A novel cell nuclei segmentation method for 3D C. elegans embryonic time-lapse images. - Long Chen 010; Leanne Lai Chan; Zhongying Zhao 002; Hong Yan 001 (BMC Bioinform., 2013)

CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data. - Daogang Guan; Jiaofang Shao; Youping Deng; Panwen Wang; Zhongying Zhao 002; Yan Liang; Junwen Wang; Bin Yan (Bioinform., 2014)

DDGni: Dynamic delay gene-network inference from high-temporal data using gapped local alignment. - Hari Krishna Yalamanchili; Bin Yan; Mulin Jun Li; Jing Qin 004; Zhongying Zhao 002; Francis Y. L. Chin; Junwen Wang (Bioinform., 2014)

PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data. - Daogang Guan; Jiaofang Shao; Zhongying Zhao 002; Panwen Wang; Jing Qin 004; Youping Deng; Kenneth R. Boheler; Junwen Wang; Bin Yan (Nucleic Acids Res., 2014)

C. elegans cell matching and tracking in a 4D imageing system. - Long Chen 010; Zhongying Zhao 002; Hong Yan 001 (ICASSP, 2015)

Gene regulatory effects inference for cell fate determination based on single-cell resolution data. - Xiao-Tai Huang; Leanne Lai Chan; Zhong-Ying Zhao 002; Hong Yan 001 (ICMLC, 2015)

A Probabilistic Relaxation Labeling (PRL) Based Method for C. elegans Cell Tracking in Microscopic Image Sequences. - Long Chen 010; Zhongying Zhao 002; Hong Yan 001 (IEEE J. Sel. Top. Signal Process., 2016)

Inference of cellular level signaling networks using single-cell gene expression data in Caenorhabditis elegans reveals mechanisms of cell fate specification. - Xiao-Tai Huang; Yuan Zhu; Leanne Lai-Hang Chan; Zhongying Zhao 002; Hong Yan 001 (Bioinform., 2017)

PlaMoM: a comprehensive database compiles plant mobile macromolecules. - Daogang Guan; Bin Yan; Christoph J. Thieme; Jingmin Hua; Hailong Zhu; Kenneth R. Boheler; Zhongying Zhao 002; Friedrich Kragler; Yiji Xia; Shoudong Zhang (Nucleic Acids Res., 2017)

Accurate Cell Segmentation Based on Biological Morphology Features. - Jianfeng Cao; Zhongying Zhao 002; Hong Yan 001 (SMC, 2018)

3DMMS: robust 3D Membrane Morphological Segmentation of C. elegans embryo. - Jianfeng Cao; Ming-Kin Wong; Zhongying Zhao 002; Hong Yan 001 (BMC Bioinform., 2019)

Bayesian Detection of Abnormal Asynchrony of Division Between Sister Cells in Mutant Caenorhabditis elegans Embryos. - Wei Liang; Yuxiao Yang; Yusi Fang; Zhongying Zhao 002; Jie Hu 020 (J. Comput. Biol., 2019)

Computable early Caenorhabditis elegans embryo with a phase field model. - Xiangyu Kuang; Guoye Guan; Ming-Kin Wong; Lu-Yan Chan; Zhongying Zhao 002; Chao Tang; Lei Zhang 061 (PLoS Comput. Biol., 2022)

Directional And Topological Transformer With Topology Priors For 4D Cellular Image Segmentation. - Zelin Li; Zhaoke Huang; Zhen Zhu; Sicheng You; Zhongying Zhao 002; Hong Yan 001 (ICIP, 2024)

CShaperApp: Segmenting and analyzing cellular morphologies of the developing Caenorhabditis elegans embryo. - Jianfeng Cao; Lihan Hu; Guoye Guan; Zelin Li; Zhongying Zhao 002; Chao Tang; Hong Yan 001 (Quant. Biol., 2024)

Volume Tells: Dual Cycle-Consistent Diffusion for 3D Fluorescence Microscopy De-noising and Super-Resolution. - Zelin Li; Chenwei Wang; Zhaoke Huang; Yiming Ma; Cunming Zhao; Zhongying Zhao 002; Hong Yan 001 (CVPR, 2025)

An effective method for quantification, visualization, and analysis of 3D cell shape during early embryogenesis. - Zelin Li; Zhaoke Huang; Jianfeng Cao; Guoye Guan; Zhongying Zhao 002; Hong Yan 001 (Quant. Biol., 2025)