Li Chen

24 papers Journal 24
YearRankTypeTitle / Venue / Authors
2025 J jnl
A Bayesian framework for genome-wide circadian rhythmicity biomarker detection.
Briefings Bioinform.
Haocheng Ding, Lingsong Meng, Yutao Zhang, Andrew J. Bryant, Chengguo Xing, Karyn A. Esser, Li Chen, Yitong Feng, Zhiguang Huo
2025 J jnl
A novel Bayesian hierarchical model for detecting differential circadian pattern in transcriptomic applications.
Briefings Bioinform.
Yutao Zhang, Haocheng Ding, Zhiguang Huo, Li Chen
2024 J jnl
AIGen: an artificial intelligence software for complex genetic data analysis.
Briefings Bioinform.
Tingting Hou, Xiaoxi Shen, Shan Zhang, Muxuan Liang, Li Chen, Qing Lu
2024 J jnl
Deep5hmC: predicting genome-wide 5-hydroxymethylcytosine landscape via a multimodal deep learning model.
Bioinform.
Xin Ma, Sai Ritesh Thela, Fengdi Zhao, Bing Yao, Zhexing Wen, Peng Jin, Jinying Zhao, Li Chen
2024 J jnl
MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants.
Bioinform.
Weijia Jin, Yi Xia, Javlon Nizomov, Yunlong Liu, Zhigang Li, Qing Lu, Li Chen
2024 J jnl
Multimodal functional deep learning for multiomics data.
Briefings Bioinform.
Yuan Zhou, Pei Geng, Shan Zhang, Feifei Xiao, Guoshuai Cai, Li Chen, Qing Lu
2024 J jnl
scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data.
PLoS Comput. Biol.
Fengdi Zhao, Xin Ma, Bing Yao, Qing Lu, Li Chen
2023 J jnl
DeepPHiC: predicting promoter-centered chromatin interactions using a novel deep learning approach.
Bioinform.
Aman Agarwal, Li Chen
2023 J jnl
TIVAN-indel: a computational framework for annotating and predicting non-coding regulatory small insertions and deletions.
Bioinform.
Aman Agarwal, Fengdi Zhao, Yuchao Jiang, Li Chen
2022 J jnl
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome.
Bioinform.
Ye Wang, Li Chen
2022 J jnl
Exploiting deep transfer learning for the prediction of functional non-coding variants using genomic sequence.
Bioinform.
Li Chen, Ye Wang, Fengdi Zhao
2021 J jnl
A novel deep learning method for predictive modeling of microbiome data.
Briefings Bioinform.
Ye Wang, Tathagata Bhattacharya, Yuchao Jiang, Xiao Qin, Yue Wang, Yunlong Liu, Andrew J. Saykin, Li Chen
2021 J jnl
Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines.
Briefings Bioinform.
Wenwen Mei, Zhiwen Jiang, Yang Chen, Li Chen, Aziz Sancar, Yuchao Jiang
2021 J jnl
WEVar: a novel statistical learning framework for predicting noncoding regulatory variants.
Briefings Bioinform.
Ye Wang, Yuchao Jiang, Bing Yao, Kun Huang, Yunlong Liu, Yue Wang, Xiao Qin, Andrew J. Saykin, Li Chen
2020 J jnl
Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules.
Bioinform.
Guodong Yang, Aiqun Ma, Zhaohui S. Qin, Li Chen
2020 J jnl
circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs.
Bioinform.
Li Chen, Feng Wang, Emily C. Bruggeman, Chao Li, Bing Yao
2020 J jnl
powmic: an R package for power assessment in microbiome case-control studies.
Bioinform.
Li Chen
2019 J jnl
Destin: toolkit for single-cell analysis of chromatin accessibility.
Bioinform.
Eugene Urrutia, Li Chen, Haibo Zhou, Yuchao Jiang
2019 J jnl
TIVAN: tissue-specific cis-eQTL single nucleotide variant annotation and prediction.
Bioinform.
Li Chen, Ye Wang, Bing Yao, Amit Mitra, Xu Wang, Xiao Qin
2017 J jnl
Omicseq: a web-based search engine for exploring omics datasets.
Nucleic Acids Res.
Xiaobo Sun, William Stephen Pittard, Tianlei Xu, Li Chen, Michael E. Zwick, Xiaoqian Jiang, Fusheng Wang, Zhaohui S. Qin
2016 J jnl
traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals.
Bioinform.
Li Chen, Zhaohui S. Qin
2015 J jnl
A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.
Bioinform.
Li Chen, Chi Wang, Zhaohui S. Qin, Hao Wu
2015 J jnl
glmgraph: an R package for variable selection and predictive modeling of structured genomic data.
Bioinform.
Li Chen, Han Liu, Jean-Pierre A. Kocher, Hongzhe Li, Jun Chen
2011 J jnl
hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data.
Bioinform.
Li Chen, George Wu, Hongkai Ji