iiinova — where your digital self keeps evolving

Amelie Stein @amelierocks.bsky.social · 26/01/2026

Big congratulations to Aleksandra Panfilova who defended her PhD last week! Aleks has been teasing apart models of protein interactions and consequences of mutations on these, preprint coming soon! She’s now looking for new opportunities in Estonia, so reach out to hear if you’re hiring 😊

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Amelie Stein @amelierocks.bsky.social · 19/01/2026

Annika raises many good points about the challenges with (not) “just putting the slides online”

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Amelie Stein @amelierocks.bsky.social · 25/11/2025

So looking forward to this meeting!

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Yury Bykov @yurabykov.bsky.social · 20/11/2025

Junior professor position at the University of Kaiserslautern! Our Department of Biology is seeking a colleague working with microalgae. This is a wonderful place to do wonderful science with great people! Please, repost :) Further details: jobs.rptu.de/jobposting/1...

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Amelie Stein @amelierocks.bsky.social · 20/11/2025

T’is the season When I scrape ice Off my saddle

Bike saddle covered in thousands of frozen droplets. Green grass and brown leaves in the background.

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Pause @ Real Scientists DE @realscientists.de · 19/11/2025

🧵 Thread👇 Heute Nachmittag im Fokus: Wissenschaftliche Karrierewege An der Uni wird oft nur das Karriereziel Professur diskutiert, aber der Weg dahin ist schwer, wenig planbar und die anderen Berufsoptionen sehr vielfältig (und zumeist sogar besser).

media.tenor.com

spongebob is writing on a piece of paper with a pen .

ALT: spongebob is writing on a piece of paper with a pen .

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Dr. Jey McCreight 🏳️‍⚧️🧬 @jeymccreight.bsky.social · 16/11/2025

I lament all the research and writing I never got to do because I was too busy fighting sex pests and institutionalized misogyny

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Oded Rechavi @odedrechavi.bsky.social · 14/11/2025

Adding citations of people who might review the paper

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Amelie Stein @amelierocks.bsky.social · 09/11/2025

Why is she referred to as Miss Franklin? Was that customary at the time also for male scientists?

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Amelie Stein @amelierocks.bsky.social · 08/11/2025

Fall is beautiful, even on gray days 🍂 🍁

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Amelie Stein @amelierocks.bsky.social · 07/11/2025

My 11yo chose Rosalind Franklin for her school project on „a person everyone should know“ and I’m having a hard time not pushing all the terrible stories that tend to get swept under a rug on her.

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Amelie Stein @amelierocks.bsky.social · 07/11/2025

My 11yo is more active in her Teams chats than I am in mine.

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Pedro Beltrao @pedrobeltrao.bsky.social · 28/10/2025

Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...

github.com

GitHub - aqlaboratory/openfold-3: OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3

OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3 - aqlaboratory/openfold-3

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Mark Peifer (He, him) @peiferlabunc.bsky.social · 27/10/2025

The UNC Department of Biology is seeking a Director of Biology Teaching Labs, a key leadership role overseeing our undergraduate laboratory program. 1/n Learn more and apply here: unc.peopleadmin.com/postings/308...

unc.peopleadmin.com

Director of Biology Teaching Labs

The Director of Biology Teaching Labs provides leadership and direction in the management of the Biology Department's undergraduate laboratories and will be responsible for the undergraduate laborator...

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Mark Hamill @markhamillofficial.bsky.social · 27/10/2025

I have a very bad feeling about this...

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Laura Howes @laurahowes.bsky.social · 25/10/2025

Alternatively, lads, might be worth thinking about supporting the German car industry to remain viable in the future rather than locking them into a dying business model. But sure, you go off...

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Amelie Stein @amelierocks.bsky.social · 20/10/2025

Fittingly, I arrived just in time for a talk from the organiser’s group @ajasjaljubetic.bsky.social 🚶‍♀️

Hotel banquet room with lots of round tables, lots of protein design aficionados, and an ongoing presentation on protein walkers

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Amelie Stein @amelierocks.bsky.social · 20/10/2025

Airplane sunrise is the reward for early departures. Looking forward to European RosettaCon 2025!

Blazing colourful sunrise seen through an airplane window

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Amelie Stein @amelierocks.bsky.social · 10/10/2025

Very similar experience moving to Spain 🇪🇸 (20 years ago, might have changed)

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Amelie Stein @amelierocks.bsky.social · 09/10/2025

I maintain that the most important is the coffee machine

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Izzy Jayasinghe @ijayas.bsky.social · 09/10/2025

Ah, a classic moment of @nature.com recognizing the scientific contributions of both genders: man and machine.

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Marcel Dickmanns | 🌿❄️🔬 @madic.bsky.social · 07/10/2025

You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly. This saves some clicking around. Neat!

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Andrew Iwaniuk @evoneuro.bsky.social · 09/10/2025

As I tell my students, if you arrived at a simple answer in biology you have done one of two things: arrived at the wrong answer or asked the wrong question

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Amelie Stein @amelierocks.bsky.social · 09/10/2025

Kindergarten teacher asks what I teach (biological sequence analyses), I try to explain. She turns to the 3yo and asks „What do you want to be when you grow up?“ Prompt and confident answer: „A butterfly 🦋!“

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 07/10/2025

The proteasome-substrate-shuttle protein UBQLN2 contains—like other quality control system proteins—a long region devoid of lysine (a lysine desert) Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation doi.org/10.1101/2025...

Fig. 1 – UBQLN2 is a conserved lysine-depleted protein. (A) Sequence comparison of
UBQLN2 orthologs in the indicated species. Intrinsically disordered regions in human
UBQLN2 based on MobiDB are shown as a blue bar. The domain organization based on the
SMART database is marked. Lysine residues are marked as black squares. (B) ESM-2
predictions of all possible single amino acid substitutions of human UBQLN2 presented as a
heat map. The wild-type residues are marked in blue. ESM-2 scores close to zero (light
yellow colors) indicate that the amino acid substitution is compatible with the ESM-2
language model, whereas negative scores (dark orange colors) indicate that the variant is
incompatible with the ESM-2 model. The domain organization (based on SMART) is aligned
above the map. Note that substitutions to lysine or cysteine in general appear detrimental, in
particular downstream of the UBL domain. (C) The AlphaFold2 predicted structured of
human UBQLN2 (AF-Q9UHD9-F1) (left panel). The UBL domain is colored blue, and the
UBA domain is colored orange and the STI1 regions green. Zoom in on the UBL domain
(right panel) with the lysine residues highlighted as stick representations and colored based
on the relative accessible surface area (rASA, dark red exposed; grey, buried).

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Elizabeth Wood, PhD @lizbwood.bsky.social · 06/10/2025

For every Nobel that goes to a criminally under-recognized woman scientist (Brunkow, Karikó), or fails to go (Candy Lee), a week of mourning and reform for an academic system wherein you can do Nobel-prize-worthy-work and still end up without a conceivable path to being a professor.

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Irina Bezsonova @irinabezsonova.bsky.social · 03/10/2025

This October I’m drawing one molecule a day inspired by proteins in pdb @rcsbpdb.bsky.social Day 2/31 Prompt WEAVE N-terminal domain of a Fibrion - a building block of silk fiber produced by silkworms. Pdb: 3UA0 Next prompt is CROWN and I would love your suggestions!

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Amelie Stein @amelierocks.bsky.social · 03/10/2025

Alternatively, we could just run a random number generator. Burns far less rainforest.

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Amelie Stein @amelierocks.bsky.social · 03/10/2025

Yes, that’s the poster child!

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Amelie Stein @amelierocks.bsky.social · 03/10/2025

Evolutionarily buffering of minor damage could be a good idea, to allow for intermediates along trajectories to other functions. Dan Tawfik looked into this trade-off between stability and evolvability quite a bit.

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Amelie Stein @amelierocks.bsky.social · 03/10/2025

Depending on the specific protein in question, if it has a dedicated transcription factor that senses whether its function/presence is needed, there could be dynamic regulation, but - as far as I know - this doesn't generally happen just for levels.

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Amelie Stein @amelierocks.bsky.social · 03/10/2025

I think, for protein stability (which I feel most qualified to comment on), the main proposed masking mechanism is that chaperones can help refold moderately affected proteins, so there is no apparent phenotype. Up to a certain level of damage, then it's down the degradation pathway.

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Amelie Stein @amelierocks.bsky.social · 03/10/2025

Ouch 😢 I’d guess it has been studied some, but not systematically enough yet to cross over to modellers?

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Amelie Stein @amelierocks.bsky.social · 03/10/2025

Some interesting thoughts on the Perspective Harper Raiken and I wrote over the summer

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Amelie Stein @amelierocks.bsky.social · 03/10/2025

and what isn’t, and why. I think e.g. organoid models can provide insight here. This is a very mechanistic perspective, sequence models informed by evolution and mutagenesis may be able to tell whether a variant is likely detrimental (patient at risk?), just not why/how (treatment development). 4/4

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Amelie Stein @amelierocks.bsky.social · 03/10/2025

to problems with oxygen transport and blood flow. Can we model each of these layers and scales individually? Perhaps. And this is a very well-studied, monogenic case. For polygenic diseases or environmental factors, we’ll need to learn how to integrate them. What is buffered by dynamic regulation 3/

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Amelie Stein @amelierocks.bsky.social · 03/10/2025

point towards gaps in our understanding of biology. As for whether we can model it, to me it depends on whether we can model emergent properties. Take sickle cell anemia. Broadly, the extra bulge on the protein surface leads to stacking, which leads to distortion of red blood cells, which leads 2/

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Amelie Stein @amelierocks.bsky.social · 03/10/2025

Thank you! I would say that us protein people are aware that we can’t explain everything bottom-up from the molecular level. But there are some things we can explain, like loss of stability, and that can be helpful. Sometimes we turn it around & say that the effects observed that we can’t explain 1/

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Dr. Jens Foell @jensfoell.de · 23/03/2024

I don’t know who wrote this, but it’s absolutely perfect

• X-Men is about civil rights. If you didn't get that, you didn't get X-Men.
• Black Panther is about civil rights. If you didn't get that, you didn't get
Black Panther.
• Captain America literally fought the Nazis. He is the embodiment of fighting the alt-right. If you didn't get that, you didn't get Captain America.
• The Empire in Star Wars is fascist. The Rebel alliance is Anti-Fascist. If you didn't get that, you didn't get Star Wars.
• The Punisher isn't meant to be a role model for police or armed forces.
So much so that the writers of The Punisher made him actively speak out against it in a comic. If you didn't get that, you didn't get The Punisher.
• Deadpool is queer. He's pansexual. Fact. If you didn't get that you didn't get Deadpool.
• Star Trek is about equality for all genders, races, and sexualities. As early as the mid-60s it was taking a pro-choice stance and defending women's right to choose. One of its clearest themes is accepting different cultures and appearances

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Sarah Shammas @sarahshammas.bsky.social · 01/10/2025

Why are transcription factors disordered? Come join us in Oxford as a postdoc and we'll find out together! Help publish 3 mature projects, AND develop cool new single molecule fluorescence binding assays! biophysics transcription protein:DNA interactions my.corehr.com/pls/uoxrecru...

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