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2020 – today
- 2024
[j57]Ruijiang Li
, Binsheng Sui, Dongjin Leng, Song He, Kunhong Liu, Xiaochen Bo:
An Ensemble Cascade Forest-Based Framework for Multi-Omics Drug Response and Synergy Prediction. Adv. Intell. Syst. 6(11) (2024)- [j56]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) - [j55]Zilin Ren, Jiarong Zhang, Yixiang Zhang, Tingting Yang, Pingping Sun, Jiguo Xue, Xiaochen Bo, Bo Zhou, Jiangwei Yan, Ming Ni:
NASTRA: accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm. Briefings Bioinform. 25(6) (2024) - [j54]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) - [j53]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: 102485 (2024) - [j52]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: 120342 (2024) - [j51]Yuyang Wang, Yu Sun, Zeyu Liu, Bijia Chen, Hebing Chen, Chao Ren, Xuanwei Lin, Pengzhen Hu, Peiheng Jia, Xiang Xu, Kang Xu, Ximeng Liu, Hao Li, Xiaochen Bo:
Effectiveness of machine learning at modeling the relationship between Hi-C data and copy number variation. Quant. Biol. 12(3): 231-244 (2024) - [i4]Jia Song, Wanru Zhuang, Yujie Lin, Liang Zhang, Chunyan Li, Jinsong Su, Song He, Xiaochen Bo:
Towards Cross-Modal Text-Molecule Retrieval with Better Modality Alignment. CoRR abs/2410.23715 (2024) - [i3]Zijun Min, Bingshuai Liu, Liang Zhang, Jia Song, Jinsong Su, Song He, Xiaochen Bo:
Exploring Optimal Transport-Based Multi-Grained Alignments for Text-Molecule Retrieval. CoRR abs/2411.11875 (2024) - 2023
- [j50]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) - [j49]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) - [j48]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) - [j47]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): 325 (2023) - [j46]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): 3941-3954 (2023) - [j45]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): 15271-15286 (2023) - [j44]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): 1432-1445 (2023) - [j43]Junting Wang, Huan Tao, Hao Li, Xiaochen Bo, Hebing Chen:
3D genomic organization in cancers. Quant. Biol. 11(2): 109-121 (2023) - [c20]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: 835-840 - [c19]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: 930-935 - [c18]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: 1054-1059 - [c17]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: 947-954 - 2022
- [j42]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) - [j41]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) - [j40]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) - [j39]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) - [j38]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) - [j37]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): 795-807 (2022) - [j36]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): 4380-4390 (2022) - [j35]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): 312-321 (2022) - [j34]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): 389-400 (2022) - [c16]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: 1423-1428 - [i2]Xu Wang, Huan Zhao, Weiwei Tu, Hao Li, Yu Sun, Xiaochen Bo:
Graph Neural Networks for Double-Strand DNA Breaks Prediction. CoRR abs/2201.01855 (2022) - 2021
- [j33]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) - [j32]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): 97 (2021) - [j31]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): 261-275 (2021) - [j30]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) - [j29]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): 2624-2634 (2021) - [c15]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: 2352-2359 - [c14]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: 465-476 - 2020
- [j28]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): 1397-1410 (2020) - [j27]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): 2848-2855 (2020) - [j26]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): 565-581 (2020) - [j25]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) - [c13]Kanghao Shao, Zhongnan Zhang, Song He, Xiaochen Bo:
DTIGCCN: Prediction of drug-target interactions based on GCN and CNN. ICTAI 2020: 337-342
2010 – 2019
- 2019
- [j24]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): 1524-1541 (2019) - [j23]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: baz011 (2019) - [j22]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): 3931-3936 (2019) - 2018
- [j21]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): 17-32 (2018) - [c12]Xiaolong Shen, Song He, Minquan Fang, Yuqi Wen, Xiaochen Bo, Yong Dou:
paraSNF: An Parallel Approach for Large-Scale Similarity Network Fusion. ACA 2018: 155-167 - [c11]Kang Yang, Zhongnan Zhang, Song He, Xiaochen Bo:
Prediction of DTIs for high-dimensional and class-imbalanced data based on CGAN. BIBM 2018: 788-791 - [c10]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: 104-114 - [i1]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 abs/1810.00867 (2018) - 2017
- [j20]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): 1930-1936 (2017) - [j19]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): 2611-2614 (2017) - [j18]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): 262:1-262:9 (2017) - [j17]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): D643-D649 (2017) - [c9]Lingwei Xie, Zhongnan Zhang, Song He, Xiaochen Bo, Xinyu Song:
Drug - target interaction prediction with a deep-learning-based model. BIBM 2017: 469-476 - 2016
- [j16]Feng Liu, Chao Ren, Hao Li, Pingkun Zhou, Xiaochen Bo, Wenjie Shu:
De novo identification of replication-timing domains in the human genome by deep learning. Bioinform. 32(5): 641-649 (2016) - [j15]Yang Cao, Yuanyuan Wang, Xiaofei Zheng, Fei Li, Xiaochen Bo:
RevEcoR: an R package for the reverse ecology analysis of microbiomes. BMC Bioinform. 17: 294 (2016) - [j14]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): W154-W159 (2016) - 2015
- [j13]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): 946-955 (2015) - [c8]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: 1-8 - 2014
- [j12]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): 3379-3386 (2014) - [c7]Yifu Luo, Qijun Liu, Wenjian Wu, Fei Li, Xiaochen Bo:
Predicting drug side effects based on link prediction in bipartite network. BMEI 2014: 729-733 - 2013
- [j11]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): 2375-2379 (2013) - 2011
- [j10]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: 93 (2011) - [c6]Fei Li, Xiuliang Cui, Dafei Xie, Xiaochen Bo, Shengqi Wang:
Topology aware functional similarity of protein interaction networks based on gene ontology. EMBC 2011: 6857-6860 - 2010
- [j9]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): 275-277 (2010) - [j8]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): 976-978 (2010)
2000 – 2009
- 2009
- [j7]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) - [c5]Fei Li, Wenjian Xu, Peng Li, Xiaochen Bo, Yuxing Peng:
Optimizing Reference Gene Set for Inter-Chip Normalization Using Genetic Algorithm. BMEI 2009: 1-4 - [c4]Fei Li, Yuxing Peng, Wenjian Xu, Guangchuang Yu, Peng Li, Xiaochen Bo, Shengqi Wang:
Towards a Comprehensive HBV-Human Interaction Map. IJCBS 2009: 311-314 - [c3]Fei Li, Yuxing Peng, Wenjian Xu, Peng Li, Xiaochen Bo:
Dynamic Propagation Properties of Virus-Host Protein Interaction Network. IJCBS 2009: 491-493 - 2008
- [j6]Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang:
A novel representation of RNA secondary structure based on element-contact graphs. BMC Bioinform. 9 (2008) - 2007
- [j5]Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang:
RSRE: RNA structural robustness evaluator. Nucleic Acids Res. 35(Web-Server-Issue): 314-319 (2007) - 2006
- [j4]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: 122 (2006) - [j3]Wenjie Shu, Xiaochen Bo, Rujia Liu, Dongsheng Zhao, Zhiqiang Zheng, Shengqi Wang:
RDMAS: a web server for RNA deleterious mutation analysis. BMC Bioinform. 7: 404 (2006) - [j2]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): 664-667 (2006) - 2005
- [j1]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): 1401-1402 (2005) - 2001
- [c2]Xiaochen Bo, Lincheng Shen, Wensen Chang:
Evaluation of the Image Degradation for a Typical Watermarking Algorithm in the Block-DCT Domain. ICICS 2001: 52-61 - [c1]Xiaochen Bo, Lincheng Shen, Wensen Chang:
Sign Correlation Detector for Blind Image Watermarking in the DCT Domain. IEEE Pacific Rim Conference on Multimedia 2001: 780-787
Coauthor Index
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