Zhisong He

SALL1 and neural microenvironmental contextspecify identity of stem cell derived humanmicroglia-like cells

This study identifies how SALL1 and neural microenvironmental context shape the identity of stem cell-derived human microglia-like cells in 2D and 3D cultures.

Decoding morphogen patterning of human neural organoids with a multiplexed single-cell transcriptomic screen

The paper uses a multiplexed single-cell transcriptomic screen to study how morphogen cues affect regional specification in human neural organoids, finding that timing, concentration, and combination of morphogens strongly influence cell type and regional composition.

DISCO-seq: 3D single-cell transcriptomics of intact biological systems

DISCO-seq enables 3D single-cell transcriptomics of whole tissues and organisms by combining tissue-clearing chemistry with imaging and transcriptomic profiling.

Unified Generation of Regionalized Neural Organoids from Single-Lumen Neuroepithelium

This paper introduces a scalable platform to generate regionally specified neural organoids from uniform single-lumen neuroepithelium, improving reproducibility and fidelity to natural brain development.

Morphodynamics of human early brain organoid development

The paper uses live imaging and single-cell transcriptomics to study how extracellular matrix influences brain organoid development and regionalization.

Fate and state transitions during human blood vessel organoid development

This study maps the cell state transitions during human blood vessel organoid development using single-cell transcriptomics and identifies key regulators and disease associations.

Multi-omic human neural organoid cell atlas of the posterior brain

The paper creates a multi-omic atlas of human neural organoids modeling the posterior brain and identifies morphogen conditions that expand organoid models.

Single-cell profiling of penta- and tetradactyl mouse limb buds identifies mesenchymal progenitors controlling digit numbers and identities

This study identifies mesenchymal progenitors in mouse limb buds that regulate digit numbers and identities through BMP signaling and GREM1-mediated antagonism.

An integrated transcriptomic cell atlas of human neural organoids

This paper integrates 36 single-cell transcriptomics datasets from human neural organoids into a unified atlas to assess cell type coverage and compare organoid protocols with primary brain tissue.

Characterization of RNA content in individual phase-separated coacervate microdroplets

The paper characterizes RNA content in individual phase-separated coacervate microdroplets using high-throughput sequencing and identifies sequence motifs associated with RNA accumulation.

Multimodal spatiotemporal phenotyping of human organoid development

This paper develops a multimodal approach to study human retinal organoid development, integrating spatial, transcriptomic, and chromatin accessibility data to create a virtual atlas of retinal development.

Inferring and perturbing cell fate regulomes in human cerebral organoids

The paper uses single-cell genomic data from human cerebral organoids to infer gene regulatory networks and assess transcription factor roles in brain development.

Cell atlas of the regenerating human liver after portal vein embolization

This study uses single-cell transcriptomics to analyze liver regeneration after portal vein embolization, identifying changes in cell states and immune interactions.

Ngn2 induces diverse neuronal lineages from human pluripotency

This study uses single-cell transcriptomics to show that Ngn2 overexpression in human iPSCs generates heterogeneous neurons, including peripheral nervous system-like populations, and that Ngn2 dosage affects neuron fate.

Cluster similarity spectrum integration of single-cell genomics data

This paper introduces a method to integrate single-cell genomics data across experiments and conditions while preserving biological information, showing it outperforms existing methods in certain scenarios.

An organoid and multi-organ developmental cell atlas reveals multilineage fate specification in the human intestine

The paper uses human intestinal organoids to create a single-cell transcriptome atlas, revealing molecular mechanisms of cell fate specification in the intestine.

Lineage recording reveals dynamics of cerebral organoid regionalization

The paper uses lineage recording techniques to study brain regionalization in cerebral organoids, finding that iPSC clones accumulate in distinct brain regions and lineage restriction increases over time.

Resolving brain organoid heterogeneity by mapping single cell genomic data to a spatial reference

This paper introduces VoxHunt, a computational method that maps single-cell genomic data from brain organoids to spatial reference data to assess patterning and cell composition.

Single-cell genomic atlas of great ape cerebral organoids uncovers human-specific features of brain development

This study uses single-cell genomics to compare brain development in humans, chimpanzees, and macaques, identifying human-specific gene regulatory features.

Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation

The paper identifies 33 functional modules associated with human neuron maturation and develops a model to quantify neuron maturity states across species.

Comprehensive investigation of temporal and autism-associated cell type composition-dependent and independent gene expression changes in human brains

The paper quantifies how cell type composition and independent gene expression changes contribute to age-related transcriptome changes in human brains.

Evaluating intra- and inter-individual variation in the human placental transcriptome

The paper evaluates gene expression variation in the human placenta, finding 33.2% within-individual, 58.9% among-individual, and 7.8% among-human-group variation, with selection pressures influencing most genes.