Igor I. Adameyko

The paper develops COSCO to map neuronal connectivity in cerebral organoids and shows self-organizing network motifs and disease-related topological changes.

The paper uses in utero barcoding and single-cell transcriptomics to map clonal relationships in mouse mesoderm-derived tissues, revealing lineage relationships in liver and heart mesenchyme.

The paper identifies chromaffin-neuroblast plasticity as a mechanism linking paraganglioma and neuroblastoma through shared developmental states and hybrid cell populations.

The paper shows that the relative abundance of transcription factors SP9 and DLX determines neuronal fate allocation in the developing basal ganglia.

The paper introduces a tissue-clearing framework and mesoSPIM-ultra system for large-scale single-neuron tracing in cleared mouse tissue.

This study uses advanced human co-culture models to show that fibroblast-derived thrombospondin-1 drives macrophage metabolic remodeling and polarization in tumor environments.

The paper introduces clone2vec, a machine learning method for analyzing lineage-resolved single-cell data, revealing clonal patterns and continuous variation in development and disease.

This study reveals GH directly stimulates human growth plate stem cell proliferation via TGF{beta} and ERK pathways, offering insights into growth mechanisms and treatment optimization.

The paper integrates single-cell, spatial, and clonal data to study cranial placode development and evolution, revealing continuous transcriptional landscapes and shared progenitors between placodes.

RETrace2 enables high-resolution retrospective lineage tracing and cell-type identification using mutable homopolymers, achieving resolution below five cell divisions in microsatellite-unstable organisms.

The paper uses chromatin state approximation to optimize stem cell differentiation protocols, finding that greedy selection based on ATAC-seq profiles improves erythroblast generation.

This study maps spatial dynamics in early human heart development using single-cell and spatial transcriptomics, identifying cell states and novel features like cardiac fibroblasts and chromaffin cells.

The paper identifies a novel epithelial population, Zippering Lambda, whose cell cycle arrest is critical for facial prominence fusion and is disrupted in orofacial clefting.

This study links EPAS1HIF2 genetic adaptations in high-altitude populations to similar mutations in hypoxia-driven tumors, showing shared mechanisms in hypoxia response and tumorigenesis.

This study identifies SOX2+ sustentacular cells as stem cells for postnatal adrenal medulla chromaffin cells, showing their ability to generate both adrenaline and noradrenaline lineages and maintain homeostasis via WNT6 secretion.

The paper profiles clonal landscapes in mouse embryos to reveal spatial modulators of clonal fate biases using single-cell lineage tracing and clone2vec.

This study shows that motor nerves guide the development of sympathetic ganglia by directing the migration and differentiation of neural crest-derived sympathoblasts.

This study uses a 3D cell-based computational model to show that oriented cell divisions and repulsive mechanical interactions drive columnar cartilage formation in embryos.

The paper creates a developmental cell atlas of the human spinal cord using single-cell and spatial transcriptomics, revealing spatiotemporal gene regulation and novel insights into ependymoma cancer stem cells.

scFates is a Python package for analyzing single-cell data trajectories, focusing on pseudotime, bifurcation, and cell fate splits, with integration into the scanpy ecosystem.

The paper shows that β-catenin signaling patterns the oral-aboral axis in Nematostella vectensis, but endoderm specification occurs opposite to nuclear β-catenin accumulation, suggesting this mechanism is a Bilateria-specific co-option.

The paper identifies microheterogeneity in embryonic chromaffin cells and their differentiation paths using single-cell transcriptomics in mice.

The paper shows that early pre-neural serotonin in zebrafish affects later serotonin synthesis and behavioral patterns without causing major developmental abnormalities.

The paper maps the regulatory landscape of neuronal and glial differentiation in the enteric nervous system using single-cell RNA sequencing and identifies gene modules and epigenetic memory associated with neurogenesis and gliogenesis.

The paper identifies and characterizes prototypical pacemaker neurons in Hydra that express immune-related genes and interact with the microbial environment.

Unspliced versus spliced mRNA in standard scRNA-seq gives RNA velocity, a per-cell vector predicting future state over hours, validated in neural crest and used to trace mouse hippocampal lineages.