Amelie Stein

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

Group Leader – Molecular Systems Biology Unit Are you ready to lead groundbreaking research in Molecular Systems Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group, addressing original biological ...

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 🤩

PhD student in Biochemistry - Uppsala University PhD student in Biochemistry, Disciplinary Domain of Science and Technology, Faculty of Chemistry, Department of Chemistry - BMC, Uppsala University

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/...

Congrats 🙌

PhD scholarship in Machine Learning for Molecules - DTU Chemistry Advance large scale data generation for chemical and biological AI in a 3 year PhD. Work on the frontier of active learning, and develop novel probabilistic machine learning techniques for experiment ...

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...

Systematic characterization of indel variants using a yeast-based protein folding sensor Larsen-Ledet et al. developed a yeast-based protein folding sensor to determine the effects of indel variants in DHFR. Using a saturated indel library, it was found that most indels are not tolerated. Several are temperature sensitive and folding is rescued by methotrexate. Rosetta and AlphaFold2 predictions correlate with the observed effects.

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

Plushies, one a turtle emerging from an egg, the other a rabbit coming out of a carrot

Which came first, the rabbit 🐰 or the carrot 🥕

#evolution

Leg and foot of a small child next to open laptop

#academicparenting

Here’s what I teach my students about finding jobs in marine biology and conservation Our field is competitive, some job postings are confusing, and some career advice is contradictory or wrong. Here’s an exercise I have my students perform that I hope can help you. Graphic vi…

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

I love this perspective

PhD Research Fellow in protein bioinformatics  (282926) | University of Bergen Job title: PhD Research Fellow in protein bioinformatics  (282926), Employer: University of Bergen, Deadline: Tuesday, July 15, 2025

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

Running vest with a single flip flop attached

Hoping the other shoe won’t drop

The dependence of the amino acid backbone conformation on the translated synonymous codon is not statistically significant | PNAS The correlation between synonymous codon usage and secondary structure in translated proteins has been widely demonstrated. This usage plays a capi...

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.

Last 90’, get writing ⌨️
#lastminutewarrior

If only the wealthy tech bros seeking to purchase the fountain of youth just for themselves would invest in the *already evidenced based* approaches that extend human lifespan in aggregate. Like childhood vaccines, safe water, access to food, housing, and education, reducing domestic violence...

Now just a few days left to submit your abstract for a chance to join this fantastic protein design meeting 📅 📜 🧬 💻

For Europeans that absolutely need to travel to the US at the moment, I suggest looking into flying through Dublin airport in Ireland and doing the US-Pre-Clearance there. That way if you get rejected by border control, you are in Europe and can return home a lot easier.

Ever wondered about who Michaelis and Menton were? Learn more here…

Casa Battlo, a famous Gaudi-building, by night

Ginormous candles and wine barrels

Bread with cured Spanish ham

Rainy day

Barcelona in off-season