelog: cryosparc.com/updates/v5.0.0

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Arjen Jakobi @cryotud.bsky.social · 29/11/2025

CCP-EM Spring Symposia have become key venues for methods-focused cryo-EM advances and an annual fixture for structural biologists worldwide. Their early adoption of online talks set the bar for inclusive meetings, and even as they have grown over the years, they have kept a family feel. Kudos!

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paulschanda.bsky.social @paulschanda.bsky.social · 18/10/2025

📢 New preprint: Experiment-guided AlphaFold3 resolves accurate protein ensembles. doi.org/10.1101/2025... AlphaFold3 is incredible, but has crucial limitations: it typically collapses to a single conformation, ignoring the inherent dynamics of proteins. And it can be wrong. Here's a solution. 🧵👇

Structures from AlphaFold3 - while often impressively good - tend to fail representing the dynamic ensembles accurately. And often parts of the structure are not correct.
Adding experimental data, directly in AlphaFold's diffusion step, provides physically realistic protein ensembles. This image shows two cases where AlphaFold3-only structures were largely improved by guiding with experimental data.

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Oli Clarke @olibclarke.bsky.social · 26/09/2025

Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup). A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.

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Arjen Jakobi @cryotud.bsky.social · 15/09/2025

We finally wrote up the paper for LocScale-2.0. edu.nl/pvhxv Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps. Code: cryotud.github.io/locscale/ Work by @alok-bharadwaj.bsky.social and Reinier.

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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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Jan Felix @janfelix.bsky.social · 02/09/2025

Now published @cp-cellreports.bsky.social! Antibody-mediated TGF-β1 activation for the treatment of diseases caused by deleterious T cell activity: www.cell.com/cell-reports... Fantastic collaboration & massive effort from Sophie Lucas Lab @ de Duve Institute. #CryoEM with @savvideslab.bsky.social.

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A. Reza Mehdipour @rezamehdipour.bsky.social · 05/08/2025

We are excited to announce the first in-cell structure of a LINC complex within a native nuclear envelope at subnanometer resolution!! #In-cell cryo-ET + #atomistic MD simulations! @tomdendooven.bsky.social et al!! www.biorxiv.org/content/10.1...

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Jan Felix @janfelix.bsky.social · 10/07/2025

Finally out @natcomms.nature.com "Single-domain antibodies directed against hemagglutinin and neuraminidase protect against influenza B viruses". Great collab between @savvideslab.bsky.social (we performed #CryoEM) and Xavier Saelens Lab, spearheaded by Arne Matthys. www.nature.com/articles/s41...

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Randy Read 🇨🇦🇬🇧 @randyjread.bsky.social · 03/07/2025

If this is true, it’s abysmally shortsighted for #NIH. The new tools nurtured by the long series of #CASP challenges probably contribute far more in one year to the scientific and industrial economies than the entire funds that have supported it.

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Misha Kudryashev @mishakudryashev.bsky.social · 08/06/2025

We have a preprint for you EHD2 forms rings on caveolae necks, in contrast to most EHDs forming helices. We determined its structure on membranes and show that N-term acts as a spacer By Elena, Vasya @vasiliimikirtumov.bsky.social, Jeff &Oli Daumke www.biorxiv.org/content/10.1...

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Arjen Jakobi @cryotud.bsky.social · 22/05/2025

We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation. Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation. cryotud.github.io/locscale/

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PLOS Biology @plosbiology.org · 14/04/2025

Reports of diverse stoichiometries have complicated our understanding of the complex between ALK kinase and its #cytokine ligand ALKAL2. @janfelix.bsky.social @savvideslab.bsky.social &co reanalyze #cryoEM data to clarify the situation @plosbiology.org 🧪 plos.io/4lvRfvu

Reanalysis of cryo-EM data from EMPIAR entry EMPIAR-10,930 deposited by Reshetnyak and colleagues, Nature (2021). (A) Ten most populated 2D class averages after performing 2D classification on 11.8 million selected particles. Classes corresponding to 2:1 ALK–ALKAL2 particles are highlighted in blue, while classes corresponding to 2:2 ALK–ALKAL2 particles are highlighted in orange. (B) Ab initio model generation in cryoSPARC results in classes corresponding to both a 2:1 ALK–ALKAL2 and 2:2 ALK–ALKAL2 assembly. Hetero-refinement of the 2:1 and 2:2 ALK–ALKAL2 classes results in the two models displaying 2:1 and 2:2 ALK–ALKAL2 assemblies, respectively. The ALK–ALKAL2 complexes with 2:1 (PDB 7nwz) and 2:2 (PDB 7n00) stoichiometries are shown fitted inside the maps, with ALK colored pink/gray and ALKAL2 colored blue/purple. (C) 3D refinement; a front view is shown of a map sharpened in RELION using a B-factor of −100 Å2, with ALK colored pink/gray and ALKAL2 colored blue. Front, side, and top views are shown of a transparent map, sharpened using deepEMhancer, with fitted structural model.

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Savvides Lab @savvideslab.bsky.social · 13/04/2025

Delighted to share our reanalysis of cryo-EM data in EMPIAR-10930, now at: journals.plos.org/plosbiology/... ; revealing the ALK-ALKAL2 assembly with 2:1 stoichiometry and resolving the conundrum introduced by the originally reported 2:2 complex. ALK/LTK-cytokine signalling getting clearer!

journals.plos.org

Reanalysis of cryo-EM data reveals ALK-cytokine assemblies with both 2:1 and 2:2 stoichiometries

The mechanistic understanding of the complex between ALK kinase and its cytokine ligand ALKAL2 has been complicated by reports of diverse stoichiometries (2:1 vs 2:2). This study reanalyzes cryo-EM da...

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Structura Biotechnology @structurabio.bsky.social · 09/04/2025

#CryoSPARC v4.7 is out! 🚀 Featuring a new automatic Micrograph Junk Detector that labels and rejects contaminants, new tools for curating subsets of particles, performance and stability fixes, and more! Full changelog: cryosparc.com/updates #cryoEM

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Florent Waltz @florentwaltz.bsky.social · 21/03/2025

I'm super happy that our story is now published! 📖 www.science.org/doi/10.1126/... But what changed compared to the original preprint? Also, I feel i should post Movie 1 🎥, that inspired the cover. Back when I did the original bluesky thread, movies were not available.

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Alisia Fadini @alisiafadini.bsky.social · 24/02/2025

Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.

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Adrià Sogues @adriasogues.bsky.social · 12/02/2025

New preprint from the @remaut-lab.bsky.social ! Happy to share our latest work on a new member of the ENA family, protein fibers found on the spore’s surface. Using CryoID @mikesleutel.bsky.social identified F-ENA in BTK. The paper dives deep into its structure analysis by integrating X-ray and AF3

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Janine Brunner @janinebrunner.bsky.social · 16/01/2025

Cryo-EM structures of mammalian membrane proteins from a single cell culture dish? Yes, Micro ISOlation (MISO) sample preparation makes it possible. www.biorxiv.org/content/10.1... Happy to be part of this exciting story and wonderful collaboration with the Rouslan Efremov lab.

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