Akis (Argyris) Papantonis
Biologist by training, basketball player at heart
Professor for Translational Epigenetics & Genome Architecture, University Medical Center Goettingen, Germany.
www.papantonislab.eu
- Reposted by Akis (Argyris) Papantonis[Not loaded yet]
- Reposted by Akis (Argyris) PapantonisI 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...
- 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...
- 2/n 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...
- 3/n ...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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View full threadThe 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.
- Reposted by Akis (Argyris) PapantonisJoin @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
- 1/ 🎄 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…
- 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…
- …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.
- Reposted by Akis (Argyris) PapantonisGreat 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!
- Reposted by Akis (Argyris) PapantonisHere 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/... 🧵👇
- Reposted by Akis (Argyris) PapantonisInterested 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... 🔄🙏🏼
- 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.
- Reposted by Akis (Argyris) PapantonisOFERTA 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 👇
- Reposted by Akis (Argyris) PapantonisHappy 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....
- Reposted by Akis (Argyris) PapantonisThe 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
- Reposted by Akis (Argyris) PapantonisOnly 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
- 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.
- Reposted by Akis (Argyris) PapantonisWe are thrilled to announce that our NEW Large Language Model will be released on 11.18.25.
- Just half a day in and it’s been a blast, with really incredible talks here on Giessen!
- What a great first day at the GfG symposium on epigenetics & chromatin. Fantastic talks by @akispapantonis.bsky.social , @apombo1.bsky.social, @marcusbuschbeck.bsky.social and Philipp Korber. And Peter Becker giving the Max-Delbrueck lecture. A real treat for the audience!
- Reposted by Akis (Argyris) PapantonisCongrats to my friends in the Boettiger lab for this really beautiful live imaging work. A big leap forward in understanding the dynamic side of genome organization. www.science.org/doi/10.1126/...
- Reposted by Akis (Argyris) PapantonisNew preprint is up, led by former postdoc Braulio Bonilla. We know these remodelers regulate nucleosome positions and occupancy, but do they have a role in regulating higher order chromatin structure? We take a peek for BAF and INO80C. www.biorxiv.org/content/10.1...
- Reposted by Akis (Argyris) PapantonisVery interesting new @wbickmor.bsky.social commentary on the mechanistic mystery that is very distal enhancer-promoter interactions www.nature.com/articles/s41...
- Reposted by Akis (Argyris) PapantonisMy lab @mpi-muenster.bsky.social is looking for a computational biologist with a passion for imaging and spatial biology. A staff scientist position with long-term perspective! Apply and spread the word 🙏 jobs.mpi-muenster.mpg.de/jobposting/0...
- Reposted by Akis (Argyris) PapantonisOn behalf of @ckadoch.bsky.social and myself, we are pleased to present our upcoming @KeystoneSymposia, #KSEpigenetics26 Epigenetics and Gene Regulation in Health and Disease, March 2-5, in Geneva, Switzerland. keysym.us/KSEpigenetic...
- In 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
- We were motivated by my old @dunnschool.bsky.social neighbors, Shona Murphy and Dawn O’Reilly, who showed that these (falsely presumed) U1 pseudo genes may actually be functional in their 2013 Genome Res paper… 2/n
- …so Kostas generated vU1-specific KOs using CRISPR-Cas9 in hiPSCs of the two most expressed variants, and Yajie analyzed their effects via total RNA-seq data, while @carmeloferrai.bsky.social provided undirected differentiation tests. 3/n
- The KO effects were far more pronounced than what the relative vU1 abundance (relative to canonical U1) would predict, and uncover an additional layer in stem cell identity regulation. Please read here: www.biorxiv.org/cgi/content/... Feedback more than welcome!
- Most read, I hear! Here is your chance to read what @mariekeoudelaar.bsky.social and I had in mind when writing this together.
- The latest Annual Review of Genomics and Human Genetics is now online 🧬 Most read article so far is "Mechanisms of Enhancer-Mediated Gene Activation in the Context of the 3D Genome" @akispapantonis.bsky.social @mariekeoudelaar.bsky.social Check it out arevie.ws/47BZEJp Full TOC: arevie.ws/4plCaPe
- This is an incredible mechanistic dissection by the @kurianlab.bsky.social and Van Nostrand labs linking splicing choice to cardiac development!
- Many conserved exons in the heart and brain utilize weak 5 ′ splice sites, yet they are accurately spliced. But how? We show that splicing fidelity is actively enforced through a QKI-U6 checkpoint at the U1→U6 handover in essential cardiac genes during organogenesis. www.biorxiv.org/content/10.1...
- Soon at a Goettingen amphitheater near us! Do join, folks! Leo always has very cool data to share.
- Excited to host my friend and collaborator Leo for the #SFB Seminar in #Göttingen on September 18, 2025, at 12:00 PM in the Center for Biostructural Imaging of Neurodegeneration seminar room. He will discuss #RNA-driven mechanisms that shape embryonic cell fate and identity. @kurianlab.bsky.social
- Reposted by Akis (Argyris) PapantonisExcited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression www.biorxiv.org/content/10.1...
- Reposted by Akis (Argyris) PapantonisPleased to see this study out, combining experimental work from our lab at the @cbitoulouse.bsky.social, in particular by @nathaliebastie.bsky.social and @beckof.bsky.social, and from Laura Chaptal and @alengronne.bsky.social at IGH Montpellier @cnrs.fr @cnrsbiologie.bsky.social Congrats to all!
- Reposted by Akis (Argyris) PapantonisCheck out this exciting meeting and register! Fantastic line-up of speakers on cell biology of the nucleus and a great venue 🔥
- 📢 Abstract submission deadline reminder for 'Cell biology of the nucleus'! Before packing your bags and leaving for your summer vacation, there is one important task left to do: submit your abstract for #EESNucleus ✍️ Deadline is 26 August: s.embl.org/ees25-07-bl
- If I wasn’t this old, I would definitely apply.
- To all post-docs: The Genome Biology dept @embl.org has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
- Reposted by Akis (Argyris) PapantonisHow do enhancer-gene contacts relate to transcription activation? In mouse embryonic stem cells, a combo of STED, oligoFISH & RNA FISH shows that 3% of Dppa3 alleles transcribe. For these, enhancers and promoters come closer (panel E). Stumberger ... Leonhardt & Harz www.biorxiv.org/content/10.1...
- Be there or be square!
- 🎉 Join us at the upcoming GfG Symposium "Epigenetics & Chromatin" in Giessen, Sept 24–26, 2025! Amazing speakers, low registration fee, € 300 prizes for best poster & short talk, + free GfG membership for non-members. Please RT! express.converia.de/frontend/ind...
- Reposted by Akis (Argyris) PapantonisFreshly launched! 🚀 Check out the new CRC 1678 website 🌐 👉 crc1678.uni-koeln.de
- Reposted by Akis (Argyris) PapantonisFantastic opportunity to launch your research group following the @embl.org model in a great environment with a solid startup package and access to state-of-the-art resources. Join us at the @ncmbm.bsky.social, part of the @nordicembl.bsky.social, at @uio.no Feel free to reach out if you have Qs.
- 📣 We’re recruiting 1-2 Group Leaders! NCMBM is looking for early-career researchers ready to establish their independent research groups! 🧬 With an attractive start-up package, help us shape the future of molecular biosciences and medicine in 🇳🇴 and be part of the @nordicembl.bsky.social!
- Reposted by Akis (Argyris) PapantonisThank you, Evgeny! I am delighted that we have a top line up of speakers confirmed for 'The 3D Regulatory Genome' for 2025: @andersshansen.bsky.social July 3rd 2025 @mariekeoudelaar.bsky.social September 4th 2025 @axelvisel.bsky.social October 2nd 2025 @efapostolou29.bsky.social November 6th 2025
- Reposted by Akis (Argyris) Papantonis🧬 New in Bioinformatics! We’re excited to share StripePy - a Python application for fast, robust detection of architectural stripes in Hi-C & Micro-C data. 🔗 Read the paper 👉 doi.org/10.1093/bioi... #3DGenomics #Bioinformatics #HiC #cool #hic @robomics.bsky.social @rea191.bsky.social
- Reposted by Akis (Argyris) PapantonisHow to represent genomes in 3D? In this paper (and video), we propose Geometric Diagrams of Genomes (GDG)—a visual grammar that aims at emulating the effect ribbon diagrams (Richardson et al 1981) had in protein structural biology. Time will tell.😅 👉🏼 genomebiology.biomedcentral.com/articles/10....
- Reposted by Akis (Argyris) Papantonis
- This is a piece that I and @karsten-rippe.bsky.social discussing a lot, and a topic that is very close to my heart. The editors @naturerevgenet.bsky.social gave us the stage to do so, and the final version of our review is now available under this link: rdcu.be/erP1u A short thread follows 1/n
- The great pace of the "condensate" field has offered frameworks that can be used to explain earlier, but still very valid experimental observations. Thus, we set out to compare and contrast (and synthesize) the "transcription factory" model with what is known about "transcriptional condensates" 2/n
- An extra motivation was to revisit the 2009 @natrevgenet.nature.com piece by @wbickmor.bsky.social: pubmed.ncbi.nlm.nih.gov/19506577/ ...as well as that by Peter Cook and I in 2013: pubmed.ncbi.nlm.nih.gov/23597155/ ..and integrate the state-of-the-art. 3/n
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View full threadFinally, it is important to state that this piece was the outcome of exchanges (and funding, of course) in the framework of the amazing @dfg.de @spp2191.bsky.social and @spp2202.bsky.social Priority Programs, as well as of the SFB1565 consortium of the Göttingen Campus @uni-goettingen.de. 6/n
- Reposted by Akis (Argyris) PapantonisTextbooks: “Enhancers are just a bunch of TFBSs” But how do they REALLY work? New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social A 🧵 (1/n) Free access link: rdcu.be/erD22
- Hear, hear! Since last week, I have the honor of serving as a Scout for the Henriette Herz program of the Humboldt Foundation. 1/n
- In a nutshell, over the next 2.5 years, I will have the responsibility (and privilege) of nomination 3 postdocs from outside of Germany to come and work with us at the University Medical Center Göttingen. Further details on the program here: www.humboldt-foundation.de/en/apply/spo...
- Some more info on our lab's work here: papantonislab.eu Do get in touch if interested!
- Mario Nicodemi kicking off SIBBM2025 with an elegant talk on phase transitions in 3D genome folding in front a wall-to-wall full house in Naples.
- Magda Bienko just gave an amazing talk on how long intronic RNAs generate a neuronal-specific nuclear architecture (picture missing because I was trying to take in the many data) #SIBBM2025
- …and now, Maria Pelizzola (from Milan) is presenting a framework called “Nanodynamo” to chart subcellular RNA dynamics in cells.
- …further extending this to epitranscriptomic RNA modifications! #SIBBM2025
- Here’s the thing: the 2025 German Pathology Congress is kicking off in a huge room with a non-pathologist as first speaker. Let’s see how Hi-C in cancer fairs today :-)
- Reposted by Akis (Argyris) PapantonisDelighted & excited to share our latest preprint on non-canonical enhancers in human pluripotent stem cells, the result of a fantastic and fun collaboration with @guenesdoganlab.bsky.social: www.biorxiv.org/content/10.1... 🧵 below
- Reposted by Akis (Argyris) PapantonisExtensive differences observed in 3D genome structure between homologous heterozygous chromosomes revealed by Genome Architecture Mapping #GAM in the @apombo1.bsky.social lab ➡️ www.embopress.org/doi/full/10....
- Reposted by Akis (Argyris) PapantonisYou want to apply #ATACseq in your emerging model organism, but you don't know where to start? Is #ATACseq the best method for my research questions? Search no more! We got you covered with our new review: doi.org/10.1002/jez.... Excellent collaboration with @gevol.bsky.social
- Reposted by Akis (Argyris) Papantonis1/ New preprint! How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites? www.biorxiv.org/content/10.1... #TranscriptionFactors #IDPs #SingleMolecule #Biophysics
- Reposted by Akis (Argyris) PapantonisHow to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭 Check out our paper - fresh off the press!!! We find widespread functional conservation of enhancers in absence of sequence homology Including: a bioinformatic tool to map sequence-diverged enhancers! rdcu.be/enVDN github.com/tobiaszehnde...
