AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis. - Thomas J. Boyle; Zhirong Bao; John I. Murray; Carlos L. Araya; Robert H. Waterston (BMC Bioinform., 2006)

A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D. - Anthony Santella; Zhuo Du; Sonja Nowotschin; Anna-Katerina Hadjantonakis; Zhirong Bao (BMC Bioinform., 2010)

A Semi-Local Neighborhood-based Framework for Probabilistic Cell Lineage Tracing. - Anthony Santella; Zhuo Du; Zhirong Bao (BMC Bioinform., 2014)

WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration. - Anthony Santella; Raúl Catena; Ismar Kovacevic; Pavak K. Shah; Zidong Yu; Javier Marquina-Solis; Abhishek Kumar; Yicong Wu; James C. Schaff; Daniel Colón-Ramos; Hari Shroff; William Mohler; et al. (BMC Bioinform., 2015)

Using High Performance Computing to Model Cellular Embryogenesis. - Gerard Vanloo; Chung Ng; Kison Osborne; Kwai Wong; Ben Ramsey; Dali Wang; Zhirong Bao (XSEDE, 2016)

Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model. - Anthony Santella; Ismar Kovacevic; Laura A. Herndon; David H. Hall; Zhuo Du; Zhirong Bao (Nucleic Acids Res., 2016)

Cell Neighbor Determination in the Metazoan Embryo System. - Zi Wang 002; Dali Wang; Husheng Li; Zhirong Bao (BCB, 2017)

Deep reinforcement learning of cell movement in the early stage of C.elegans embryogenesis. - Zi Wang 002; Dali Wang; Chengcheng Li; Yichi Xu; Husheng Li; Zhirong Bao (Bioinform., 2018)

AceTree: a major update and case study in the long term maintenance of open-source scientific software. - Braden Katzman; Doris Tang; Anthony Santella; Zhirong Bao (BMC Bioinform., 2018)

Deep Reinforcement Learning of Cell Movement in the Early Stage of C. elegans Embryogenesis. - Zi Wang 002; Dali Wang; Chengcheng Li; Yichi Xu; Husheng Li; Zhirong Bao (CoRR, 2018)

Cellular Structure Image Classification With Small Targeted Training Samples. - Dali Wang; Zheng Lu; Yichi Xu; Zi Wang 002; Anthony Santella; Zhirong Bao (IEEE Access, 2019)

Augmenting C. elegans Microscopic Dataset for Accelerated Pattern Recognition. - Dali Wang; Zheng Lu; Zhirong Bao (CoRR, 2019)

Hierarchical deep reinforcement learning reveals a modular mechanism of cell movement. - Zi Wang 002; Yichi Xu; Dali Wang; Jiawei Yang; Zhirong Bao (Nat. Mach. Intell., 2022)