Zhirong Bao

Transient morphogenetic constraints organize self-assembling axon neighborhoods for robust yet flexible wiring

The paper shows how transient morphogenetic structures and stochastic innervation models shape reproducible yet flexible wiring in C. elegans nervous systems through a trade-off between physical constraints and molecular specificity.

A Single-cell Spatiotemporal Manifold of Tissue Morphology and Dynamics

This paper introduces a learned single-cell spatiotemporal manifold to analyze tissue morphology and dynamics over time.

A compound PCP scheme underlies sequential rosettes-based cell intercalation

The paper identifies a novel PCP-related polarity scheme that regulates sequential rosettes in C. elegans embryos, distinct from known PCP mechanisms in convergent extension.

A single-cell transcriptome atlas of human early embryogenesis

This study creates a single-cell transcriptome atlas of human early embryogenesis, identifying 313 cell types and their spatial organization across 18 developmental systems.

Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification

The paper investigates the role of homeobox genes in neuronal identity specification in C. elegans, finding that 111 of 118 neuron classes require homeobox genes for proper differentiation.

Cross-modality Synthesis of EM Time Series and Live Fluorescence Imaging

The paper develops a cross-modality image alignment method to integrate EM and fluorescence imaging data in C. elegans, revealing dynamic cell behaviors during nervous system development.

Differential adhesion regulates neurite placement via a retrograde zippering mechanism

The paper investigates how differential adhesion controls neurite placement in C. elegans brain neuropils through a retrograde zippering mechanism.

A landscape model for cell fate decisions during mesoendoderm differentiation in C. elegans based on Wnt dynamics

The paper constructs a Waddington landscape model to predict cell fate decisions during C. elegans mesoendoderm differentiation based on Wnt dynamics and mutant penetrance data.

A Genetic Screen for Temperature-sensitive Morphogenesis-defective Caenorhabditis elegans Mutants

The paper identifies temperature-sensitive embryonic-lethal mutants in C. elegans with morphogenesis defects and characterizes their genetic and cellular basis.

Structural and developmental principles of neuropil assembly in C. elegans

The paper uses diffusion condensation to analyze the C. elegans nerve ring neuropil, revealing its stratified structure and developmental principles.

A single-cell analysis of the molecular lineage of chordate embryogenesis

This study maps the molecular lineage of chordate embryogenesis using single-cell transcriptomics in Ciona savignyi, identifying 47 cell types and revealing fate determination mechanisms.

Cadherin Preserves Cohesion Across Involuting Tissues During C. elegans Neurulation

This study shows that HMR-1/Cadherin mediates tissue cohesion during C. elegans neurulation, suggesting a potential homology with vertebrate neurulation.

Multicellular rosettes organize neuropil formation

The paper shows multicellular rosettes organize the nerve ring neuropil in C. elegans by guiding axon outgrowth and structural formation.

A multicellular rosette-mediated collective dendrite extension

The paper shows that C. elegans amphid neurons form a multicellular rosette to collectively extend dendrites, using adhesion molecules and mechanical cues from surrounding tissues.

Cellular structure image classification with small targeted training samples

The paper presents a deep learning method using GANs and feature transfer to classify cell shapes with minimal training samples, achieving high accuracy in detecting multicellular rosettes in C. elegans embryos.