Allon Moshe Klein

The paper shows that neuropeptide tachykinin and Wnt signaling regulate cardiomyocyte progenitor proliferation in Ciona robusta, with neuronal innervation playing a key role.

The paper develops CAGEs to enable high-throughput multi-step assays on live cells, measuring gene expression persistence in expanding clones.

This paper introduces a mannitol-based buffer (PBS-M) that improves scRNA-seq quality for high-salt marine cells, revealing previously undetected cell states.

This paper shows that tissue fluidity regulates the speed and accuracy of adhesion-based cell sorting through a trade-off between cell motility and adhesion.

The paper uses single-cell RNA sequencing to analyze inner ear development in zebrafish, identifying cell states and genes involved in sensory patches, semicircular canals, and endolymphatic sac formation.

The paper constructs a single-cell transcriptomic atlas of Botryllus schlosseri budding, identifying dedifferentiating founder cells that drive asexual development.

This study identifies immune cell types in the basal chordate Ciona robusta using single-cell RNA sequencing and finds divergence from vertebrate immune cells.

This study shows IL-17A enhances erythropoietic response to hypoxia by sensitizing progenitors to erythropoietin, balancing reactivity and steady-state burden.

This study shows cell division is dispensable for differentiation of embryonic tissues in zebrafish but affects cell state proportions.

The paper constructs a signaling-response map of the human airway epithelium by analyzing 17 receptor-mediated pathways, revealing convergent and ligand-specific responses and linking TGFB1 to lung disease.

scDiffEq models single-cell dynamics using neural stochastic differential equations, improving trajectory reconstruction and fate prediction in hematopoiesis.

The paper identifies Spock1 as a neuronal signal that regulates blood-brain barrier permeability by altering extracellular matrix and vascular gene expression in zebrafish and mice.

This paper introduces CoSpar, a computational method that integrates single-cell genomics with lineage tracing to infer cell dynamics, revealing previously undetected fate biases in hematopoiesis, reprogramming, and differentiation.

This study uses DNA barcodes to trace single-cell transcriptomes during differentiation, identifying fate biases and developmental hierarchies in hematopoiesis.

Scrublet detects scRNA-seq doublets by simulating doublets from random cell pairs and scoring cells by simulated-doublet neighbor fraction, reaching AUC 0.99 on human-mouse mixtures.

The paper introduces scGESTALT, a method that combines single-cell RNA sequencing with lineage tracking to identify cell types and their developmental relationships in the zebrafish brain.

This paper identifies fundamental limits on inferring gene expression dynamics from single-cell snapshots and introduces an algorithmic approach to constrain dynamic solutions.

The paper uses single-cell transcriptomics and fate potential assays to map the erythroid differentiation trajectory from multipotent hematopoietic stem cells in mice, revealing novel regulators and transcriptional programs.

SPRING visualizes high-dimensional single-cell expression data using force-directed layouts, revealing more detailed biological relationships and greater reproducibility than existing methods.

The paper quantifies protein and phospho-site dynamics during fertilization and meiotic exit in Xenopus eggs using mass spectrometry-based proteomics, revealing limited degradation and extensive dephosphorylation.

This study compares two mouse motor neuron differentiation protocols, showing that direct programming can reach the same final state through a different intermediate state with distinct gene expression.