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Plos Biology|July 29, 2024
FURNA: A database for functional annotations of RNA structuresChengxin Zhang, Lydia FreddolinoBriefings in Bioinformatics|July 22, 2024
A large-scale assessment of sequence database search tools for homology-based protein function predictionChengxin Zhang, Lydia FreddolinoBiorxiv : the Preprint Server for Biology|January 8, 2024
FURNA: a database for function annotations of RNA structuresChengxin Zhang, P Lydia FreddolinoBiorxiv : the Preprint Server for Biology|November 28, 2023
A large-scale assessment of sequence database search tools for homology-based protein function predictionChengxin Zhang, P Lydia FreddolinoBiorxiv : the Preprint Server for Biology|August 12, 2025
EZpred: improving deep learning-based enzyme function prediction using unlabeled sequence homologsChengxin Zhang, Quancheng Liu, Lydia FreddolinoBioinformatics (Oxford, England)|November 5, 2024
InterLabelGO+: unraveling label correlations in protein function predictionQuancheng Liu, Chengxin Zhang, Lydia FreddolinoMethods in Molecular Biology (Clifton, N.J.)|July 2, 2025
Using InterLabelGO+ for Accurate Protein Language Model-Based Function PredictionChengxin Zhang, Quancheng Liu, Lydia FreddolinoNucleic Acids Research|May 5, 2017
COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction informationChengxin Zhang, Lydia Freddolino, Yang ZhangNature Protocols|July 3, 2025
A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-alignChengxin Zhang, Lydia Freddolino, Yang ZhangGenomics, Proteomics & Bioinformatics|April 6, 2026
StarFunc: Fusing Template-based and Deep Learning Approaches for Accurate Protein Function PredictionChengxin Zhang, Quancheng Liu, Lydia FreddolinoPageof 26