Austin G Smith

Branching topology of the human embryo transcriptome revealed by entropy sort feature weighting

This paper introduces cESFW for scRNA-seq analysis, revealing high-resolution developmental trajectories in human embryos and identifying lineage-specific markers.

ERK signalling orchestrates metachronous transition from naive to formative pluripotency

This study shows ERK signalling dismantles the naive pluripotent state and preserves pluripotency during transition to formative pluripotency in mouse embryonic stem cells.

Suppression of YAP Safeguards Human Naïve Pluripotency

This study identifies YAP suppression as the mechanism by which tankyrase inhibition maintains human naive pluripotency without inducing differentiation.

Entropy sorting of single cell RNA sequencing datareveals the inner cell mass in the humanpre-implantation embryo

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

Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

The paper shows that disabling de novo DNA methylation in embryonic stem cells causes them to adopt a trophoblast fate instead of proper differentiation, due to misexpression of Ascl2.

Human Naive Epiblast Cells Possess Unrestricted Lineage Potential

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.

Capture of mouse and human stem cells with features of formative pluripotency

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.

Embryonic stem cells commit to differentiation by symmetric divisions following a variable lag period

The paper tracks mouse embryonic stem cells during differentiation, finding symmetric divisions and variable lag periods before loss of pluripotency.

Efficient RNA-mediated reprogramming of human somatic cells to naive pluripotency facilitated by tankyrase inhibition

This paper demonstrates that tankyrase inhibition enables efficient, transgene-free reprogramming of human somatic cells to naive pluripotency, with clonal expansion and differentiation capabilities.

A common molecular logic determines embryonic stem cell self-renewal and reprogramming

This study identifies a common molecular logic governing embryonic stem cell self-renewal and reprogramming through Boolean network analysis and experimental validation.

Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

This study compares single-cell transcriptomes of human, marmoset, and mouse embryos to identify conserved and divergent features of preimplantation development.

Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast

Reanalysis of three human embryo scRNA-seq datasets resolves cell-type ambiguities, defines epiblast and primitive endoderm prototypes, and identifies t2iLGö and 5i/L/A naïve stem cells as epiblast-like.

Gene editing in rat embryonic stem cells to produce in vitro models and in vivo reporters

This study uses CRISPR/Cas9 to edit rat embryonic stem cells, generating in vitro models and in vivo reporters for genetic studies.

Epigenetic resetting of human pluripotency

This paper describes a method to reset human pluripotent stem cells to a naive state through transient histone deacetylase inhibition, showing transcriptomic and epigenomic changes similar to the inner cell mass.

Nodal secures pluripotency upon embryonic stem cell progression from the ground state

This study shows that Nodal maintains pluripotency in mouse ES cells as they exit the ground state, enabling competence for germline and somatic lineage specification.

Tracking the embryonic stem cell transition from ground state pluripotency

The paper tracks the transition of mouse embryonic stem cells from ground state pluripotency to a formative phase, showing acute exit from naive status and transcriptome changes similar to early post-implantation epiblast.