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Biological 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 ChengBiorxiv : the Preprint Server for Biology|March 31, 2025
Improving AlphaFold2 and 3-based protein complex structure prediction with MULTICOM4 in CASP16Jian Liu, Pawan Neupane, Jianlin ChengCommunications Chemistry|November 1, 2025
Multimodal deep learning integration of cryo-EM and AlphaFold3 for high-accuracy protein structure determinationRajan Gyawali, Ashwin Dhakal, Jianlin ChengBioinformatics Advances|August 13, 2025
Estimating protein complex model accuracy using graph transformers and pairwise similarity graphsJian Liu, Pawan Neupane, Jianlin ChengBioinformatics (Oxford, England)|October 24, 2025
MPBind: a multitask protein binding site predictor using protein language models and equivariant GNNsYanli Wang, Frimpong Boadu, Jianlin ChengProteins|September 7, 2020
DNSS2: Improved ab initio protein secondary structure prediction using advanced deep learning architecturesZhiye Guo, Jie Hou, Jianlin ChengPageof 54