hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. - Li Chen 029; George Wu; Hongkai Ji (Bioinform., 2011)

glmgraph: an R package for variable selection and predictive modeling of structured genomic data. - Li Chen 029; Han Liu 001; Jean-Pierre A. Kocher; Hongzhe Li; Jun Chen (Bioinform., 2015)

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets. - Li Chen 029; Chi Wang 003; Zhaohui S. Qin; Hao Wu 003 (Bioinform., 2015)

traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals. - Li Chen 029; Zhaohui S. Qin (Bioinform., 2016)

Omicseq: a web-based search engine for exploring omics datasets. - Xiaobo Sun; William S. Pittard; Tianlei Xu; Li Chen 029; Michael E. Zwick; Xiaoqian Jiang; Fusheng Wang 001; Zhaohui S. Qin (Nucleic Acids Res., 2017)

TIVAN: tissue-specific cis-eQTL single nucleotide variant annotation and prediction. - Li Chen 029; Ye Wang 024; Bing Yao; Amit Mitra; Xu Wang 026; Xiao Qin 001 (Bioinform., 2019)

Destin: toolkit for single-cell analysis of chromatin accessibility. - Eugene Urrutia; Li Chen 029; Haibo Zhou; Yuchao Jiang (Bioinform., 2019)

powmic: an R package for power assessment in microbiome case-control studies. - Li Chen 029 (Bioinform., 2020)

circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs. - Li Chen 029; Feng Wang; Emily C. Bruggeman; Chao Li; Bing Yao (Bioinform., 2020)

Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules. - Guodong Yang; Aiqun Ma; Zhaohui S. Qin; Li Chen 029 (Bioinform., 2020)

Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines. - Wenwen Mei; Zhiwen Jiang; Yang Chen 063; Li Chen 029; Aziz Sancar; Yuchao Jiang (Briefings Bioinform., 2021)

A novel deep learning method for predictive modeling of microbiome data. - Ye Wang 024; Tathagata Bhattacharya; Yuchao Jiang; Xiao Qin 001; Yue Wang; Yunlong Liu; Andrew J. Saykin; Li Chen 029 (Briefings Bioinform., 2021)

WEVar: a novel statistical learning framework for predicting noncoding regulatory variants. - Ye Wang 024; Yuchao Jiang; Bing Yao; Kun Huang; Yunlong Liu; Yue Wang; Xiao Qin 001; Andrew J. Saykin; Li Chen 029 (Briefings Bioinform., 2021)

Exploiting deep transfer learning for the prediction of functional non-coding variants using genomic sequence. - Li Chen 029; Ye Wang 024; Fengdi Zhao (Bioinform., 2022)

DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome. - Ye Wang 024; Li Chen 029 (Bioinform., 2022)

DeepPHiC: predicting promoter-centered chromatin interactions using a novel deep learning approach. - Aman Agarwal; Li Chen 029 (Bioinform., 2023)

TIVAN-indel: a computational framework for annotating and predicting non-coding regulatory small insertions and deletions. - Aman Agarwal; Fengdi Zhao; Yuchao Jiang; Li Chen 029 (Bioinform., 2023)

A novel Bayesian hierarchical model for detecting differential circadian pattern in transcriptomic applications. - Yutao Zhang; Haocheng Ding; Zhiguang Huo; Li Chen 029 (Briefings Bioinform., 2024)

scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data. - Fengdi Zhao; Xin Ma; Bing Yao; Qing Lu; Li Chen 029 (PLoS Comput. Biol., 2024)