Akis (Argyris) Papantonis

Tread -1- EpiSci - I am very proud to share with you our new study that you can access on @biorxivpreprint.bsky.social (see link below)
"The Interaction with Nanotopographical Environment regulates nuclear mechanoresponse in mESCs via Histone Demethylase KDM3A.
www.biorxiv.org/content/10.6...

Michal Gdula group leader at @uam-ibmib.bsky.social is saerching for a postdoc to work on the epigenetics of pancreatic cancer within colaborative OPUS-LAP funded by @ncn.gov.pl and @dfg.de - reach out! #3Dgenome #cancer #pancreas

Expected. If you ask me: cruel. If you asked my lab members: understated.

Seeing into Hi-C: How our scientific connectivity revealed the close connections in our DNA to be a work of art Scientific data can be beautiful. An example where the data itself have a particularly striking appearance even before any scientific meaning has been ascribed

I had the privilege to meet artist Mary Griffiths. Mary got inspired by Hi-C maps and over zooms we spoke about Hi-C maps, patterns and drawings. Mary’s Hi-C inspired art has been exhibited eg the Royal Academy. We wrote this piece about this art-science collaboration

pubs.aip.org/aip/bpr/arti...

GitHub - YajieZhu018/LoopBin: A deep-learning-based pipeline to cluster genomic loop types with micro-C and Cut&Tag data. A deep-learning-based pipeline to cluster genomic loop types with micro-C and Cut&Tag data. - YajieZhu018/LoopBin

The LoopBin code is already available here: github.com/YajieZhu018/...

So feel free to try it out and come back to us with praise or complaints! We would be happy for any feedback.

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We then used MD simulations to test whether these loop classes are the result of the same or different underlying mechanisms with some surprising conclusions ― so do read the preprint and lets us know!

This work was supported by the DFG SPP2202 priority program (@spp2202.bsky.social).

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...which allowed the automated and unbiased clustering of >20,000 loops into 6 well-separated clusters, with distinct epigenomic and physical attributes.

The key here is that raw signal structure is considered (not peaks) allowing the neural network to identify differences in signal structure.

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Yajie and Mariano implemented a variational deep embedding (VaDE) neural network trained on Micro-C loop signal structure and concatenated CUT&Tag signal overlapping the anchors of these loops...

Preprint alert! 🥸

Yajie Zhu (PhD graduate) and Mariano Barbieri (postdoc, @spp2202.bsky.social Accelerator award) produced a package that will classify loops in your #3Dgenomics data based on (whichever) epigenomic data you have available. Keep reading...

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www.biorxiv.org/content/10.6...

Join @stirlingchurchman.bsky.social,
@moffittlab.bsky.social, @saramostafavi.bsky.social, me and all speakers for the 2026 CSHL meeting Systems Biology: Global Regulation of Gene Expression, March 11-14. Abstract deadline January 9! More infos and registration at meetings.cshl.edu/meetings.asp...

Our Xmas present all wrapped and nicely packaged, a collab with @karsten-rippe.bsky.social lab within the realm of the @spp2202.bsky.social

I feel very ready for retirement :-)

…I feel very grateful for how this coincidence has come about: via the generosity of my mentors, many collaborators, and all members of our lab. Let's see what the next two decades have in store for us.

By coincidence, this year my 100th peer-reviewed paper was published―on the subject closest to my heart. Although scientific output is not a mere reflection of the number of papers published (or so we hope), looking back at these two decades…

As 2025 comes to a close, I am realising that it has been 20(!) years since the publication of the very first article featuring me as a co-author…

Great news for @uam-ibmib.bsky.social! Three @ncn.gov.pl OPUS grants to our researchers: @juliadluzewska.bsky.social, Wojciech Szlachcic and a collaborative Polish-German OPUS-LAP grant to @michal-gdula.bsky.social & @akispapantonis.bsky.social from @uni-goettingen.de. Big congrats to everyone!

Here is a copy of last year's Twitter thread explaining our preprint - jump to (21) for the new stuff 👀

Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function

now revised and journal accepted at www.science.org/doi/10.1126/...

🧵👇

Doctoral INPhINIT fellowships - Incoming Call 2026 We grant 30 fellowships for researchers of any nationality who wish to pursue a doctorate in a STEM discipline at research centres of excellence in Spain or Portugal.

Interested in #3DGenomics #4Dnucleome? Like #Barcelona? Would like to enjoy doing #science and to have fun during your #PhD?

Apply now to La Caixa Foundation Doctoral #INPhINIT fellowships with us. DM or email in case of interest... 👇🏼👍🏼

lacaixafoundation.org/en/doctoral-...

Please, repost... 🔄🙏🏼

Are you being pleasantly sarcastic????

Last day of the @spp2202.bsky.social Closing Retreat in Goettingen ending in a high note with Stavros Lomvardas discussing the peculiar 3D attributes of the OR chromatin landscape!

@karsten-rippe.bsky.social rocking down memory lane and along single cell genomics data in Day 2 of the @spp2202.bsky.social Closing Retreat in Goettingen!

The Closing Scientific Retreat of @spp2202.bsky.social is under way in Goettingen with Gerd Blobel delivering the first Keynote lecture on LDB11-mediated looping of chromatin.

OFERTA DE EMPLEO (por favor difundir):

Ofrecemos un contrato predoctoral de 4 años asociado a nuestro proyecto PID2024-157249OB-I00. El objetivo del proyecto es evaluar un nuevo mecanismo patológico según el cual la competición entre promotores puede llegar a ocasionar enfermedades congénitas
👇

Happy to share our latest publication, in which we show that the arrangement of nucleosomes around CTCF sites contributes to higher-order organisation of chromatin into TADs: www.embopress.org/doi/full/10....

Characterization of induced cohesin loop extrusion trajectories in living cells Nature Genetics - This study introduces a system called TArgeted Cohesin Loader (TACL) that recruits cohesin complexes at defined genomic regions and induces loop extrusion events in living cells,...

The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project!

If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!

rdcu.be/eLiT5

Only two days left to apply for the open tenure track professorship in Computational Biology here in @uni-goettingen.de
uni-goettingen.de/en/700631.html

Thanks, Maria!

Merci merci!

Thank you, Sandra — hope a German version appears soon!

Science-peripheral post (ignore unless you read in Greek or French): I was surprised and truly honored to receive the Aix-Marseille Metropolitain for the French translation of my novel ‘The last bear of the woods’ (Kichli 2023)—a great thanks to my translators M. Volkich and H. Zervas.