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Joost Snijder

@joostsnijder.bsky.social
2.8K followers 471 following 301 posts

a sort of scientist. viruses and antibodies. structure and biophysics. mass spec and cryoEM

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Reposted by Joost Snijder
Matti Pronker @mfpronker.bsky.social · 6h
Check out our new preprint: Affinity maturation of a single-domain antibody via rational mutagenesis informed by artificial intelligence 🧬🧫🧪🤖 www.biorxiv.org/content/10.6...
biorxiv.org
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 14/10/2026
LoL-align is out in @natmethods.nature.com! It aligns protein structures without superposition. More sensitive than TM-align and DALI, producing better alignments 5–20× faster. Now available in Foldseek! 📄 www.nature.com/articles/s41... 💾 github.com/steineggerlab/foldseek 🌐 search.foldseek.com
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 13/10/2026
Version 1.3.2 of PearTree released: github.com/artic-networ... Fixes many of the remaining niggling bugs. WebApp updated at peartree.live
The logo of the PearTree phylogenetic tree viewer app - a partridge in a pear tree.
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 09/10/2026
"Temporal and Phylodynamic analyses of the 2026 Bundibugyo virus disease outbreak in the Democratic Republic of the Congo" - www.medrxiv.org/content/10.6...
medrxiv.org
Temporal and Phylodynamic analyses of the 2026 Bundibugyo virus disease outbreak in the Democratic Republic of the Congo
The Democratic Republic of the Congo is experiencing a major outbreak of Ebola disease caused by Orthoebolavirus bundibugyoense (Bundibugyo virus), which was declared on May 15, 2026. To investigate t...
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GlycoShape @glycoshape.org · 09/10/2026
Phenomenal #glycotime by Meg Lunn-Halbert, Joel Allen and colleagues demonstrates through de novo protein design how steric hindrance controls N-glycan maturation ⬇️ doi.org/10.64898/202... Protein design with RFdiffusionAA coupled with glycosylation with GlycoShape 🧪
screenshot of Fig. 2 in the paper, titled "Systematically altering steric restriction controls glycan processing" the following corresponds to the figure caption in the paper.
Panel a, AF3-predicted protein with GlycoShape-modeled Man9 glycan (green) for glycoproteins THRgly1-4. b-d, Deconvoluted intact
mass spectra for analyzing native glycosylation with 1–3 major peaks corresponding to glycosylation shifts labeled. Glycans
matching in theoretical molecular weight to the corresponding shift are schematically annotated as follows: mannose residues as
green circles, N-acetyl glucosamine residues as blue squares, galactose as yellow circles, sialic acid as pink diamonds, and glucose
as blue circles. Unglycosylated sizes are estimated based on predicted MW and labeled, when present. b: Native glycosylation. c:
Native protein digested with Endo H. d: Overlaid protein from kifunensine-treated cells (color, solid line) and digested with Endo H
(gray, dotted line). Estimated predominant glycans present are shown in MW (Da) differences from predicted unglycosylated size.
For peak table see Supplementary Data S3; amino acid sequences provided in Supplementary Data S1.
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Friedrich Förster @fridof.bsky.social · 07/10/2026
Can RNA itself drive toxicity in Huntington’s disease? Join the Kaiser lab (Bijvoet Centre, Utrecht University) to tackle this question using cutting-edge single-molecule biophysics, optical tweezers & fluorescence microscopy. www.uu.nl/en/organisat...
uu.nl
PhD Position on Biophysical Origins of RNA Toxicity in Huntington’s Disease
Exciting Opportunity for a PhD Researcher: Join our team to investigate molecular mechanisms in Huntington’s Disease!
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Joost Snijder @joostsnijder.bsky.social · 07/10/2026
The gall it would take to complain about zero points for that answer 😅
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Lukas Käll @lukaskall.bsky.social · 07/10/2026
Self-supervised pretraining can improve de novo peptide sequencing. To our knowledge, our new model dIon is the first to show it. Preprint with Alfred Nilsson, Joel Lapin, Samuel Payne and Mathias Wilhelm. doi.org/10.48550/arX... 1/9
doi.org
dIon: Fragmentation-Based Invariance for Self-Supervised Learning of Tandem Mass Spectra
We introduce a novel invariance for peptide tandem mass spectrometry data, unlocking self-supervised representation learning that improves de novo sequencing of peptides. This invariance exploits the ...
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Joost Snijder @joostsnijder.bsky.social · 07/10/2026
“Fragmentizing the microisotopic peak” - correcting exams don’t know whether to laugh or cry 😅
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Michael MacCoss @maccoss.bsky.social · 06/10/2026
The @uwgenome.bsky.social has two open faculty positions. One recruitment will be for an Assistant Professor and the second is an open rank position. ap.washington.edu/ahr/position...
ap.washington.edu
Position Details - Academic Personnel & Faculty
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Renske Leijten @renskeleijten.bsky.social · 06/10/2026
Liefst was ik niet herinnerd aan het bestaan van deze dame. Maar de Belastingdienst flikte het toch weer dat velen een nare herbeleving kregen aan donkere tijden. Nieuwe column! open.substack.com/pub/nijman/p...
open.substack.com
‘Deze dame, die ik twee keer martelend aan de slag heb gezien, oh precies deze dame’ - Renske Leijten
‘Wat is de Belastingdienst toch voor plek, dat dit maar blijft gebeuren?’
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Sjors Scheres @sjorsscheres.bsky.social · 06/10/2026
We have 2 new preprints on @biorxivpreprint.bsky.social that describe reconstitution of #Alzheimers paired helical filaments in experimental model systems: one in human brain organoids and one in murine primary cultures. www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6...
biorxiv.org
Templated seeding induces the formation of Alzheimer paired helical tau filaments in human brain organoids
The prion concept postulates that seeded aggregation results in the recruitment of soluble protein monomers and their assembly into amyloid filaments with the same structures as those of the seeds. He...
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Daniel Hurdiss @danielhurdiss.bsky.social · 04/10/2026
Mechanism of spike opening in a mammalian gammacoronavirus www.biorxiv.org/content/10.6...
biorxiv.org
Mechanism of spike opening in a mammalian gammacoronavirus
Coronavirus spike proteins mediate receptor binding and fusion and are key determinants of viral host range. To bind protein receptors, some CoV spikes undergo conformational changes termed opening, w...
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Daniel Hurdiss @danielhurdiss.bsky.social · 04/10/2026
Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes www.biorxiv.org/content/10.6...
biorxiv.org
Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes
Mechanistic understanding of viral protein-protein interactions enables global health security and pandemic preparedness, yet experimental characterisation remains difficult, costly, and often restric...
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Amy Maxmen, PhD @amymaxmen.bsky.social · 02/10/2026
The Ebola outbreak in Congo is now exploding in North Kivu, where 34% of Ebola patients are being treated in bare-bones health facilities instead of Ebola Treatment Units, according to @msf.org 3,982 confirmed deaths 😔 www.doctorswithoutborders.org/latest/ebola...
doctorswithoutborders.org
Ebola outbreak spreading like “wildfire” across North Kivu
The province is bearing an increasing share of the Ebola burden in DR Congo, while access to specialized care remains insufficient.
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Joost Snijder @joostsnijder.bsky.social · 01/10/2026
Fantastic evening at ARTIS cheering on Miguel for his @heinekenprizes.bsky.social Young Scientist award. Here with @danielhurdiss.bsky.social and @fmattiroli.bsky.social 😁
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Kai Yi @kaiyi94.bsky.social · 29/09/2026
1/7 Excited to share GuideFlip! We use guided discrete flow matching to co-design protein sequences and structures for flexible interactions, with experimental validation across three systems: α-synuclein, RBX1 and active-state GPCR nanobodies.
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Elisa Fadda @elisafadda.bsky.social · 25/09/2026
Got a glycoprotein as a target for your binder design competition on Monday? Look no further ⬇️ we got you 😎 #glycotime 🧪🔥
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Arnaud Vanden Broeck @avbroeck.bsky.social · 23/09/2026
Very happy to share the first paper from our lab, out now in Nature Communications!🎉🥳 Structural basis of step II Spliced Leader RNA trans-splicing in trypanosomatid parasites 🧬🔬 🔗 www.nature.com/articles/s41... @natcomms.nature.com @universitedeliege.bsky.social @rockefeller.edu #cryoEM #cryo-EM
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Maya Voichek @mayavoichek.bsky.social · 24/09/2026
Super excited to share my postdoctoral work at @imbavienna.bsky.social @viennabiocenter.bsky.social - We discovered that some retrotransposons, or "jumping genes" 🧬, are able to spread from cell to cell via a new viral infectivity route. A short thread: 🧵👇 (1/7)
AI-generated illustration of the soma-to-germline transmission of retrotransposons described in our work
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Meryl Haas @merylhaas.bsky.social · 24/09/2026
Happy to see that the first paper of my PhD journey has been published in Nature Communications. A big thank you to all the collaborators and authors that made this possible.
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Colin Carlson @colincarlson.bsky.social · 23/09/2026
What's behind this tidal wave of epidemics? In the largest study ever conducted on emerging infectious diseases, we show that the popular explanation - "our relationship with nature is out of balance" - doesn't hold up. Out now in Nature, after half a decade of work: www.nature.com/articles/s41...
nature.com
The anthropogenic fingerprint on emerging infectious diseases - Nature
Emerging infectious disease outbreak risks are ubiquitous worldwide, and highest in landscapes where people, livestock and fragmented natural ecosystems coexist, but detection and data ...
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Cathy Spangler @cathyspangler.bsky.social · 22/09/2026
I'm excited to share our new preprint, where we show that fine-tuning gold nanoparticle conjugation to different Fab structural elements can produce powerful, rigidly coupled, labeling tools for in-situ cryo-ET. Take a look if you want to see an AuNP in an EM map!🔬🧠 www.biorxiv.org/content/10.6...
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Philippe Le Mercier, ViralZone @viralzone.bsky.social · 22/09/2026
A clever new tool for building full icosahedral capsids from AlphaFold models — from the talented team behind ViperDB. FoldaVirus, a knowledge-based icosahedral capsid prediction tool using AlphaFold www.pnas.org/doi/10.1073/...
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Nature Communications @natcomms.nature.com · 22/09/2026
Co-authors @merylhaas.bsky.social, @danielhurdiss.bsky.social from @utrechtvirology.bsky.social and others show that the norovirus  NS3 protein forms an RNA-engaging molecular motor that may transport viral RNA during infection. #Virology #CryoEM dlvr.it/TVbP01
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Ed Hutchinson @socialinfluenza.bsky.social · 21/09/2026
🚨New paper!🚨 Delighted to have played a small part in this study from Jason Botten's lab (and unusually for us, not on a respiratory virus) on a global map of the Zika virus phosphoproteome
journals.plos.org
A global map of the Zika virus phosphoproteome reveals host-driven regulation of viral particle release and cytopathogenicity
Author summary Zika virus can cause neurological complications and birth defects in humans. The proteins made by viruses are the tools used to hijack human cells to repurpose them into virus productio...
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Diego del Alamo @delalamo.xyz · 21/09/2026
The preprint for Structure-based Antibody Renumbering is now on biorxiv. The method, which I developed while I was between jobs last year, gives ANARCI-like annotations to antibodies and related systems using only the 3d coordinates of main chain atoms. www.biorxiv.org/content/10.6...
biorxiv.org
Structure-based Antibody Renumbering
Antibody numbering schemes like IMGT and Chothia assign each residue in the variable domain a consistent index based on substructural position. These annotations standardize sequences with different l...
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Daniel Hurdiss @danielhurdiss.bsky.social · 21/09/2026
Excited to share that our norovirus NS3 study is now online in Nature Communications! 🎉 These enzymes, found across an entire order of RNA viruses, have long been molecular motors in search of a function. We think we’ve uncovered their role. (🧵) www.nature.com/articles/s41... #virology #cryoEM
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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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Joost Snijder @joostsnijder.bsky.social · 21/09/2026
Time for our Advanced BioMS course this week! Here’s Kelly kicking things off.
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cryoEM papers @cryoempapers.bsky.social · 19/09/2026
Antigenic landscape of rabies and related lyssaviruses revealed by cryo-EM pubmed.ncbi.nlm.nih.gov/42758589/ #cryoEM
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Bloom lab @jbloomlab.bsky.social · 17/09/2026
We have measured 47,851 neutralization titers of current human sera vs current influenza strains to inform vaccine update & analyses of viral evolution. New H1N1 strains (eg, D.3.1.1 + G155E) have reduced neutralization, as do some H3N2 subclade K descendants. www.biorxiv.org/content/10.6...
biorxiv.org
Near real-time data on the human neutralizing antibody landscape to influenza virus in summer of 2026 shows antigenic advance of H3N2 subclade K region D mutants and H1N1 D.3.1.1 Sa mutants
Human seasonal influenza evolves rapidly, necessitating twice yearly decisions about whether to update the strains in the vaccine. To help inform this decision, we have been using high-throughput sequ...
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cryoEM papers @cryoempapers.bsky.social · 17/09/2026
Structural basis of diverse antibody recognition of conserved coronavirus spike S2 epitopes that contribute to protective immunity www.biorxiv.org/content/10.64898/2026.09.13.750764v1 #cryoEM
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Joost Snijder @joostsnijder.bsky.social · 17/09/2026
At the Dutch Vaccine Symposium 😁 with Frerik presenting our work on flavivirus antigen design.
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Abraham lab at Harvard Medical School @abrahamlabhms.bsky.social · 16/09/2026
Excited to share our newest publication revealing the structural and biophysical basis for monkeypox virus replisome activation! @hhmi-science.bsky.social @harvardmicro.bsky.social @hc2em.bsky.social @harvardmed.bsky.social @nature.com www.nature.com/articles/s41...
nature.com
Structure and operating principles of a monkeypox virus replisome - Nature
During replisome assembly of monkeypox virus, the hexameric helicase–primase E5 undergoes large-scale conformational changes that allow two of its primase domains to interact with the polymerase F8 th...
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Laboratory of Functional Viromics (LETKO) @fviromics.bsky.social · 16/09/2026
Our hedgehog coronavirus receptor study is now out in Nature Microbiology! Exciting new data has been added since the pre-print, including structure-guided mutagenesis showing species barriers, TMPRSS2 experiments and more details on the curious temperature adaptation in hedgehogs. (1/4)
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Kelvin Lau @klausenhauser on 🙅‍♂️🐘🪡 @klausenhauser.bsky.social · 16/09/2026
Did some reviews and…. Why do ppl show biophysical assays without the actual data? KD values with no curves or fits. An ITC table without a single raw thermogram. You wouldn’t publish a Western without the blot, but for binding assays we just say “trust me bro”. Free the curves!!
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Naomi Klein @naomiaklein.bsky.social · 15/09/2026
Today is the day! A journey that Astra and I started as an essay in The Guardian is now officially out in the world. End Times Fascism – And the Fight for the Living World is in bookstores now. If you are inclined, please buy one from an indie bookseller or borrow it from your local library.
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Sjors Scheres @sjorsscheres.bsky.social · 15/09/2026
Michel Goedert and myself are looking for two postdocs to work on #cryoEM and #masspec of #alphasynuclein filaments from neurodegenerative disease. Come join our bubbly and friendly team at the @mrclmb.ac.uk in lovely Cambridge, UK. www.nature.com/naturecareer...
nature.com
Postdoctoral Scientist | Neurobiology | Dr Michel Goedert | LMB 2842 - Cambridgeshire job with MRC Laboratory of Molecular Biology | 12864505
Postdoctoral Scientist Salary £42,694 per annum Fixed term, 3 years MRC Laboratory of Molecular Biology, Cambridge, UK To work in the group of Dr M...
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Tulilab.com @tulilab.bsky.social · 14/09/2026
IU is hiring a virologist. I am so excited. Come join a great group of scientists and people.
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Nature Biotechnology @natbiotech.nature.com · 14/09/2026
An engineered nanopore identifies saccharides, amino acids, peptides and ribonucleotides - @huang-nanopore.bsky.social www.nature.com/articles/s41...
nature.com
An engineered nanopore identifies saccharides, amino acids, peptides and ribonucleotides - Nature Biotechnology
Modified nanopore simultaneously identifies diverse biomolecules and their modifications.
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Sergey Ovchinnikov @sokrypton.org · 14/09/2026
Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)
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Follow the Money @ftm.nl · 13/09/2026
Minder verslavende algoritmes en meer privacy voor gebruikers: daar strijdt Evelyn Austin voor. Als directeur van Bits of Freedom zet ze zich al jaren in voor regulering van big tech-bedrijven – en met succes. Zo won ze in maart nog een hevige juridische strijd tegen Meta.
ftm.nl
‘Meta moet nu aanpassingen doen’: burgerrechten­activist sleepte big tech voor de rechter
In maart van dit jaar kreeg Meta een gevoelige tik op de vingers van de Nederlandse rechter. Het techbedrijf moet Nederlandse gebruikers van Instagram en Facebook de mogelijkheid bieden een tijdlijn t...
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Mart Krupovic @mkrupovic.bsky.social · 11/09/2026
Why did some #viruses evolve to be #giants while others did not? Our perspective piece on this topic with Eugene Koonin. www.pnas.org/doi/10.1073/...
pnas.org
Why did some viruses evolve to be giants while others did not? | PNAS
Viruses are ubiquitous mobile genetic elements that are obligate symbionts of cellular life forms and replicate exclusively within host cells. The ...
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Philippe Le Mercier, ViralZone @viralzone.bsky.social · 11/09/2026
Mechanism of membrane perforation in rotavirus cell entry | Science www.science.org/doi/10.1126/...
science.org
Mechanism of membrane perforation in rotavirus cell entry
Cell entry of nonenveloped animal viruses requires translocation of a macromolecular assembly across a cellular membrane. Double-stranded RNA viruses introduce into the target cell an inner capsid par...
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Kranzusch Lab @kranzuschlab.bsky.social · 10/09/2026
Stunning cryo-ET analysis from the Harrison Lab capturing every stage of how non-membrane viruses infect animal cells www.science.org/doi/10.1126/...
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cryoEM papers @cryoempapers.bsky.social · 09/09/2026
Structure-based design of soluble prefusion-stabilized herpes simplex virus type 2 glycoprotein B antigens pubmed.ncbi.nlm.nih.gov/42709545/ #cryoEM
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Leonie Anton @leonieanton.bsky.social · 03/09/2026
I am excited to share that I will start my group @embl.org in Grenoble in February 2027, where we will investigate host-pathogen interactions using in situ cryo electron microscopy🦠❄️🔬! I am recruiting PhD students through the current open call of the EMBL PhD Program: www.embl.org/about/info/e...
embl.org
Anton Group – Cellular structural biology of host-pathogen interactions
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Kermit Murray @kkmurray.bsky.social · 09/09/2026
(BioRxiv All) Allosteric remodelling of the Ebola virus glycoprotein underlies differences in entry mechanisms across species: During Ebolavirus transit through the endo-lysosomal pathway, the glycoprotein GP undergoes a series of conformational rearrangements upon cathepsin… #BioRxiv #MassSpecRSS
dlvr.it
Allosteric remodelling of the Ebola virus glycoprotein underlies differences in entry mechanisms across species
During Ebolavirus transit through the endo-lysosomal pathway, the glycoprotein GP undergoes a series of conformational rearrangements upon cathepsin cleavage and NPC1 receptor binding, culminating in host-virus membrane fusion. While these rearrangements underpin viral entry, their molecular mechanisms remain poorly understood. Here, we combine hydrogen/deuterium-exchange mass spectrometry and mass photometry to resolve structural dynamic and energetic transitions of GP of two major species, Zaire (EBOV) and Sudan (SUDV). We describe the allosteric axes that govern reorganization of the cleavage sites, opening of the receptor binding cavity and priming for fusion upon NPC1 engagement. We show that GP cathepsin cleavage and receptor binding exhibit different mechanisms and kinetics across species, and are allosterically coupled in a species-specific manner. We reveal that fusion priming is optimized via distinct routes in EBOV and SUDV GP. These data suggest that GP structural dynamics and allosteric remodelling underlie differences in entry mechanisms across Ebolavirus species.
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Daniel Hurdiss @danielhurdiss.bsky.social · 09/09/2026
Our first #cryoEM map from the Krios 5 recently installed at Utrecht University as part of the EMPower-funded upgrades to NeCEN. Hopefully the first of many more!
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