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Michalis Averof

@michalis-averof.bsky.social
2.6K followers 801 following 177 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 · 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 · 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
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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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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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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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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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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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 · 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 · 27/06/2026
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Michalis Averof @michalis-averof.bsky.social · 24/06/2026
How depressing – another pretentious and artificial way to promote the star system, without ever reading and thinking about the science
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Michalis Averof @michalis-averof.bsky.social · 20/05/2026
Pomaks, a slavic-speaking ethnicity, have faced isolation & exclusion in mountainous areas of northern Greece. When borders opened, Pomak men emigrated and Pomak society experienced an unusual transformation. Article by my daughter Marta, based on 2023 fieldwork.
ecmi.de
ECMI Minorities Blog. Pomak Minority Women and the Fallout of Male Migration
After decades of strict movement restrictions, socioeconomic and political isolation, widespread male migration has profoundly transformed the lifestyles of the Pomak minority in North-Eastern Greece....
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Michalis Averof @michalis-averof.bsky.social · 14/05/2026
Mapping neurons in the brain of a beetle, by Gregor Bucher's team @bucherlab.bsky.social www.biorxiv.org/content/10.6... Happy we could make a minor contribution by providing a Brainbow construct, which the team used to map neuronal projections Tribolium Brainbow soon available on Addgene
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Michalis Averof @michalis-averof.bsky.social · 20/04/2026
I almost forgot: a big thank you to Development's @dev-journal.bsky.social editorial and production teams for being supportive, flexible and responsive re: editorial communication and deadlines, during a period when I faced a serious health problem. It means a lot to have this support.
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Michalis Averof @michalis-averof.bsky.social · 19/04/2026
These images show live embryos of animals (jellyfish, crustacean, worm, sea urchin, sea squirt, beetle) and one of animals closest single-celled relatives. They were captured taking advantage of fluorescent proteins localised on the outer membrane of cells, allowing us to observe cell outlines. 1/9
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Michalis Averof @michalis-averof.bsky.social · 15/03/2026
Οur recent preprint includes data from 3 new Parhyale species: aquilina & plumicornis from the Mediterranean, darvishi from the Persian Gulf I started looking for such species in 2021. Amphipod expert Oliver Coleman gave me some key contacts: Farzaneh Momtazi (Iran) & Sabrina Lo Brutto (Palermo) /1
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Marco Grillo @mgrillo.bsky.social · 12/03/2026
Do you work with a strange model species and are frustrated by the lack of antibodies for immunos? Here's a web app that does some computational pre-screening for you. sixpack-abscan.serve.scilifelab.se
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Michalis Averof @michalis-averof.bsky.social · 09/03/2026
In animals with large genomes, finding cis-regulatory elements can be very challenging. Enhancers can be located tens/hundreds of kb away from their target promoters. We face this challenge in Parhyale, with >3 Gbp genome. We just published a preprint describing how we are tackling this problem. /1
biorxiv.org
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John Burns @burnsajohn.bsky.social · 16/02/2026
I like this concept of the genome as a compressed representation of an organism. Not like a ZIP file that recreates the same file in smaller form, but more like an AI model where a compact sequence (DNA) generates an organism through probabilistic interactions using molecules that it encodes itself.
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Michalis Averof @michalis-averof.bsky.social · 04/02/2026
Just discovered the wonderful covers of 'Genes to Cells', the journal of the Molecular Biology Society of Japan @mbsj-official.bsky.social – absolutely beautiful! here some examples inspired by mitosis, CRISPR, the DNA helix, and plant pigments
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Michalis Averof @michalis-averof.bsky.social · 27/01/2026
À quoi ressemble le quotidien dans un laboratoire de recherche ? En 2025, Arthur Monternier, étudiant en art, a passé six mois dans notre laboratoire. Il raconte son expérience dans cette bande dessinée. popsciences.universite-lyon.fr/ressources/l... popsciences.universite-lyon.fr/app/uploads/...
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Michalis Averof @michalis-averof.bsky.social · 27/01/2026
How is everyday life in a research lab? Last year Arthur Monternier, an art student, joined our lab for 6 months. He conveys his experience in this comic strip. popsciences.universite-lyon.fr/ressources/l... popsciences.universite-lyon.fr/app/uploads/...
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Michalis Averof @michalis-averof.bsky.social · 01/01/2026
Happy new year to all! (photo by Karl Blossfeldt, Art Forms in Nature, 1928)
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Michalis Averof @michalis-averof.bsky.social · 05/11/2025
That's what 'the napolitans' we up to when they briefly invaded our lab! Wonderful memories from December 2021 and November 2022. Congratulations!!
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Michalis Averof @michalis-averof.bsky.social · 27/10/2025
Our lab studies how animals regenerate their body, e.g. how crustaceans regenerate broken legs. One of our aims is to understand if regeneration re-uses the gene networks that built the legs in the first place. Arthur Monternier, an artist in our team, captured the question in this cartoon.
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Michalis Averof @michalis-averof.bsky.social · 26/10/2025
What are these? You are looking at embryos of a sea squirt. Each of the 'soap bubbles' is a living cell, about a fourtieth of a millimetre in size. The outlines of the cells are visible thanks to fluorescent markers identified by Hitoyoshi Yasuo @hitoyas.bsky.social see doi.org/10.1101/2024... 🧵
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Michalis Averof @michalis-averof.bsky.social · 23/10/2025
How can we see the cells that make up a living organism? Membrane-localising tags can drive fluorescent proteins to the cell's outer membrane, making their outlines visible. But the tags don't work well in all organisms. How do you find one for your species of interest? 🧵 Check our latest preprint
biorxiv.org
A toolkit for testing membrane-localising tags across species
Transgenic markers and tools have revolutionised how we study cells and developing organisms. Some of the elements needed to construct those tools are universally applicable (e.g. fluorescent proteins...
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Michalis Averof @michalis-averof.bsky.social · 09/10/2025
interesting article by @yoginho.spore.social.ap.brid.gy Artificial Intelligence is algorithmic mimicry: why artificial “agents” are not (and won’t be) proper agents arxiv.org/pdf/2307.07515
arxiv.org
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Michalis Averof @michalis-averof.bsky.social · 03/10/2025
Here it is! Postdoctoral position to identify the progenitors sensory organs in the regenerating legs of Parhyale apply here: www.averof-lab.org/pages/tracman 1/3
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Michalis Averof @michalis-averof.bsky.social · 24/09/2025
X-ray imaging of crustacean legs at the DESY synchrotron, Hamburg. Cross-section of regenerating Parhyale leg (~1/10 of a mm in width). X-rays give accurate 3D view with almost cellular resolution. With Angelika Svetlove, Kevin Grüner & Mathilde Paris @zoocell.biologists.social.ap.brid.gy
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Michalis Averof @michalis-averof.bsky.social · 02/09/2025
Interested in a sabbatical in Lyon? The Collegium de Lyon provides accommodation and attractive interdisciplinary environment for 1 or 2 semesters. Open to all disciplines. You can be affiliated with any local department/lab. Apply now for 2026-27. collegium.universite-lyon.fr/2026-2027-un...
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Michalis Averof @michalis-averof.bsky.social · 08/08/2025
Latest paper elifesciences.org/articles/107... closes an important cycle in our efforts to study regeneration: week-long recordings allow us to observe the behaviour of cells during the entire course of regeneration in a crustacean leg – bright objects in movie are fluorescent nuclei of cells. 1/6
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Michalis Averof @michalis-averof.bsky.social · 13/07/2025
We've just been awarded a grant to study the cellular basis of regeneration – to track the progenitors of sensory organs in the context of leg regeneration, in our favourite crustacean tinyurl.com/parhyale, based on live imaging and cell tracking. The project involves some cool collaborations... 1/3
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Reposted by Michalis Averof
Arvid Ågren @arvidagren.bsky.social · 27/06/2025
John Maynard Smith on natural history. (London Review of Books, April 1982)
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Michalis Averof @michalis-averof.bsky.social · 23/06/2025
In the brain of intertidal crustaceans (Eurydice and Parhyale), circadian clock genes are expressed with a daily rhythm (24h) in some cells and a tidal rhythm (12.4h) in other cells. Two different clocks working in the same brain, using the same components.
sciencedirect.com
Expression of clock genes tracks daily and tidal time in brains of intertidal crustaceans Eurydice pulchra and Parhyale hawaiensis
Intertidal organisms, such as the crustaceans Eurydice pulchra and Parhyale hawaiensis, express daily and tidal rhythms of physiology and behavior to …
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Michalis Averof @michalis-averof.bsky.social · 10/05/2025
Trichoplax adhaerens is one of the simplest and most enigmatic animals on earth. Its body shows incredible fluidity, changing shape within minutes. In a recent visit by Andrea Pasini we had the chance to host and observe these amazing animals live. [movie accelerated 3x; animal 0.5 to 1 mm in size]
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Cnidarian developmental mechanisms group @clytia-vlfr.bsky.social · 05/05/2025
Intriguing findings from our Sendai collaborators Ruka Kitsui and Ryusaku Deguchi. While C. hemispherica spawns at dawn, Clytia IZ-D species spawns at dusk. This is not triggered by dark but, unexpectedly, by light-mediated extension of an autonomously-running 20h cycle. doi.org/10.1101/2025...
Cartoon of autonomous and light-modulated spwning cycles in Clytia IZ-D
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Michalis Averof @michalis-averof.bsky.social · 07/03/2025
#StandUpForScience Lyon France
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Michalis Averof @michalis-averof.bsky.social · 05/03/2025
I prepared these as banners for the #StandUpForScience demonstration on Friday. Happy to share the high-res files, if anyone wants to use them.
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Michalis Averof @michalis-averof.bsky.social · 28/02/2025
Do you have experience in generating transgenic tools and fluorescent markers? Are you interested in developing new tools in a non-conventional model, to observe and genetically manipulate cells during leg regeneration? We are recruiting! www.averof-lab.org/pages/3560
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Michalis Averof @michalis-averof.bsky.social · 27/02/2025
Rita Levi-Montalcini defied fascism, which excluded her from university due to her jewish ancestry, by setting up a clandestine lab in her own bedroom. During 1940-42 she carried out experiments that set the foundations for her Nobel-prize-winning research a decade later. nautil.us/a-lab-of-her...
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Michalis Averof @michalis-averof.bsky.social · 26/02/2025
As the world of science wakes up to modern fascism, it's worth remembering older generations who stood up for humanity in much harsher circumstances. Jacques Monod worked actively for the resistance in WWII, while pursuing early stages of his research in occupied Paris. @standupforscifr.bsky.social
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Michalis Averof @michalis-averof.bsky.social · 18/11/2024
thenode.biologists.com/please-show-...
thenode.biologists.com
Please, show me your boundaries - the Node
from Irene Karapidaki, Béryl Laplace-Builhé and Michalis Averof What is this? These are crustacean embryos injected with mRNA encoding a red fluorescent
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Michalis Averof @michalis-averof.bsky.social · 12/11/2024
Looking for a tag to localise fluorescent proteins to the plasma membrane? Unsure which tag might work in your species? We generated a toolkit of 11 membrane-localising tags, which can be screened rapidly by microinjecting mRNA in your species of interest. 1/4 www.biorxiv.org/content/10.1...
biorxiv.org
A toolkit for testing membrane localisation tags across species
Transgenic markers and tools have revolutionised how we study cells and developing organisms. Some of the elements needed to construct those tools are universally applicable (e.g. fluorescent proteins...
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Michalis Averof @michalis-averof.bsky.social · 12/09/2024
Can we observe how the injured leg of an animal is regenerated? We have figured out how to do this in the crustacean Parhyale. Over the course of a week, we can record the entire process of regeneration at cell-by-cell resolution. 1/3 vimeo.com/802413847
vimeo.com
Time lapse movie of regenerating crustacean leg
Video made by Cagri Cevrim. (hpa = hours post amputation)
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Michalis Averof @michalis-averof.bsky.social · 13/07/2024
Looking for a membrane localisation tag? unclear what will work in your spp? We gathered 10 tags (diff mechanisms of memb localisation) + fused them with red FP. Interested in joining us for a comparative screen? We'll share plasmids for making mRNA, you can inject in your favourite model. #evodevo
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Michalis Averof @michalis-averof.bsky.social · 28/04/2024
thenode.biologists.com/the-shrimp-p...
thenode.biologists.com
The shrimp Parhyale hawaiensis – a non-model organism research story with Prof. Michalis Averof - the Node
Earlier this year, my co-correspondent for the Node Brent Foster and I published a pot pourri-style interview article asking biology researchers about
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Michalis Averof @michalis-averof.bsky.social · 21/02/2024
Remembering Claus Nielsen for his gentleness and dry humour while teaching us about marine organisms in Kristineberg www.nature.com/articles/d41...
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