Sergey V. Isaev

Connectomics by Sequencing Reveals Self-Organizing Principles of Neuronal Networks in Cerebral Organoids

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

In utero barcoding of mouse mesoderm reveals the clonal architecture of organ mesenchyme

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.

Stoichiometric transcription factor partnerships control GABAergic neuron fate allocation

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

Fibroblast-derived thrombospondin-1 shapes macrophage polarization in advanced human co-culture models

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

Clonal embeddings allow exploratory analysis of lineage-resolved single-cell data

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.

Single-cell, clonal and spatial atlases of cranial placodes illuminate their specification and evolution

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.

Unbiased profiling of multipotency landscapes reveals spatial modulators of clonal fate biases

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