- Jing Yang and Hong-Bin Shen, MemBrain-contact 2.0: A new two-stage deep learning model for the prediction enhancement of transmembrane protein residue contacts in the full chain, Submitted, 2017.
- Feng Xiao and Hong-Bin Shen, Prediction enhancement of residue real-value relative accessible surface area in transmembrane helical proteins by solving the output preference problem of machine learning-based predictors, Journal of Chemical Information and Modeling, 2015, 55: 2464-2474.
- Jing Yang, Richard Jang, Yang Zhang, and Hong-Bin Shen, High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling, Bioinformatics, 2013, 29: 2579-2587.
- Hongbin Shen, James J. Chou, MemBrain: Improving the Accuracy of Predicting Transmembrane Helices, PLoS ONE, 2008, 6: e2399.
- Hong-Bin Shen, Kuo-Chen Chou, Signal-3L: a 3-layer approach for predicting signal peptides, Biochemical and Biophysical Research Communications, 2007, 363: 297-303.