Benjamin D. Simons

This paper develops a xeno-free human iPSC-derived prostate organoid platform that enables multilineage differentiation and genetic manipulation for studying prostate biology and disease.

VeloTrace unifies RNA velocity and trajectory inference using NeuralODEs, improving accuracy and coherence in single-cell transcriptomic analysis.

The paper shows that pre-cancerous niche remodeling by early tumour cells determines nascent tumour survival in mice.

The paper develops a mechanistic framework showing how cell cycle criticality enables robust population control by balancing self-renewal and differentiation through sensitivity to mitogenic signals.

The paper investigates how periodic changes in cell polarity during migration are controlled by pulsations in Rac1 activity in live zebrafish embryos.

The paper shows how DNA methylation aging emerges from a hierarchy of molecular processes across different timescales.

The paper identifies shared proliferation acceleration and heterogeneous transcriptional changes during B-lymphoid and neutrophil/monocyte lineage restriction from CD34+ cord blood cells.

The paper develops a computational framework to jointly analyze transcriptional and mechanical signals in spatial transcriptomics data from mouse embryos, identifying predictive signatures of tissue compartment boundaries.

The paper shows that coupling cell proliferation to the segmentation clock ensures uniform PSM growth and precise somite scaling in mouse embryos.

The paper uses live imaging and mathematical modeling to show how self-organization of cell turnover in mouse testes sustains sperm production through phase waves and retinoic acid signaling.

The paper uses spatial transcriptomics to map the temporal dynamics of the seminiferous epithelial cycle in mouse testis, revealing synchronized transcriptional patterns between Sertoli and germ cells.

The paper introduces Red2Flpe-SCON, a multicolor system for generating mosaic conditional knockout mice, and uses it to show Sox2 is not essential for stem cell maintenance but for proliferation and differentiation.

This study identifies a foetal-like state 0B in human spermatogonial stem cells that maintains a suppressive transcriptomic program, contrasting with rodent models where this state is not maintained into adulthood.

The paper shows that transgenerational gene silencing in C. elegans is maintained by a self-tuning mechanism based on resource competition, leading to long-term memory-like persistence.

The paper identifies distinct neural processing patterns in children with dyslexia and Developmental Language Disorder using EEG and speech listening tasks, showing different oscillation dynamics and spatial patterns.

The paper identifies the origin, fate, and clonal contribution of endocardial progenitors to the development of the cardiac mitral valve using single-cell RNA sequencing and genetic tracing in mice.

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 skin-like epithelial cells that contribute to colonic wound healing in mouse models of colitis.

The paper identifies extrinsic cues from chondrogenic progression that inhibit AER cell formation and limit limb regeneration in Xenopus tadpoles.

The paper identifies factors that disrupt neural stem cells in the adult hippocampus and shows that Abl1 inhibition can enhance NSC proliferation in middle-aged brains.

The paper quantifies the progenitor cell behavior and gliogenesis program in the mouse neocortex, revealing a 60%:15%:25% propensity for astrocytes, oligodendrocytes, and both, and links gliogenesis to tumor suppressor loss.

This study investigates the role of centrosomes in epidermal stratification, finding that early stratification depends on proliferation and delamination, while later stages are less dependent on division orientation.

This study shows that OPC proliferation is required for differentiation during CNS remyelination, revealing a link between proliferation and differentiation in OPCs.

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.

This study shows that THRA mutations impair neural progenitor cell proliferation and organisation in human cortical development using patient-derived iPSCs.

The paper identifies Lgr5+ hepatoblasts as bi-potent liver progenitors that contribute to liver development and reside at the apex of the embryonic hepatoblast hierarchy.

Cardelino integrates whole exomes and single-cell transcriptomes to identify clone-of-origin and reveal phenotypic impacts of somatic variants in human fibroblasts.

The paper shows that during exit from pluripotency, coexpression of DNMT3s and TETs drives genome-scale DNA methylation oscillations, with amplitude dependent on CpG density, observed both in vitro and in vivo.