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Briefings in Functional Genomics|October 18, 2015
An overview of bioinformatics methods for modeling biological pathways in yeastJie Hou, Lipi Acharya, Dongxiao Zhu, et al.Biorxiv : the Preprint Server for Biology|November 14, 2023
CryoTransformer: A Transformer Model for Picking Protein Particles from Cryo-EM MicrographsAshwin Dhakal, Rajan Gyawali, Liguo Wang, et al.Scientific Data|June 22, 2023
A large expert-curated cryo-EM image dataset for machine learning protein particle pickingAshwin Dhakal, Rajan Gyawali, Liguo Wang, et al.Bioinformatics (Oxford, England)|November 17, 2007
TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteinsArlo Randall, Jianlin Cheng, Michael Sweredoski, et al.Methods in Molecular Biology (Clifton, N.J.)|October 28, 2016
Assessing Predicted Contacts for Building Protein Three-Dimensional ModelsBadri Adhikari, Debswapna Bhattacharya, Renzhi Cao, et al.Nature Communications|November 15, 2022
Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networksZhiye Guo, Jian Liu, Jeffrey Skolnick, et al.Biorxiv : the Preprint Server for Biology|April 1, 2025
A Labeled Dataset for AI-based Cryo-EM Map EnhancementNabin Giri, Xiao Chen, Liguo Wang, et al.Bioinformatics (Oxford, England)|September 11, 2019
Analysis of several key factors influencing deep learning-based inter-residue contact predictionTianqi Wu, Jie Hou, Badri Adhikari, et al.Proteins|February 4, 2021
Combination of deep neural network with attention mechanism enhances the explainability of protein contact predictionChen Chen, Tianqi Wu, Zhiye Guo, et al.BMC Bioinformatics|January 26, 2021
DeepDist: real-value inter-residue distance prediction with deep residual convolutional networkTianqi Wu, Zhiye Guo, Jie Hou, et al.Pageof 30