References

[1] Akalin PK. Introduction to bioinformatics. Molecular Nutrition & Food Research. 2006;50(7):610-619.

[2] Azad RK, Shulaev V. Metabolomics technology and bioinformatics for precision medicine. Briefings in Bioinformatics. 2019;20(6):1957-1971.

[3] Gauthier J, Vincent AT, Charette SJ, et al. A brief history of bioinformatics. Briefings in Bioinformatics. 2019;20(6):1981-1996.

[4] Simpson RC, Shanahan ER, Scolyer RA, et al. Towards modulating the gut microbiota to enhance the efficacy of immune-checkpoint inhibitors. Nature Reviews Clinical Oncology. 2023;20:697-715.

[5] Zhao Y, Cheng MY, Zou L, et al. Hidden link in gut-joint axis: gut microbes promote rheumatoid arthritis at early stage by enhancing ascorbate degradation. Gut. 2022;71(5):1041-1043.

[6] Deng L, Gao BB, Zhao L, et al. Diurnal RNAPII-tethered chromatin interactions are associated with rhythmic gene expression in rice. Genome Biology. 2022;23:7.

[7] Almeida A, Mitchell AL, Boland M, et al. A new genomic blueprint of the human gut microbiota. Nature. 2019;568:499-504.

[8] Chen XW, Hao YJ, Cui Y, et al. LncVar: deciphering genetic variations associated with long noncoding genes. Methods in Molecular Biology. 2019;1870:189-198.

[9] Jiang Y, Sun AH, Zhao Y, et al. Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma. Nature. 2019;567:257-261.

[10] Zhong SJ, Zhang S, Fan XY, et al. A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. Nature. 2018;555:524-528.

[11] Zhu GT, Wang SC, Huang ZJ, et al. Rewiring of the fruit metabolome in tomato breeding. Cell. 2018;172:249-261.

[12] Zhang ZY, Wang M, Xie DF, et al. METTL3-mediated N6-methyladenosine mRNA modification enhances long-term memory consolida-tion. Cell Research. 2018;28:1050-1061.

[13] Gates AJ, Gysi DM, Kellis M, et al. A wealth of discovery built on the Human Genome Project-by the numbers. Nature. 2021;590:212-215.

[14] Martinez-Jimenez F, Muinos F, Sentis I, et al. A compendium of mutational cancer driver Genes. Nature Reviews Cancer. 2020;20(10):555-572.

[15] Esteva A, Robicquet A, Ramsundar B, et al. A guide to deep learning in healthcare. Nature Medicine. 2019;25:24-29.

[16] Zhou Y, Zhang YT, Lian XC, et al. Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents. Nucles Acids Research. 2022;50:1398-1407.

[17] Su X, Wang HX, Zhao N, et al. Trends in innovative drug development in China. Nature Reviews Drug Discovery. 2022;21(10):709-710.

[18] Zeng XX, Zhu SY, Lu WQ, et al. Target identification among known drugs by deep learning from heterogeneous networks. Chemical Science. 2020;11:1775-1797.

[19] Shang J, Wan YS, Luo CM, et al. Cell entry mechanisms of SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(21):11727-11734.

[20] Zhou C, Chen ZK, Zhang L, et al. SEPPA 3.0-enhanced spatial epitope prediction enabling glycoprotein antigens. Nucleic Acids Research. 2019;47:388-394.

[21] Qiu TY, Yang YY, Qiu JX, et al. CE-BLAST makes it possible to compute antigenic similarity for newly emerging pathogens. Nature Communications. 2018;9:1772.

[22] CNCB-NGDC Members & Partners. Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Research. 2022;50:27-38.

[23] Koppad S, Basava A, Gkoutos GV, et al. Cloud computing enabled big multi-omics data analytics. Bioinformatics Biology Insights. 2021;15:1-16.

[24] Chen F, Zhang ZQ, Ding CJ, et al. Analysis of global biosafety strategy and recommendations to China. Bulletin of Chinese Academy of Sciences. 2020;35(2):204-211.

[25] Cao ZJ, Gao G. Multi-omics single-cell data integration and regulatory inference with graph-linked embedding. Nature Biotechnology. 2022;40:1458-1466.

[26] Chowdhury R, Bouatta N, Biswas S, et al. Single-sequence protein structure prediction using a language model and deep learning. Nature Biotechnology. 2022;40:1617-1623.

[27] Vamathevan J, Apweiler R, Birney E. Biomolecular data resources: bioinformatics infrastructure for biomedical data science. Annual Review of Biomedical Data Science. 2019;2:199-222.

[28] Kundu S, Ashinsky BG, Bouhrara M, et al. Enabling early detection of osteoarthritis from presymptomatic cartilage texture maps via transport-based learning. Proceedings of the National Academy of Sciences of the National Academy of Sciences. 2020;117:24709-24719.

[29] Liu XF, Lu Z. Progress of bioinformatics studies for multi-omics and multi-modal data in complex diseases. Chinese Science Bulletin. 2024;69(30):4432-4446.

[30] Sayers EW, Bolton EE, Brister JR, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research. 2022;50:20-26.