Nicolas Dray

Kontext: Kernel-based method bridging spatial domain identification and cell-cell communication

Kontext identifies spatial domains and cell-cell communication by integrating ligand-receptor interactions, outperforming existing methods in spatial transcriptomics.

EpiCure (Epithelial Curation): a versatile and handy tool for curation of epithelial segmentation

EpiCure is a tool for curating epithelial segmentation errors in 2D movies, improving accuracy and efficiency in single-cell dynamics analysis.

Linking transcriptome to cell behavior in real time uncovers molecular fate-asymmetry and a quiescence cycle among adult neural stem cells

This study links transcriptomic data with real-time cell behavior to uncover molecular fate asymmetry and a quiescence cycle in adult neural stem cells.

Jagged-mediated lateral induction patterns Notch3 signaling within adult neural stem cell populations

The paper measures Notch3 signaling in zebrafish adult neural stem cells and shows it correlates with quiescence and stemness, with jagged1b promoting stemness through lateral induction.

FishFeats: streamlined quantification of multimodal labeling at the single-cell level in 3D tissues

FishFeats provides a streamlined pipeline for quantifying multimodal labeling in 3D tissues, integrating image analysis steps into a user-friendly tool for non-computational users.

Non-apoptotic caspase events and Atf3 expression underlie direct neuronal differentiation of adult neural stem cells

Apical size and deltaA expression predict adult neural stem cell decisions along lineage progression

The paper links apical size and deltaA expression to neural stem cell activation and division modes in zebrafish, showing their independence from Notch signaling.

LocalZProjector and DeProj: A toolbox for local 2D projection and accurate morphometrics of large 3D microscopy images.

The paper introduces LocalZProjector and DeProj, tools for accurate 2D projection and morphometric analysis of 3D microscopy images, showing they handle complex data and correct projection distortions.

Dynamic spatiotemporal coordination of neural stem cell fate decisions through local feedback in the adult vertebrate brain

The paper shows neural stem cells use local feedback mechanisms with delays to coordinate their division and maintain homeostasis in the adult brain.

Lineage hierarchies and stochasticity ensure the long-term maintenance of adult neural stem cells

The paper investigates the dynamics of adult neural stem cells in zebrafish, showing a hierarchical organization with reservoir and operational stem cells and an upstream progenitor population supporting long-term neurogenesis.

Rere-dependent Retinoic Acid signaling controls brain asymmetry and handedness

The paper shows that Retinoic Acid signaling, specifically through Rere, controls brain asymmetry and handedness in zebrafish and mouse.