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Michalis Averof

@michalis-averof.bsky.social
2.6K followers 808 following 191 posts

Comparative developmental biology, regeneration, non-conventional model organisms, live imaging; see www.averof-lab.org

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Michalis Averof @michalis-averof.bsky.social · 2h
My understanding is that AI has taken in everything, including copyrighted, non-licensed material, so I'm not even sure this is a consequence of licensing under OA.
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Michalis Averof @michalis-averof.bsky.social · 3h
Indeed. So is it ok to turn human bad practice into standard practice?
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Michalis Averof @michalis-averof.bsky.social · 3h
When AI companies claim to discover a drug or to solve a mathematical problem based (partly) on the work of others, they neither attribute, cite, or in any way acknowledge those contributions. This, I think, is the problem.
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Michalis Averof @michalis-averof.bsky.social · 3h
not if it's done without acknowledging others' contributions
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Michalis Averof @michalis-averof.bsky.social · 11h
it's standard for internships >3 months in France
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Michalis Averof @michalis-averof.bsky.social · 21h
The results of this work will be used to explore and compare the regulatory networks that guide development and regeneration. To apply, please email mparis@ens-lyon.fr, michalis.averof@ens-lyon.fr and yad.ghavi-helm@ens-lyon.fr, including background, motivation and CV
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Michalis Averof @michalis-averof.bsky.social · 21h
We are interested in identifying cis-reg elements (enhancers & promoters) that underpin leg development and regeneration in the crustacean Parhyale. The recruited student will establish a chromosome conformation capture method to reveal genome organisation and promoter-enhancer contacts in Parhyale.
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Michalis Averof @michalis-averof.bsky.social · 21h
Understanding how cis-regulatory elements direct gene expression in complex genomes is a major unsolved puzzle. There are 2 elements to resolving this puzzle: identifying the CREs (see our recent paper) and understanding they interactions/contacts across the genome (focus of Ghavi-Helm lab).
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Michalis Averof @michalis-averof.bsky.social · 21h
6-month internship to explore (genome-wide) enhancer-promoter interactions in the crustacean Parhyale – Hosted by the Averof and Ghavi-Helm teams at IGFL Lyon – Early 2027 – Student (any level) with some prior experience in mol biol – Stipend 695 €/month
Activity of neuron-specific cis-regulatory elements in Parhyale embryos (Averof lab)Enhancer-promoter interactions in Drosophila embryos (Ghavi-Helm lab)
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Michalis Averof @michalis-averof.bsky.social · 13/10/2026
I didn't know him so well, but I also remember him as a kind and determined person
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Michalis Averof @michalis-averof.bsky.social · 13/10/2026
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Michalis Averof @michalis-averof.bsky.social · 11/10/2026
😂😂 I was trying to figure out what you meant
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Michalis Averof @michalis-averof.bsky.social · 11/10/2026
in greek it is kukuvagia (κουκουβάγια), from the sound 'kukuvau' - animal sounds do not translate well ;)
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Michalis Averof @michalis-averof.bsky.social · 09/10/2026
Waddington's epigenetic landscape at the Biennale d'Art Contemporain in Lyon (though not what the artist, Miguel Rothchild, intended to portray ;)
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Michalis Averof @michalis-averof.bsky.social · 01/10/2026
Cis-regulatory elements neuro5 and neuro6 driving fluorescent protein expression in a late Parhyale embryo. See article elifesciences.org/articles/111...
Cis-regulatory elements neuro5 and neuro6 driving fluorescent protein expression in a late Parhyale embryo (pseudocoloured, inverted image).
See article https://elifesciences.org/articles/111378
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Michalis Averof @michalis-averof.bsky.social · 01/10/2026
Here again is the story on how we got the three additional Parhyale species, with the help of our field experts /collaborators
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Michalis Averof @michalis-averof.bsky.social · 01/10/2026
Thanks to all co-authors for a great collaboration. @gillian-forbes.bsky.social, @irenekarapidaki.bsky.social and Emilia Skafida did most of the work. Mathilde Paris led the omics and data crunching. Thanks to @frm-officiel.bsky.social, @erc.europa.eu & EU Marie Curie for supporting our research.
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Michalis Averof @michalis-averof.bsky.social · 01/10/2026
A cost-effective method for finding cis-regulatory elements in a large genome (Parhyale, 3.6 Gb), combining info from chromatin accessibility (bulk & single-nucleus ATACseq) and cross-species sequence conservation (low coverage sequencing from 3 additional Parhyale species) Now published in eLife!
elifesciences.org
Genome-wide discovery of cis-regulatory elements in a large genome
Integrating genome-wide maps of chromatin accessibility and sequence conservation provides an accessible low-cost approach for identifying cis-regulatory elements in large genomes, validated in the em...
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Michalis Averof @michalis-averof.bsky.social · 01/10/2026
I would not lump them all as gimmicky. I think some are great. e.g. "A haystack in the needle: packaging sperm DNA in insects"
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Reposted by Michalis Averof
Michalis Averof @michalis-averof.bsky.social · 30/09/2026
Difficult to think how this could work in practice. One idea that comes to mind is a pre-selection by interview, before written proposal. In the arts, I think this kind of 'pitching' of the idea is quite common. Would it work in science? Would it succeed in selecting good proposals? Not sure.
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Michalis Averof @michalis-averof.bsky.social · 30/09/2026
The idea I put forward was pre-selecting based on (in-person) pitching. No algorithm involved on either side. I'm not sure it's a good idea, just wondering.
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Michalis Averof @michalis-averof.bsky.social · 30/09/2026
I guess it depends on the scale. If you bring in more people to assess 10x more AI-written proposals, that's a huge waste of everyone's time.
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Michalis Averof @michalis-averof.bsky.social · 30/09/2026
I understand, but the I think the increased workload comes from the surge of AI-written proposals. I wonder whether a pre-selection by pitching (in-person) would quell that surge.
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Michalis Averof @michalis-averof.bsky.social · 30/09/2026
Difficult to think how this could work in practice. One idea that comes to mind is a pre-selection by interview, before written proposal. In the arts, I think this kind of 'pitching' of the idea is quite common. Would it work in science? Would it succeed in selecting good proposals? Not sure.
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Michalis Averof @michalis-averof.bsky.social · 23/09/2026
beautiful work, thanks David
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Michalis Averof @michalis-averof.bsky.social · 23/09/2026
Yes, that's what I understood. If AF needs to be guided by additional information (here presumably a pattern of sequence conservation), then it's not fully capable of predicting how a protein folds itself based on primary sequence. No?
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Michalis Averof @michalis-averof.bsky.social · 23/09/2026
here is the paper: www.pnas.org/doi/10.1073/...
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Michalis Averof @michalis-averof.bsky.social · 23/09/2026
Nice example of how AI predictions are limited by the training set. AlphaFold has not learned the rules of protein folding, it's just great at predicting structures based on what it has already seen. Added constraints (e.g. alignment revealing conservation patterns) can help make a good prediction.
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Reposted by Michalis Averof
James Briscoe @jamesbriscoe.bsky.social · 22/09/2026
Our latest paper on building models of cell fate decisions -with David Rand, Marine Fontaine & @joadelas.bsky.social- combines developmental biology, dynamical systems theory and bioinformatics. I wrote a short piece to summarise it & explain ideas behind the approach briscoelab.org/blog-quantif...
briscoelab.org
Quantifying Waddington's Landscape | Briscoe Lab
I have written before about how two conceptual frameworks have shaped our thinking about cell fate, Waddington's epigenetic landscape and Davidson's gene...
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Michalis Averof @michalis-averof.bsky.social · 20/09/2026
Marie Curie fellowships are all about providing the best support and training to your fellows. A disengaged group leader who supports 10 or 20 applicants is not providing that support. I think it would be fair to fail these applications and set a rule of maximum 2 applicants per team.
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Reposted by Michalis Averof
Arnaud Martin @evolvwing.bsky.social · 20/09/2026
Such an essential piece. To share with students, trainees, and colleagues all around. (from 7 years ago) www.nature.com/articles/d41...
nature.com
Novelist Cormac McCarthy’s tips on how to write a great science paper
The Pulitzer prizewinner shares his advice for pleasing readers, editors and yourself.
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Reposted by Michalis Averof
Michalis Averof @michalis-averof.bsky.social · 17/09/2026
If you're proposing more tools to explore the data in papers, then yes, great! But why would we ever choose an AI agent _instead_ of a paper in which we can read the authors describe their ideas, motivations & conclusions? Would you like if your ideas were communicated exclusively via an AI agent?
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Michalis Averof @michalis-averof.bsky.social · 17/09/2026
If you're proposing more tools to explore the data in papers, then yes, great! But why would we ever choose an AI agent _instead_ of a paper in which we can read the authors describe their ideas, motivations & conclusions? Would you like if your ideas were communicated exclusively via an AI agent?
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Michalis Averof @michalis-averof.bsky.social · 24/08/2026
Article on the Pomaks by Marina Rafenberg @marinaraf.bsky.social, drawing on observations from Marta's fieldwork in September 2023. www.courrierdesbalkans.fr/petits-peupl...
courrierdesbalkans.fr
Petits peuples des Balkans (8/10) | En Grèce, les villages pomaks de Thrace au défi du changement - Le Courrier des Balkans
Dans les montagnes de Thrace occidentale, au nord-est de la Grèce, les villages pomaks se transforment rapidement. Les hommes partent travailler dans les chantiers navals d’Europe occidentale. Les jeu...
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Reposted by Michalis Averof
The Company of Biologists @biologists.bsky.social · 22/08/2026
We are gathering feedback from our readers, authors and reviewers about the use of AI tools in scholarly publishing. Have your say at: www.surveymonkey.com/r/ZBFC663
Community survey - The role of AI tools in scholarly publishing
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Michalis Averof @michalis-averof.bsky.social · 06/08/2026
I find that you need to understand the Brusselish but you don't need to speak it yourself. The reviewers of your grant will probably be happy to read plain english.
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Reposted by Michalis Averof
ZooCELL MSCA-Doctoral Network @zoocell.bsky.social · 21/07/2026
🔬 Meet Michalis Averof, ZooCELL PI at IGFL @michalis-averof.bsky.social What sparked his interest in EvoDevo? What keeps him curious after all these years? And what does he hope to discover next? 🧵 Read on to get to know Michalis through his own words. #ZooCELL#EvoDevo#genomics#IGFL#MSCA
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Michalis Averof @michalis-averof.bsky.social · 18/07/2026
both rare in budding yeast
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Michalis Averof @michalis-averof.bsky.social · 18/07/2026
and breakpoints for alternative splicing
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Michalis Averof @michalis-averof.bsky.social · 14/07/2026
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Michalis Averof @michalis-averof.bsky.social · 14/07/2026
Probably the first scientific description of regeneration in crustaceans was published by Réaumur in 1712. The paper starts like this: Scholars are as wary of the marvellous as common people are ready to believe it. ... 🧵 1/3
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Michalis Averof @michalis-averof.bsky.social · 14/07/2026
The people who frequent the banks of rivers or the sea assert that when crayfish, lobsters, crabs etc., have by accident lost one of their large legs, another grows back in its place. 3/3 www.academie-sciences.fr/pdf/dossiers...
academie-sciences.fr
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Michalis Averof @michalis-averof.bsky.social · 14/07/2026
This is a wise disposition, yet they should never deny the most surprising facts in the same way that the common people accept them – that is, without having examined them with sufficient care. 2/3
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Michalis Averof @michalis-averof.bsky.social · 14/07/2026
Probably the first scientific description of regeneration in crustaceans, by Réaumur 1712 The paper starts like this: Scholars are as wary of the marvellous as common people are ready to believe it. ... 🧵 1/3
drawing of regenerating crustacean leg by Arthur Monternier
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Michalis Averof @michalis-averof.bsky.social · 13/07/2026
Where did you watch this? it doesn't seem to be available in continental Europe.
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Michalis Averof @michalis-averof.bsky.social · 01/07/2026
Tribolium Brainbow plasmids are now available at www.addgene.org/browse/artic...
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Michalis Averof @michalis-averof.bsky.social · 29/06/2026
I have not been able to have a good discussion with AI yet, so no, I would hate if peer review was replaced by arguing with an AI bot. I fear that's the path this is leading to.
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Michalis Averof @michalis-averof.bsky.social · 29/06/2026
I disagree. I think it does specifically compromise preprints, because most preprints are still submitted for publication to journals. I think AI-based ranking or reviewing will further degrade/undermine peer review.
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Michalis Averof @michalis-averof.bsky.social · 27/06/2026
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Michalis Averof @michalis-averof.bsky.social · 25/06/2026
no hope, as @maxjtelford.bsky.social once suggested, we will all be digging for coal to feed the needs of AI servers
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