The EMBL PhD programme is open until 13th October (entry ~Sep 2026): www.embl.org/about/info/e... We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them

Job opportunities at an absolutely amazing place for molecular biology 🧫

Almost done, just need to add a bit of background.

Different supervision task today 🍿

Deadline extended - last chance, second edition!

Cool project with the Pless lab on disease-associated variants in a membrane protein, NALCN, that needs to be in complex to function. Most of our computational work was done by PhD student Aleks Panfilova.

Interested in structural biology, membrane proteins, biophysics and working to understand hormone transport in plants?☘️🔬👩‍🔬🧪 We have an open PhD position: - 3 years fully funded. - Details and application link: www.linkedin.com/posts/plant-... Please repost 💚

The journal version of "Biophysics-based protein language models for protein engineering" with @philromero.bsky.social is live! Mutational Effect Transfer Learning (METL) is a protein language model trained on biophysical simulations that we use for protein engineering. 1/ doi.org/10.1038/s415...

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🚨 We're hiring, please share! The FMI seeks a tenure-track Group Leader (Assistant Prof) in Structural Biology 🔬 Innovative scientists in genome regulation, RNA metabolism, or protein homeostasis—especially using cutting-edge approaches—apply now at www.fmi.ch/education-ca...

One of those days when Copenhagen is trying to play San Francisco 🌫️ Fortunately we got to keep the trains.

"We can and should reject that AI output is ‘good enough,’ not only because it is not good, but also because there is inherent value in thinking for ourselves."

BIG NEWS!! We will be hiring a new professor with 25 years of endowed funding at the @biozentrum.unibas.ch @unibas.ch, focused on using biophysics and structural biology to explore climate-related fundamental science topics. Come start an innovative research cluster with us! 🧪🔬🧶🧬🌾🌍

Successfully taught my first bioinformatics class in Danish 🇩🇰 Based on feedback, the most helpful bit was rather language-Independent, when I said that affine gap scores are kinda like Affinity in Magic The Gathering 🧙‍♀️ 📜

A very relatable rant on why manuscript revisions can be frustrating. And it doesn’t even mention „you should have cited these 7 tangentially related articles, all written by the same author“ 📜

This is where German clearly was much easier. To this day I can find myself in an English audiobook and realise „oh that’s how you pronounce it“ 😅

Final reminder to nominate yourself / your outstanding group members for the inaugural ISBUC Best Paper Award 📅 Submission deadline: September 3rd 🏆 Prize: 10.000kr stipend for research and training-related travel expenses ✏️ Submit nominees: isbuc.ku.dk/junior-isbuc...

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

#lørdagslik (Saturday sweets) from Frauke Gräter at the SBiNLab 25th anniversary symposium: Natural proteins are like soft candy (gummy bears) while current designed proteins are like hard candy 🍭

starting to suspect my neighbor is a large language model

Last chance to register for the 2025 European RosettaCon - we had a blast last year, and @ajasjaljubetic.bsky.social is putting together a great program. With Easter eggs 🥚 in the submission system!

If you use Boltz1/2, BioEmu, Chai1, or other MSA-dependent models, you’re likely using our ColabFold server. Please be considerate! Avoid large submissions across many IPs instead generate the MSA locally. Our server is an old-timer from 2014 and can’t handle that load.

RosettaFold 3 is here! 🧬🚀 AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release! Congratulations @simonmathis.bsky.social and team!!! ❤️ bioRxiv preprint: www.biorxiv.org/content/10.1...

I'm in this picture and I don't like it

Testing how AI-proof my homework and exam questions are. Images and graphs are a real challenge for current LLMs. This "HMM" for membrane proteins look nothing like the real deal.

Instead of regurgitating the bromide that LLMs are just "autocomplete on steroids" (even by people who know better), maybe we can actually engage in some public education. The problem with genAI is better expressed through a classic computer science concept, known as SYMBOL GROUNDING. 🧵

“Mom, your Danish 🇩🇰 is a little embarrassing.” 😳 Apparently I’m raising little language snobs. Just what I needed to hear a month before starting to teach in Danish.

Villum Sabbatical grant: For US-based researchers wishing to visit a Danish university for up to 12 months Deadline Aug. 15th 2025 villumfonden.dk/en/group/cha...

food for thought mailchi.mp/rawsignal/no...

Side story: While working on the Google Colab notebook for MSA pairformer. We encountered a problem: The MMseqs2 ColabFold MSA did not show any contacts at protein interfaces, while our old HHblits alignments showed clear contacts 🫥... (2/4)

Trip description by 3yo: “First we drive with the car. Then we take a kind of boat ⛴️ and we’ve eaten fries 🍟 on it before!” #priorities

Ready to lead pioneering research that bridges systems-level investigations of biological systems to molecular mechanism? The EMBL Molecular Systems Biology Unit in Heidelberg is hiring a Group Leader!

This thread has so much amazing biology 🤩

We are looking for a PhD student in (mostly )wet-lab biochemistry to work on short linear motifs, intrinsically disordered regions, in the context of the Marie Curie network "IDPro". More info an apply here: www.uu.se/en/about-uu/...

I'm looking for my first PhD student! We will push the frontiers of probabilistic machine learning for the molecular sciences, and study how to design new algorithms that exploit the unique properties of molecular systems to learn about the world. efzu.fa.em2.oraclecloud.com/hcmUI/Candid...

In our new paper we characterize the effects of indel variants on protein folding and stability using a new yeast-based protein folding sensor. The work was led by Sven Larsen-Ledet and supported by the @novo-nordisk.bsky.social. Link to paper: www.cell.com/structure/fu...

Curious about how protein variants affect interactions and networks? Check out our review on both experimental 🧫 and computational 💻 approaches

Which came first, the rabbit 🐰 or the carrot 🥕 #evolution

I keep seeing heartbreaking stories about people who spend years in grad school, apply to jobs, and only then learn that their dream job needs a skill they didn’t learn during grad school. Looking at job ads *now*, years before you’re applying, can help identify skills to develop. 🧪🌎🦑🐠

Excellent thread that everyone who thinks gender and sex are as simple as you learned in school should read before they ever offer up an opinion of any kind on trans or intersex people

Open PhD position in my group: protein bioinformatics and protein-lipid interactions. Competences required: experience with protein bioinformatics, good programing skills, machine learning, interest for beautiful protein structures! Deadline: Aug 1st 2025. Official info => tinyurl.com/LTPbioinfo

Hoping the other shoe won’t drop

The dependence of the amino acid backbone conformation on the translated synonymous codon is not statistically significant doi.org/10.1073/pnas... [Following: Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon doi.org/10.1038/s414...

10yo reading. “Mommy, what does j-e-n-e-s-a-i-s-p-a-s mean?” I’m puzzled, and walk over. “Ah - ‘I don’t know’. It’s French 🇫🇷 “ “Ok” A minute later “Mommy, can you look it up, I really want to know” #lostintranslation

AlphaFold is amazing but gives you static structures 🧊 In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃 Code: github.com/KULL-Centre/... Colab: github.com/matteo-cagia...

K1 learned about twitter and Bluesky today. „Makes sense, the sky is usually blue… no wait, it’s usually grey. It should be called GreySky.“ Tell me you live in 🇩🇰 without telling me you live in 🇩🇰

As a person who has professionally done my own research on a number of things, let me say: I do not want to have to do my own research on most things. I am happy for experts to do research in their fields and publish their finds, and for service providers to read and summarize it for me.

New Postdoc position alert: a very exciting opportunity to join a new group led by @sumanasharma.bsky.social who is a visionary scientist and a fantastic person. Looking for a computational person to work on a project related to studying immune checkpoint signalling: my.corehr.com/pls/uoxrecru...

PSA: be careful with the classic dark-gray-on-light-gray colour scheme. On old projectors, this can look like light brown on light pink. In particular, avoid for violin plots.