Akis (Argyris) Papantonis
@akispapantonis.bsky.social
Biologist by training, basketball player at heart Professor for Translational Epigenetics & Genome Architecture, University Medical Center Goettingen, Germany. www.papantonislab.eu
🚨 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
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...
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...
nature.com
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
@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...
Nature Protocols@natprot.nature.com · 3w agoNew Article! Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC)
“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...
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...
biorxiv.org
A really cool set of findings.
Nitika Taneja @TanejaLab@nitikataneja.bsky.social · last mo.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!
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!
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.
nature.com
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.
Lluis Montoliu@lluismontoliu.bsky.social · last mo.Frank Grosveld, born in 1948, passed away last Friday. He was a colossal scientist in the transcriptional control of gene expression during development and helped us understand the complex regulation of beta-globin genes. His work will remain as a reference. May he rest in peace.
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.
Marc A. Marti-Renom@mamartirenom.bsky.social · last mo.1/4 *Embrace AI cautiously* AI is a tool: powerful and scary. Like calculators, computers, office tools, or scripting, it will reshape many jobs. If we recognize that, we should embrace it wisely. For me, it has freed time to think about biology and tackle projects I would not have dared before.
I have spent a long time resisting the use of AI in my everyday task, let alone in the process of scientific production (text, figures, ideas) which is anyway the bit of this weird profession that I enjoy the most. In the ensuing mini-rant, echoing Aydan’s thoughts, I want to highlight few things…
Aydan Bulut-Karslioglu@bulutkarslioglu.bsky.social · last mo.I have been thinking since yesterday about why I find the 1% thing so, so disturbing. It's a visceral reaction of 'just no', which goes beyond the general yuck towards the enshittification of/via AI. I have finally put my finger on it: it is the feeling you get when
Yours truly staring at a picture of the historical Sternwarte during Day 2 of the great CLEPIC2026 meeting, followed by @dewitlab.bsky.social, @radaiglesiaslab.bsky.social with amazing talks.
Hello #world, meet 1,000× Expansion Microscopy. A small gel would grow to the size of an Olympic swimming pool, while amino-acid-scale distances become visible with ordinary light microscopy. Led by Helena Hu from @eboyden3.bsky.social's lab, in collab with us. Story: www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6... Check this pure magic by @alishaib.bsky.social and collegues
biorxiv.org
I know that this might only concern my Greek friends and colleagues, and I know that it has nothing to do with my science… but I always so thrilled when I get to see my fiction in print — this time, a collection of 26 short stories about losing and finding affection at different life stages.
I am very happy (and proud) of our good friend and neighbor @mariekeoudelaar.bsky.social — and equally sad to see her and her lab leave Goettingen. A great hire for @mpi-ie.bsky.social!
MPI for Multidisciplinary Sciences@mpi-nat.bsky.social · 2mo ago@mariekeoudelaar.bsky.social becomes a director at the MPI of Immunobiology and Epigenetics (@mpi-ie.bsky.social) in Freiburg - congratulations! 🎉 Thank you for the experience & expertise you shared with us at MPI-NAT and all the best in your new department of Genome Biology.
Our preprint on how variant U1 snRNAs control transcriptional and splicing homeostasis of hiPSCs is now officially out in @natcomms.nature.com and accessible via this link: www.nature.com/articles/s41... This has been the culmination of our work as part of the SPP1935 program funded by @dfg.de 1/n
Variant U1 snRNAs contribute to cell cycle and differentiation control of human iPS cells - Nature Communications
Stem cell identity and differentiation require precise gene regulation, yet key regulatory components remain poorly understood. Here, the authors show that variant U1 snRNAs have distinct and essentia...
nature.com
Akis (Argyris) Papantonis @akispapantonis.bsky.social · 11mo agoIn our latest preprinted work, Yajie and Kostas combine computational analysis with precision KO of single variant U1 snRNA genes in human iPSCs to find pronounced deregulation of both gene expression and splicing that seem to affect the cell cycle and the differentiation potency of stem cells. 1/n
Hello all, our lab is recruiting a PhD candidate to study how 3D genome folding impacts gene regulation in development. We're located at the Center for Integrative Genomics department of the University of Lausanne, Switzerland. Please email me if interested. #PhDPosition, #PhDOpportunity
We are looking for a new group leader to join the IGH (Montpellier, France). I can’t wait to meet my future colleague! Apply :-) More infos here: igh.cnrs.fr/join-igh-as-...
Join IGH as Group Leader - IGH
The Institute of Human Genetics invites applications for a Principal Investigator position in its main research areas. Read more...
igh.cnrs.fr
🚨 Job Alert - Please share! 🙏 Interested in 3D gene regulation in development & evolution? 🤓🧬 💥 Our lab at @cabd-upo-csic.bsky.social is expanding! We’re recruiting: ✅ PhD students ✅ Postdocs 💻🧪 Experimental or computational backgrounds welcome 👇 Details below
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
Michal Gdula@michal-gdula.bsky.social · 6mo agoWe’re recruiting! Three-year, fully funded #postdoc opportunity: pancreatic cancer #epigenetics & potential new treatments (funded by @ncn.gov.pl & @dfg.de ). Collaboration with @akispapantonis.bsky.social, University of Göttingen (OPUS-LAP). See the ad & contact me! drive.google.com/file/d/1vrFd...
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...
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
pubs.aip.org
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... 1/n www.biorxiv.org/content/10.6...
LoopBin – a VaDE-based neural network for chromatin loop classification
Classifying chromatin loops from 3D genomics data according to their epigenetic and structural attributes is important for inferring their functional roles. Currently, such classification typically relies on the manual intersection of epigenomic signal peaks and loop anchor locations. To automate this, remove peak-calling biases and include information inherent to 3D genomics signal structure, we developed LoopBin, a framework based on a variational deep embedding (VaDE) neural network. We applied LoopBin to kilobase-resolution Micro-C data and segmented tens of thousands of loops into clusters with distinct features using minimal histone modification and transcription factor-binding data. These features were indicative of apparently distinct biological function by each subgroup of loops. Therefore, LoopBin can provide insights into the dynamic shifts in loop classification that can occur upon perturbation of cell homeostasis or signaling. ### Competing Interest Statement The authors have declared no competing interest.
biorxiv.org
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
Karsten Rippe@karsten-rippe.bsky.social · 7mo ago1/ 🎄 We got our Christmas present today: "Two distinct chromatin modules regulate proinflammatory gene expression" is now published @natcellbio.nature.com doi.org/10.1038/s415.... Our study introduces a scATAC-seq-based framework for genome-wide analysis of gene regulation features.
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/... 🧵👇
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... 🔄🙏🏼
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.
lacaixafoundation.org