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Akis (Argyris) Papantonis

@akispapantonis.bsky.social
993 followers 452 following 151 posts

Biologist by training, basketball player at heart Professor for Translational Epigenetics & Genome Architecture, University Medical Center Goettingen, Germany. www.papantonislab.eu

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Reposted by Akis (Argyris) Papantonis
Harmit Singh Malik @harmitmalik.bsky.social · 21/09/2026
Thanks to the generosity of the Bezos Family Foundation, @basicsci.fredhutch.org is excited to announce a new search to recruit a Bezos Family Distinguished Scholar : apply.interfolio.com/193655
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Reposted by Akis (Argyris) Papantonis
Marcus Buschbeck and Lab @marcusbuschbeck.bsky.social · 17/09/2026
OPPORTUNITY TO JOIN US! We are looking for motivated PhD candidate who would like to work on improving blood cancer therapy. This is a mechanistic / translational project. More info and how to apply here: carreraspathfinders.eu
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 01/09/2026
Come and join us!
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 30/08/2026
Very interesting work by Nick Gilbert’s group and collaborators.
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 26/08/2026
Thank you, Marc :-)
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 26/08/2026
LOL Thanks, Elzo! (I have generally done a poor job in hiding this...)
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 26/08/2026
Agreed, and also very unexpected to me that we would land here!
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 25/08/2026
7/ And here is the link to the actual OA paper: linkinghub.elsevier.com/retrieve/pii...
linkinghub.elsevier.com
Redirecting
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 25/08/2026
6/ In our eyes, this is critical as it can constitute the basis for combinatorial therapy in the not-so-distant future (hence the lack of preprinting). Equally important though is how a 'basic science' observation in studies of 3D genome reorganization during senescence can lead to 'applications'!
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 25/08/2026
5/ But most interesting, we could repurpose a senogenic small molecule inhibitor to target HMG2 and induce irreversible growth arrest to cancer cells, PDAC organoids, and mouse tumors in vivo!
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 25/08/2026
4/ ...to cut a long story (very) short, we combined single-cell and 3D genomics to show that > Tumor cells overexpress HMGB2 > HMGB2 binds hundreds of cell proliferation/growth genes > HMGB2 depletion reduces accessibility and looping
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 25/08/2026
3/ In this latest work, we put this proposition to the test in the context of pancreatic cancer and via the heroic efforts of first author Adi Mackay-Danieli and the support of the local Clinical Research Unit 5002 on PDAC Genome Dynamics @kfo5002.bsky.social funded by the @dfg.de
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 25/08/2026
...and few years back I proposed that HMGB2 should perhaps be viewed as a "rheostat" of chromatin and cell homeostasis: www.sciencedirect.com/science/arti...
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 25/08/2026
We have long been working with the highly abundant, but functionally elusive HMGB2 chromatin binder. And work from 2018 (Zirkel et al, Mol Cell), but also from this year (Palikyras et al, Nat Aging; www.nature.com/articles/s43...) have consolidated that its loss from cell nuclei induces senescence.
nature.com
Senescent cells cluster CTCF on nuclear speckles to instruct an alternative splicing program - Nature Aging
Palikyras and colleagues investigate chromatin reorganization upon senescence induction, reporting that components of nuclear speckles coordinate chromatin rewiring and a senescence-associated splicin...
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 25/08/2026
Newest from the lab - and the only of our manuscripts since the introduction of bioRxiv that we did not preprint (it will become obvious why). "Targeting addiction to HMGB2-driven transcriptional programs in pancreatic cancer" A thread...
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 09/08/2026
Really nice, Marc!
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Reposted by Akis (Argyris) Papantonis
Marc A. Marti-Renom @mamartirenom.bsky.social · 08/08/2026
🚨the latest from the lab! 😃👇🏻 www.science.org/doi/10.1126/...
science.org
3D genome organization in tissue regeneration involves long-range chromatin loops
Chromosome conformation analysis in Drosophila wing discs reveals the requirement of specific meta-loops during regeneration.
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 28/07/2026
Nice new work by the lab of @eddaschulz.bsky.social
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 22/07/2026
Cheers, Marc!
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Reposted by Akis (Argyris) Papantonis
Darío Lupiáñez @dariloops.bsky.social · 21/07/2026
🚨 Job Alert - Please share 🙏 Interested in 3D gene regulation in development & evolution? 🤓🧬 💥 Our lab at @cabd-upo-csic.bsky.social is expanding! ✅ 4 years fully funded PhD position 💻🧪 Experimental or computational backgrounds welcome 👇 Details below #PhDPosition #PhDOpportunity #AcademicJobs
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 21/07/2026
Thanks (for everything), Sir
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 21/07/2026
PS: this is also an opportunity to showcase our powerful senescence model using a small molecule inhibitor. See thread on this here: bsky.app/profile/akis...
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 21/07/2026
8/n Finally, a thanks to the many structures supporting us at the @UMG especially to SFB1565, @spp2191.bsky.social and @spp2202.bsky.social of the @dfg.de, and to our amazing PhD program @imprsgs.bsky.social!
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 21/07/2026
7/n This work would reach here without my resilient lab (the story from preprinting to publication I might narrate another time) and amazing collaborators @goettingen-campus.de and beyond @kurianlab.bsky.social, @mariekeoudelaar.bsky.social, @ellenberglab.bsky.social, and @kaibeckwith.bsky.social.
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 21/07/2026
6/n Equally strikingly, many of these splicing changes manifesting upon senescence induction can be recorded in RNA-seq data from aging human tissues, while interventions that hinder CTCF clustering extended the replicative lifespan of human cells nearing senescence!
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 21/07/2026
5/n The net result of all these genomic changes is not transcriptional, but rather splicing-centric, with most effects manifesting in speckle-associated genes. Strikingly, interventions preventing CTCF clustering almost fully revert splicing patterns to those seen in proliferating cells!
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 21/07/2026
4/n ...which we further validated at the single cell-level using high-resolution DNA tracing in collaboration with Jan Ellenberg and Kai Beckwith and their powerful LoopTrace approach, thanks to intramural @spp2202.bsky.social funding.
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 21/07/2026
3/n CTCF clustering leads to the 3D reorganisation of chromatin with the emergence of new and longer CTCF-anchored loops predominantly in the speckle-associated A1 subcompartment of the genome.
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 21/07/2026
2/n Here, we find that a protein of the nuclear periphery important in mitosis, BANF1 (see PMID: 28841419) and the key speckle component, SRRM2, are both necessary for this clustering. In fact, 62 aa of the SRRM2 RNA-binding domain suffice to induce CTCF clusters even in proliferating cells!
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 21/07/2026
A thread... 1/n Cells entering senescence cluster CTCF, our original finding already in 2018 by Zirkel et al: www.cell.com/molecular-ce... ...but how and for what reason?
cell.com
HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types
Zirkel et al. use three distinct primary human cell types to show that nuclear depletion of HMGB2 constitutes an early event on the path to replicative senescence controlling heterochromatic and trans...
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 21/07/2026
Our latest is now out in @nataging.nature.com giving reason to celebrate! Led by talented Spiros Palikyras, it improves our preprint (posted 2 years ago!) dissecting the mechanism and functional consequences of CTCF clustering upon senescence commitment of human cells. www.nature.com/articles/s43...
nature.com
Senescent cells cluster CTCF on nuclear speckles to instruct an alternative splicing program - Nature Aging
Palikyras and colleagues investigate chromatin reorganization upon senescence induction, reporting that components of nuclear speckles coordinate chromatin rewiring and a senescence-associated splicin...
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Reposted by Akis (Argyris) Papantonis
Elias Friman @eliasfriman.bsky.social · 11/05/2026
Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/ www.biorxiv.org/content/10.6...
biorxiv.org
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Reposted by Akis (Argyris) Papantonis
Anders Sejr Hansen @andersshansen.bsky.social · 14/07/2026
@mileshuseyin.bsky.social and the lab have put together a comprehensive protocol for genome-wide Micro-C and for Region-Capture Micro-C in @natprot.nature.com : www.nature.com/articles/s41... See also the GitHub for a user-friendly end-to-end computational pipeline: github.com/ahansenlab/M...
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Reposted by Akis (Argyris) Papantonis
Richard Sever @richardsever.bsky.social · 06/07/2026
“move from preprint to peer-reviewed publication leaves the central claims of most abstracts intact, indicating preprints are a reliable source…papers that were never posted as preprints were retracted at roughly twice the rate of those that were…” www.biorxiv.org/content/10.6...
biorxiv.org
Tracking claim changes from preprint to publication across 72,644 biomedical studies using large language models
Preprints now disseminate a large share of biomedical research before peer review. Because they have not yet passed peer review, some scientists regard preprint claims as unverified or potentially unr...
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 01/07/2026
A really cool set of findings.
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Reposted by Akis (Argyris) Papantonis
Nitika Taneja @TanejaLab @nitikataneja.bsky.social · 01/07/2026
Very excited to share our new Nature study! We discovered that replication stress stabilizes CTCF-dependent chromatin loops enclosing stressed nascent DNA, where G9a-mediated heterochromatin protects it from nucleolytic degradation. rdcu.be/frzLg Huge thanks to all our collaborators and co-authors!
nature.com
Replication-stress-induced chromatin loops protect fork stability - Nature
Replication stress induces the formation of transient chromatin loops that enclose de novo heterochromatin-enriched stalled replication forks.
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 28/06/2026
When the news of Frank’s death reached me, I could only utter: f*ck! He was an exceptional mind and a true scientist, always asking the next question. I was lucky to have interacted with him so often. He is already dearly missed.
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 27/06/2026
Having read Marc's nuanced thread, I am glad I put him on the spot! Plus, he didn't have to go on forever (like I did) in order to share his thoughts.
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 27/06/2026
15/n …nor, of course, should we settle for the status quo. It is time to be brave and transparent and stand up for the few things we really believe in. I am sure that most of this started with best intentions at heart and that it can be used in productive ways. But can we afford it not used such?
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 27/06/2026
14/n …not just for biologists but for humanity as a whole. Being true to my Greek genes, I tend to always see the glass half empty (if not totally empty!), but I cannot help but think that we should not let this get away from us (like previous generations let publishing take over science appraisal)…
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 27/06/2026
13/n …I gladly acknowledge that their ‘Feed’ feature is useful in navigating literature and I would happily use this. I also acknowledge that I was happy with my 99% paper — and until I wasn’t because I started thinking about it long term. These are both trying and turning times…
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 27/06/2026
12/n …nor of course do I need journal editorial teams using scores derived from such models (surely there are others around the corner) to defer their judgement. I have a story about our ‘80%’ manuscript that speaks volumes on this! Yet, in trying to remain fair towards QED and their efforts…
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 27/06/2026
11/n I can name a number of colleagues in my field who really produce glamorous work (meant here as the best possible praise) and I both love and am jealous of their great papers. I think this applies to all of us and I don’t need any AI-derived score to convince me for or against that…
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 27/06/2026
10/n …seems to merely reflect our deeply embedded need for relative rankings (myself included) and was, in my view, a mistake given the original thesis of the QED team as communicated via @odedrechavi.bsky.social, especially as regards the need to disentangle ourselves from ‘glam’ science.
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 27/06/2026
9/n …it is fast and does this based on ‘common knowledge’ (ie. its training knowledge base). In my experience, many of the gaps contain misinterpretations and issues in qualitatively assessing prior art, but still good to see since a scientist can actually dismiss those. The scoring however…
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 27/06/2026
8/n And, much more importantly, why would journals and funding agencies, which I assume are the target group of the QED company, adopt this? To score papers and decide which to review? In fact, if the model were to only analyze the paper and identify gaps, it’d be reasonably useful — mostly because…
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 27/06/2026
7/n I actually browsed through the Genomics 1% papers (so marketing worked!) and found some I had already read and appreciated, as well as, for example, last single cell atlases. And? What am I to take away? That a 89% score is a bit less innovative than a 99% one? How does the model appraise this?
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 27/06/2026
6/n …to veer back to QED and the now infamous 1%, I cannot help but wonder exactly how a (presumably) LLM-based approach can really have qualitative criteria and how these scores can be interpreted. (For transparency, I tested 3 preprints of mine and scored 99, 80 and 63%, so this is not bitterness)
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 27/06/2026
5/n …is to become the norm, I cannot but worry that future generations who grow up amidst AI-driven creativity will only become dependent on it (not to delve into its environmental aspects in addition)! I might be wrong, but the three recent ‘coscientist’ Nature papers clearly signal this. But…
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Akis (Argyris) Papantonis @akispapantonis.bsky.social · 27/06/2026
4/n …arguments on this and my lab will host him soon to explain his process on this). However, I am deeply worried about AI taking over the creative process in modern biology, ie. the thing most of us most enjoy in a profession that has a fair share of disappointments attached to it. And if this…
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