Andreas Panagopoulos
@apanagopoulos.bsky.social
Postdoc @UZH. Interested in Genome stability, Cellular heterogeneity & Imaging.
Pinned
Multigenerational cell tracking of DNA replication and heritable DNA damage - Nature
A multigenerational single-cell tracking approach provides a framework to dissect phenotypic plasticity at the single-cell level, offering insights into cellular processes that may resemble early even...
doi.org
Delighted to share that the results of my main postdoc project are now published in @nature.com
🔗 doi.org/10.1038/s415...
🔗 doi.org/10.1038/s415...
Reposted by Andreas Panagopoulos
Our protocol for imaging-based quantification of RNAPII clearance during transcription-coupled DNA repair is now online. 👇
Well done, Bram, Diana, and Paula!
star-protocols.cell.com/protocols/45...
Well done, Bram, Diana, and Paula!
star-protocols.cell.com/protocols/45...
Cell Press: STAR Protocols
STAR Protocols is an open access, peer-reviewed journal from Cell Press. We offer structured, transparent, accessible, and repeatable step-by-step experimental and computational protocols from all are...
star-protocols.cell.com
November 22, 2025 at 8:29 AM
Our protocol for imaging-based quantification of RNAPII clearance during transcription-coupled DNA repair is now online. 👇
Well done, Bram, Diana, and Paula!
star-protocols.cell.com/protocols/45...
Well done, Bram, Diana, and Paula!
star-protocols.cell.com/protocols/45...
Reposted by Andreas Panagopoulos
Check out this beautiful paper by @richardcsilva.bsky.social et al., out now in @natcomms.nature.com. Great new DSB sensors to track DNA break formation and repair in real-time
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Engineered chromatin readers track damaged chromatin dynamics in live cells and animals - Nature Communications
DNA damage threatens genome stability, but its dynamics in living systems remain difficult to track. Here, the authors engineer MCPH1-based protein probes that specifically recognize γH2AX, enabling r...
www.nature.com
November 22, 2025 at 12:13 PM
Check out this beautiful paper by @richardcsilva.bsky.social et al., out now in @natcomms.nature.com. Great new DSB sensors to track DNA break formation and repair in real-time
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Honored to have participated in the Talent Forum — what an inspiring event! Truly grateful to @metorrespadilla.bsky.social for the kind invitation and outstanding organization.
The Helmholtz Munich Talent Forum (Nov 18–19) brought 8 emerging global talents in epigenetics & nucleic acids research to our Neuherberg Campus! Inspiring talks, a keynote by @boyanbonev.bsky.social & vibrant networking—science at its best! bit.ly/4o2ftxr
November 21, 2025 at 3:57 PM
Honored to have participated in the Talent Forum — what an inspiring event! Truly grateful to @metorrespadilla.bsky.social for the kind invitation and outstanding organization.
Reposted by Andreas Panagopoulos
Our paper is out in @nature.com! Oncogenes are often copy-number amplified on extrachromosomal DNA (ecDNA) in cancer, but how is ecDNA inherited by dividing cells? Here we identified elements within ecDNA that promote its retention in dividing cells. 1/11
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Genetic elements promote retention of extrachromosomal DNA in cancer cells - Nature
A combination of genome-wide functional screening, imaging and chromatin profiling identifies a new class of highly prevalent genomic elements that help retain extrachromosomal DNA copies in dividing ...
www.nature.com
November 19, 2025 at 7:03 PM
Our paper is out in @nature.com! Oncogenes are often copy-number amplified on extrachromosomal DNA (ecDNA) in cancer, but how is ecDNA inherited by dividing cells? Here we identified elements within ecDNA that promote its retention in dividing cells. 1/11
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Andreas Panagopoulos
So awesome to have this great paper from Sam Reffsin and Sara Cherry out! In it, we use retrospective clone tracing to show that there are particular single cell states that are more susceptible to viral infection (both SARS-CoV-2 and flu)!
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Single-cell susceptibility to viral infection is driven by variable cell states
Not all cells that can be infected by a virus become infected with that virus. Single-cell
clone tracing reveals intrinsic cell states with variable expression patterns that
increase susceptibility to...
www.cell.com
November 14, 2025 at 4:47 PM
So awesome to have this great paper from Sam Reffsin and Sara Cherry out! In it, we use retrospective clone tracing to show that there are particular single cell states that are more susceptible to viral infection (both SARS-CoV-2 and flu)!
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by Andreas Panagopoulos
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
biorxiv.org
November 12, 2025 at 9:26 PM
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Reposted by Andreas Panagopoulos
Registration is open!🧬
Join us at Egmond aan Zee (April 19–24, 2026) for the next DNA Repair Meeting. We have an amazing line-up of speakers.
📅 Deadline for early registration: Jan 10, 2026
🔗 dnarepairmeeting-egmond2026.com
Join us at Egmond aan Zee (April 19–24, 2026) for the next DNA Repair Meeting. We have an amazing line-up of speakers.
📅 Deadline for early registration: Jan 10, 2026
🔗 dnarepairmeeting-egmond2026.com
November 12, 2025 at 3:04 PM
Registration is open!🧬
Join us at Egmond aan Zee (April 19–24, 2026) for the next DNA Repair Meeting. We have an amazing line-up of speakers.
📅 Deadline for early registration: Jan 10, 2026
🔗 dnarepairmeeting-egmond2026.com
Join us at Egmond aan Zee (April 19–24, 2026) for the next DNA Repair Meeting. We have an amazing line-up of speakers.
📅 Deadline for early registration: Jan 10, 2026
🔗 dnarepairmeeting-egmond2026.com
Reposted by Andreas Panagopoulos
🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)
November 11, 2025 at 12:52 PM
🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)
Reposted by Andreas Panagopoulos
‼️ Excited to share our new paper out now in @science.org ‼️
We describe a new tetrameric RAD51 paralog complex – XRCC3-RAD51C-RAD51D-XRCC2 – which caps the end of RAD51 filaments.
Link: www.science.org/doi/epdf/10....
Thread ⬇️ (1/8)
We describe a new tetrameric RAD51 paralog complex – XRCC3-RAD51C-RAD51D-XRCC2 – which caps the end of RAD51 filaments.
Link: www.science.org/doi/epdf/10....
Thread ⬇️ (1/8)
November 7, 2025 at 10:15 AM
‼️ Excited to share our new paper out now in @science.org ‼️
We describe a new tetrameric RAD51 paralog complex – XRCC3-RAD51C-RAD51D-XRCC2 – which caps the end of RAD51 filaments.
Link: www.science.org/doi/epdf/10....
Thread ⬇️ (1/8)
We describe a new tetrameric RAD51 paralog complex – XRCC3-RAD51C-RAD51D-XRCC2 – which caps the end of RAD51 filaments.
Link: www.science.org/doi/epdf/10....
Thread ⬇️ (1/8)
Reposted by Andreas Panagopoulos
𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n
Repair of DNA double-strand breaks leaves heritable impairment to genome function
Upon DNA breakage, a genomic locus undergoes alterations in three-dimensional chromatin architecture to facilitate signaling and repair. Although cells possess mechanisms to repair damaged DNA, it is ...
tinyurl.com
November 6, 2025 at 11:05 PM
𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n
Reposted by Andreas Panagopoulos
Now published on @plos.org Computational Biology!
Same findings as the preprint, with improved analyses suggested by reviewers!
Check it out and let us know how RepliFlow works for you!
journals.plos.org/ploscompbiol...
Same findings as the preprint, with improved analyses suggested by reviewers!
Check it out and let us know how RepliFlow works for you!
journals.plos.org/ploscompbiol...
October 27, 2025 at 6:09 PM
Now published on @plos.org Computational Biology!
Same findings as the preprint, with improved analyses suggested by reviewers!
Check it out and let us know how RepliFlow works for you!
journals.plos.org/ploscompbiol...
Same findings as the preprint, with improved analyses suggested by reviewers!
Check it out and let us know how RepliFlow works for you!
journals.plos.org/ploscompbiol...
Reposted by Andreas Panagopoulos
Ever wondered how chromosomal instability (CIN) influences tumorigenesis? And how does it contribute to shaping the tumor microenvironment?
In our latest preprint, we used the CiMKi model to induce and monitor skin tumors across five levels of CIN
tinyurl.com/52tuk88z
Here's what we find (1/5):
In our latest preprint, we used the CiMKi model to induce and monitor skin tumors across five levels of CIN
tinyurl.com/52tuk88z
Here's what we find (1/5):
Non-cell-autonomous mechanisms of tumor initiation and relapse by chromosomal instability
Chromosomal instability (CIN) is a hallmark of cancer, and a primary cause of genetic heterogeneity in tumors. Depending on the degree of CIN and the affected tissue, CIN can promote or suppress tumor...
tinyurl.com
November 4, 2025 at 11:41 AM
Ever wondered how chromosomal instability (CIN) influences tumorigenesis? And how does it contribute to shaping the tumor microenvironment?
In our latest preprint, we used the CiMKi model to induce and monitor skin tumors across five levels of CIN
tinyurl.com/52tuk88z
Here's what we find (1/5):
In our latest preprint, we used the CiMKi model to induce and monitor skin tumors across five levels of CIN
tinyurl.com/52tuk88z
Here's what we find (1/5):
Reposted by Andreas Panagopoulos
Our paper in Science is out! @souravagrawal.bsky.social, @rlynn.bsky.social, @susvirkar.bsky.social, and the rest of the team show human RPA is a telomerase processivity factor essential for telomere maintenance. This reshapes our thinking about telomerase regulation. www.science.org/doi/10.1126/...
Human RPA is an essential telomerase processivity factor for maintaining telomeres
Telomerase counteracts telomere shortening by repeatedly adding DNA repeats to chromosome ends. We identified the replication protein A (RPA) heterotrimer as a telomerase processivity factor critical ...
www.science.org
October 30, 2025 at 10:07 PM
Our paper in Science is out! @souravagrawal.bsky.social, @rlynn.bsky.social, @susvirkar.bsky.social, and the rest of the team show human RPA is a telomerase processivity factor essential for telomere maintenance. This reshapes our thinking about telomerase regulation. www.science.org/doi/10.1126/...
Reposted by Andreas Panagopoulos
Want to know how homologous recombination defects are caused upon loss of BRCA2? Check out our recent efforts in uncovering this phenomenon just out in Science!
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
FIGNL1 inhibits homologous recombination in BRCA2 deficient cells by dissociating RAD51 filaments
Homologous recombination (HR) deficiency upon Breast Cancer Gene 2 (BRCA2) loss arises from defects in the formation of RAD51 nucleoprotein filaments. We demonstrate that loss of the anti-recombinase ...
www.science.org
October 30, 2025 at 9:52 PM
Want to know how homologous recombination defects are caused upon loss of BRCA2? Check out our recent efforts in uncovering this phenomenon just out in Science!
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Andreas Panagopoulos
Among the anti-recombinases, FIGNL1 rules them all. So much that inactivating it brings BRCA2-deficient cells to life. Who is responsible for RAD51 loading without BRCA2/FIGNL1, check out the paper to find out! Great collaboration with @raychaudhurilab.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
October 30, 2025 at 8:41 PM
Among the anti-recombinases, FIGNL1 rules them all. So much that inactivating it brings BRCA2-deficient cells to life. Who is responsible for RAD51 loading without BRCA2/FIGNL1, check out the paper to find out! Great collaboration with @raychaudhurilab.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Andreas Panagopoulos
🧬 Excited to share Nicheformer out now in Nature Methods!
A transformer foundation model linking single-cell & spatial omics, learning spatial context from gene expression to map tissue organization.
Led by Ale Tejada & Anna Schaar 👏
👉 www.nature.com/articles/s41...
A transformer foundation model linking single-cell & spatial omics, learning spatial context from gene expression to map tissue organization.
Led by Ale Tejada & Anna Schaar 👏
👉 www.nature.com/articles/s41...
October 30, 2025 at 7:19 PM
🧬 Excited to share Nicheformer out now in Nature Methods!
A transformer foundation model linking single-cell & spatial omics, learning spatial context from gene expression to map tissue organization.
Led by Ale Tejada & Anna Schaar 👏
👉 www.nature.com/articles/s41...
A transformer foundation model linking single-cell & spatial omics, learning spatial context from gene expression to map tissue organization.
Led by Ale Tejada & Anna Schaar 👏
👉 www.nature.com/articles/s41...
Reposted by Andreas Panagopoulos
Very happy to share our latest work extending iterative immunofluorescence to in toto imaging of early zebrafish embryos (3D-4i), integrated with a 3D-dedicated image analysis pipeline! 🐟🔬📊
Huge kudos to Max Hess for this PhD milestone! 💪
@lucaspelkmans.bsky.social shorturl.at/cO0u7
Let's zoom in!
Huge kudos to Max Hess for this PhD milestone! 💪
@lucaspelkmans.bsky.social shorturl.at/cO0u7
Let's zoom in!
October 29, 2025 at 2:20 PM
Very happy to share our latest work extending iterative immunofluorescence to in toto imaging of early zebrafish embryos (3D-4i), integrated with a 3D-dedicated image analysis pipeline! 🐟🔬📊
Huge kudos to Max Hess for this PhD milestone! 💪
@lucaspelkmans.bsky.social shorturl.at/cO0u7
Let's zoom in!
Huge kudos to Max Hess for this PhD milestone! 💪
@lucaspelkmans.bsky.social shorturl.at/cO0u7
Let's zoom in!
Reposted by Andreas Panagopoulos
Can an AI tool help us better understand the origins of cancer?
Researchers from EMBL's Korbel Group have developed a new AI method – MAGIC – which, through a game of molecular laser tag, is shedding light on how chromosomal abnormalities form in cells.
www.embl.org/news/science...
Researchers from EMBL's Korbel Group have developed a new AI method – MAGIC – which, through a game of molecular laser tag, is shedding light on how chromosomal abnormalities form in cells.
www.embl.org/news/science...
October 29, 2025 at 4:11 PM
Can an AI tool help us better understand the origins of cancer?
Researchers from EMBL's Korbel Group have developed a new AI method – MAGIC – which, through a game of molecular laser tag, is shedding light on how chromosomal abnormalities form in cells.
www.embl.org/news/science...
Researchers from EMBL's Korbel Group have developed a new AI method – MAGIC – which, through a game of molecular laser tag, is shedding light on how chromosomal abnormalities form in cells.
www.embl.org/news/science...
Reposted by Andreas Panagopoulos
Nektarios Tavernarakis on why curiosity-driven research, not focusing on application, is fundamental to problem solving and requires government support in @emboreports.org doi.org/10.1038/s443...
For the love of frontier research, or why Elon’s rockets keep blowing up | EMBO reports
EMBO Press is an editorially independent publishing platform for the development of EMBO scientific publications.
doi.org
October 29, 2025 at 11:57 AM
Nektarios Tavernarakis on why curiosity-driven research, not focusing on application, is fundamental to problem solving and requires government support in @emboreports.org doi.org/10.1038/s443...
Reposted by Andreas Panagopoulos
📢 Excited to share that our study has just been published in Nature Communications! We uncover how CRL4-DCAF12 regulates the cellular levels of MCMBP, a chaperone essential for assembling nascent MCM2-7 complexes, to ensure accurate and error-free genome duplication.
October 28, 2025 at 3:04 PM
📢 Excited to share that our study has just been published in Nature Communications! We uncover how CRL4-DCAF12 regulates the cellular levels of MCMBP, a chaperone essential for assembling nascent MCM2-7 complexes, to ensure accurate and error-free genome duplication.
Reposted by Andreas Panagopoulos
Sometimes #Cas9 is too dang big. But mini Cas proteins are bad at both NHEJ & HDR. PhD student Fedor Gorbenko used mammalian cell evolution for *HDR* to make REALLY super #Cas12f1 and #TnpB. As good as or better than Cas9! Base editors included! www.biorxiv.org/cgi/content/short/2025.10.27.684765v1
Directed evolution of compact RNA-guided nucleases for homology-directed repair in mammalian cells
RNA-guided nucleases enable DNA editing and offer promise for treating genetic diseases, particularly when used for precise sequence replacement. However, many of the most effective enzymes, such as S...
www.biorxiv.org
October 28, 2025 at 1:28 PM
Sometimes #Cas9 is too dang big. But mini Cas proteins are bad at both NHEJ & HDR. PhD student Fedor Gorbenko used mammalian cell evolution for *HDR* to make REALLY super #Cas12f1 and #TnpB. As good as or better than Cas9! Base editors included! www.biorxiv.org/cgi/content/short/2025.10.27.684765v1
Reposted by Andreas Panagopoulos
See our paper “Mechanism of trinucleotide repeat expansion by MutSβ-MutLγ and contraction by FAN1”. Using biochemistry, we show how DNA incisions by the MutLγ nuclease can lead to expansions, and how expansion is prevented by FAN1. Well done Issam and Valentina!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
October 27, 2025 at 1:12 PM
See our paper “Mechanism of trinucleotide repeat expansion by MutSβ-MutLγ and contraction by FAN1”. Using biochemistry, we show how DNA incisions by the MutLγ nuclease can lead to expansions, and how expansion is prevented by FAN1. Well done Issam and Valentina!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Andreas Panagopoulos
🚀 Our new Science paper is out (w/ B DeMeo, D Burkhardt, A Shalek, M Cortes): www.science.org/doi/10.1126/...
We show that active learning + transcriptomic perturbations can guide which exps to run next, boosting phenotypic hit rates >13x. AI not just predicting bio, but designing it. 🔁
We show that active learning + transcriptomic perturbations can guide which exps to run next, boosting phenotypic hit rates >13x. AI not just predicting bio, but designing it. 🔁
October 25, 2025 at 1:24 PM
🚀 Our new Science paper is out (w/ B DeMeo, D Burkhardt, A Shalek, M Cortes): www.science.org/doi/10.1126/...
We show that active learning + transcriptomic perturbations can guide which exps to run next, boosting phenotypic hit rates >13x. AI not just predicting bio, but designing it. 🔁
We show that active learning + transcriptomic perturbations can guide which exps to run next, boosting phenotypic hit rates >13x. AI not just predicting bio, but designing it. 🔁
Reposted by Andreas Panagopoulos
Ever noticed that #CRISPR editing results differ between cells? Awesome PhD student Moritz Schlapansky developed "scOUT-seq" to measure single cell transcriptomes + editing. 1.2 million cells, 74 cell types, living 🐭. Cell subtypes differ wildly from bulk average! www.biorxiv.org/content/10.1...
Cell-stereotyped DNA repair outcomes are widespread during genome editing
Genome editing outcomes are governed by DNA repair pathways that vary with cell type and state. We developed scOUT-seq (single-cell Outcomes Using Transcript sequencing), a scalable approach that join...
www.biorxiv.org
October 24, 2025 at 8:44 AM
Ever noticed that #CRISPR editing results differ between cells? Awesome PhD student Moritz Schlapansky developed "scOUT-seq" to measure single cell transcriptomes + editing. 1.2 million cells, 74 cell types, living 🐭. Cell subtypes differ wildly from bulk average! www.biorxiv.org/content/10.1...
Reposted by Andreas Panagopoulos
The CRG PhD call is open! 🌟
A truly special place, world-class facilities, an inspiring community, and a training team that really cares about helping each student reach their full potential.
My lab will be recruiting (moving next year), as will many amazing new colleagues!
#CRGPhD2026 #CRGBarcelona
A truly special place, world-class facilities, an inspiring community, and a training team that really cares about helping each student reach their full potential.
My lab will be recruiting (moving next year), as will many amazing new colleagues!
#CRGPhD2026 #CRGBarcelona
Are you looking for a PhD? Join us in Barcelona! You'll dive into a community of >100 PhD students from 30 countries exploring the frontiers of biology. You can also join an online workshop on 6 November (15:00 CET) to learn how to find the right lab for you.
More info: www.crg.eu/en/content/t...
More info: www.crg.eu/en/content/t...
October 23, 2025 at 10:14 AM
The CRG PhD call is open! 🌟
A truly special place, world-class facilities, an inspiring community, and a training team that really cares about helping each student reach their full potential.
My lab will be recruiting (moving next year), as will many amazing new colleagues!
#CRGPhD2026 #CRGBarcelona
A truly special place, world-class facilities, an inspiring community, and a training team that really cares about helping each student reach their full potential.
My lab will be recruiting (moving next year), as will many amazing new colleagues!
#CRGPhD2026 #CRGBarcelona