Yinan Wan

Generative modeling reveals the connection between nuclear morphology and gene expression

COSMIC, a generative model, quantifies the relationship between nuclear morphology and gene expression using paired single-cell data, revealing morphology-associated genes in prostate cancer and spatial transcriptomics of zebrafish embryos.

FOCUS-3D: Robust, generalizable volumetric cell segmentation for three-dimensional fluorescence microscopy

FOCUS-3D segments cells in 3D fluorescence microscopy data across species and tissues, revealing phases of notochord morphogenesis in zebrafish.

Odor preference maps to cohesive transcriptional domains in the olfactory bulb

The paper identifies transcriptional domains in the zebrafish olfactory bulb that correlate with odor preference and shows specific neuronal subtypes are recruited based on odor preference.

High-Fidelity Long-term Whole-embryo Lineage and Fate Reconstruction by Iterative Tracking with Error Correction

ITEC reconstructs high-fidelity cell lineages and fate maps of embryos with over 99.7% accuracy using iterative tracking and error correction.

Whole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesis

The paper introduces a whole-embryo spatial transcriptomics method and generates a comprehensive gene expression and chromatin accessibility atlas in zebrafish embryos.

Imaging cellular activity simultaneously across all organs of a vertebrate reveals body-wide circuits

The paper introduces WHOLISTIC, a method to image cellular activity across all organs of a vertebrate, revealing body-wide circuits and responses to stimuli.

Automated Reconstruction of Whole-Embryo Cell Lineages by Learning from Sparse Annotations

This paper introduces a method for automated lineage reconstruction in developing embryos using sparse annotations, achieving 75.8% accuracy on mouse embryos compared to 31.8% previously.

Interkinetic nuclear migration in the zebrafish retina as a diffusive process

The paper uses imaging to analyze nuclear migration in zebrafish retinas and models it as a diffusive process influenced by nuclear concentration gradients.