ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. - Jing Qin 004; Mulin Jun Li; Panwen Wang; Michael Q. Zhang; Junwen Wang (Nucleic Acids Res., 2011)

DDGni: Dynamic delay gene-network inference from high-temporal data using gapped local alignment. - Hari Krishna Yalamanchili; Bin Yan; Mulin Jun Li; Jing Qin 004; Zhongying Zhao 002; Francis Y. L. Chin; Junwen Wang (Bioinform., 2014)

PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data. - Daogang Guan; Jiaofang Shao; Zhongying Zhao 002; Panwen Wang; Jing Qin 004; Youping Deng; Kenneth R. Boheler; Junwen Wang; Bin Yan (Nucleic Acids Res., 2014)

The Current Status and Challenges in Computational Analysis of Genomic Big Data. - Yiming Qin; Hari Krishna Yalamanchili; Jing Qin 004; Bin Yan; Junwen Wang (Big Data Res., 2015)

ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks. - Panwen Wang; Jing Qin 004; Yiming Qin; Yun Zhu; Lily Yan Wang; Mulin Jun Li; Michael Q. Zhang; Junwen Wang (Nucleic Acids Res., 2015)

Applications of integrative OMICs approaches to gene regulation studies. - Jing Qin 004; Bin Yan; Yaohua Hu; Panwen Wang; Junwen Wang (Quant. Biol., 2016)

Group Sparse Optimization via lp, q Regularization. - Yaohua Hu; Chong Li 002; Kaiwen Meng; Jing Qin 004; Xiaoqi Yang 001 (J. Mach. Learn. Res., 2017)

ENPD - A Database of Eukaryotic Nucleic Acid Binding Proteins: Linking Gene Regulations to Proteins. - Ricky Wai Tak Leung; Xiaosen Jiang; Ka Hou Chu; Jing Qin 004 (Nucleic Acids Res., 2019)

Cell fate conversion prediction by group sparse optimization method utilizing single-cell and bulk OMICs data. - Jing Qin 004; Yaohua Hu; Jen-Chih Yao; Ricky Wai Tak Leung; Yongqiang Zhou; Yiming Qin; Junwen Wang (Briefings Bioinform., 2021)

CORN - Condition Orientated Regulatory Networks: bridging conditions to gene networks. - Ricky Wai Tak Leung; Xiaosen Jiang; Xueqing Zong; Yanhong Zhang; Xinlin Hu; Yaohua Hu; Jing Qin 004 (Briefings Bioinform., 2022)

A self-attention-driven deep learning framework for inference of transcriptional gene regulatory networks. - Yong Liu; Le Zhong; Bin Yan; Zhuobin Chen; Yanjia Yu; Dan Yu; Jing Qin 004; Junwen Wang (Briefings Bioinform., 2024)