Sign in

Antonio Scialdone

@antonio-scialdone.bsky.social
516 followers 475 following 12 posts

Group Leader at Helmholtz Munich - single-cell/spatial omics & mathematical modelling of cell fate decision

PostsRepliesMedia
Antonio Scialdone @antonio-scialdone.bsky.social · 03/03/2026
Transposable elements are increasingly studied in single-cell data, but how reliable are current locus-level quantification methods in short-read scRNA-seq data? If you work with single-cell RNA-seq or TEs, we hope this is a useful resource — feedback very welcome!
1146
Reposted by Antonio Scialdone
ME Torres-Padilla @metorrespadilla.bsky.social · 09/02/2026
We go live!!! Join us Munich July5-7th to hear exciting research on #Replication by leaders in the field AND !! registration is FREE 🥳 (but mandatory) - we hope to see many in Munich 🍺 @helmholtzmunich.bsky.social @replifate.bsky.social @epicrossborders.bsky.social replifate.eu/event/meetin...
replifate.eu
Events for February 2026
06-07 July 2026 | Munich, GermanyDNA Replication and Its Impact on Genome and Chromatin MaintenanceWe are RepliFate, a European Training Doctoral Network dedicated to understanding how DNA replication...
13228
Antonio Scialdone @antonio-scialdone.bsky.social · 23/12/2025
Our new preprint is out: www.biorxiv.org/content/10.6... We show that GRN benchmarks commonly used can overestimate performance due to negative-sampling choices, sometimes allowing simple degree-based baselines to rival more complex GNNs. A reminder of why bias-aware evaluation matters!
biorxiv.org
Hidden sampling biases inflate performance in gene regulatory network inference
Accurate reconstruction of gene regulatory networks (GRNs) from single-cell transcriptomic data remains a major methodological challenge. Recent machine learning approaches, particularly graph neural ...
12111
Reposted by Antonio Scialdone
Eva Hörmanseder @evahoermanseder.bsky.social · 22/12/2025
We probably shouldn’t have favourites amongst projects in the lab, but this one was mine. I’m so pleased we can finally share it: Our work is now out in Nature Communications: 🔗 nature.com/articles/s41467-025-67692-7
nature.com
22710
Antonio Scialdone @antonio-scialdone.bsky.social · 25/07/2025
How can we quantify cell potency from scRNAseq data? In our latest preprint, we show that intrinsic dimensionality (ID) tracks potency in single cells across reprogramming datasets, and we provide IDEAS, a Python toolkit for ID-based potency analysis: www.biorxiv.org/content/10.1...
biorxiv.org
Intrinsic dimensionality of single-cell transcriptomic data reveals potency landscapes during cell reprogramming
Cell potency, the ability of a cell to generate other cell types, is a fundamental property that drives development, regeneration, and reprogramming. Recent computational advances have en- abled estim...
2123
Reposted by Antonio Scialdone
ME Torres-Padilla @metorrespadilla.bsky.social · 15/07/2025
🎤 Apply to speak @our TALENT FORUM by July 31! Showcase YOUR research in Epigenetics & NucleicAcids @www.helmholtz-munich.de & connect with leading scientists 🧳Travel+accommodation covered if selected! 📝 Info+how to apply: lnkd.in/drkRvz7N #postdoc #career #groupleader #HelmholtzMunich #research
01312
Reposted by Antonio Scialdone
Epigenetics at Helmholtz Munich @epihmgu.bsky.social · 01/04/2025
NEW PAPER ALERT!! 🥚And a new powerful tool for modeling early human development! @antonio-scialdone.bsky.social ’s lab @www.helmholtz-munich.de & A. Surani’s lab at University Cambridge uncover key insights into early #humandevelopment with 3D human #gastruloids. Read our news: shorturl.at/7FjGT
052
Reposted by Antonio Scialdone
Alfonso Martinez Arias @amartinezarias.bsky.social · 27/03/2025
Human #gastruloids as a model for the emergence of #PGCs www.science.org/doi/10.1126/...; early days but it promises as it follows the earlier work of @nmoris.bsky.social on mouse PGCs shorturl.at/FO1p0
science.org
The emergence of human primordial germ cell–like cells in stem cell–derived gastruloids
3D human gastruloids mimic gastrulation and postgastrulation development, forming the three germ layer derivatives and hPGCLCs.
063
Antonio Scialdone @antonio-scialdone.bsky.social · 27/03/2025
Here’s our latest study on human gastruloids: www.science.org/doi/10.1126/... With the Surani lab, we combine imaging, scRNA-seq and genetic perturbation to investigate the emergence of amnion-&PGC-like cells. Congrats to Jitesh Neupane, Gabriele Lubatti and all co-authors for their great work!
science.org
The emergence of human primordial germ cell–like cells in stem cell–derived gastruloids
3D human gastruloids mimic gastrulation and postgastrulation development, forming the three germ layer derivatives and hPGCLCs.
1176
Antonio Scialdone @antonio-scialdone.bsky.social · 13/03/2025
Why do some cells resist nuclear reprogramming? Using nuclear transfer, we tracked single-cell fate changes in vivo and uncovered cell-type-specific barriers to reprogramming. Suppressing the old identity boosts success! www.cell.com/stem-cell-re...
cell.com
Differentiation success of reprogrammed cells is heterogeneous in vivo and modulated by somatic cell identity memory
This study investigates how reprogramming success in vivo varies across cell types, revealing that gene expression of the previous somatic cell identity hinders proper differentiation. By following si...
1124
Antonio Scialdone @antonio-scialdone.bsky.social · 12/02/2025
How can we improve gene regulatory network inference from noisy scRNA-seq data? Our new review in @molsystbiol.org explores the latest methods integrating prior knowledge to enhance reliability. Plus, some suggestions on how to improve benchmarking! www.embopress.org/doi/full/10....
embopress.org
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data | Molecular Systems Biology
EMBO Press is an editorially independent publishing platform for the development of EMBO scientific publications.
22514
Antonio Scialdone @antonio-scialdone.bsky.social · 10/02/2025
Join our lab for a summer internship at Helmholtz Munich! Only 1 week left to apply!
031
Reposted by Antonio Scialdone
Meghana Oak @meghana-oak.bsky.social · 22/01/2025
✨ Excited to share my latest preprint on how H3K4 methylation promotes transcriptional memory from gametes to embryos across a transcriptionally silent window — crucial for proper zygotic genome activation and development. 🐸🧬✨ 📄 Check it out here:
doi.org/10.1101/2025... 👇 Highlights below
doi.org
H3K4 methylation-promoted transcriptional memory ensures faithful zygotic genome activation and embryonic development
In the life of a vertebrate embryo, gene expression is initiated for the first time at zygotic genome activation (ZGA). Maternally expressed transcription factors present in the embryo are essential f...
14820
Reposted by Antonio Scialdone
Mario Nicodemi @marionicodemi.bsky.social · 08/12/2024
Join us at the next conference on the frontiers between Biological Physics and Statistical Mechanics: indico.unina.it/event/91/ Contributed talk submission is open.
indico.unina.it
Biological Physics and Statistical Mechanics: from molecules to cells and beyond (09-13 giugno 2025)
Overview The conference on "Biological Physics and Statistical Mechanics" will be held in Napoli, Italy, from June 9 to June 13, 2025. The meeting aims at bringing together the Italian scientific co...
011
Reposted by Antonio Scialdone
Rob Schneider @robertife.bsky.social · 08/12/2024
Please RS/RT. #GordonConference on "Histone and DNA Modifications" #epigenetics #chromatin 20-25. July 2025. Il Ciocco, Italy. Great speaker lineup. ➡️Register now www.grc.org/histone-and-...
04640