Zhirong Bao
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View article: A Single-cell Spatiotemporal Manifold of Tissue Morphology and Dynamics
A Single-cell Spatiotemporal Manifold of Tissue Morphology and Dynamics Open
Complex tissues are now characterizable at single-cell resolution, but the spatial logic underlying tissue organization remains challenging to access without effective single-cell spatial descriptors. We present a learned single-cell manif…
View article: SwiftKV: A Metadata Indexing Scheme Integrating LSM-Tree and Learned Index for Distributed KV Stores
SwiftKV: A Metadata Indexing Scheme Integrating LSM-Tree and Learned Index for Distributed KV Stores Open
Optimizing metadata indexing remains critical for enhancing distributed file system performance. The Traditional Log-Structured Merge-Trees (LSM-Trees) architecture, while effective for write-intensive operations, exhibits significant limi…
View article: Single-cell topographical profiling of the immune synapse reveals a biomechanical signature of cytotoxicity
Single-cell topographical profiling of the immune synapse reveals a biomechanical signature of cytotoxicity Open
Immune cells have intensely physical lifestyles characterized by structural plasticity and force exertion. To investigate whether specific immune functions require stereotyped mechanical outputs, we used super-resolution traction force mic…
View article: Modeling Cell Migration with Convolutional Neural Network and Deep Reinforcement Learning
Modeling Cell Migration with Convolutional Neural Network and Deep Reinforcement Learning Open
Cell migration modeling is a longstanding biological challenge, which is regulated by a highly complex set of regulatory mechanisms at multiple scales in a developmental system. This study presents a generic framework for regulatory mechan…
View article: Vibration monitoring of optical fiber composited in overhead transmission line using φ-OTDR
Vibration monitoring of optical fiber composited in overhead transmission line using φ-OTDR Open
In order to evaluate the vibration state of the overhead line, the φ-OTDR (phase-sensitive optical time-domain reflectometry) is applied to the vibration monitoring for the optical fiber composited in overhead transmission line. The princi…
View article: Topographical analysis of immune cell interactions reveals a biomechanical signature for immune cytolysis
Topographical analysis of immune cell interactions reveals a biomechanical signature for immune cytolysis Open
Immune cells live intensely physical lifestyles characterized by structural plasticity, mechanosensitivity, and force exertion. Whether specific immune functions require stereotyped patterns of mechanical output, however, is largely unknow…
View article: A compound PCP scheme underlies sequential rosettes-based cell intercalation
A compound PCP scheme underlies sequential rosettes-based cell intercalation Open
The formation of sequential rosettes is a type of collective cell behavior recently discovered in the Caenorhabditis elegans embryo that mediates directional cell migration through sequential formation and resolution of multicellular roset…
View article: A compound PCP scheme underlies sequential rosettes-based cell intercalation
A compound PCP scheme underlies sequential rosettes-based cell intercalation Open
SUMMARY Sequential rosettes are a type of collective cell behavior recently discovered in the C. elegans embryo to mediate directional cell migration through sequential formation and resolution of multicellular rosettes involving the migra…
View article: Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification
Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification Open
Homeobox genes are prominent regulators of neuronal identity, but the extent to which their function has been probed in animal nervous systems remains limited. In the nematode Caenorhabditis elegans , each individual neuron class is define…
View article: Visualizing and quantifying molecular and cellular processes in <i>Caenorhabditis elegans</i> using light microscopy
Visualizing and quantifying molecular and cellular processes in <i>Caenorhabditis elegans</i> using light microscopy Open
Light microscopes are the cell and developmental biologists’ “best friend,” providing a means to see structures and follow dynamics from the protein to the organism level. A huge advantage of Caenorhabditis elegans as a model organism is i…
View article: 3D+time nuclei tracking dataset of confocal fluorescence microscopy time series of C. elegans embryos
3D+time nuclei tracking dataset of confocal fluorescence microscopy time series of C. elegans embryos Open
The dataset consists of 3 confocal microscopy time series of C. elegans embryos, fully tracked with StarryNite followed by manual curation 3 raw time-series and the corresponding tracks/lineage trees temporal resolution; 75s tempo…
View article: 3D+time nuclei tracking dataset of confocal fluorescence microscopy time series of C. elegans embryos
3D+time nuclei tracking dataset of confocal fluorescence microscopy time series of C. elegans embryos Open
The dataset consists of 3 confocal microscopy time series of C. elegans embryos, fully tracked with StarryNite followed by manual curation 3 raw time-series and the corresponding tracks/lineage trees temporal resolution; 75s tempo…
View article: Cross-modality synthesis of EM time series and live fluorescence imaging
Cross-modality synthesis of EM time series and live fluorescence imaging Open
Analyses across imaging modalities allow the integration of complementary spatiotemporal information about brain development, structure, and function. However, systematic atlasing across modalities is limited by challenges to effective ima…
View article: Author response: Cross-modality synthesis of EM time series and live fluorescence imaging
Author response: Cross-modality synthesis of EM time series and live fluorescence imaging Open
View article: Widespread employment of conserved <i>C. elegans</i> homeobox genes in neuronal identity specification
Widespread employment of conserved <i>C. elegans</i> homeobox genes in neuronal identity specification Open
Homeobox genes are prominent regulators of neuronal identity, but the extent to which their function has been probed in animal nervous systems remains limited. In the nematode Caenorhabditis elegans , each individual neuron class is define…
View article: Small RNAs couple embryonic developmental programs to gut microbes
Small RNAs couple embryonic developmental programs to gut microbes Open
Embryogenesis has long been known for its robustness to environmental factors. Although developmental tuning of embryogenesis to the environment experienced by the parent may be beneficial, little is understood on whether and how developme…
View article: Cross-modality Synthesis of EM Time Series and Live Fluorescence Imaging
Cross-modality Synthesis of EM Time Series and Live Fluorescence Imaging Open
Analyses across imaging modalities allow the integration of complementary spatiotemporal information about brain development, structure and function. However, systematic atlasing across modalities is limited by challenges to effective imag…
View article: Hierarchical deep reinforcement learning reveals a modular mechanism of cell movement
Hierarchical deep reinforcement learning reveals a modular mechanism of cell movement Open
View article: A single-cell transcriptome atlas of human early embryogenesis
A single-cell transcriptome atlas of human early embryogenesis Open
The early window of human embryogenesis is largely a black box for developmental biologists. Here we probed the cellular diversity of 4- to 6-week human embryos when essentially all organs are just laid out. Based on over 180,000 single-ce…
View article: Author response: Differential adhesion regulates neurite placement via a retrograde zippering mechanism
Author response: Differential adhesion regulates neurite placement via a retrograde zippering mechanism Open
Article Figures and data Abstract Editor's evaluation Introduction Results Discussion Materials and methods Appendix 1 Data availability References Decision letter Author response Article and author information Metrics Abstract During deve…
View article: A landscape model for cell fate decisions during mesoendoderm differentiation in C. elegans based on Wnt dynamics
A landscape model for cell fate decisions during mesoendoderm differentiation in C. elegans based on Wnt dynamics Open
Geometric models allow us to quantify topography of the Waddington landscape and gain quantitative insights of gene interaction in cell fate differentiation. Often mutant phenotypes show partial penetrance and there is a dearth of quantita…
View article: A genetic screen for temperature-sensitive morphogenesis-defective <i>Caenorhabditis elegans</i> mutants
A genetic screen for temperature-sensitive morphogenesis-defective <i>Caenorhabditis elegans</i> mutants Open
Morphogenesis involves coordinated cell migrations and cell shape changes that generate tissues and organs, and organize the body plan. Cell adhesion and the cytoskeleton are important for executing morphogenesis, but their regulation rema…
View article: Kathryn Anderson (1952–2020)
Kathryn Anderson (1952–2020) Open
View article: Structural and developmental principles of neuropil assembly in C. elegans
Structural and developmental principles of neuropil assembly in C. elegans Open
View article: A Genetic Screen for Temperature-sensitive Morphogenesis-defective<i>Caenorhabditis elegans</i>Mutants
A Genetic Screen for Temperature-sensitive Morphogenesis-defective<i>Caenorhabditis elegans</i>Mutants Open
Morphogenesis involves coordinated cell migrations and cell shape changes that generate tissues and organs, and organize the body plan. Cell adhesion and the cytoskeleton are important for executing morphogenesis, but their regulation rema…
View article: Small RNAs couple embryonic developmental programs to gut microbes
Small RNAs couple embryonic developmental programs to gut microbes Open
Maternal exposure to microbes and other environmental factors is known to induce adaptive changes in the progeny, but little is understood about how development of the progeny is changed. We show that Caenorhabditis elegans undergoes addit…
View article: A single-cell analysis of the molecular lineage of chordate embryogenesis
A single-cell analysis of the molecular lineage of chordate embryogenesis Open
scRNA-seq of an invariant cell lineage reveals insights into asymmetric cell division, FGF signaling, and notochord specification.
View article: Cadherin preserves cohesion across involuting tissues during C. elegans neurulation
Cadherin preserves cohesion across involuting tissues during C. elegans neurulation Open
The internalization of the central nervous system, termed neurulation in vertebrates, is a critical step in embryogenesis. Open questions remain regarding how force propels coordinated tissue movement during the process, and little is know…
View article: Author response: Cadherin preserves cohesion across involuting tissues during C. elegans neurulation
Author response: Cadherin preserves cohesion across involuting tissues during C. elegans neurulation Open
Article Figures and data Abstract Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract The internalization of the central nervous…
View article: Rapid image deconvolution and multiview fusion for optical microscopy
Rapid image deconvolution and multiview fusion for optical microscopy Open