LSCplus: a fast solution for improving long read accuracy by short read alignment. - Ruifeng Hu 002; Guibo Sun; Xiaobo Sun (BMC Bioinform., 2016)

lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics. - Ruifeng Hu 002; Xiaobo Sun (J. Bioinform. Comput. Biol., 2016)

ANCO-GeneDB: annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence. - Ruifeng Hu 002; Yulin Dai; Peilin Jia; Zhongming Zhao (Database J. Biol. Databases Curation, 2018)

6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes. - Hao-Dong Xu; Ruifeng Hu 002; Peilin Jia; Zhongming Zhao (Bioinform., 2020)

TSEA-DB: a trait?tissue association map for human complex traits and diseases. - Peilin Jia; Yulin Dai; Ruifeng Hu 002; Guangsheng Pei; Astrid Marilyn Manuel; Zhongming Zhao (Nucleic Acids Res., 2020)

VISDB: a manually curated database of viral integration sites in the human genome. - Deyou Tang; Bingrui Li; Tianyi Xu; Ruifeng Hu 002; Daqiang Tan; Xiaofeng Song; Peilin Jia; Zhongming Zhao (Nucleic Acids Res., 2020)

KinaseMD: kinase mutations and drug response database. - Ruifeng Hu 002; Hao-Dong Xu; Peilin Jia; Zhongming Zhao (Nucleic Acids Res., 2021)

CSEA-DB: an omnibus for human complex trait and cell type associations. - Yulin Dai; Ruifeng Hu 002; Astrid Marilyn Manuel; Andi Liu; Peilin Jia; Zhongming Zhao (Nucleic Acids Res., 2021)

DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner. - Guangsheng Pei; Ruifeng Hu 002; Peilin Jia; Zhongming Zhao (Nucleic Acids Res., 2021)

WebCSEA: web-based cell-type-specific enrichment analysis of genes. - Yulin Dai; Ruifeng Hu 002; Andi Liu; Kyung Serk Cho; Astrid Marilyn Manuel; Xiaoyang Li; Xianjun Dong; Peilin Jia; Zhongming Zhao (Nucleic Acids Res., 2022)

A Framework for Detecting Thyroid Cancer from Ultrasound and Histopathological Images Using Deep Learning, Meta-Heuristics, and MCDM Algorithms. - Rohit Sharma; Gautam Kumar Mahanti; Ganapati Panda; Adyasha Rath; Sujata Dash; Saurav Mallik; Ruifeng Hu 002 (J. Imaging, 2023)

Benchmark of embedding-based methods for accurate and transferable prediction of drug response. - Peilin Jia; Ruifeng Hu 002; Zhongming Zhao (Briefings Bioinform., 2023)

MetaDegron: multimodal feature-integrated protein language model for predicting E3 ligase targeted degrons. - Mengqiu Zheng; Shaofeng Lin; Kunqi Chen; Ruifeng Hu 002; Liming Wang; Zhongming Zhao; Haodong Xu (Briefings Bioinform., 2024)