Jennifer Nichols

This paper optimizes a protocol for generating human gastruloids by adjusting culture conditions, improving efficiency and cost-effectiveness for studying early development.

The paper compares WNT/{beta}-catenin signalling and TCF/LEF gene expression in human and mouse pluripotent stem cells, revealing species-specific differences in early development.

The paper describes a resource of clonal human pluripotent stem cell lines derived from embryos, showing intra- and inter-embryo variation and potential for modeling chromosomal mosaicism.

This study creates a spatiotemporal atlas of mouse gastrulation and early organogenesis using spatial transcriptomics and scRNA-seq, revealing gene expression dynamics and mesodermal fate decisions.

The paper shows that donor ESCs displace host cells from the epiblast in chimeras through crowding and FGF4 signalling, with FGF4 acting after physical displacement.

This study shows that STAT3 signaling is crucial for tissue expansion during postimplantation mouse development by promoting cell proliferation and differentiation.

The paper identifies epigenetically primed enhancers in early embryonic development and shows their role in regulating developmental gene networks across species.

This study creates a single-cell transcriptomic atlas of pig gastrulation, revealing conserved and divergent gene programs and fate dynamics across species.

This study uses human naive PSC models to show FGF signaling is critical for hypoblast specification, revealing conservation with mouse lineage specification.

The paper uses scRNA-Seq and computational methods to predict and validate differentiation trajectories during early mammalian organogenesis, showing agreement between computational predictions and experimental outcomes.

The paper develops statistical tools to analyze gene knockouts in mouse embryos and applies them to study developmental disruptions and cancer therapy responses.

The paper introduces insideOutside, a method to classify interior and exterior cells in embryos using spatial data, showing improved accuracy over existing methods.

This study shows that mouse gastruloids generate PGC-like cells (Gld-PGCLCs) through self-organized interactions, mimicking in vivo PGC development without exogenous signals.

This study constructs a rabbit developmental atlas and compares it with mouse data to identify species-specific differences in gene regulation and extra-embryonic tissues.

The paper identifies the sequential activation of hypoblast marker genes in the human blastocyst, supporting a model of sequential lineage commitment.

The paper shows STAT3 and TFCP2L1 are essential for epiblast self-renewal during diapause, but only TFCP2L1 is needed for deriving embryonic stem cells in vitro.

Entropy Sorting identifies meaningful cellular heterogeneity in scRNA-seq data, revealing the inner cell mass in human pre-implantation embryos.

This study shows that Plakoglobin regulates naive pluripotency in mouse ESCs through mechanosensitivity, with expression specific to the blastocyst stage in human and mouse embryos.

This study shows that STAT3 phosphorylation variants regulate naïve pluripotency and developmental timing in mouse embryos, with loss of active STAT3 causing developmental delay and metabolic defects.

The paper identifies dynamic cell surface fluctuations as a key factor in early embryonic lineage sorting, showing that increased surface fluctuations in primitive endoderm precursors drive their segregation from epiblast precursors.

This paper identifies 8-cell like cells (8CLCs) in human naive stem cells that model zygotic genome activation, expressing ZGA markers and transposable elements, and can be manipulated to enhance ZGA-like transcription.

The paper introduces VASA-seq, a method for total single-cell RNA-seq in mice, revealing non-coding RNA expression and alternative splicing during development.

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.

The paper identifies coordinated step-changes in gene expression kinetics during erythropoiesis in both mouse and human, challenging assumptions of RNA velocity analysis.

This study shows that Rreb1 is essential for mouse embryonic development, regulating epithelial architecture and invasiveness during gastrulation.

The paper shows human naive epiblast cells can generate trophectoderm and trophoblast cells, unlike mouse embryonic stem cells, and identifies key regulators of this process.

This study identifies OCT4's role in maintaining pluripotency through metabolic regulation and Stat3 signaling in mouse embryos.

The paper identifies and characterizes formative stem cells in mice and humans, showing they have unique transcriptional and epigenetic features compared to naive and primed pluripotent cells.

The paper uses single cell triple-omics analysis to reveal how epigenetic changes drive germ layer specification in mouse embryos, showing distinct epigenetic priming and remodeling in different lineages.