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Biorxiv : 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 ChengBMC Genomics|November 9, 2016
Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealingBadri Adhikari, Tuan Trieu, Jianlin ChengBiorxiv : the Preprint Server for Biology|February 20, 2025
Estimating Protein Complex Model Accuracy Using Graph Transformers and Pairwise Similarity GraphsJian Liu, Pawan Neupane, Jianlin ChengBiorxiv : the Preprint Server for Biology|January 27, 2025
Accurate Prediction of Protein Complex Stoichiometry by Integrating AlphaFold3 and Template InformationJian Liu, Pawan Neupane, Jianlin ChengMethods in Molecular Biology (Clifton, N.J.)|November 22, 2024
Improving Protein Secondary Structure Prediction by Deep Language Models and Transformer NetworksTianqi Wu, Weihang Cheng, Jianlin ChengBiorxiv : the Preprint Server for Biology|September 24, 2024
CryoTEN: Efficiently Enhancing Cryo-EM Density Maps Using TransformersJoel Selvaraj, Liguo Wang, Jianlin ChengPageof 56