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)

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)

Bayesian peptide peak detection for high resolution TOF mass spectrometry. - Jianqiu Zhang 002; Xiaobo Zhou 001; Honghui Wang; Anthony Suffredini; Lin Zhang 015; Yufei Huang 001; Stephen T. C. Wong (IEEE Trans. Signal Process., 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)

trumpet: transcriptome-guided quality assessment of m6A-seq data. - Teng Zhang; Shao-Wu Zhang 001; Lin Zhang 015; Jia Meng 001 (BMC Bioinform., 2018)

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)

MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data. - Xiaodong Cui; Lin Zhang 015; Jia Meng 001; Manjeet K. Rao; Yidong Chen 002; Yufei Huang 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 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)

Development of an Open-Access and Explainable Machine Learning Prediction System to Assess the Mortality and Recurrence Risk Factors of Clostridioides Difficile Infection Patients. - Yui-Lun Ng; Michelle C. K. Lo; Kit-Hang Lee; Xiaochen Xie; Thomas N. Y. Kwong; Margaret Ip; Lin Zhang 015; Jun Yu 009; Joseph J. Y. Sung; William Ka Kei Wu; Sunny Hei Wong; Ka-Wai Kwok (Adv. Intell. Syst., 2021)

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)

Multi-omic analysis suggests tumor suppressor genes evolved specific promoter features to optimize cancer resistance. - Dan Huang; Xiansong Wang; Yingzhi Liu; Ziheng Huang; Xiaoxu Hu; Wei Hu; Qing Li; Hung Chan; Yidan Zou; Idy H. T. Ho; Yan Wang; Alfred S. L. Cheng; et al. (Briefings Bioinform., 2021)

Bioinformatic analysis of SMN1-ACE/ACE2 interactions hinted at a potential protective effect of spinal muscular atrophy against COVID-19-induced lung injury. - Zheng Li; Xingye Li; Jianxiong Shen; Haining Tan; Tianhua Rong; Youxi Lin; Erwei Feng; Zhengguang Chen; Yang Jiao; Gang Liu; Lin Zhang 015; Matthew Tak Vai Chan; 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)

Pedestrian Detection with Multi-View Convolution Fusion Algorithm. - Yuhong Liu; Chunyan Han; Lin Zhang 015; Xin Gao 001 (Entropy, 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)

BDBB: A Novel Beta-Distribution-Based Biclustering Algorithm for Revealing Local Co-Methylation Patterns in Epi-Transcriptome Profiling Data. - Zhaoyang Liu 002; Yuteng Xiao; Hongsheng Yin 001; Xiaodan Li; Shutao Chen; Kaijian Xia; Lin Zhang 015 (IEEE J. Biomed. Health Informatics, 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)

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)

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)

MSCAN: multi-scale self- and cross-attention network for RNA methylation site prediction. - Honglei Wang; Tao Huang; Dong Wang; Wenliang Zeng; Yanjing Sun; Lin Zhang 015 (BMC Bioinform., 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)