Xiaochen Bo

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 55

Top Topics

Biomedical Data

Gene Expression Profiling

Top Venues

Briefings Bioinform.

Nucleic Acids Res.

Publications

Bijia Chen, Chao Ren, Zhangyi Ouyang, Jingxuan Xu, Kang Xu, Yaru Li, Hejiang Guo, Xuemei Bai, Mengge Tian, Xiang Xu, Yuyang Wang, Hao Li, Xiaochen Bo, Hebing Chen
Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair. Briefings Bioinform. 25 (4) (2024)
Ruiqing Wang, Chao Ren, Tian Gao, Hao Li, Xiaochen Bo, Dahai Zhu, Dan Zhang, Hebing Chen, Yong Zhang
SEPDB: a database of secreted proteins. Database J. Biol. Databases Curation 2024 (2024)
Xiaoqi Wang, Yuqi Wen, Yixin Zhang, Chong Dai, Yaning Yang, Xiaochen Bo, Song He, Shaoliang Peng
A hierarchical attention network integrating multi-scale relationship for drug response prediction. Inf. Fusion 110 (2024)
Qiong Tan, Yuqi Wen, Yong Xu, Kunhong Liu, Song He, Xiaochen Bo
Multi-view uncertainty deep forest: An innovative deep forest equipped with uncertainty estimation for drug-induced liver injury prediction. Inf. Sci. 667 (2024)
Hongyan Ye, Yingying Song, Binyu Wang, Lianlian Wu, Song He, Xiaochen Bo, Zhongnan Zhang
HSGCL-DTA: Hybrid-scale Graph Contrastive Learning based Drug-Target Binding Affinity Prediction. ICTAI (2023)
Lianlian Wu, Xiaona Ye, Yixin Zhang, Jie Gao, Zhikai Lin, Binsheng Sui, Yuqi Wen, Qingqiang Wu, Kunhong Liu, Song He, Xiaochen Bo
A Genetic Algorithm-Based Ensemble Learning Framework for Drug Combination Prediction. J. Chem. Inf. Model. 63 (12) (2023)
Binyu Wang, Yunhao Zhang, Hongyan Ye, Lianlian Wu, Song He, Xiaochen Bo, Zhongnan Zhang
Drug-target and Drug-disease Association Prediction based on Drug-target-disease Network and Multi-task Learning. BIBM (2023)
Jing Chen, Lianlian Wu, Kunhong Liu, Yong Xu, Song He, Xiaochen Bo
EDST: a decision stump based ensemble algorithm for synergistic drug combination prediction. BMC Bioinform. 24 (1) (2023)
Junting Wang, Huan Tao, Hao Li, Xiaochen Bo, Hebing Chen
3D genomic organization in cancers. Quant. Biol. 11 (2) (2023)
Xinjian Chen, Chenyang Xie, Yunhao Zhang, Song He, Xiaochen Bo, Zhongnan Zhang
MoSCHG: Multi-omics Single-cell Classification based on Heterogeneous Graphs and Supervised Contrastive Learning. BIBM (2023)
Lianlian Wu, Bowei Yan, Junshan Han, Ruijiang Li, Jian Xiao, Song He, Xiaochen Bo
TOXRIC: a comprehensive database of toxicological data and benchmarks. Nucleic Acids Res. 51 (D1) (2023)
Siyang Chen, Lianlian Wu, Yong Xu, Kunhong Liu, Song He, Xiaochen Bo
A Multi-View Learning-Based Bayesian Ruleset Extraction Algorithm For Accurate Hepatotoxicity Prediction. BIBM (2023)
Qiao Li, Bin Jiang, Xiaochen Bo, Chao Yang, Xu Wu
Effective low-light image enhancement with multiscale and context learning network. Multim. Tools Appl. 82 (10) (2023)
Xiaojing Wu, Mingfei Han, Xinyu Song, Song He, Xiaochen Bo, Yunping Zhu
COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods. Bioinform. 39 (12) (2023)
Hong Wang, Chong Dai, Yuqi Wen, Xiaoqi Wang, Wenjuan Liu, Song He, Xiaochen Bo, Shaoliang Peng
GADRP: graph convolutional networks and autoencoders for cancer drug response prediction. Briefings Bioinform. 24 (1) (2023)
Yuqi Wen, Linyi Zheng, Dongjin Leng, Chong Dai, Jing Lu, Zhongnan Zhang, Song He, Xiaochen Bo
Deep Learning-Based Multiomics Data Integration Methods for Biomedical Application. Adv. Intell. Syst. 5 (5) (2023)
Qingyu Li, Xiaochang Zhang, Lianlian Wu, Xiaochen Bo, Song He, Shengqi Wang
PLA-MoRe: A Protein-Ligand Binding Affinity Prediction Model via Comprehensive Molecular Representations. J. Chem. Inf. Model. 62 (18) (2022)
Yuting Zhong, Bowei Yan, KunHong Liu, Yong Xu, Song He, Xiaochen Bo
A Multi-View Learning-Based Rule Extraction Algorithm For Accurate Hepatotoxicity Prediction. BIBM (2022)
Hao Li, Yu Sun, Hao Hong, Xin Huang, Huan Tao, Qiya Huang, Longteng Wang, Kang Xu, Jingbo Gan, Hebing Chen, Xiaochen Bo
Inferring transcription factor regulatory networks from single-cell ATAC-seq data based on graph neural networks. Nat. Mach. Intell. 4 (4) (2022)
X. U. Wang, Huan Zhao, Weiwei Tu, Hao Li, Yu Sun, Xiaochen Bo
Graph Neural Networks for Double-Strand DNA Breaks Prediction. CoRR (2022)
Dafei Xie, Song He, Lu Han, Lianlian Wu, Hai Huang, Huan Tao, Pingkun Zhou, Xunlong Shi, Hui Bai, Xiaochen Bo
Systematic optimization of host-directed therapeutic targets and preclinical validation of repositioned antiviral drugs. Briefings Bioinform. 23 (3) (2022)
Limin Shang, Yuehui Zhang, Yuchen Liu, Chaozhi Jin, Yanzhi Yuan, Chunyan Tian, Ming Ni, Xiaochen Bo, Li Zhang, Dong Li, Fuchu He, Jian Wang
A Yeast BiFC-seq Method for Genome-wide Interactome Mapping. Genom. Proteom. Bioinform. 20 (4) (2022)
Jing Wang, Qinglong Zhang, Junshan Han, Yanpeng Zhao, Caiyun Zhao, Bowei Yan, Chong Dai, Lianlian Wu, Yuqi Wen, Yixin Zhang, Dongjin Leng, Zhongming Wang, Xiaoxi Yang, Song He, Xiaochen Bo
Computational methods, databases and tools for synthetic lethality prediction. Briefings Bioinform. 23 (3) (2022)
Weiping Lin, Lianlian Wu, Yixin Zhang, Yuqi Wen, Bowei Yan, Chong Dai, Kun-Hong Liu, Song He, Xiaochen Bo
An enhanced cascade-based deep forest model for drug combination prediction. Briefings Bioinform. 23 (2) (2022)
Kanghao Shao, Yunhao Zhang, Yuqi Wen, Zhongnan Zhang, Song He, Xiaochen Bo
DTI-HETA: prediction of drug-target interactions based on GCN and GAT on heterogeneous graph. Briefings Bioinform. 23 (3) (2022)
Lianlian Wu, Yuqi Wen, Dongjin Leng, Qinglong Zhang, Chong Dai, Zhongming Wang, Ziqi Liu, Bowei Yan, Yixin Zhang, Jing Wang, Song He, Xiaochen Bo
Machine learning methods, databases and tools for drug combination prediction. Briefings Bioinform. 23 (1) (2022)
Xian Liu, Kaikun Xu, Xin Tao, Ronghua Yin, Guangming Ren, Miao Yu, Changyan Li, Hui Chen, Ke Zhao, Shensi Xiang, Huiying Gao, Xiaochen Bo, Cheng Chang, Xiaoming Yang
ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data. Nucleic Acids Res. 50 (W1) (2022)
Peng Ke, Yuqi Wen, Zhongnan Zhang, Song He, Xiaochen Bo
A Metagraph-Based Model for Predicting Drug-Target Interaction on Heterogeneous Network. ICANN (1) (2021)
Yuqi Wen, Xinyu Song, Bowei Yan, Xiaoxi Yang, Lianlian Wu, Dongjin Leng, Song He, Xiaochen Bo
Multi-dimensional data integration algorithm based on random walk with restart. BMC Bioinform. 22 (1) (2021)
Lianlian Wu, Yuqi Wen, Xiaoxi Yang, Bowei Yan, Song He, Xiaochen Bo
Synthetic Lethal Interactions Prediction Based on Multiple Similarity Measures Fusion. J. Comput. Sci. Technol. 36 (2) (2021)
Jie Yang, Song He, Zhongnan Zhang, Xiaochen Bo
NegStacking: Drug-Target Interaction Prediction Based on Ensemble Learning and Logistic Regression. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (6) (2021)
Song He, Xinyu Song, Xiaoxi Yang, Jijun Yu, Yuqi Wen, Lianlian Wu, Bowei Yan, Jiannan Feng, Xiaochen Bo
COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data. PLoS Comput. Biol. 17 (3) (2021)
Yihua Ye, Yuxin Chen, Zhongnan Zhang, Yuqi Wen, Song He, Xiaochen Bo
Drug-target interaction prediction based on nonnegative and self-representative matrix factorization. BIBM (2021)
Shuai Jiang, Hao Li, Hao Hong, Guifang Du, Xin Huang, Yu Sun, Junting Wang, Huan Tao, Kang Xu, Cheng Li, Yang Chen, Hebing Chen, Xiaochen Bo
Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains. Briefings Bioinform. 22 (3) (2021)
Kanghao Shao, Zhongnan Zhang, Song He, Xiaochen Bo
DTIGCCN: Prediction of drug-target interactions based on GCN and CNN. ICTAI (2020)
Hebing Chen, Zhuo Zhang, Shuai Jiang, Ruijiang Li, Wanying Li, Chenghui Zhao, Hao Hong, Xin Huang, Hao Li, Xiaochen Bo
New insights on human essential genes based on integrated analysis and the construction of the HEGIAP web-based platform. Briefings Bioinform. 21 (4) (2020)
Hao Hong, Shuai Jiang, Hao Li, Guifang Du, Yu Sun, Huan Tao, Cheng Quan, Chenghui Zhao, Ruijiang Li, Wanying Li, Xiaoyao Yin, Yangchen Huang, Cheng Li, Hebing Chen, Xiaochen Bo
DeepHiC: A generative adversarial network for enhancing Hi-C data resolution. PLoS Comput. Biol. 16 (2) (2020)
Song He, Yuqi Wen, Xiaoxi Yang, Zhen Liu, Xinyu Song, Xin Huang, Xiaochen Bo
PIMD: An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion. Genom. Proteom. Bioinform. 18 (5) (2020)
Lingwei Xie, Song He, Zhongnan Zhang, Kunhui Lin, Xiaochen Bo, Shu Yang, Boyuan Feng, Kun Wan, Kang Yang, Jie Yang, Yufei Ding
Domain-adversarial multi-task framework for novel therapeutic property prediction of compounds. Bioinform. 36 (9) (2020)
Xin Huang, Xudong Gao, Wanying Li, Shuai Jiang, Ruijiang Li, Hao Hong, Chenghui Zhao, Pingkun Zhou, Hebing Chen, Xiaochen Bo, Hao Li
Stable H3K4me3 is associated with transcription initiation during early embryo development. Bioinform. 35 (20) (2019)
Zhuo Zhang, Hao Li, Shuai Jiang, Ruijiang Li, Wanying Li, Hebing Chen, Xiaochen Bo
A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data. Briefings Bioinform. 20 (4) (2019)
Gaole An, Jiaqi Sun, Chao Ren, Zhangyi Ouyang, Lingyun Zhu, Xiaochen Bo, Shaoliang Peng, Wenjie Shu
LIVE: a manually curated encyclopedia of experimentally validated interactions of lncRNAs. Database J. Biol. Databases Curation 2019 (2019)
Lingwei Xie, Song He, Shu Yang, Boyuan Feng, Kun Wan, Zhongnan Zhang, Xiaochen Bo, Yufei Ding
Domain-Adversarial Multi-Task Framework for Novel Therapeutic Property Prediction of Compounds. CoRR (2018)
Xiaolong Shen, Song He, Minquan Fang, Yuqi Wen, Xiaochen Bo, Yong Dou
paraSNF: An Parallel Approach for Large-Scale Similarity Network Fusion. ACA (2018)
Xiaoping Zheng, Song He, Xinyu Song, Zhongnan Zhang, Xiaochen Bo
DTI-RCNN: New Efficient Hybrid Neural Network Model to Predict Drug-Target Interactions. ICANN (1) (2018)
Kang Yang, Zhongnan Zhang, Song He, Xiaochen Bo
Prediction of DTIs for high-dimensional and class-imbalanced data based on CGAN. BIBM (2018)
Chensi Cao, Feng Liu, Hai Tan, Deshou Song, Wenjie Shu, Weizhong Li, Yiming Zhou, Xiaochen Bo, Zhi Xie
Deep Learning and Its Applications in Biomedicine. Genom. Proteom. Bioinform. 16 (1) (2018)
Wenjian Xu, Yang Cao, Ziwei Xie, Haochen He, Song He, Hao Hong, Xiaochen Bo, Fei Li
NFPscanner: a webtool for knowledge-based deciphering of biomedical networks. BMC Bioinform. 18 (1) (2017)
Bite Yang, Feng Liu, Chao Ren, Zhangyi Ouyang, Ziwei Xie, Xiaochen Bo, Wenjie Shu
BiRen: predicting enhancers with a deep-learning-based model using the DNA sequence alone. Bioinform. 33 (13) (2017)
Yiming Lu, Cheng Quan, Hebing Chen, Xiaochen Bo, Chenggang Zhang
3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes. Nucleic Acids Res. 45 (Database-Issue) (2017)
Hebing Chen, Shuai Jiang, Zhuo Zhang, Hao Li, Yiming Lu, Xiaochen Bo
Exploring spatially adjacent TFBS-clustered regions with Hi-C data. Bioinform. 33 (17) (2017)
Lingwei Xie, Zhongnan Zhang, Song He, Xiaochen Bo, Xinyu Song
Drug - target interaction prediction with a deep-learning-based model. BIBM (2017)
Feng Liu, Chao Ren, Hao Li, Pingkun Zhou, Xiaochen Bo, Wenjie Shu
identification of replication-timing domains in the human genome by deep learning. Bioinform. 32 (5) (2016)
Yang Cao, Yuanyuan Wang, Xiaofei Zheng, Fei Li, Xiaochen Bo
RevEcoR: an R package for the reverse ecology analysis of microbiomes. BMC Bioinform. 17 (2016)
Song He, Haochen He, Wenjian Xu, Xin Huang, Shuai Jiang, Fei Li, Fuchu He, Xiaochen Bo
ICM: a web server for integrated clustering of multi-dimensional biomedical data. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Xiaoyao Yin, Lu Han, Hui Bai, Xiaochen Bo, Yun Bai, Cong Niu, Naiyang Guan, Zhigang Luo
New insights into the landscape relationships of host response to bacterial pathogens. IJCNN (2015)
Yang Liu, Dafei Xie, Lu Han, Hui Bai, Fei Li, Shengqi Wang, Xiaochen Bo
EHFPI: a database and analysis resource of essential host factors for pathogenic infection. Nucleic Acids Res. 43 (Database-Issue) (2015)
Yifu Luo, Qijun Liu, Wenjian Wu, Fei Li, Xiaochen Bo
Predicting drug side effects based on link prediction in bipartite network. BMEI (2014)
Ming Ni, Fuqiang Ye, Juanjuan Zhu, Zongwei Li, Shuai Yang, Bite Yang, Lu Han, Yongge Wu, Ying Chen, Fei Li, Shengqi Wang, Xiaochen Bo
ExpTreeDB: Web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO. Bioinform. 30 (23) (2014)
Zhenpeng Li, Xiuliang Cui, Fei Li, Peng Li, Ming Ni, Shengqi Wang, Xiaochen Bo
Exploring the role of human miRNAs in virus-host interactions using systematic overlap analysis. Bioinform. 29 (19) (2013)
Zhenpeng Li, Fei Li, Ming Ni, Peng Li, Xiaochen Bo, Shengqi Wang
Characterization the regulation of herpesvirus miRNAs from the view of human protein interaction network. BMC Syst. Biol. 5 (2011)
Fei Li, Xiuliang Cui, Dafei Xie, Xiaochen Bo, Shengqi Wang
Topology aware functional similarity of protein interaction networks based on gene ontology. EMBC (2011)
Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, Shengqi Wang
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinform. 26 (7) (2010)
Fei Li, Peng Li, Wenjian Xu, Yuxing Peng, Xiaochen Bo, Shengqi Wang
PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks. Bioinform. 26 (2) (2010)
Fei Li, Wenjian Xu, Peng Li, Xiaochen Bo, Yuxing Peng
Optimizing Reference Gene Set for Inter-Chip Normalization Using Genetic Algorithm. BMEI (2009)
Wenjie Shu, Ming Ni, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang
EvoRSR: an integrated system for exploring evolution of RNA structural robustness. BMC Bioinform. 10 (2009)
Fei Li, Yuxing Peng, Wenjian Xu, Peng Li, Xiaochen Bo
Dynamic Propagation Properties of Virus-Host Protein Interaction Network. IJCBS (2009)
Fei Li, Yuxing Peng, Wenjian Xu, Guangchuang Yu, Peng Li, Xiaochen Bo, Shengqi Wang
Towards a Comprehensive HBV-Human Interaction Map. IJCBS (2009)
Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang
A novel representation of RNA secondary structure based on element-contact graphs. BMC Bioinform. 9 (2008)
Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang
RSRE: RNA structural robustness evaluator. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Xiaochen Bo, Shaoke Lou, Daochun Sun, Jing Yang, Shengqi Wang
AOBase: a database for antisense oligonucleotides selection and design. Nucleic Acids Res. 34 (Database-Issue) (2006)
Xiaochen Bo, Shaoke Lou, Daochun Sun, Wenjie Shu, Jing Yang, Shengqi Wang
Selection of antisense oligonucleotides based on multiple predicted target mRNA structures. BMC Bioinform. 7 (2006)
Wenjie Shu, Xiaochen Bo, Rujia Liu, Dongsheng Zhao, Zhiqiang Zheng, Shengqi Wang
RDMAS: a web server for RNA deleterious mutation analysis. BMC Bioinform. 7 (2006)
Xiaochen Bo, Shengqi Wang
TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA. Bioinform. 21 (8) (2005)
Xiaochen Bo, Lincheng Shen, Wensen Chang
Sign Correlation Detector for Blind Image Watermarking in the DCT Domain. IEEE Pacific Rim Conference on Multimedia (2001)
Xiaochen Bo, Lincheng Shen, Wensen Chang
Evaluation of the Image Degradation for a Typical Watermarking Algorithm in the Block-DCT Domain. ICICS (2001)