Who would have thought you could use so many tokens getting Claude to do the hard work to ingest GEO datasets. The scRNA-seq world is wild.

I love this concept so much. Haven’t checked out the architecture, but I bet its a bunch of wasm running this. I notice that Claude is on the contributors on github. The tool has really been transformational in making wasm available to me personally, as it generated standard tooling.

I have recently ventured deep into python notebook land these days, and I would love to know how people handle moderately complex notebooks. For simple stuff code+output is easy. But anything larger and it becomes quickly unreadable. Jupyter code hiding/folding is completely inscrutable…

🧵 New paper from @proteaglyco.bsky.social out in Analytical Chemistry! We used anion supercharging to unlock next-generation O-glycan structural analysis: - 4× greater signal - 5× better fragmentation Here's a thread, digging into each figure: doi.org/10.1021/acs....

I am hiring an associate scientist (non-PhD). If you have interest in #glycotime and antibody de novo sequencing please consider applying: regeneron.wd1.myworkdayjobs.com/en-US/Career...

This looks to be a follow up on the glycofibrils from a little while back. Really interesting to see the glycans resolved there. Does anyone have any feeling about how much we should rely on modelled structures/conformations into the cryo? What do people use to check their work?

It all makes chemical sense, and one might say: well, why not? Given that the amino-acid residues in a protein can form highly specific H-bond arrangements - that's often what they use for their selective binding and catalysis - why shouldn't those be arranged to mimic a nucleotide base? /14

We are proud to announce the discovery of Glyco-Carbohydrates, a paradigm shift in glycobiology! Traditional glycoconjugates (proteins, lipids & RNA) max out at 50% carbohydrate. Ours are 100% carbohydrate AND glycans, unlocking truly homogenous properties. TBA April 1st, 2027! 🍬 #glycotime

Look, I haven’t seen the code, maybe Claude helped out implementing it, maybe it was hand crafted. It doesn’t matter to me. The fact that software is fun and quirky again makes me happy.

The three enzymes ALG3, ALG9, and ALG12 catalyze the synthesis of the branched mannose core in N-glycans in four distinct steps. Now, their structures reveal the molecular logic of oligomannose core assembly #glycotime www.nature.com/articles/s41...

This will be great if it comes to fruition - I have this dream that we can eventually ditch journals, and move to collections of communities (society review) for peer review. A system of closed review, that then opens up when finished will be amazing, and could be built with this.

Finally, a detailed review about C-mannosylation: mechanism of C-mannosyltransferases and the influence of the C-mannosylation on the function of several proteins. Highly recommended to everyone in this type of post-translational modification! tinyurl.com/3ywjmfk3 #glycotime

"Structural analysis enabled us to convert Tn-specific mAbs into STn-specific mAbs through modification of VH complementarity-determining region 3, demonstrating the versatility of this approach" #glycotime 😎🧪 www.nature.com/articles/s41...

Just a reminder that when the Nazis were marching in to Copenhagen, Neils Bohr chose to dissolve his medal rather than have any Nazi take possession of it.

Authors use “Siglec-7 and -15…Fc chimera to demonstrate that CHST1-mediated 6-O-sulfation markedly enhanced binding to select O-glycoproteins, namely MAdCAM1, CD43, and PSGL-1” www.biorxiv.org/content/10.6...

The robots are not coming for your jobs, but bullshitters with robots ARE competing for your jobs, and unless we decouple publishing metrics from career paths (financial gain), we are going to lose both careers and our capacity to share information. doi.org/10.1126/science.adw3000

A tribute to Stuart Kornfeld, pioneering #glycotime scientist whose work on mannose-6-phosphate receptor lysosomal trafficking (among many other contributions) was highly influential to our work 🫡 www.jci.org/articles/vie...

There are so many quotes in this article that read as dystopian satire - but the worst has to be the overall idea that the one thing conservation efforts need is the Silicon Valley treatment. Pauli’s phrasing of “not even wrong” seems very apt here.

🚨 Are you into comp chem/biophys? Do you like glycobiology? Are you located around Freiburg Germany? Do you like me as a person? Want to see an open lecture about Computational Glycobiology/Biophysics in Freiburg, Germany, delivered by me?! 15 Dec, 17:15 HS Chemie @ Alberstrasse 21, 79104 Freiburg

We are looking for a motivated PhD student to join our lab! #SPPL3 #glycotime #Golgi #UniKiel

Last stretch for these positions, as the deadline for this is on Sunday!

Hey @biorxivpreprint.bsky.social @altmetric.com , I haven’t been able to see the BlueSky metrics for preprints for a while now on the BioRxiv website, so I am missing out on all the salacious gossip about the preprints. Is this a known bug?

Another bump for the postdoc and PhD positions still open at the center and postdoc specifically within my group (same link to apply). We’re looking for wet/dry lab, and I’m specifically after people who do magic with computers!

Reminder: our postdoc and PhD positions are still open. We work across different areas (wet and dry lab), but I am especially after people with a computational biology, bioinformatics, pytorch whisperer kind of background. Protein design and OpenFold/AF also counts.

First neurons didn’t appear overnight. We trace their roots to ancient secretory cells - showing how lifestyle & behavior shaped the evolution of first synapses.🧠🌊 #Evolution #Neuroscience Our latest in @natrevneuro.nature.com Link: rdcu.be/eMX3E @jeffcolgren.bsky.social @msarscentre.bsky.social

We will be hiring soon! #SPPL3 #glycotime #Golgi

Pretty low-effort example of plagiarism here.

I have a PhD position available in my lab at the University of Freiburg!! If you, or someone you know, might be looking for a position using modeling and simulations to uncover secrets in (glyco-)protein structure/function relationships please take a look at our website! www.kearnslab.org

It’s cool to see more stuff being built on top of Joshua Klein’s mzdata libraries. I’ve been playing around with a version that compiles down to WASM, which has been great to work with.

We all agree that LinkedIn is absolutely awful, right? Every other click on there is some highly optimised funnel to extract money from you. Hard to believe that people think it’s a good network for “science” discussions.

Also, on top of the postdoc and PhD positions open, you should also get in touch if you would like to try your hand at an EMBO or Marie Curie fellowship with us to get a headstart on your independent career.

employment.ku.dk/faculty/?sho... Hi all! We’re hiring at our brand new Center for Glycocalyx Research, across all areas - but I am also looking for postdocs to join my group specifically!

Multi-domain O-GlcNAcase structures reveal allosteric regulatory mechanisms pubmed.ncbi.nlm.nih.gov/41044083/ #cryoem

It is awesome that this work keeps going on. No idea where it’s going, but it looks fun!

Vaguely remember differences in glycosylation for spike alone vs native virus, and another paper that implicated N in slowing Golgi transit. Anyone with a better memory than me remember the refs? No doubt that viral protein effects on endomembranes are complex and overlapping.

This is a cool dive into AF3, with a really nice way to get AF3 to do something much more closely matching reality.

This might be be a dumb question, but do we know which glycans end up on the surfaces here after GGTA1/B4GALNT2/neuGc knockouts? Would obviously guess we miss these epitopes, but are they truncated, or replaced with some other epitope (apart from the obvious NeuAc)? www.nature.com/articles/s41...

A cryptic pocket allosterically modulates oligosaccharide binding to DC-SIGN www.biorxiv.org/content/10.1101/2025.08.19.671048v1 #cryoem

Sad, but probably inevitable news from Vodafone AU. I have been sitting on an ancient mobile phone plan for the past 25 years, with no minimum cost for infrequent usage, and they’re finally removing the plan. Are there any reputable places to port Australian mobile numbers to for e.g., VOIP?

Check the great commentary on @natcomms.nature.com from Trayambak Basak and colleagues about our work on #collagen GLT25D1 and the paper from Cao et al. about the LH3/GLT21D1 complex! #glycotime www.nature.com/articles/s41...

Kim Jong-un inspects the latest in North Korean shark tank technology.

If anyone is keen on testing the reglycosylation plugin for PyMOL, please get in touch! There’s a few rough edges I’d like to iron out, and would appreciate feedback.

This Lorenz Oken guy might just be on to something. The article mixes slime and mucus interchangeably, but it is a good read about the relative rarity of complex life. www.asimov.press/p/slime

CCG (incl @manno.se and @xylobecs.bsky.social) representing at the half marathon across the Øresund bridge today. Lovely weather for it!

Well, it turns out that you can actually make PyMOL do quite a lot of stuff. Here's the full workflow, integrating the amazing ReGlyco into PyMOL to re-glycosylate the LDLA linker. There's some serious magic needed to get it running as fast as it is within PyMOL. @elisafadda.bsky.social

Glycosylation of Structured Protein Domains in Cell-Free Reaction Environments | ACS Synthetic Biology pubs.acs.org/doi/10.1021/...

Interesting thread below! One thing I have been trying to understand is how NNs can store so much info in such a relatively “small” parameter space, such that the concepts are stored in the “direction” in a latent space. This idea would fit nicely with this model.

Looks intriguing! granta.com/slime/

This looks like a great resource to gain a conceptual understanding of deep learning models. It would be amazing to have a “Design Patterns” style book a la Gang of Four, just with patterns to detect, and the method to train it.