James Briscoe

The paper shows that boundary constraints influence the spatial patterning of cell fates during development through a reaction-diffusion model and Wnt signaling.

The paper shows that RA induces a transient co-expression state of PAX6 and FOXA2 in neural tube organoids, leading to two opposing cell fates that determine cell-type proportions through feedback signaling.

The paper shows that a truncated ASH2L isoform, generated via a lineage-specific retrotransposon, primes developmental gene promoters during pluripotency and is required for later developmental transitions.

ESFS improves scRNA-seq data interpretability by identifying gene sets with complex expression dynamics, outperforming traditional methods in diverse biological contexts.

This paper introduces a computational framework to reconstruct developmental landscapes from single-cell data, revealing morphogen-dependent cell fate transitions in neural progenitors.

The paper uses genomic barcoding and single-cell RNA sequencing to reveal hierarchical lineage architecture in human and avian spinal cord development, showing conserved lineage restriction and developmental routes.

This study investigates how multiscale mechanical and chemical interactions drive the functional maturation of the zebrafish heart during development.

This study identifies a global temporal chromatin programme in vertebrate neural progenitors that integrates with spatial patterning to regulate cell fate and identity.

This study identifies a reversible basal-like cell state in AKT-inhibitor resistant triple negative breast cancer using multimodal profiling and lineage tracing.

This paper introduces a framework to model cell fate decisions using single-cell data, revealing conserved decision-making architectures across species.

The paper identifies a spatiotemporal cancer cell trajectory in glioblastoma that explains tumor heterogeneity across regions and subclones.

The paper tracks mesodermal cell migration and lineage during mouse gastrulation, revealing distinct progenitor behaviors and fate allocation in cardiac development.

The paper uses scATAC-seq to study chromatin accessibility changes during neural plate border cell fate specification, identifying new regulatory mechanisms involving Foxk2.

The paper develops a method to engineer synthetic cis-regulatory elements that control gene expression in response to signals, showing they can be designed using quantitative rules.

The paper uses an in vivo CRISPR screen in chick embryos to identify MLLT3 as a regulator of neural fate specification from the caudal epiblast.

The paper uses single-cell transcriptomics to study vertebrate trunk formation, identifying signaling pathways that regulate notochord and tissue development in human pluripotent stem cells.

This paper develops a 3D model of human CNS development from naive hiPSCs, showing their ability to form neuroepithelial cysts and model FXS with epigenetic changes.

The paper compares protein dynamics in mouse and human neural progenitors, finding that human NPs have longer protein half-lives and lower proteasomal activity, which influences developmental tempo.

PUFFFIN labels cell neighbourhoods using a fluorescent protein fusion, enabling tracking of cell interactions and profiling non-cell-autonomous responses in mammalian cells.

The paper quantifies positional information in the vertebrate neural tube using information theory and shows that signaling dynamics enhance positional precision.

This paper introduces an optogenetic system to control morphogen production and study patterning dynamics in vitro, revealing how Shh concentration and duration affect neural progenitor domain formation.

This paper uses optimal control theory to model morphogen-driven tissue patterning, showing how cells can achieve precise and reproducible fate decisions despite noise and dynamic feedback.

The paper uses single-cell RNA sequencing to study cell fate decisions at the neural plate border in chick ectoderm, proposing a gradient border model for fate allocation.

The paper introduces a deep learning framework called velvet to model gene expression dynamics from single-cell data, outperforming existing methods and capturing developmental decision-making processes.

The paper shows how floorplate organiser forms autonomously in neural tube organoids through BMP-mediated cluster competition and FOXA2 dynamics.

The paper identifies two distinct cis regulatory strategies used by CREs to translate graded Shh signaling into differential gene expression in neural progenitors.

The paper identifies a temporal patterning program in vertebrate neurons controlled by transcription factors and the TGFβ pathway, showing its role in generating neuronal diversity.

This paper uses spatial transcriptomics to study mouse organogenesis, revealing spatial gene expression patterns and cell fate decisions not captured by single-cell RNA sequencing.

Human embryonic spinal cord scRNA-seq (71,219 cells, CS12-CS19) mirrors mouse patterning and neurogenesis but shows floor-plate PAX7, broad ventral NKX6.2 and early OLIG2/NKX2.2 progenitors.

The paper identifies spatial and molecular differences in cardiac progenitor origins in mouse embryos, showing distinct regions of the primitive streak contribute to different heart structures.