PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data. - Lu Zhang 061; Jing Zhang; Jing Yang; Dingge Ying; Yu-Lung Lau; Wanling Yang (Bioinform., 2013)

Reconstructing directed gene regulatory network by only gene expression data. - Lu Zhang 061; Yen Kaow Ng; Shuaicheng Li 001 (BIBM, 2015)

More accurate models for detecting gene-gene interactions from public expression compendia. - Lu Zhang 061; Jiaxing Chen; Shuai Cheng Li 001 (BIBM, 2016)

An ensemble deep learning framework to refine large deletions in linked-reads. - Yunfei Hu; V. Mangal Sanidhya; Lu Zhang 061; Zhou Xin (BIBM, 2021)

DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data. - Jiaxing Chen; Chinwang Cheong; Liang Lan; Xin Zhou; Jiming Liu 001; Aiping Lyu; William K. Cheung 001; Lu Zhang 061 (Briefings Bioinform., 2021)

METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs. - Zhenmiao Zhang; Lu Zhang 061 (BMC Bioinform., 2021)

A machine learning model for disease risk prediction by integrating genetic and non-genetic factors. - Yu Xu; Chonghao Wang; Zeming Li; Yunpeng Cai; Ouzhou Young; Aiping Lyu; Lu Zhang 061 (BIBM, 2022)

dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data. - Yu Xu; Jiaxing Chen; Aiping Lyu; William K. Cheung 001; Lu Zhang 061 (Briefings Bioinform., 2022)

A comprehensive investigation of statistical and machine learning approaches for predicting complex human diseases on genomic variants. - Chonghao Wang; Jing Zhang; Werner Pieter Veldsman; Xin Zhou; Lu Zhang 061 (Briefings Bioinform., 2023)

Benchmarking genome assembly methods on metagenomic sequencing data. - Zhenmiao Zhang; Chao Yang; Werner Pieter Veldsman; Xiaodong Fang; Lu Zhang 061 (Briefings Bioinform., 2023)

Accurate and interpretable gene expression imputation on scRNA-seq data using IGSimpute. - Ke Xu; Chinwang Cheong; Werner Pieter Veldsman; Aiping Lyu; William K. Cheung 001; Lu Zhang 061 (Briefings Bioinform., 2023)

Benchmarking multi-platform sequencing technologies for human genome assembly. - Jingjing Wang; Werner Pieter Veldsman; Xiaodong Fang; Yufen Huang; Xuefeng Xie; Aiping Lyu; Lu Zhang 061 (Briefings Bioinform., 2023)

Med-PRSIMD: Enhanced Complex Disease Risk Prediction through Integrative Analysis of Multi-Type Data and Medical History Records. - Zeming Li; Yu Xu; Debajyoti Chowdhury; Hip Fung Yip; Chonghao Wang; Lu Zhang 061 (BCB, 2024)

Integrated analysis of gut microbiome compositional and genomic alterations reveals strain diversity and actionable biomarkers across multiple colorectal cancer cohorts. - Chao Yang; Jingjing Wang; Lu Zhang 061 (BCB, 2024)

A multi-modal deep language model for contaminant removal from metagenome-assembled genomes. - Bohao Zou; Jingjing Wang; Yi Ding; Zhenmiao Zhang; Yufen Huang; Xiaodong Fang; Ka Chun Cheung; Simon See; Lu Zhang 061 (Nat. Mac. Intell., 2024)

RAPID: Reliable and efficient Automatic generation of submission rePortIng checklists with large language moDels. - Zeming Li; Xufei Luo; Zhenhua Yang; Huayu Zhang; Bingyi Wang; Long Ge; Zhaoxiang Bian; James Zou; Yaolong Chen; Lu Zhang 061; Ye Wang; Haodong Li; et al. (J. Am. Medical Informatics Assoc., 2025)