Zhang L, Li H, Shi M, Ren K, Zhang W, Cheng Y, Wang Y, Xia X-Q. FishSNP: a high quality cross-species SNP database of fishes. Scientific Data, 2024, 11:386. 10.1038/s41597-024-03111-8.
Li H, Zhang W, Ren K, Yang H, Zhang L, Younas W, Cheng Y, Wang Y, Shi M, Xia X-Q. FishCODE: a web-based information platform for comprehensive omics data exploration in fish research. Journal of Genetics and Genomics, 2024, 51: 1525-1528. 10.1016/j.jgg.2024.09.019.
Guo C, Ye W, Cao D, Shi M, Zhang W, Cheng Y, Wang Y, Xia X-Q. Unraveling the stereoscopic gene transcriptional landscape of zebrafish using FishSED, a fish spatial expression database with multispecies scalability. Science China Life Sciences, 2024, 67(4): 843-846. 10.1007/s11427-023-2418-2.
Guo C, Duan Y, Ye W, Zhang W, Cheng Y, Shi M, Xia X-Q, FishGET: a fish gene expression and transcriptome database with improved accuracy and visualization. iScience, 2023, 26: 106539. 10.1016/j.isci.2023.106539.
Guo C, Ye W, Shi M, Duan Y, Zhang W, Cheng Y, Xia X-Q. FishSCT: a zebrafish-centric database for exploration and visualization of fish single-cell transcriptome. Science China Life Sciences, 2023, 66(9): 2185-2188. 10.1007/s11427-022-2293-4.
Li H, Shi M, Ren K, Zhang L, Ye W, Zhang W, Cheng Y, Xia X-Q. Visual Omics: A web-based platform for omics data analysis and visualization with rich graph-tuning capabilities. Bioinformatics, 2023, 39(1): btac777. 10.1093/bioinformatics/btac777.
Chen Y, Shi M, Zhang W, Cheng Y, Wang Y, Xia X-Q. The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations. Database, 2017, 2017: bax051. 10.1093/database/bax051.
TOOLS
Cao D, Yang H, Guo C, Cheng Y, Zhang W, Shi M, Xia X-Q. ESC-YOLOv8-seg: A real-time non-destructive detection framework for small-target surface anomalies in zebrafish underwater monitoring. Ecological Informatics, 2025, 92: 103473. 10.1016/j.ecoinf.2025.103473.
Cao D, Guo C, Shi M, Liu Y, Fang Y, Yang H, Cheng Y, Zhang W, Wang Y, Li Y, Xia X-Q. A method for custom measurement of fish dimensions using the improved YOLOv5-keypoint framework with multi-attention mechanisms. Water Biology and Security, 2024, 3: 100293. 10.1016/j.watbs.2024.100293.
Xia L, Shi M, Li H, Zhang W, Cheng Y, Xia X-Q. PMSeeker: a scheme based on the greedy algorithm and the exhaustive algorithm to screen low-redundancy marker sets for large-scale parentage assignment with full parental genotyping. Biology, 2024, 13(2): 100. 10.3390/biology13020100.
Chen Y, Shi M, Cheng Y, Zhang W, Tang Q, Xia X-Q. FVD: The fish-associated virus database. Infection, Genetics and Evolution, 2018, 58: 23-26. 10.1016/j.meegid.2017.11.004.
Tang Q, Song Y, Shi M, Cheng Y, Zhang W, Xia X-Q. Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition. Scientific Reports, 2015, 5: 17155. 10.1038/srep17155.
Wang Y, McClelland M, Xia XQ. Analyzing microarray data using WebArray. Cold Spring Harbor Protocols, 2009. 4(8). 10.1101/pdb.prot5260.
Xia XQ, McClelland M, Porwollik S et al. WebArrayDB: Cross-platform microarray data analysis and public data repository. Bioinformatics, 2009, 25(18): 2425-2429. 10.1093/bioinformatics/btp430.
Xia X, McClelland M, Wang Y. WebArray: an online platform for microarray data analysis. BMC Bioinformatics, 2025, 6(1): 306. 10.1186/1471-2105-6-306.
