GPTCelltype: Hou, W., Ji, Z.*(2023). Reference-free and cost-effective automated cell type annotation with GPT-4 in single-cell RNA-seq analysis. bioRxiv. PMID/PMCID to be announced.

Paella: Hou, W., Ji, Z.*(2022). Decomposing spatial heterogeneity of cell development trajectories with Paella. bioRxiv. PMID/PMCID to be announced.

Palo: Hou, W., Ji, Z.*(2022). Spatially-aware color palette optimization for single-cell and spatial data. Bioinformatics, June 01, 2022. PMID: 35642896.

scubi: Hou, W., Ji, Z. (2022). Single-cell Unbiased Visualization with SCUBI. Cell Reports Methods, 100135, 2022. PMID: 35224531. PMCID: PMC8871596.

Lamian: Hou, W., Ji, Z., Chen, Z., Wherry, E.J., Hicks, S.C.*, and Ji, H.*, (2021) A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples. Preprint in bioRxiv. PMID: 34282418. PMCID: PMC8288148

SCATE, SCATEData: Ji, Z., Zhou, W., Hou, W. and Ji, H.*, (2020). SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement. Genome Biology, 21,161 (2020). PMID: 32620137. PMCID: PMC7333383.