生物大数据整合审编技术及平台：研发标准化和自动化的数据收集与整合、实体识别与知识提取、数据与知识关联融合技术，应用于疾病与健康、非编码RNA、分子进化等主题特色数据库建设，服务于国家应急攻关任务、人类基因组注释、物种多样性研究等，支撑国家生物信息中心数据资源体系建设。未来将利用人工智能算法、大语言模型等前沿技术，研发智能化的生物大数据整合审编技术，提升数据资源平台服务能力。

RNA调控信息学：RNA是一种古老且具有多种功能的特殊生物大分子。以往研究主要关注其遗传信息传递功能，对其调控功能缺乏系统深入研究。我们利用生物信息学分析方法，基于生命多组学数据整合挖掘，研究不同类型RNA的调控功能，回答以下问题：1）哪些RNA具有调控功能？例如，除了ncRNA，是否还存在大量有调控功能的mRNA；2）RNA调控功能的分子基础是什么？期望建立RNA的新型鉴定和分类方法；3）RNA的调控功能如何影响人类进化和健康疾病？除了RNA疫苗，RNA世界能给予人类社会的可能更多。

代表论文（#共同第一，*共同通讯）：

1. Ma Lina# as co-first author in CNCB-NGDC Members & Partners. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024. Nucleic Acids Res 2024;52(D1):D18-D32.

2. Gao Xinxin#, Chen Kai#, Xiong Jie#, Zou Dong#, Yang Fangdian, Ma Yingke, Jiang Chuanqi, Gao Xiaoxuan, Wang Guangying, Gu Siyu, Zhang Peng, Luo Shuai, Huang Kaiyao, Bao Yiming, Zhang Zhang*, Ma Lina*, Miao Wei*. The P10K Database: A Data Portal for the Protist 10 000 Genomes Project. Nucleic Acids Res 2024;52(D1):D747-D755.

3. Li Cuiping#, Ma Lina#, Zou Dong#, Zhang Rongqin#, Bai Xue, Li Lun, Wu Gangao, Huang Tianhao, Zhao Wei, Jin Enhui, Bao Yiming*, Song Shuhui*. RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variant Monitoring, and Risk Pre-warning. Genomics, Proteomics & Bioinformatics 2023:S1672-0229(23)00116-X.

4. Ma Lina#,*, Zhao Wei#, Huang Tianhao#, Jin Enhui#, Wu Gangao, Zhao Wenming, and Bao Yiming*. On the collection and integration of SARS-CoV-2 genome data. Biosafety and Health 2023, 5(4):204-210.

5. Ma Lina* and Zhang Zhang*. The contribution of databases towards understanding the universe of long non-coding RNAs. Nat Rev Mol Cell Biol 2023. doi: 10.1038/s41580-023-00612-z.

6. Li Zhao#, Liu Lin#, Feng Changrui#, Qin Yuxin, Xiao Jingfa, Zhang Zhang*, Ma Lina*. LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations. Nucleic Acids Res 2023, 51(D1):D186-D191.

7. Ma Lina# as co-first author in CNCB-NGDC Members & Partners: Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023. Nucleic Acids Res 2023, 51(D1):D18-D28.

8. Ma Lina#,*, Zou Dong#, Liu Lin#, Shireen Huma, Abbasi A. Amir, Bateman Alex, Xiao Jingfa, Zhao Wenming, Bao Yiming, Zhang Zhang*. Database Commons: A Catalog of Worldwide Biological Databases. Genomics Proteomics Bioinformatics. 2022 Dec 23:S1672-0229(22)00169-3. doi: 10.1016/j.gpb.2022.12.004. Epub ahead of print.

9. Liu Lin#, Li Zhao#, Liu Chang#, Zou Dong, Li Qianpeng, Feng Changrui, Jing Wei, Luo Sicheng, Zhang Zhang*, Ma Lina*. LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system. Nucleic Acids Research, 2022, 50(D1):D190-D195

10. Liu Lin#, Zhang Yang#, Niu Guangyi#, Li Qianpeng, Li Zhao, Zhu Tongtong, Feng Changrui, Liu Xiaonan, Zhang Yuansheng, Xu Tianyi, Chen Ruru, Teng Xufei, Zhang Rongqin, Zou Dong, Ma Lina*, Zhang Zhang*. BrainBase: a curated knowledgebase for brain diseases, Nucleic Acids Research, 2022, 5 0(D1): D1131-D1138

11. Jiang Shuai#, Du Qiang#, Feng Changrui#, Ma Lina*, Zhang Zhang*. CompoDynamics: a comprehensive database for characterizing sequence composition dynamics. Nucleic Acids Research, 2022, 50(D1):D962-D969

12. Ma Lina# as co-first author in CNCB-NGDC Members and Partners: Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Research, 2022, 50(D1):D27-D38

13. Li Zhao#, Liu Lin#, Jiang Shuai, Li Qianpeng, Feng Changrui, Du Qiang, Zou Dong, Xiao Jingfa, Zhang Zhang* and Ma Lina*. LncExpDB: an expression database of human long non-coding RNAs. Nucleic Acids Research, 2021, 49(D1): D962-D968

14. Ma Lina# as co-first author in National Genomics Data Center Members and Partners. Database Resources of the National Genomics Data Center in 2021. Nucleic Acids Research, 2021, 49(D1):D18-D28.

15. Ma Lina is authored in RNAcentral Consortium. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Research, 2021, 49(D1): D212-D220

16. Song Shuhui#, Ma Lina#, Zou Dong#, Tian Dongmei#, Li Cuiping#, Zhu Junwei#, Chen Meili, Wang Anke, Ma Yingke, Li Mengwei, Teng Xufei, Cui Ying, Duan Guangya, Zhang Mochen, Jin Tong, Shi Chengmin, Du Zhenglin, Zhang Yadong, Liu Chuandong, Li Rujiao, Zeng Jingyao, Hao Lili, Jiang Shuai, Chen Hua, Han Dali, Xiao Jingfa, Zhang Zhang*, Zhao Wenming *, Xue Yongbiao *, Bao Yiming *. The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR, Genomics Proteomics Bioinformatics, 2020, 18(6): 749-759

17. Li Qianpeng#, Li Zhao#, Feng Changrui, Jiang Shuai, Zhang Zhang*, Ma Lina*. Multi-omics annotation of human long non-coding RNAs. Biochemical Society Transactions, 2020, 48(4): 1545-1556 (invited review)

18. 赵文明*,#; 宋述慧#; 陈梅丽#; 邹东#; 马利娜#; 马英克; 李茹姣; 郝丽丽; 李翠萍; 田东梅; 唐碧霞; 王彦青; 朱军伟; 陈焕新; 章张; 薛勇彪*; 鲍一明*; 2019新型冠状病毒信息库, 遗传, 2020, 42(02): 212-221

19. Ma Lina# as co-first author in National Genomics Data Center Members and Partners. Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Research 2020, 48(D1): D24-D33

20. Liu Lin#, Wang Guangyu#, Wang Liguo, Yu Chunlei, Li Mengwei, Song Shuhui, Hao Lili, Ma Lina* & Zhang Zhang*. Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling. Biology Direct, 2020, volume 15, Article number: 10

21. Wang Guangyu, Yin Hongyan, Li Boyang, Yu Chunlei, Wang Fan, Xu Xingjian, Cao Jiabao, Bao Yiming, Wang Liguo, Abbasi A. Amir, Bajic B. Vladimir, Ma Lina* and Zhang Zhang*. Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics, 2019, doi: 10.1093/bioinformatics/btz008

22. Ma Lina*,#, Cao Jiabao#, Liu Lin#, Du Qiang, Li Zhao, Zou Dong, Bajic B. Vladimir, Zhang Zhang*. LncBook: a curated knowledgebase of human long non-coding RNAs. Nucleic Acids Research, 2019, 47(D1): D128-D134

23. Ma Lina*,#, Cao Jiabao#, Liu Lin#, Li Zhao, Shireen Huma, Pervaiz Nashaiman, Batool Fatima, Raza Z Rabail, Zou Dong, Bao Yiming, Abbasi A. Amir, Zhang Zhang*: Community curation and expert curation of human long non-coding RNAs. Current Protocols in Bioinformatics, 2019, 67(1):e82 (invited protocol)

24. Ma Lina# as co-first author in BIG Data Center Members. Database Resources of the BIG Data Center in 2019. Nucleic Acids Research, 2019, 47(D1): D8-D14

25. Ma Lina# as co-first author in BIG Data Center Members. Database Resources of the BIG Data Center in 2018. Nucleic Acids Research, 2018, 46(D1): D14-D20

26. Ma Lina# as co-first author in BIG Data Center Members. The BIG Data Center: from deposition to integration to translation. Nucleic Acids Research, 2017, 45(D1): D18-D24

27. Ma Lina#, Li Ang#, Zou Dong, Xu Xingjian, Xia Lin, Yu Jun, Bajic B. Vladimir* and Zhang Zhang*. LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs, Nucleic Acids Research, 2015, 43: D187-D192

28. Zou Dong#, Ma Lina#, Yu Jun, Zhang Zhang: Biological databases for human research. Genomics Proteomics Bioinformatics, 2015, 13(1):55-63.

29. Ma Lina, Cui Peng, Zhu Jiang, Zhang Zhihua, Zhang Zhang: Translational selection in human: more pronounced in housekeeping genes. Biology Direct, 2014, 9:17.

30. Ma Lina, Bajic B. Vladimir, Zhang Zhang. On the classification of long non-coding RNAs. RNA Biology, 2013, 10(6): 924-933 (Google Scholar Citations > 930)

31. Ma Lina, Nie Linghu, Liu Jing, Zhang Bing, Song Shuhui, Sun Min, Yang Jin, Yang Yadong, Fang Xiangdong, Hu Songnian, Zhao Yongliang*, Yu Jun*: An RNA-seq-based gene expression profiling of radiation-induced tumorigenic mammary epithelial cells. Genomics Proteomics Bioinformatics, 2013, 10(6):326-335.

32. Ma Lina, Huang Yanyan, Zhu Wangyu, Zhou Shiquan, Zhou Jihang, Zeng Fang, Liu Xiaoguang, Zhang Yongkui, Yu Jun: An integrated analysis of miRNA and mRNA expressions in non-small cell lung cancers. PLoS One, 2011, 6(10): e26502.

33. Ma Lina, Meng Qingshu, Cheng Weihung, Sung Yunju, Tang Petrus, Hu Songnian*, Yu Jun*: Involvement of the GP63 protease in infection of Trichomonas vaginalis. Parasitology Research, 2011, 109(1):71-79.

34. Ma Lina, Chen Kaifu, Meng Qingshu, Liu Qingyou, Tang Petrus, Hu Songnian*, Yu Jun*: An evolutionary analysis of trypanosomatid GP63 proteases. Parasitology Research, 2011, 109(4):1075-1084. 

软件著作权

马利娜; 邹东; 刘琳; 章张; 全球生物数据库目录平台 [简称: DBC] V1.0, 2023SR0619912, 原始取得, 全部权利, 2022-12-14

李昭; 刘琳; 冯昶瑞; 章张; 马利娜; 人类长非编码RNA整合及多组学注释平台 [简称: LncBook] V2.0, 2023SR0620714, 原始取得, 全部权利, 2022-7-1

刘琳; 李昭; 刘畅; 章张; 马利娜; 基于优化的审编模型和网站系统的长非编码RNA群体审编平台 [简称: LncRNAWiki] V2.0, 2022SR0319145, 原始取得, 全部权利, 2021-7-1

李昭; 刘琳; 章张; 马利娜; 人类长非编码RNA表达数据库系统 [简称: LncExpDB] V1.0, 2022SR0319157, 原始取得, 全部权利, 2020-8-30

马利娜; 曹佳宝; 刘琳; 章张; 基于专业审编的人类长非编码RNA知识库系统 [简称: LncBook] V1.0, 2019SR0347237, 原始取得, 全部权利, 2018-6-30

降帅; 杜强; 冯昶瑞; 马利娜; 章张; 分子序列组分动态图谱数据库系统 [简称: CompoDynamics] V 1.0, 2022SR0319146, 原始取得, 全部权利, 2021-9-16

刘琳; 张阳; 牛广艺; 马利娜; 章张; 脑疾病知识库系统 [简称: BrainBase] V1.0, 2022SR0319144 , 原始取得, 全部权利, 2021-7-1

降帅；朱军伟；陈梅丽；马利娜；新冠病毒基因组组装及注释在线分析软件V1.0，2021SR2039216，原始取得, 全部权利, 2020-4-6（新冠病毒基因组注释软件部分）

马利娜; 邹东; 张陌尘; 崔莹; 段光亚; 金彤; 鲍一明; 新冠病毒基因组信息标准化整合与展示平台 [简称: 基因组序列发布] V2.0, 2021SR2060037, 原始取得, 全部权利, 2020-07-1

王光煜; 马利娜; 章张; 基于序列特征关系的长非编码RNA鉴定软件 [简称: LGC] V1.0, 2019SR0347231, 原始取得, 全部权利, 2018-1-10

马利娜; 李昂; 章张; 基于wiki的长非编码RNA审编平台 [简: LncRNAWiki] V1.0, 2015SR265449, 原始取得, 全部权利, 2014-11-15

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