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A Deep Learning approach for time-consistent cell cyclephase prediction from microscopy data
  • Articles scientifiques
A Deep Learning approach for time-consistent cell cyclephase prediction from microscopy data
Thomas Walter // The cell cycle consists of four phases and impacts most cellular processes. In imaging assays, the cycle phase can be identified using dedicated cell-cycle markers. However, such markers occupy fluorescent channels that may be needed for other reporters. Here, we propose to address this limitation by inferring the phase from a widely used fluorescent reporter: SiR-DNA.
14 novembre 2025
STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport
  • Articles scientifiques
STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport
Laura Cantini // In dynamic biological processes such as development, spatial transcriptomics is revolutionizing the study of the mechanisms underlying spatial organization within tissues. Inferring cell fate trajectories from spatial transcriptomics profiled at several time points has thus emerged as a critical goal, requiring novel computational methods.
14 novembre 2025
Loop extrusion provides mechanical robustness to chromatin
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Loop extrusion provides mechanical robustness to chromatin
Hossein Salari, Daniel Jost // Chromosomes are complex biopolymers folded into dynamic loops via a loop extrusion process and may experience various mechanical forces in vivo. We develop a force-dependent model of chromatin loop extrusion and investigate its mechanical consequences on chromosome organization using simulations and analytical theory. We show that loop extrusion alters the force–extension behavior of DNA in a non-monotonic manner: extrusion stiffens the chain at low forces but softens it at intermediate and high forces.
14 novembre 2025
FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format
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FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format
Marcelo Nollmann // A key output of the NIH-Common Fund 4D Nucleome (4DN) project 1,2 is the open publication of datasets related to the structure of the human cell nucleus and the genome. Recent years have seen a rapid expansion of multiplexed Fluorescence In Situ Hybridization (FISH) or FISH-omics methods, which quantify the spatial organization of chromatin in single cells, sometimes together with RNA and protein measurements, and provide an expanded understanding of how 3D higher-order chromosome structure relates to transcriptional activity and cell development in both health and disease.
13 novembre 2025
AAP
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  • Autres
AAP
En juin 2025, nous avons lancé un appel à projets ouvert avec l’ANR pour le PEPR Cell-ID ! C’est un appel de 5 millions d’euros pour des projets de 3 à 4 ans pouvant atteindre 1 million d’euros. L’appel est aujourd’hui clos et les projets sont en cours de sélection.
5 novembre 2025
Postdoctoral position in neurodevelopment
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  • Postdoc
Postdoctoral position in neurodevelopment
The Davy team is looking for a highly motivated postdoctoral fellow to study acquisition of cell identities in innovative mouse and human brain organoid models in the frame of the Cell-ID research program (https://www.pepr-cell-id.fr/) whose main goal is to deploy interceptive medicine in the field of pediatric brain cancer. The proposed project is part of the CELL EXP challenge and includes methodologies in the fields of tissue engineering, single cell transcriptomics, as well as advanced imaging.
2 octobre 2025
Au cœur des cellules souches : comment les variants des histones protègent leur génome
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Au cœur des cellules souches : comment les variants des histones protègent leur génome
Dans le noyau des cellules de mammifères, l’ADN doit être compacté pour tenir dans un espace restreint. Ce rôle est assuré par les histones, des protéines qui modulent l’organisation et l’activité du génome. Dans une étude publiée dans Nature Communications, des scientifiques ont montré l’importance de l’équilibre entre différents variants d’histones dans la stabilité nucléaire, particulièrement dans les cellules souches.
1 septembre 2025
Appel à projets – ANR
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Appel à projets – ANR
PEPR Cell-ID : « Identités et destins cellulaires » – Appel à projets – 2025 | ANR…
25 août 2025
Cell-ID Scientific meeting
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Cell-ID Scientific meeting
10, 11 & 12 september 2025 Institut Jacques Monod, 15 rue Hélène Brion, Paris 13ᵉ Deadline : August 1st,…
20 juin 2025
Appel à idées visuelles !
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Appel à idées visuelles !
Et si vous participiez à imaginer l’identité visuelle de notre programme de recherche Cell-ID ? 🎨🧠 Cell-ID est un programme scientifique dédié à la médecine d’interception, une approche innovante pour prévenir la réapparition des cancers du cerveau pédiatriques, en intervenant à l’échelle de la cellule. Pour représenter cette ambition, nous cherchons à créer un pictogramme porteur de sens et d’espoir 💫 Pas besoin d’être graphiste ! Ce que l’on cherche : un croquis, un prompt IA, un texte desciptif… Tout ce qui peut faire germer une image !
14 avril 2025
Call for applications
  • Recrutement
Call for applications
Join the Cell-ID (Cell identity and Destiny) Research Program for your PhD in 2025 to participate in a multidisciplinary research program that involves a network of 29 French labs. We are seeking outstanding, creative, and motivated young researchers for a highly collaborative effort using advanced technologies and approaches to understand how cells contribute to both normal development and derail in certain pediatric brain cancers and pave the way toward interceptive medicine. Paired Labs with Available PhD Positions.
3 février 2025
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A point cloud segmentation framework for image-based spatial transcriptomics | Nature
Recent progress in image-based spatial RNA profiling enables to spatially resolve tens to hundreds of distinct RNA species with high spatial resolution. It presents new avenues for comprehending tissue organization. In this context, the ability to assign detected RNA transcripts to individual cells is crucial for downstream analyses, such as in-situ cell type calling…
6 juillet 2024
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Multiplexed chromatin imaging reveals predominantly pairwise long-range coordination between Drosophila Polycomb genes | Cell Reports
Polycomb (Pc) group proteins are transcriptional regulators with key roles in development, cell identity, and differentiation. Pc-bound chromatin regions form repressive domains that interact in 3D to assemble repressive nuclear compartments. Here, we use multiplexed chromatin imaging to investigate whether Pc compartments involve the clustering of multiple Pc domains during Drosophila development….
25 mai 2024
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EZH2 mutations in follicular lymphoma distort H3K27me3 profiles and alter transcriptional responses to PRC2 inhibition | Nature Communications
Mutations in chromatin regulators are widespread in cancer. Among them, the histone H3 lysine 27 methyltransferase Polycomb Repressive Complex 2 (PRC2) shows distinct alterations according to tumor type. This specificity is poorly understood. Here, we model several PRC2 alterations in one isogenic system to reveal their comparative effects…
24 avril 2024
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Transient loss of Polycomb components induces an epigenetic cancer fate | Nature
Although cancer initiation and progression are generally associated with the accumulation of somatic mutations, substantial epigenomic alterations underlie many aspects of tumorigenesis and cancer susceptibility, suggesting that genetic mechanisms might not be the only drivers of malignant transformation.
24 avril 2024
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Reconstruction of macroglia and adult neurogenesis evolution through cross-species single-cell transcriptomic analyses | Nature
Macroglia fulfill essential functions in the adult vertebrate brain, producing and maintaining neurons and regulating neuronal communication. However, we still know little about their emergence and diversification. We used the zebrafish D. rerio as a distant vertebrate model with moderate glial diversity as anchor to reanalyze datasets covering over 600 million years of evolution…
17 avril 2024
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A cell fate decision map reveals abundant direct neurogenesis bypassing intermediate progenitors in the human developing neocortex | Nature Cell Biology
The human neocortex has undergone strong evolutionary expansion, largely due to an increased progenitor population, the basal radial glial cells. These cells are responsible for the production of a diversity of cell types, but the successive cell fate decisions taken by individual progenitors remain unknown. Here we developed a semi-automated live/fixed correlative imaging method to map basal radial glial cell division modes in early fetal tissue and cerebral organoids…
28 mars 2024
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Regulation of replicative histone RNA metabolism by the histone chaperone ASF1 | Molecular Cell
In S phase, duplicating and assembling the whole genome into chromatin requires upregulation of replicative histone gene expression. Here, we explored how histone chaperones control histone production in human cells to ensure a proper link with chromatin assembly. Depletion of the ASF1 chaperone specifically decreases the pool of replicative histones both at the protein and RNA levels…
15 février 2024
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Chromatin compartmentalization regulates the response to DNA damage | Nature
The DNA damage response is essential to safeguard genome integrity. Although the contribution of chromatin in DNA repair has been investigated1,2, the contribution of chromosome folding to these processes remains unclear3. Here we report that, after the production of double-stranded breaks (DSBs) in mammalian cells, ATM drives the formation of a new chromatin compartment (D compartment) through the clustering of damaged topologically associating domains, decorated with γH2AX and 53BP1…
18 octobre 2023
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Self-organizing models of human trunk organogenesis recapitulate spinal cord and spine co-morphogenesis
Integrated in vitro models of human organogenesis are needed to elucidate the multi-systemic events underlying development and disease. Here we report the generation of human trunk-like structures that model the co-morphogenesis, patterning and differentiation of the human spine and spinal cord. We identified differentiation conditions for human pluripotent stem cells favoring the formation of an embryo-like extending antero-posterior (AP) axis…
14 septembre 2023
Lancement du programme Cell-ID
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Lancement du programme Cell-ID
Lancement officiel du programme de recherche 22 novembre 2024 Institut Curie Présentation Le programme…
3 janvier 2023

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