A comprehensive study of a SVM-based miRNA target prediction algorithm. - Hui Liu 024; Dong Yue 002; Yidong Chen 002; Yufei Huang 001 (GENSiPS, 2009)

A Bayesian Approach for Identifying miRNA Targets by Combining Sequence Prediction and Expression Profiling. - Hui Liu 024; Lin Zhang 015; Shou-Jiang Gao; Yufei Huang 001 (IJCBS, 2009)

A Bayesian decision fusion approach for microRNA target prediction. - Dong Yue 002; Hui Liu 024; Mingzhu Lu; Philip Chen 001; Yidong Chen 002; Yufei Huang 001 (BCB, 2010)

SysMicrO: A Novel Systems Approach for miRNA Target Prediction. - Hui Liu 024; Lin Zhang 015; Qilong Sun; Yidong Chen 002; Yufei Huang 001 (ICIC (2), 2010)

miRNA Target Prediction Method Based on the Combination of Multiple Algorithms. - Lin Zhang 015; Hui Liu 024; Dong Yue 002; Hui He; Yufei Huang 001 (ICIC (1), 2010)

Improving performance of mammalian microRNA target prediction. - Hui Liu 024; Dong Yue 002; Yidong Chen 002; Shou-Jiang Gao; Yufei Huang 001 (BMC Bioinform., 2010)

Clustering DNA methylation expressions using nonparametric beta mixture model. - Lin Zhang 015; Jia Meng 001; Hui Liu 024; Yufei Huang 001 (GENSiPS, 2011)

An investigation of clinical outcome prediction from integrative genomic profiles in ovarian cancer. - Lin Zhang 015; Hui Liu 024; Tzu-Hung Hsiao; Yidong Chen 002; Yufei Huang 001 (GENSiPS, 2012)

Unveiling the dynamics in RNA epigenetic regulations. - Jia Meng 001; Xiaodong Cui; Hui Liu 024; Lin Zhang 015; Shaowu Zhang 001; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (BIBM, 2013)

Integration of gene expression, genome wide DNA methylation, and gene networks for clinical outcome prediction in ovarian cancer. - Lin Zhang 015; Hui Liu 024; Jia Meng 001; Xuesong Wang 001; Yidong Chen 002; Yufei Huang 001 (BIBM, 2013)

Detecting differentially methylated mRNA from MeRIP-Seq with likelihood ratio test. - Lin Zhang 015; Jia Meng 001; Hui Liu 024; Xiaodong Cui; Shao-Wu Zhang 001; Yidong Chen 002; Yufei Huang 001 (GlobalSIP, 2014)

Differential analysis of RNA methylome with improved spatial resolution. - Yu-Chen Zhang; Shao-Wu Zhang 001; Lian Liu; Lin Zhang 015; Hui Liu 024; Xiaodong Cui; Yufei Huang 001; Jia Meng 001 (GlobalSIP, 2014)

Sketching the distribution of transcriptomic features on RNA transcripts with Travis coordinates. - Xiaodong Cui; Zhen Wei; Lin Zhang 015; Hui Liu 024; Lei Sun; Shaowu Zhang 001; Yufei Huang 001; Jia Meng 001 (BIBM, 2015)

MeT-DB: a database of transcriptome methylation in mammalian cells. - Hui Liu 024; Mario A. Flores; Jia Meng 001; Lin Zhang 015; Xinyu Zhao; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (Nucleic Acids Res., 2015)

Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net. - Lin Zhang 015; Hui Liu 024; Yufei Huang 001; Xuesong Wang 001; Yidong Chen 002; Jia Meng 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome. - Hui Liu 024; Huaizhi Wang; Zhen Wei; Songyao Zhang; Gang Hua 002; Shao-Wu Zhang 001; Lin Zhang 015; Shou-Jiang Gao; Jia Meng 001; Xing Chen 001; Yufei Huang 001 (Nucleic Acids Res., 2018)

RNA methylation and diseases: experimental results, databases, Web servers and computational models. - Xing Chen 001; Ya-Zhou Sun; Hui Liu 024; Lin Zhang 015; Jian-Qiang Li 001; Jia Meng 001 (Briefings Bioinform., 2019)

m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network. - Xiangyu Wu; Zhen Wei; Kunqi Chen; Qing Zhang; Jionglong Su; Hui Liu 024; Lin Zhang 015; Jia Meng 001 (BMC Bioinform., 2019)

REW-ISA: unveiling local functional blocks in epi-transcriptome profiling data via an RNA expression-weighted iterative signature algorithm. - Lin Zhang 015; Shutao Chen; Jingyi Zhu; Jia Meng 001; Hui Liu 024 (BMC Bioinform., 2020)

Lysosome activation in peripheral blood mononuclear cells and prognostic significance of circulating LC3B in COVID-19. - Shisong Fang; Lin Zhang 015; Yingzhi Liu; Wenye Xu; Weihua Wu; Ziheng Huang; Xin Wang; Hui Liu 024; Ying Sun; Renli Zhang; Bo Peng; Xiaodong Liu; et al. (Briefings Bioinform., 2021)

m7GDisAI: N7-methylguanosine (m7G) sites and diseases associations inference based on heterogeneous network. - Jiani Ma; Lin Zhang 015; Jin Chen; Bowen Song; Chenxuan Zang; Hui Liu 024 (BMC Bioinform., 2021)

EDLm6APred: ensemble deep learning approach for mRNA m6A site prediction. - Lin Zhang 015; Gangshen Li; Xiuyu Li; Honglei Wang; Shutao Chen; Hui Liu 024 (BMC Bioinform., 2021)

ARMS Net: Overlapping chromosome segmentation based on Adaptive Receptive field Multi-Scale network. - Guangjie Wang; Hui Liu 024; Xianpeng Yi; Jinjun Zhou; Lin Zhang 015 (Biomed. Signal Process. Control., 2021)

LRTCLS: low-rank tensor completion with Laplacian smoothing regularization for unveiling the post-transcriptional machinery of N6-methylation (m6A)-mediated diseases. - Jiani Ma; Hui Liu 024; Yumeng Mao; Lin Zhang 015 (Briefings Bioinform., 2022)

EMDLP: Ensemble multiscale deep learning model for RNA methylation site prediction. - Honglei Wang; Hui Liu 024; Tao Huang; Gangshen Li; Lin Zhang 015; Yanjing Sun (BMC Bioinform., 2022)

FBCwPlaid: A Functional Biclustering Analysis of Epi-Transcriptome Profiling Data Via a Weighted Plaid Model. - Shutao Chen; Lin Zhang 015; Lin Lu; Jia Meng 001; Hui Liu 024 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

BRPCA: Bounded Robust Principal Component Analysis to Incorporate Similarity Network for N7-Methylguanosine(m7G) Site-Disease Association Prediction. - Jiani Ma; Lin Zhang 015; Shaojie Li; Hui Liu 024 (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

FGFICA: Independent Component Analysis of Fusion Genomic Features for Mining Epi-Transcriptome Profiling Data. - Shutao Chen; Lin Zhang 015; Xiangzhi Chen 003; Hui Liu 024 (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Surrogate Sample-Assisted Particle Swarm Optimization for Feature Selection on High-Dimensional Data. - Xianfang Song; Yong Zhang 016; Dunwei Gong; Hui Liu 024; Wanqiu Zhang (IEEE Trans. Evol. Comput., 2023)

MULGA, a unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning. - Jiani Ma; Chen Li 021; Yiwen Zhang; Zhikang Wang; Shanshan Li; Yuming Guo 001; Lin Zhang 015; Hui Liu 024; Xin Gao 001; Jiangning Song (Bioinform., 2023)

scDBImpute: Dual-branch imputation for single-cell RNA-seq data dropouts. - Lin Zhang 015; Feng Wang 064; Jiani Ma; Hui Liu 024 (BCB, 2024)

'Bingo' - a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data. - Jiani Ma; Jiangning Song; Neil D. Young; Bill C. H. Chang; Pasi K. Korhonen; Tulio L. Campos; Hui Liu 024; Robin B. Gasser (Briefings Bioinform., 2024)

DaCSeg: Divide and conquer for accurate overlapping chromosome instance segmentation in metaphase cell images. - Xinyu Fan; Hui Liu 024; Hongdang Zheng; Jingfang Zhai; Lin Zhang 015 (Biomed. Signal Process. Control., 2024)

DBDNMF: A Dual Branch Deep Neural Matrix Factorization method for drug response prediction. - Hui Liu 024; Feng Wang 064; Jian Yu; Yong Pan; Chaoju Gong; Liang Zhang; Lin Zhang 015 (PLoS Comput. Biol., 2024)

pMHChat, characterizing the interactions between major histocompatibility complex class II molecules and peptides with large language models and deep hypergraph learning. - Jiani Ma; Zhikang Wang; Cen Tong; Qi Yang; Lin Zhang 015; Hui Liu 024 (Briefings Bioinform., 2025)

FDDSeg: Unleashing the Power of Scribble Annotation for Cardiac MRI Images Through Feature Decomposition Distillation. - Lin Zhang 015; Wenzong Li; Kaiyue Bi; Pei Li; Liang Zhang; Hui Liu 024 (IEEE J. Biomed. Health Informatics, 2025)

MPGLNet: Multi-scale progressive global-local fusion dental point cloud complementation network. - Lin Zhang 015; Hongfei Zhang; Fucheng Niu; Zekuan Yu; Zhongwei Zhou; Hui Liu 024 (Biomed. Signal Process. Control., 2026)