VisFeature: a stand-alone program for visualizing and analyzing statistical features of biological sequences. - Jun Wang 081; Pu-Feng Du; Xin-Yu Xue; Guang-Ping Li 005; Yuan-Ke Zhou; Wei Zhao; Hao Lin 001; Wei Chen 064 (Bioinform., 2020)

NPI-GNN: Predicting ncRNA-protein interactions with deep graph neural networks. - Zi-Ang Shen; Tao Luo; Yuan-Ke Zhou; Han Yu; Pu-Feng Du (Briefings Bioinform., 2021)

KNIndex: a comprehensive database of physicochemical properties for k-tuple nucleotides. - Wen-Ya Zhang; Junhai Xu; Jun Wang 081; Yuan-Ke Zhou; Wei Chen 064; Pu-Feng Du (Briefings Bioinform., 2021)

Predicting protein subchloroplast locations: the 10th anniversary. - Jian Sun; Pu-Feng Du (Frontiers Comput. Sci., 2021)

NPI-RGCNAE. - Han Yu; Zi-Ang Shen; Pu-Feng Du (IEEE DataPort, 2021)

NPI-RGCNAE: Fast Predicting ncRNA-Protein Interactions Using the Relational Graph Convolutional Network Auto-Encoder. - Han Yu; Zi-Ang Shen; Pu-Feng Du (IEEE J. Biomed. Health Informatics, 2022)

iEssLnc: quantitative estimation of lncRNA gene essentialities with meta-path-guided random walks on the lncRNA-protein interaction network. - Ying-Ying Zhang; De-Min Liang; Pu-Feng Du (Briefings Bioinform., 2023)

PLA-GNN: Computational inference of protein subcellular location alterations under drug treatments with deep graph neural networks. - Ren-Hua Wang; Tao Luo; Han-Lin Zhang; Pu-Feng Du (Comput. Biol. Medicine, 2023)

SilenceREIN: seeking silencers on anchors of chromatin loops by deep graph neural networks. - Jian-Hua Pan; Pu-Feng Du (Briefings Bioinform., 2024)

Vislocas: Vision transformers for identifying protein subcellular mis-localization signatures of different cancer subtypes from immunohistochemistry images. - Jing-Wen Wen; Han-Lin Zhang; Pu-Feng Du (Comput. Biol. Medicine, 2024)

scMUG: deep clustering analysis of single-cell RNA-seq data on multiple gene functional modules. - De-Min Liang; Pu-Feng Du (Briefings Bioinform., 2025)