Evaluation of the Image Degradation for a Typical Watermarking Algorithm in the Block-DCT Domain. - Xiaochen Bo; Lincheng Shen; Wensen Chang (ICICS, 2001)

Sign Correlation Detector for Blind Image Watermarking in the DCT Domain. - Xiaochen Bo; Lincheng Shen; Wensen Chang (IEEE Pacific Rim Conference on Multimedia, 2001)

TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA. - Xiaochen Bo; Shengqi Wang (Bioinform., 2005)

Selection of antisense oligonucleotides based on multiple predicted target mRNA structures. - Xiaochen Bo; Shaoke Lou; Daochun Sun; Wenjie Shu; Jing Yang; Shengqi Wang (BMC Bioinform., 2006)

RDMAS: a web server for RNA deleterious mutation analysis. - Wenjie Shu; Xiaochen Bo; Rujia Liu; Dongsheng Zhao; Zhiqiang Zheng 005; Shengqi Wang (BMC Bioinform., 2006)

AOBase: a database for antisense oligonucleotides selection and design. - Xiaochen Bo; Shaoke Lou; Daochun Sun; Jing Yang; Shengqi Wang (Nucleic Acids Res., 2006)

RSRE: RNA structural robustness evaluator. - Wenjie Shu; Xiaochen Bo; Zhiqiang Zheng 005; Shengqi Wang (Nucleic Acids Res., 2007)

A novel representation of RNA secondary structure based on element-contact graphs. - Wenjie Shu; Xiaochen Bo; Zhiqiang Zheng 005; Shengqi Wang (BMC Bioinform., 2008)

Optimizing Reference Gene Set for Inter-Chip Normalization Using Genetic Algorithm. - Fei Li 004; Wenjian Xu; Peng Li; Xiaochen Bo; Yuxing Peng 001 (BMEI, 2009)

Dynamic Propagation Properties of Virus-Host Protein Interaction Network. - Fei Li 004; Yuxing Peng 001; Wenjian Xu; Peng Li; Xiaochen Bo (IJCBS, 2009)

Towards a Comprehensive HBV-Human Interaction Map. - Fei Li 004; Yuxing Peng 001; Wenjian Xu; Guangchuang Yu; Peng Li; Xiaochen Bo; Shengqi Wang (IJCBS, 2009)

EvoRSR: an integrated system for exploring evolution of RNA structural robustness. - Wenjie Shu; Ming Ni; Xiaochen Bo; Zhiqiang Zheng 005; Shengqi Wang (BMC Bioinform., 2009)

PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks. - Fei Li 004; Peng Li; Wenjian Xu; Yuxing Peng 001; Xiaochen Bo; Shengqi Wang (Bioinform., 2010)

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. - Guangchuang Yu; Fei Li 004; Yide Qin; Xiaochen Bo; Yibo Wu; Shengqi Wang (Bioinform., 2010)

Topology aware functional similarity of protein interaction networks based on gene ontology. - Fei Li 004; Xiuliang Cui; Dafei Xie; Xiaochen Bo; Shengqi Wang (EMBC, 2011)

Characterization the regulation of herpesvirus miRNAs from the view of human protein interaction network. - Zhenpeng Li; Fei Li 004; Ming Ni; Peng Li; Xiaochen Bo; Shengqi Wang (BMC Syst. Biol., 2011)

Exploring the role of human miRNAs in virus-host interactions using systematic overlap analysis. - Zhenpeng Li; Xiuliang Cui; Fei Li 004; Peng Li; Ming Ni; Shengqi Wang; Xiaochen Bo (Bioinform., 2013)

Predicting drug side effects based on link prediction in bipartite network. - Yifu Luo; Qijun Liu; Wenjian Wu; Fei Li 004; Xiaochen Bo (BMEI, 2014)

ExpTreeDB: Web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO. - Ming Ni; Fuqiang Ye; Juanjuan Zhu; Zongwei Li; Shuai Yang; Bite Yang; Lu Han; Yongge Wu; Ying Chen; Fei Li 004; Shengqi Wang; Xiaochen Bo (Bioinform., 2014)

New insights into the landscape relationships of host response to bacterial pathogens. - Xiaoyao Yin; Lu Han; Hui Bai; Xiaochen Bo; Yun Bai; Cong Niu; Naiyang Guan; Zhigang Luo (IJCNN, 2015)

EHFPI: a database and analysis resource of essential host factors for pathogenic infection. - Yang Liu 273; Dafei Xie; Lu Han; Hui Bai; Fei Li 004; Shengqi Wang; Xiaochen Bo (Nucleic Acids Res., 2015)

De novo identification of replication-timing domains in the human genome by deep learning. - Feng Liu 054; Chao Ren; Hao Li 035; Pingkun Zhou; Xiaochen Bo; Wenjie Shu (Bioinform., 2016)

RevEcoR: an R package for the reverse ecology analysis of microbiomes. - Yang Cao; Yuanyuan Wang; Xiaofei Zheng; Fei Li 004; Xiaochen Bo (BMC Bioinform., 2016)

ICM: a web server for integrated clustering of multi-dimensional biomedical data. - Song He; Haochen He; Wenjian Xu; Xin Huang 005; Shuai Jiang; Fei Li 004; Fuchu He; Xiaochen Bo (Nucleic Acids Res., 2016)

Drug - target interaction prediction with a deep-learning-based model. - Lingwei Xie; Zhongnan Zhang; Song He; Xiaochen Bo; Xinyu Song 002 (BIBM, 2017)

Exploring spatially adjacent TFBS-clustered regions with Hi-C data. - Hebing Chen; Shuai Jiang; Zhuo Zhang; Hao Li 035; Yiming Lu; Xiaochen Bo (Bioinform., 2017)

BiRen: predicting enhancers with a deep-learning-based model using the DNA sequence alone. - Bite Yang; Feng Liu 054; Chao Ren; Zhangyi Ouyang; Ziwei Xie; Xiaochen Bo; Wenjie Shu (Bioinform., 2017)

NFPscanner: a webtool for knowledge-based deciphering of biomedical networks. - Wenjian Xu; Yang Cao; Ziwei Xie; Haochen He; Song He; Hao Hong; Xiaochen Bo; Fei Li 004 (BMC Bioinform., 2017)

3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes. - Yiming Lu; Cheng Quan; Hebing Chen; Xiaochen Bo; Chenggang Zhang (Nucleic Acids Res., 2017)

paraSNF: An Parallel Approach for Large-Scale Similarity Network Fusion. - Xiaolong Shen; Song He; Minquan Fang; Yuqi Wen; Xiaochen Bo; Yong Dou (ACA, 2018)

Prediction of DTIs for high-dimensional and class-imbalanced data based on CGAN. - Kang Yang; Zhongnan Zhang; Song He; Xiaochen Bo (BIBM, 2018)

DTI-RCNN: New Efficient Hybrid Neural Network Model to Predict Drug-Target Interactions. - Xiaoping Zheng; Song He; Xinyu Song 002; Zhongnan Zhang; Xiaochen Bo (ICANN (1), 2018)

Domain-Adversarial Multi-Task Framework for Novel Therapeutic Property Prediction of Compounds. - Lingwei Xie; Song He; Shu Yang; Boyuan Feng; Kun Wan 001; Zhongnan Zhang; Xiaochen Bo; Yufei Ding 001 (CoRR, 2018)

Deep Learning and Its Applications in Biomedicine. - Chensi Cao; Feng Liu 054; Hai Tan; Deshou Song; Wenjie Shu; Weizhong Li 001; Yiming Zhou; Xiaochen Bo; Zhi Xie (Genom. Proteom. Bioinform., 2018)

A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data. - Zhuo Zhang; Hao Li 035; Shuai Jiang; Ruijiang Li; Wanying Li; Hebing Chen; Xiaochen Bo (Briefings Bioinform., 2019)

LIVE: a manually curated encyclopedia of experimentally validated interactions of lncRNAs. - Gaole An; Jiaqi Sun; Chao Ren; Zhangyi Ouyang; Lingyun Zhu; Xiaochen Bo; Shaoliang Peng; Wenjie Shu (Database J. Biol. Databases Curation, 2019)

Stable H3K4me3 is associated with transcription initiation during early embryo development. - Xin Huang 005; Xudong Gao; Wanying Li; Shuai Jiang; Ruijiang Li; Hao Hong; Chenghui Zhao; Pingkun Zhou; Hebing Chen; Xiaochen Bo; Hao Li 035 (Bioinform., 2019)

DTIGCCN: Prediction of drug-target interactions based on GCN and CNN. - Kanghao Shao; Zhongnan Zhang; Song He; Xiaochen Bo (ICTAI, 2020)

New insights on human essential genes based on integrated analysis and the construction of the HEGIAP web-based platform. - Hebing Chen; Zhuo Zhang; Shuai Jiang; Ruijiang Li; Wanying Li; Chenghui Zhao; Hao Hong; Xin Huang 005; Hao Li 035; Xiaochen Bo (Briefings Bioinform., 2020)

Domain-adversarial multi-task framework for novel therapeutic property prediction of compounds. - Lingwei Xie; Song He; Zhongnan Zhang; Kunhui Lin; Xiaochen Bo; Shu Yang; Boyuan Feng; Kun Wan 001; Kang Yang; Jie Yang; Yufei Ding 001 (Bioinform., 2020)

PIMD: An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion. - Song He; Yuqi Wen; Xiaoxi Yang; Zhen Liu 017; Xinyu Song 002; Xin Huang 005; Xiaochen Bo (Genom. Proteom. Bioinform., 2020)

DeepHiC: A generative adversarial network for enhancing Hi-C data resolution. - Hao Hong; Shuai Jiang; Hao Li 035; Guifang Du; Yu Sun; Huan Tao; Cheng Quan; Chenghui Zhao; Ruijiang Li; Wanying Li; Xiaoyao Yin; Yangchen Huang; et al. (PLoS Comput. Biol., 2020)

Drug-target interaction prediction based on nonnegative and self-representative matrix factorization. - Yihua Ye; Yuxin Chen; Zhongnan Zhang; Yuqi Wen; Song He; Xiaochen Bo (BIBM, 2021)

A Metagraph-Based Model for Predicting Drug-Target Interaction on Heterogeneous Network. - Peng Ke; Yuqi Wen; Zhongnan Zhang; Song He; Xiaochen Bo (ICANN (1), 2021)

Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains. - Shuai Jiang; Hao Li 035; Hao Hong; Guifang Du; Xin Huang 005; Yu Sun; Junting Wang 003; Huan Tao; Kang Xu; Cheng Li; Yang Chen; Hebing Chen; et al. (Briefings Bioinform., 2021)

Multi-dimensional data integration algorithm based on random walk with restart. - Yuqi Wen; Xinyu Song 002; Bowei Yan; Xiaoxi Yang; Lianlian Wu; Dongjin Leng; Song He; Xiaochen Bo (BMC Bioinform., 2021)

Synthetic Lethal Interactions Prediction Based on Multiple Similarity Measures Fusion. - Lianlian Wu; Yuqi Wen; Xiaoxi Yang; Bowei Yan; Song He; Xiaochen Bo (J. Comput. Sci. Technol., 2021)

COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data. - Song He; Xinyu Song 002; Xiaoxi Yang; Jijun Yu; Yuqi Wen; Lianlian Wu; Bowei Yan; Jiannan Feng; Xiaochen Bo (PLoS Comput. Biol., 2021)

NegStacking: Drug-Target Interaction Prediction Based on Ensemble Learning and Logistic Regression. - Jie Yang; Song He; Zhongnan Zhang; Xiaochen Bo (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

A Multi-View Learning-Based Rule Extraction Algorithm For Accurate Hepatotoxicity Prediction. - Yuting Zhong; Bowei Yan; KunHong Liu 001; Yong Xu 009; Song He; Xiaochen Bo (BIBM, 2022)

An enhanced cascade-based deep forest model for drug combination prediction. - Weiping Lin; Lianlian Wu; Yixin Zhang; Yuqi Wen; Bowei Yan; Chong Dai; Kun-Hong Liu 001; Song He; Xiaochen Bo (Briefings Bioinform., 2022)

DTI-HETA: prediction of drug-target interactions based on GCN and GAT on heterogeneous graph. - Kanghao Shao; Yunhao Zhang; Yuqi Wen; Zhongnan Zhang; Song He; Xiaochen Bo (Briefings Bioinform., 2022)

Computational methods, databases and tools for synthetic lethality prediction. - Jing Wang; Qinglong Zhang; Junshan Han; Yanpeng Zhao; Caiyun Zhao; Bowei Yan; Chong Dai; Lianlian Wu; Yuqi Wen; Yixin Zhang; Dongjin Leng; Zhongming Wang; et al. (Briefings Bioinform., 2022)

Machine learning methods, databases and tools for drug combination prediction. - Lianlian Wu; Yuqi Wen; Dongjin Leng; Qinglong Zhang; Chong Dai; Zhongming Wang; Ziqi Liu; Bowei Yan; Yixin Zhang; Jing Wang; Song He; Xiaochen Bo (Briefings Bioinform., 2022)

Systematic optimization of host-directed therapeutic targets and preclinical validation of repositioned antiviral drugs. - Dafei Xie; Song He; Lu Han; Lianlian Wu; Hai Huang; Huan Tao; Pingkun Zhou; Xunlong Shi; Hui Bai; Xiaochen Bo (Briefings Bioinform., 2022)

Graph Neural Networks for Double-Strand DNA Breaks Prediction. - Xu Wang; Huan Zhao 002; Weiwei Tu; Hao Li 035; Yu Sun; Xiaochen Bo (CoRR, 2022)

PLA-MoRe: A Protein-Ligand Binding Affinity Prediction Model via Comprehensive Molecular Representations. - Qingyu Li; Xiaochang Zhang; Lianlian Wu; Xiaochen Bo; Song He; Shengqi Wang (J. Chem. Inf. Model., 2022)

ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data. - Xian Liu; Kaikun Xu; Xin Tao; Ronghua Yin; Guangming Ren; Miao Yu; Changyan Li; Hui Chen; Ke Zhao; Shensi Xiang; Huiying Gao; Xiaochen Bo; et al. (Nucleic Acids Res., 2022)

Inferring transcription factor regulatory networks from single-cell ATAC-seq data based on graph neural networks. - Hao Li 035; Yu Sun; Hao Hong; Xin Huang 005; Huan Tao; Qiya Huang; Longteng Wang; Kang Xu; Jingbo Gan; Hebing Chen; Xiaochen Bo (Nat. Mach. Intell., 2022)

A Yeast BiFC-seq Method for Genome-wide Interactome Mapping. - Limin Shang; Yuehui Zhang; Yuchen Liu; Chaozhi Jin; Yanzhi Yuan; Chunyan Tian; Ming Ni; Xiaochen Bo; Li Zhang 097; Dong Li 018; Fuchu He; Jian Wang (Genom. Proteom. Bioinform., 2022)

A Multi-View Learning-Based Bayesian Ruleset Extraction Algorithm For Accurate Hepatotoxicity Prediction. - Siyang Chen; Lianlian Wu; Yong Xu 009; Kunhong Liu 001; Song He; Xiaochen Bo (BIBM, 2023)

MoSCHG: Multi-omics Single-cell Classification based on Heterogeneous Graphs and Supervised Contrastive Learning. - Xinjian Chen 007; Chenyang Xie; Yunhao Zhang; Song He; Xiaochen Bo; Zhongnan Zhang (BIBM, 2023)

Drug-target and Drug-disease Association Prediction based on Drug-target-disease Network and Multi-task Learning. - Binyu Wang; Yunhao Zhang; Hongyan Ye; Lianlian Wu; Song He; Xiaochen Bo; Zhongnan Zhang (BIBM, 2023)

HSGCL-DTA: Hybrid-scale Graph Contrastive Learning based Drug-Target Binding Affinity Prediction. - Hongyan Ye; Yingying Song; Binyu Wang; Lianlian Wu; Song He; Xiaochen Bo; Zhongnan Zhang (ICTAI, 2023)

GADRP: graph convolutional networks and autoencoders for cancer drug response prediction. - Hong Wang; Chong Dai; Yuqi Wen; Xiaoqi Wang; Wenjuan Liu; Song He; Xiaochen Bo; Shaoliang Peng (Briefings Bioinform., 2023)

TOXRIC: a comprehensive database of toxicological data and benchmarks. - Lianlian Wu; Bowei Yan; Junshan Han; Ruijiang Li; Jian Xiao; Song He; Xiaochen Bo (Nucleic Acids Res., 2023)

Effective low-light image enhancement with multiscale and context learning network. - Qiao Li; Bin Jiang 006; Xiaochen Bo; Chao Yang 015; Xu Wu (Multim. Tools Appl., 2023)

Deep Learning-Based Multiomics Data Integration Methods for Biomedical Application. - Yuqi Wen; Linyi Zheng; Dongjin Leng; Chong Dai; Jing Lu; Zhongnan Zhang; Song He; Xiaochen Bo (Adv. Intell. Syst., 2023)

A Genetic Algorithm-Based Ensemble Learning Framework for Drug Combination Prediction. - Lianlian Wu; Xiaona Ye; Yixin Zhang; Jie Gao; Zhikai Lin; Binsheng Sui; Yuqi Wen; Qingqiang Wu 001; Kunhong Liu 001; Song He; Xiaochen Bo (J. Chem. Inf. Model., 2023)

3D genomic organization in cancers. - Junting Wang 003; Huan Tao; Hao Li 035; Xiaochen Bo; Hebing Chen (Quant. Biol., 2023)

COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods. - Xiaojing Wu; Mingfei Han 001; Xinyu Song 002; Song He; Xiaochen Bo; Yunping Zhu (Bioinform., 2023)

EDST: a decision stump based ensemble algorithm for synergistic drug combination prediction. - Jing Chen; Lianlian Wu; Kunhong Liu 001; Yong Xu 009; Song He; Xiaochen Bo (BMC Bioinform., 2023)

Exploring Optimal Transport-Based Multi-Grained Alignments for Text-Molecule Retrieval. - Zijun Min; Bingshuai Liu; Liang Zhang; Jia Song; Jinsong Su; Song He; Xiaochen Bo (BIBM, 2024)

Towards Cross-Modal Text-Molecule Retrieval with Better Modality Alignment. - Jia Song; Wanru Zhuang; Yujie Lin; Liang Zhang; Chunyan Li 002; Jinsong Su; Song He; Xiaochen Bo (BIBM, 2024)

CPDT: A Novel Cluster-based Paired Decision Tree for Identifying Biomedical Entity Interactions. - Jiayu Zou; Lianlian Wu; Weiping Lin; Kunhong Liu 001; Yong Xu 009; Song He; Xiaochen Bo (BIBM, 2024)

Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair. - Bijia Chen; Chao Ren; Zhangyi Ouyang; Jingxuan Xu; Kang Xu; Yaru Li; Hejiang Guo; Xuemei Bai; Mengge Tian; Xiang Xu; Yuyang Wang; Hao Li 035; et al. (Briefings Bioinform., 2024)

ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing. - Kechen Fan; Mengfan Li; Jiarong Zhang; Zihan Xie; Daguang Jiang; Xiaochen Bo; Dongsheng Zhao; Shenghui Shi; Ming Ni (Briefings Bioinform., 2024)

NASTRA: accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm. - Zilin Ren; Jiarong Zhang; Yixiang Zhang; Tingting Yang; Pingping Sun; Jiguo Xue; Xiaochen Bo; Bo Zhou; Jiangwei Yan; Ming Ni (Briefings Bioinform., 2024)

DeepPFP: a multi-task-aware architecture for protein function prediction. - Han Wang; Zilin Ren; Jinghong Sun; Yongbing Chen; Xiaochen Bo; Jiguo Xue; Jingyang Gao; Ming Ni (Briefings Bioinform., 2024)

A hierarchical attention network integrating multi-scale relationship for drug response prediction. - Xiaoqi Wang; Yuqi Wen; Yixin Zhang; Chong Dai; Yaning Yang; Xiaochen Bo; Song He; Shaoliang Peng (Inf. Fusion, 2024)

Multi-view uncertainty deep forest: An innovative deep forest equipped with uncertainty estimation for drug-induced liver injury prediction. - Qiong Tan; Yuqi Wen; Yong Xu 009; Kunhong Liu 001; Song He; Xiaochen Bo (Inf. Sci., 2024)

Reusability report: exploring the utility of variational graph encoders for predicting molecular toxicity in drug design. - Ruijiang Li; Jiang Lu; Ziyi Liu; Duoyun Yi; Mengxuan Wan; Yixin Zhang; Peng Zan; Song He; Xiaochen Bo (Nat. Mac. Intell., 2024)

Effectiveness of machine learning at modeling the relationship between Hi-C data and copy number variation. - Yuyang Wang; Yu Sun; Zeyu Liu; Bijia Chen; Hebing Chen; Chao Ren; Xuanwei Lin; Pengzhen Hu; Peiheng Jia; Xiang Xu; Kang Xu; Ximeng Liu; et al. (Quant. Biol., 2024)

SEPDB: a database of secreted proteins. - Ruiqing Wang; Chao Ren; Tian Gao; Hao Li 035; Xiaochen Bo; Dahai Zhu; Dan Zhang; Hebing Chen; Yong Zhang (Database J. Biol. Databases Curation, 2024)

An Ensemble Cascade Forest-Based Framework for Multi-Omics Drug Response and Synergy Prediction. - Ruijiang Li; Binsheng Sui; Dongjin Leng; Song He; Kunhong Liu 001; Xiaochen Bo (Adv. Intell. Syst., 2024)

37.5 SKADI: A 28nm Complete K-SAT Solver Featuring Dual-Path SRAM-Based Macro and Incremental Update with 100% Solvability. - Zihan Wu 005; Xiyuan Tang; Tao Zhang; Lishan Lin; Haoyang Luo; Bocheng Xu; Zhongyi Wu; Jiahao Song; Yitao Liang; Xiaochen Bo; Yuan Wang 001 (ISSCC, 2025)

IECata: interpretable bilinear attention network and evidential deep learning improve the catalytic efficiency prediction of enzymes. - Jingjing Wang; Yanpeng Zhao; Zhijiang Yang; Ge Yao; Penggang Han; Jiajia Liu; Chang Chen; Peng Zan; Xiukun Wan; Xiaochen Bo; Hui Jiang (Briefings Bioinform., 2025)

Multi-task multi-view and iterative error-correcting random forest for acute toxicity prediction. - Jie Gao; Lianlian Wu; Guangyi Lin; Jiayu Zou; Bowei Yan; Kunhong Liu 001; Song He; Xiaochen Bo (Expert Syst. Appl., 2025)

RL-GCL: Reinforcement Learning-Guided Contrastive Learning for molecular property prediction. - Yanran Fu; Junshan Han; Yong Xu 009; Kunhong Liu 001; Jiang Lu; Song He; Xiaochen Bo (Inf. Fusion, 2025)

A feature pair-based neural network embedded decision tree for synergistic drug combination prediction. - Jiayu Zou; Lianlian Wu; Kunhong Liu 001; Yong Xu 009; Song He; Xiaochen Bo (Pattern Recognit., 2025)

The Dance of Atoms-De Novo Protein Design with Diffusion Model. - Yujie Qin; Ming He; Changyong Yu; Ming Ni; Xian Liu; Xiaochen Bo (CoRR, 2025)

A Variation-Tolerant Continuous-Time Ising Machine With eDRAM-Based Spin Interaction and Leaked Negative Feedback Annealing. - Zihan Wu 005; Jiahao Song; Xiyuan Tang; Bocheng Xu; Haoyang Luo; Youming Yang 002; Runsheng Wang; Xiaochen Bo; Yuan Wang 001 (IEEE J. Solid State Circuits, 2025)