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Proteins|June 2, 2025
Improving AlphaFold2- and AlphaFold3-Based Protein Complex Structure Prediction With MULTICOM4 in CASP16Jian Liu, Pawan Neupane, Jianlin ChengScientific Data|May 6, 2024
Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein StructuresNabin Giri, Liguo Wang, Jianlin ChengBioinformatics (Oxford, England)|June 5, 2026
A unified multimodal model for generalizable zero-shot and supervised protein function predictionFrimpong Boadu, Yanli Wang, Jianlin ChengBMC Bioinformatics|February 3, 2011
DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learningJesse Eickholt, Xin Deng, Jianlin ChengJournal of Proteomics & Bioinformatics|October 31, 2017
A Template-Based Protein Structure Reconstruction Method Using Deep Autoencoder LearningHaiou Li, Qiang Lyu, Jianlin ChengBiological Procedures Online|May 4, 2019
An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C DataOluwatosin Oluwadare, Max Highsmith, Jianlin ChengBMC Bioinformatics|December 23, 2009
PreDisorder: ab initio sequence-based prediction of protein disordered regionsXin Deng, Jesse Eickholt, Jianlin ChengIEEE/ACM Transactions on Computational Biology and Bioinformatics|March 10, 2015
A Deep Learning Network Approach to ab initio Protein Secondary Structure PredictionMatt Spencer, Jesse Eickholt, Jianlin ChengBioinformatics (Oxford, England)|May 5, 2023
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformerTianqi Wu, Zhiye Guo, Jianlin ChengMethods in Molecular Biology (Clifton, N.J.)|July 2, 2025
TransFun: A Tool of Integrating Large Language Models, Transformers, and Equivariant Graph Neural Networks to Predict Protein FunctionFrimpong Boadu, Ahhyun Lee, Jianlin ChengPageof 56