近期论文
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Struct2GO: protein function prediction based on Graph pooling algorithm and AlphaFold2 structure information. Jiao P, Wang B, Wang X, Liu B, Wang Y, Li J. Bioinformatics. 2023 October, doi:10.1093/bioinformatics/btad637.
ScCCL: Single-cell data clustering based on self-supervised contrastive learning. Du L, Han R, Liu B, Wang Y, Li J. IEEE/ACM Trans Comput Biol Bioinform. 2023 January; doi: 10.1109/TCBB.2023.3241129.
SLGNN: Synthetic lethality prediction in human cancers based on factor-aware knowledge graph neural network. Zhu Y, Zhou Y, Liu Y, Wang X, Li J. Bioinformatics. 2023 January; doi:10.1093/bioinformatics/btad015.
PSPGO: cross-species heterogeneous network propagation for protein function prediction. Wu K, Wang L, Liu B, Liu Y, Wang Y, Li J. IEEE/ACM Trans Comput Biol Bioinform. 2022 October; 10.1109/TCBB.2022.3215257.
MEAHNE: miRNA–disease association prediction based on semantic information in a heterogeneous network. Huang C, Cen K, Zhang Y, Liu B, Wang Y, Li J. Life. 2022 October; 12, 1578. doi: 10.3390/life12101578.
Correction of Out-of-focus Microscopic Images by Deep Learning. Jiang H, Liu W, Zhang C, Li J, Tang S, Juhas M, Zhang Y. Computational and Structural Biotechnology Journal. Accepted; 2022 April.
MDGNN：Microbial drug prediction based on heterogeneous multi-attention graph neural network. Pi J, Jiao P, Zhang Y, Li J. Frontiers in Microbiology. 2022 Apr 7;13:819046. doi: 10.3389/fmicb.2022.819046.
OTUCD: Unsupervised GCN-based Metagenomics Nonoverlapping Community Detection. Zhang Z, Jiao Q, Zhang Y, Liu B, Wang Y, Li J.Computational Biology and Chemistry. 2022 Mar 24;98:107670. doi: 10.1016/j.compbiolchem.2022.107670.
Deep Learning for Microscopic Examination of Protozoan Parasites. Zhang C, Jiang H, Jiang HL, Xi H, Chen B, Liu Y, Juhas M, Li J, Zhang Y. Computational and Structural Biotechnology Journal. 2022 February；22:1036. doi.org/10.1016/j.csbj.2022.02.005.
Prediction of the Disease Causal Genes Based on Heterogeneous Network and Multi-Feature Combination Method. Wang L, Wu M, Wu Y, Zhang X, Li S, He M, Zhang F, Wang Y, Li J. Computational Biology and Chemistry. 2022 February; 97:107639. doi: 10.1016/j.compbiolchem.2022.107639.
SmileGNN: Drug–Drug Interaction Prediction Based on the SMILES and Graph Neural Network. Han X, Xie R, Li X, Li J. Life. 2022 February; 12(2), 319. doi: 10.3390/life12020319
Prot2GO: predicting GO annotations from protein sequences and interactions. Zhang X, Wang L, Liu H, Zhang X, Liu B,Wang Y, Li J. IEEE/ACM Trans Comput Biol Bioinform. 2021 December; doi: 10.1109/TCBB.2021.3139841.
DRBin: Metagenomic binning based on deep representation learning. Mao G, Wu Y, Zhang Y, Wang X, Zhu Y, Liu B, Wang Y, Li J. Journal of Genetics and Genomics. 2021 December; doi: 10.1016/j.jgg.2021.12.005.
HNetGO: protein function prediction via heterogeneous network transformer. Zhang X, Cai Y, Wang X, Wu K, Zhang F, Qiu S, Liu B, Wang Y, Hu Y, Li J. Briefings in Bioinformatics. Accepted; 2021 December.
Deep learning driven drug discovery: tackling SARS-CoV-2. Zhang Y, Ye T, Xi H, Juhas M, Li J. Frontiers in Microbiology. 2021 October; 12:739684. doi: 10.3389/fmicb.2021.739684.
Deepgmd: a Graph-neural-network-based method to detect gene regulator module. Ye X, Wu Y, Pi J, Li H, Liu B, Wang Y, Li J. IEEE/ACM Trans Comput Biol Bioinform. 2021 Sept; doi: 10.1109/TCBB.2021.3114281.
Mixed-protocol multi-party computation framework towards complex computation tasks with malicious security. Wu Y, Wang X, Susilo W, Yang G, Jiang L, Li J, Liu X. Computer Standards & Interfaces. 2021 August; 80:103570. doi: 10.1016/j.csi.2021.103570.
PanSVR: pan-genome augmented short read realignment for sensitive detection of structural variations. Li G, Jiang T, Li J and Wang Y. Frontiers in Genetics. 2021 August; 12:1486(2021). doi:10.3389/fgene.2021.731515
IIMLP: Integrated Information-entropy-based Method for LncRNA Prediction. Li J, Li H, Ye X, Zhang L, Xu Q, Ping Y, Jing X, Jiang W, Liao Q, Liu B and Wang Y. BMC Bioinformatics. 2021 May; 22:243(2021). doi:10.1186/s12859-020-03884-w
Factor Graph-Aggregated Heterogeneous Network Embedding for Disease-Gene Association Prediction. He M, Huang C, Liu B, Wang Y and Li J. BMC Bioinformatics. 2021 Mar; 22:165 (2021). doi: 10.1186/s12859-021-04099-3
Fast and accurate classification of meta-genomics long reads with deSAMBA. Li G, Liu Y, Liu B, Li J, Hu Y and Wang Y. Frontiers in Cell and Developmental Biology. 2021 April; doi:10.3389/fcell.2021.643645
Genome assembly and transcriptome analysis provide insights into the anti-schistosome mechanism of Microtus fortis. Li H, Wang Z, Chai S, Bai X, Ding G, Li Y, Li J, Xiao Q, Miao B, Lin W, Feng J, Huang M, Gao C, Li B, Hu W, Lin J, Fu Z, Xie J, Li Y. Journal of Genetics and Genomics. 2021 Feb. doi: 10.1016/j.jgg.2020.11.009.
PmDNE: Prediction of miRNA-disease association based on network embedding and network similarity analysis. Li J, Liu Y, Zhang Z, Liu B and Wang Y. Biomed Res Int. vol. 2020, 6248686, 9 pages, 2020 Dec 07. doi：10.1155/2020/6248686
ScGSLC: An Unsupervised Graph Similarity Learning Framework for Single-cell RNA-seq Data Clustering. Li J, Jiang W, Han H, Liu J, Liu B and Wang Y. Computational Biology and Chemistry. 2020 Nov 18. doi：10.1016/j.compbiolchem.2020.107415.
Pan-Cancer Classification based on Self-Normalizing Neural Networks and Feature Selection. Li J, Xu Q, Wu M, Huang T, Wang Y. Front. Bioeng. Biotechnol. 2020 Aug 4; 8:766. doi: 10.3389/fbioe.2020.00766
Long-read-based human genomic structural variation detection with cuteSV. Jiang T, Liu Y, Jiang Y, Li J, Gao Y, Cui Z, Liu Y, Liu B and Wang Y. Genome Biol. 2020 Aug; 21, 189. doi: 10.1186/s13059-020-02107-y
Prognostic prediction of carcinoma by a differential-regulatory-network-embedded deep neural network. Li J, Ping Y, Li H, Li HN, Liu Y, Liu B, Wang Y. Computational Biology and Chemistry. 2020 Jun 24; 88:107317.doi: 10.1016/j.compbiolchem.2020.107317.
deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index. Liu B, Liu Y, Li J, Guo H, Zang T, Wang Y. Genome Biol. 2019 Dec; 20(1):274. doi: 10.1186/s13059-019-1895-9
rMETL: sensitive mobile element insertion detection with long read realignment. Jiang T, Liu B, Li J, Wang Y. Bioinformatics. 2019 Sep 15;35(18):3484-3486. doi: 10.1093/bioinformatics/btz106.
Integrated entropy-based approach for analyzing exons and introns in DNA sequences. Li J, Zhang L, Li H, Ping Y, Xu Q, Wang R, Tan R, Wang Z, Liu B, Wang Y. BMC Bioinformatics. 2019 Jun 10;20(Suppl 8):283. doi: 10.1186/s12859-019-2772-y.
deGSM: memory scalable construction of large scale de Bruijn Graph. Guo H, Fu Y, Gao Y, Li J, Wang Y, Liu B. IEEE/ACM Trans Comput Biol Bioinform. 2019 Apr 30. doi: 10.1109/TCBB.2019.2913932.
BdBG: a bucket-based method for compressing genome sequencing data with dynamic de Bruijn graphs. Wang R, Li J, Bai Y, Zang T, Wang Y. PeerJ. 2018 Oct 19;6:e5611. doi: 10.7717/peerj.5611. eCollection 2018.
rMFilter: acceleration of long read-based structure variation calling by chimeric read filtering. Liu B, Jiang T, Yiu SM, Li J, Wang Y. Bioinformatics. 2017 Sep 1;33(17):2750-2752. doi: 10.1093/bioinformatics/btx279.
Differential regulation analysis reveals dysfunctional regulatory mechanism involving transcription factors and microRNAs in gastric carcinogenesis. Li Q, Li J, Dai W, Li YX, Li YY. Artif Intell Med. 2017 Mar;77:12-22. doi: 10.1016/j.artmed.2017.02.006. Epub 2017 Mar 1.
The Safety of Ovarian Preservation in Stage I Endometrial Endometrioid Adenocarcinoma Based on Propensity Score Matching. Hou T, Sun Y, Li J, Liu C, Wang Z, Li Y, Lu Y. Comb Chem High Throughput Screen. 2017;20(7):647-655. doi: 10.2174/1386207320666170417145856.
Integrated Differential Regulatory Analysis Reveals a Novel Prognostic 36-Gene Signature for Gastric Cancer in Asian Population. Li J, Wu S, Yang L, Li YX, Liu BY, Li YY. Comb Chem High Throughput Screen. 2017;20(2):174-181. doi: 10.2174/1386207320666170117121543.
Differential Regulatory Analysis Based on Coexpression Network in Cancer Research. Li J, Li YX, Li YY. Biomed Res Int. 2016;2016:4241293. doi: 10.1155/2016/4241293. Epub 2016 Aug 11.
A novel integrated gene coexpression analysis approach reveals a prognostic three-transcription-factor signature for glioma molecular subtypes. Wu S, Li J, Cao M, Yang J, Li YX, Li YY. BMC Syst Biol. 2016 Aug 26;10 Suppl 3:71. doi: 10.1186/s12918-016-0315-y.
Hyperlipidemia-associated gene variations and expression patterns revealed by whole-genome and transcriptome sequencing of rabbit models. Wang Z, Zhang J, Li H, Li J, Niimi M, Ding G, Chen H, Xu J, Zhang H, Xu Z, et al., Chen YE, Li Y. Sci Rep. 2016 Jun 1;6:26942. doi: 10.1038/srep26942.
Integrated analysis of transcriptome in cancer patient-derived xenografts. Li H, Zhu Y, Tang X, Li J, Li Y, Zhong Z, Ding G, Li Y. PLoS One. 2015 May 7;10(5):e0124780. doi: 10.1371/journal.pone.0124780. eCollection 2015.
Evidence for widespread exonic small RNAs in the glaucophyte alga Cyanophora paradoxa. Gross J, Wajid S, Price DC, Zelzion E, Li J, Chan CX, Bhattacharya D. PLoS One. 2013 Jul 3;8(7):e67669. doi: 10.1371/journal.pone.0067669. Print 2013.
会议论文及发表演说
NIEE: Modeling Edge Embeddings for Drug-Disease Association Prediction via Neighborhood Interactions. Jiang Y, Zhou J, Zhang Y, Wu Y, Wang X and Li J. ICIC 2023 : International Conference On Intelligent Computing, Zhengzhou, China, 2023.8
NSAP: A neighborhood subgraph aggregation method for drug-disease association prediction. Jiao Q, Jiang Y, Zhang Y, Wang Y and Li J. ICIC 2022 : International Conference On Intelligent Computing, on line, 2022.8
ScSSC: semi-supervised single cell clustering based on 2D embedding. Shi N, Du L, Liu B, Wang Y and Li J. ICIC 2021 : International Conference On Intelligent Computing, Shenzhen, on line, 2021.8
GONET: A Deep Network to Annotate Proteins via Recurrent Convolution Networks. Li J, Wang L, Zhang X, Liu B and Wang Y. BIBM 2020: International Conference on Bioinformatics & Biomedicine, 2020.12
HGAlinker: drug-disease association prediction based on attention mechanism of heterogeneous graph. Jing X, Jiang W, Zhang Z, Wang Y and Li J. ICIC 2020 : International Conference On Intelligent Computing, on line, 2020.10
Prediction of human lncRNAs based on integrated information entropy features. Li J, Li H, Zhang L, Xu Q, Ping Y, Jing X, Jiang W, Liu B, Wang Y. ICIC 2019 : International Conference On Intelligent Computing, Nanchang, China, 2019.8
Prognostic prediction of carcinoma by a differential-regulatory-network-embedded deep neural network. Li J, Ping Y, Li H, Xu Q, Wang L, Liu Y, Liu B, Wang Y. IDMB 2019: International Conference on Data Science in Medicine and Bioinformatics, 2019.6
DeGSM: memory scalable construction of large scale de Bruijn graph. Hongzhe Guo H, Fu Y, Gao Y, Li J, Wang Y, Liu B. The 17th Asia Pacific Bioinformatics Conference, 2019.1
DeepDNA: a hybrid convolutional and recurrent neural network for compressing human mitochondrial genomes. Wang R, Bai Y, Chu Y, Wang Z, Wang Y, Sun M, Li J, Zang T, Wang Y. BIBM 2018: International Conference on Bioinformatics & Biomedicine, 2018.12
Integrated entropy-based approach for analyzing exons and introns in DNA sequences. Li J, Zhang L, Li H, Ping Y, Xu Q, Wang R, Tan R, Wang Z, Liu B, Wang Y. IDMB 2018: International Conference on Data Science in Medicine and Bioinformatics, 2018.6
Integrated gene co-expression analysis approach reveals a prognostic three-transcription-factor signature for glioma molecular subtypes. Wu S, Li J, Cao M, Yang J, Li YX, Li YY. ICIBM 2015: International Conference on Intelligent Biology and Medicine，Indianapolis，US，2015.11.
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