Benjamin D. Simons

WNT/β-catenin increases 3D chromatin mobility and reorganisation during posterior cell state transitions

Xeno-free human iPSC-derived prostate organoid platform for multilineage differentiation and genetic manipulation

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 Reconciles Divergent Velocity and Trajectory in Single-cell Transcriptomics with Deep Neural ODE

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

Pre-cancerous Niche Remodelling Dictates Nascent Tumour Survival

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

Cell cycle criticality as a mechanism for robust cell population control

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.

Recovery of human upper airway epithelium after smoking cessation is driven by a slow-cycling stem cell population and immune surveillance

Corrections in single cell migration path in vivo are controlled by pulses in polar Rac1 activation

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

A temporal hierarchy determines epigenetic aging

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

A computational pipeline for spatial mechano-transcriptomics

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.

Coupling of cell proliferation to the segmentation clock ensures robust somite scaling

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

Self-organization of spermatogenic wave coordinates sustained sperm production in the mouse testis

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.

Spatial Transcriptomics Reveals the Temporal Architecture of the Seminiferous Epithelial Cycle and Precise Sertoli-Germ Synchronization

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.

Red2Flpe-SCON: A Versatile, Multicolor Strategy for Generating Mosaic Conditional Knockout Mice

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.

Human spermatogonial stem cells retain states with a foetal-like signature

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.

Epigenetic inheritance of gene-silencing is maintained by a self-tuning mechanism based on resource competition

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.

Atypical cortical encoding of speech identifies children with Dyslexia versus Developmental Language Disorder

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.

Birth, cell fate and behavior of progenitors at the origin of the cardiac mitral valve

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.

Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis

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.

Anal skin-like epithelium mediates colonic wound healing

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

Secreted inhibitors drive the loss of regeneration competence in Xenopus limbs

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

Early Stem Cell Aging in the Mature Brain

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.

Distinct progenitor behavior underlying neocortical gliogenesis related to tumorigenesis

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.

A two-phase model of skin epidermal stratification: lessons from centrosomes

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.

Proliferation is a requirement for differentiation of oligodendrocyte progenitor cells during CNS remyelination

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

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.

Mutations in thyroid hormone receptor α1 cause premature neurogenesis and progenitor cell depletion in human cortical development

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

Lgr5+ stem/progenitor cells reside at the apex of the embryonic hepatoblast pool

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: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants

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

Genome-scale oscillations in DNA methylation during exit from pluripotency

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.