iiinova — where your digital self keeps evolving

Dawid Zyla @dzyla.bsky.social · 12/06/2026

I recently had the pleasure of speaking with Teddy Rosenbluth at The New York Times about our work on measles. The article covers our efforts and those of others in the field who are working toward anti-measles therapeutic solutions. You can read it here: www.nytimes.com/2026/06/11/w...

nytimes.com

With Measles Roaring Back, the Search for a Treatment Is On

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cryoEM papers @cryoempapers.bsky.social · 09/05/2026

Human neutralizing antibodies targeting the measles virus hemagglutinin and fusion surface proteins pubmed.ncbi.nlm.nih.gov/42102820/ #cryoEM

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Dawid Zyla @dzyla.bsky.social · 07/05/2026

Read about our story in the Washington Post!

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Dawid Zyla @dzyla.bsky.social · 07/05/2026

Measles is coming back. Until now, we didn't know how human antibodies actually recognize and neutralize the virus. No structure of either measles surface protein bound to a human antibody had ever been reported. We set out to change that.

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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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Jason McLellan @mclellanlab.bsky.social · 02/03/2026

Our fourth installment on prefusion herpesvirus gB proteins is available as a preprint: doi.org/10.64898/202.... Working with Ivelin Georgiev's group, we isolated and characterized prefusion-specific HSV gB antibodies from humans!

Cryo-EM structures of prefusion HSV-2 gB in complex with human antibodies.

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Lars-Anders Carlson @lacarlson.bsky.social · 23/01/2026

I am super happy to share this paper in its final form. We used FIB milling to "dig in to" cell lines and mouse brains infected with tick-borne flaviviruses, followed by cryo-ET to study the virus replication. It's open access, so have a look! #virology #teamtomo www.nature.com/articles/s41...

nature.com

Cryo-electron tomography reveals coupled flavivirus replication, budding and maturation - Nature Communications

In this study, Dahmane et al use a method called cryo-electron tomography to uncover new details of how tick-borne flaviviruses transform cells into virus factories.

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Dawid Zyla @dzyla.bsky.social · 21/01/2026

I never imagined I'd be writing this, but I am happy to share that, starting this June, I will be joining @cuanschutz.bsky.social @cu-bmg.bsky.social as an Assistant Professor.

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Hanjin Liu @liu-hanjin.bsky.social · 23/12/2025

CryoEM folks, If you want to handle huge STAR file efficiently in Python, please try starfile-rs! github.com/hanjinliu/star… Reading a motion data of a particle from a 15 MB file is just like this ↓🤩

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Helen Branswell 🇨🇦 @helenbranswell.bsky.social · 23/12/2025

The US #measles count for this year has topped 2,000 cases for the first time since 1992. These are confirmed cases only, ie there have been more. 3 reported deaths. The vast majority of the cases are in unvaccinated kids & adults. 11% needed hospitalization. www.cdc.gov/measles/data...

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cryoEM papers @cryoempapers.bsky.social · 26/11/2025

Stabilized Full-Length Measles Fusion Protein Elicits Potent Immunity and Protection In Vivo pubmed.ncbi.nlm.nih.gov/41278811/ #cryoEM

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Daniel Hurdiss @danielhurdiss.bsky.social · 25/11/2025

It’s been a while since I put together the Structural Virology starter pack, and I’m sure some new folks have joined Bluesky since then. There’s still plenty of space to fill, so if you’d like to be added to the list just let me know. #virology #cryoEM go.bsky.app/Qxv95BL

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Dawid Zyla @dzyla.bsky.social · 23/11/2025

Proteins are dynamic structures, but structural biology often shows them as static snapshots. Inspired by long-exposure photography and generative art, I built ProteinCHAOS, an artistic tool inspired by molecular dynamics to capture protein flexibility over time, much like long-exposure images.

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Grant Jacobs BioinfoTools/NotJustDNA 🔬🧬🖥️✍️📚🇳🇿 @notjustdna.bsky.social · 31/10/2025

#NZ measles 🦠 - Now 14 cases - Needs a week-plus to know if there will be a surge in cases (owing to the non-symptomatic phase), and how widespread - vaccination is free RNZ: Extent of measles outbreak will be confirmed over coming days, an epidemiologist says ⬇️

rnz.co.nz

Extent of measles outbreak will be confirmed over coming days, an epidemiologist says

There are currently no hospitalisations linked to the outbreak.

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Ian M. Mackay, PhD (he/him) 🦠🤧🧬📑🦟🧀 @mackayim.bsky.social · 25/04/2025

Interesting side-quest. Has #measles immunity in children declined in Austria due to the #COVID19 pandemic, driving measles outbreaks? (It also tangentially addresses a group's assumption that SARS-CoV-2 "destroys our immune system" and is "airborne AIDS" or whatever). Answer: no, it did not. 1/2

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bioRxiv Immunology @biorxiv-immuno.bsky.social · 09/10/2025

Stabilized Full-Length Measles Fusion Protein Elicits Potent Immunity and Protection In Vivo www.biorxiv.org/content/10.1101/202…

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Florian Schur @schurlab.bsky.social · 25/09/2025

Huntingtin binds and bundles F-actin! Thrilled to team up with the Humbert (Sorbonne Université) and Song (KAIST) labs on this discovery. We had a blast doing cryo-ET on this unexpected complex — and now so many new questions lie ahead! #TeamTomo #CryoET #HTT #actin doi.org/10.1126/scia...

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Dawid Zyla @dzyla.bsky.social · 17/09/2025

Our second paper explores the mechanism by which fusion-targeting antibodies neutralize the measles virus. It was exciting to integrate structural biology, virology, and biophysics to demonstrate that these F-targeting antibodies can provide complete protection against measles infection.

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Dawid Zyla @dzyla.bsky.social · 16/09/2025

One of our new manuscripts is now available on bioRxiv! Stay tuned!

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Roger Castells @rcastellsg.bsky.social · 07/05/2025

Hi everyone! I’m a #NewPI just starting my lab and would love to hear your advice on lab management and building the lab culture. Any tips, lessons learned, or resources you’ve found helpful are very welcome! Feel free to reply, message me, or email me at rcastellsg(at)cnio.es thanks a lot!! 🤗

media.tenor.com

a cat is sitting in front of a laptop computer asking for advice

ALT: a cat is sitting in front of a laptop computer asking for advice

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Ricardo D. Righetto @lifeonthewedge.bsky.social · 07/05/2025

My colleagues @phaips.vd.st and @florentwaltz.bsky.social have put together this wonderful website with step-by-step tutorials for in situ subtomogram averaging using different software packages 🤩 Check it out, especially if you are a newcomer to the field! #CryoET #TeamTomo #ChlamyDataset

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Ben Engel @cellarchlab.com · 07/05/2025

“The Website” is here! It can be intimidating getting into analysis of #CryoET data, and software is evolving all the time👩‍💻🚀. @phaips.vd.st & @florentwaltz.bsky.social put our lab’s workflows into an online guide. We hope this helps lower the bar to joining #TeamTomo. Feedback much appreciated! 🧪🧶🧬🔬

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Sebastian S. Cocioba @atinygreencell.bsky.social · 02/05/2025

I got hit by some rather sudden and extreme financial hardship so if anyone is in need of remote wetlab contract research, strictly BSL1, do let me know. Currently scrambling for gigs. Plant, Bacterial, Archaeal Non-model Bioeng Custom Lab Hardware Turn Key Genetic Design Please repost for reach 💚

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Dawid Zyla @dzyla.bsky.social · 27/04/2025

1/5: Over the last few months, I have been working on an update for the #FollowRelionGracefully dashboard, which offers improved real-time job previews for #cryoEM #Relion jobs.

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Jan Philipp Kreysing @jpkreysing.bsky.social · 11/04/2025

New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇

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Aaron Whiteley @aaronwhiteley.bsky.social · 08/04/2025

Check out our new story led by @aesully98.bsky.social describing how bacteria turn immune evasion against phage! In collaboration with @benmorehouse.bsky.social lab, we discover that bacteria guard their nucleotide second messenger pool using a nucleotidyltransferase related to Cas10/CRISPR enzymes

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Rommie Amaro @rommieamaro.bsky.social · 28/03/2025

✨✨ It's #glycotime for #HIV Env ✨✨ N-linked glycans modulate flexibility & MPER epitope exposure #glycotime Huge effort by @shehata92.bsky.social @lcasalino88.bsky.social with cryoET of Env in VLPs by @thevillalab.bsky.social & team 💪 Would love feedback! www.biorxiv.org/content/10.1...

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Dawid Zyla @dzyla.bsky.social · 02/04/2025

Happy to share that our manuscript on the anti-measles antibody is mentioned in this article: Measles can ravage the immune system and brain, causing long-term damage – a virologist explains theconversation.com/measles-can-...

theconversation.com

Measles can ravage the immune system and brain, causing long-term damage – a virologist explains

Complications from measles infection are surprisingly common.

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eLife @elife.bsky.social · 29/03/2025

Herpes viruses are among the most widespread human viruses. Scientists have shown how HSV-1, known for oral and genital sores, assembles in cells thanks to advanced imaging techniques.

buff.ly

Viruses: How herpes is assembled

A combination of imaging techniques reveals how herpes simplex virus type 1 assembles within infected cells, highlighting the roles of essential viral proteins in viral assembly and exit.

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Ben Engel @cellarchlab.com · 21/03/2025

Press release from @unibas.ch and @biozentrum.unibas.ch about our new #cryoET study on mitochondrial respirasomes. Led by the unstoppable @florentwaltz.bsky.social 🙌 🧪🧶🧬 #TeamTomo

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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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La Jolla Institute for Immunology (LJI) @lji.org · 18/03/2025

New in @elife.bsky.social: LJI Instructor Dawid Zyla (@dzyla.bsky.social) highlights recent research into how herpes simplex virus type 1 assembles within infected cells — revealing the roles of essential viral proteins in viral assembly and exit. elifesciences.org/articles/106... #virology

The key stages of Herpes simplex virus 1 (HSV-1) assembly and the roles of specific viral proteins, based on advanced imaging data.
(A; lower left) In the host cell nucleus, HSV-1 DNA is replicated, and a protein capsid that encloses the viral genome is assembled. These capsids (purple hexagons) bind to pUL34, a component of the nuclear egress complex (NEC) and move towards the inner nuclear membrane of the host cell (INM). The capsid-protein complexes then bud into the perinuclear space (PNS) between the inner and outer membrane of the cell nucleus, where they acquire a temporary envelope from the INM (depicted as a circle around the hexagon). (B) The viral complexes then fuse with the outer nuclear membrane (ONM), where they shed their temporary envelope and are released into the cytoplasm. The viral kinase pUS3 regulates the NEC and thus influences the efficiency of the capsids transit through the nuclear envelope. (C) Once in the cytoplasm, VP16 binds to the capsid to stabilize it for further maturation. Then, pUL16 starts to form the tegument (gray dotted circle), a protein-rich layer that surrounds the capsid and connects it to the outer layer, the envelope, with pUL21 assisting in cytoplasmic transport of molecules between the two layers (D) VP16 delivers the capsids to the envelopment compartment (EC), where they associate with cytoplasmic vesicles (CV, gray circles) to form secondary envelopes with the help of pUL11, pUL51, gK and gE. (E) Finally, the mature virus particle is transported within the vesicle originating from the envelopment compartment, which then fuses with the cell membrane (CM) to release the mature virion with viral glycoproteins (GP) into the extracellular space.

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Dawid Zyla @dzyla.bsky.social · 17/03/2025

I am pleased to share my eLife Insight related to an outstanding manuscript by Nahas et al. This manuscript discusses the assembly of the Herpes simplex virus through a combination of light microscopy and X-ray tomography. You can find my Insight here: elifesciences.org/articles/106....

elifesciences.org

Viruses: How herpes is assembled

A combination of imaging techniques reveals how herpes simplex virus type 1 assembles within infected cells, highlighting the roles of essential viral proteins in viral assembly and exit.

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Artologica aka Michele Banks @artologica.net · 16/03/2025

Risk is often hard to understand. @beebrookshire.bsky.social takes a look at how parents assess the risks of MMR vaccine against the risk of measles #scicomm

open.substack.com

The risk you see, and the risk you don't

On vaccines as victim of their own success.

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Dawid Zyla @dzyla.bsky.social · 09/03/2025

Another update for [MSS]! Along with some graphical improvements and a faster search, it now supports date filtering! You can specify a date range for your search results. Plus, [MSS] now indicates whether a full, free publication text is available on PubMed Central. mssearch.xyz

mssearch.xyz

Streamlit

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La Jolla Institute for Immunology (LJI) @lji.org · 05/03/2025

LJI recently unveiled a new "pocket" art gallery to showcase breathtaking images of immune cells at work! www.lji.org/blog/new-lji... #SanDiego #STEM #Science #Microscopy #Immunology #ImmuneSystem #SciArt

lji.org

New LJI art gallery celebrates the body’s microscopic ‘landscape’

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Sven Klumpe @svenklumpe.bsky.social · 05/03/2025

Happy to share our manuscript on the in situ visualization of the copia retrotransposon in its final form today published in @cellcellpress.bsky.social www.cell.com/cell/fulltex.... What’s new?

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Kelsey Atherton @atherton.bsky.social · 03/03/2025

"Kennedy has since emphasized that HHS is aiding Texas health officials with their measles response, but declined so far to explicitly call for people to get vaccinated." Politico underrated as carrying water for monsters. Name the measles outbreak RFK Jr exacerbated in American Samoa you cowards!

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Dawid Zyla @dzyla.bsky.social · 03/03/2025

I updated the metadata extraction from PubMed files, improving the abstracts in the [MSS]. However, only 70% of PubMed entries include abstracts, limiting their contribution to semantic search. To test the new database, check here: mssearch.xyz

The database logos within the manuscript search app that allows searching for manuscripts from PubMed, bioRxiv, medRxiv and arxiv.

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Dawid Zyla @dzyla.bsky.social · 01/03/2025

High-quality search is now available. Previously, [MSS] returned many empty abstracts or titles; now, you can ensure that only quality entries are displayed. This does not solve the root problem but makes the manuscript search better.

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Rosa Isela Gálvez @rig-scientist.bsky.social · 26/02/2025

JCI Insight - Frequency of dengue virus–specific T cells is related to infection outcome in endemic settings insight.jci.org/articles/vie...

insight.jci.org

JCI Insight - Frequency of dengue virus–specific T cells is related to infection outcome in endemic settings

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Dawid Zyla @dzyla.bsky.social · 21/02/2025

Search in peace 🔍 arXiv was added to Manuscript Semantic Search [MSS] (database updated 250216)! Check it here: mssearch.xyz

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Diego del Alamo @delalamo.xyz · 20/02/2025

Inverse folding models fine-tuned on ddG data are SOTA on stability/thermostability prediction, & can be further improved by including features from PLMs; additionally, these help identify conserved AAs whose functional importance isn't obvious from structure alone www.biorxiv.org/content/10.1...

Performance of SPURS (the paper here) against baselines on the Megascale test set and ten independent test datasets

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John Rubinstein @johnrubinstein.bsky.social · 19/02/2025

In @justinditrani.bsky.social final postdoc paper (with contributions from many others) we show that forming/purifying vesicles (here from M. smegmatis) allows structure det'n of *endogenous* membrane proteins in their *native lipid bilayer* 🧵 on methods & TB biology... www.pnas.org/doi/full/10....

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