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Lina Ma
Lina Ma

Associate Professor

Team Leader, LncRNA Resources

Email: malina (AT) big.ac.cn

Tel: +86 (10) 8409-7845

PROFESSIONAL EXPERIENCE

  • Young Professor, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation (CNCB), China, 2024−Present

  • Associate Professor, Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation (CNCB), China, 2018−2024

  • Assistant Professor, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2012−2018

  • Assistant Professor, Zhoushan Hospital, China, 2010−2012

EDUCATION

  • Ph.D. in Bioinformatics, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), China, 2010

  • B.S. in Biotechnology, Ocean University of China, China, 2005

RESEARCH INTERESTS

  • Function and Molecular Evolution of Non-coding RNA

  • Big Data Integration and Analytics

PROJECTS & RESOURCES

  • LncBook 2.0 and LncBook 1.0 (integration and multi-omics annotation of human lncRNAs, China's Top Ten Bioinformatics Databases of 2019, expert database of RNAcentral)

  • LncRNAWiki 2.0 and LncRNAWiki 1.0 (community-curation based knowledgebase of lncRNAs)

  • LncExpDB (expression database of human lncRNAs)

  • LGC (characterization and identification of lncRNAs based on feature relationship)

  • CompoDynamics (sequence composition dynamics of genes and genomes)

  • BrainBase (a curated knowledgebase of brain diseases)

  • The P10K Database (protist 10,000 genomes project)

  • RCoV19 (previously known as 2019nCoVR, highly accessed, China's Top Ten Bioinformatics Advances of 2020)

  • Database Commons (a curated catalogue of biological databases, highly accessed, China's Top Ten Bioinformatics Advances of 2022)

  • ScienceWikis (a catalog of biological knowledge wikis and wiki extensions)

  • MIA (multi-omics integrative analysis)

SOFTWARE COPYRIGHT

  • 全球生物数据库目录平台 [简称: DBC] V1.0, 2023SR0619912

  • 人类长非编码RNA整合及多组学注释平台 [简称: LncBook] V2.0, 2023SR0620714

  • 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

  • 人类长非编码RNA表达数据库系统 [简称: LncExpDB] V1.0, 2022SR0319157

  • 分子序列组分动态图谱数据库系统 [简称: CompoDynamics] V 1.0, 2022SR0319146

  • 脑疾病知识库系统 [简称: BrainBase] V1.0, 2022SR0319144

  • 新冠病毒基因组标准化整合与展示平台 [简称: 基因组序列发布] V2.0，2021SR2060037

  • 新冠病毒基因组组装及注释在线分析软件V1.0，2021SR2039216

  • 基于序列特征关系的长非编码RNA鉴定软件 [简称: LGC] V1.0，2019SR0347231

  • 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

  • 基于wiki的长非编码RNA审编平台 [简称：LncRNAWiki] V1.0，2015SR265449

FUNDING

  • National Natural Science Foundation of China (Grant No. 32470608): The bioinformatics method for large-scale identification of regulatory messenger RNA, 50w RMB, 2025.01-2028.12

  • Outstanding Member of the Youth Innovation Promotion Association, CAS (Y2021038), 200w RMB, 2024.1-2026.12

  • Strategic Priority Research Program, CAS, 44w RMB, 2020.01-2024.12

  • Member of the Youth Innovation Promotion Association, CAS (No. 2019104), 80w RMB, 2019.01-2022.12

  • National Natural Science Foundation of China (Grant No. 31200978): Building transcriptomic interactive networks for miR-21-related mechanisms in cancer cells based on deep RNA-seq (Ribo-minus) data, 20w RMB, 2013.01-2015.12

ACADEMIC ACTIVITIE

    EDITOR

    REVIEWER

  • Reviewer: Nucleic Acids Research, Clinical and Translational Medicine, Communications Biology, Biomedicine & Pharmacotherapy, Genomics Proteomics & Bioinformatics, Biology Direct, MAMMALIAN GENOME, BioMed Research International (formerly titled Journal of Biomedicine and Biotechnology), GIW(International Conference on Genome Informatics), Human Genetics, PLoS ONE, SCIENCE CHINA Life Sciences, F1000Research

    TRAINING

  • Training: 全球生物数据库归档与检索（NGDC用户培训，腾讯会议，2022.12.02）

  • Training: LncRNA数据库与算法工具的应用（NGDC用户培训，腾讯会议，2022.12.02）

  • Training: 人类长非编码RNA注释资源（清华大学基因测序与分析平台，腾讯会议，2021.01.07）

  • Hands-on training in Pakistan-China Genomics Workshop (17-19 July, 2018): Database Commons: a curated catalogue of biological databases; GSA: Genome Sequence Archive; Genome Variation Map: a repository of genome variations for animals and plants.

    POSTER

  • Poster: International Conference of Genomics 2015, Database Commons: a curated catalogue of biological databases (The third poster prize).

  • Poster: Biocuration 2015, LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.

  • Poster: SMBE 2014, Translational selection in human: more pronounced in housekeeping genes.

  • Poster: SMBE 2014, Heterogeneity of translational selection in human tissues.

  • Poster: 2013 Transcriptional Regulation in Eukaryotes, Cold Spring Harbor Laboratory, A knowledge base for community curation of human long non-coding RNAs.

  • Poster: 2013 International Conference of Genomics, A knowledge base for community curation of human long non-coding RNAs.

    TALK

  • Talk: Identify non-mutational p53 loss of function in human cancers (The 2nd Conference on Bioinformatics and Translational Medicine, Beijing, 2024.04.12-13)

  • Talk: 基因与基因组学大数据（中国科学院青年创新促进会2022 年度学术年会，深圳，2023.04.10-13）

  • Talk: 人类长非编码RNA整合审编与功能解析（第十一届全国生物信息学与系统生物学学术大会，广州，2023.02.25-27）

  • Talk: LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system (RNAcentral Consortium 2021, 2021.11.19, Over Zoom)

  • Talk: Identification, characterization and curation of long non-coding RNAs (The 6th Big Data Forum for Life and Health Science, Online, 2021.10.15)

  • Conference Committee, Noncoding RNA World: From Mechanism to Therapy, 2021.07.21-23

  • Talk: 人类长非编码RNA多生物学场景表达图谱（第三届青年生命科学论坛，北京，2021.06.04-06）

  • Talk：生物信息大数据管理与共享（大科学装置交叉学科论坛，广东东莞，2020.12.12）

  • Talk: RNAcentral Consortium 2020 (20 November, 2020; Cambridge, United Kingdom, Over Zoom), Expression profiles of human lncRNAs across diverse biological contexts/conditions.

  • Talk: Multi-omics annotation of human long non-coding RNAs (第二届青年生命科学论坛，武汉，2020.09.24-26；第九届全国生物信息学与系统生物学学术大会，上海，2020.0926-0929)

  • Talk: The 4th Big Data Forum for Life and Health Sciences (13-16 October, 2019; Beijing, China), Annotation of human lncRNAs based on multi-omics data integration and analysis.

  • Talk: RNA Informatics 2019 (9-11 September, 2019; Cambridge, United Kingdom), Annotation of human lncRNAs based on multi-omics data integration and analysis.

  • Talk: 第一届青年生命科学论坛（乌鲁木齐，2019.07.12-16），长非编码RNA跨物种鉴定及功能研究.

  • Talk: RNAcentral Consortium 2018 (Cambridge, United Kingdom), LncBook: a curated knowledgebase of human long non-coding RNAs.

  • Workshop Talk: Biocuration 2018, LncRNAWiki: community curation of human long non-coding RNAs.

SCIENCE POPULARIZATION

  • 生命的密码——基因，科普报告，海淀实验小学，2024.05.28

  • 认识生命——什么是基因，科普报告，中国科学院附属实验学校（小学部），2024.04.11

  • 从基因到基因组大数据，科普报告，中国科学院第十九届公众科学日，2023.05.13

  • 从基因到基因组大数据，科普报告，北京基因组研究所（北京一零一中上地校区初二瑾瑜十班），2023.04.16

  • 第七届全国青年科普创新实验暨作品大赛，科普实验单元-生物环境命题（大学组），决赛评委， 2021.07.20-21

  • 国家生物信息中心公众号科普文章，动物与新冠病毒，2021.06.11

  • 北京基因组研究所科普水果拼盘比赛，评委，2020.11.07

  • 从基因到基因组大数据，科普报告，甘家口街道（2019.12.20）、羊坊店街道（2020.01），中科院行管局与海淀区文明委共同组织的走进中科院的科普活动

  • “环球自然日”青少年自然科学知识挑战赛，北京赛区中小学组评委，国家自然博物馆，2019.05.2

PUBLICATIONS (Google Scholar citations: 5178, as of 2024.09; H index: 28)

  1. Li Q#, Zhang Y#, Luo S, Zhang Z, Oberg A, Kozono D, Lu H, Sarkaria J, Ma L*, Wang L*. Identify non-mutational p53 functional deficiency in human cancers. Genomics, Proteomics & Bioinformatics 2024 (in proof).

  2. Ma L# 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.

  3. Gao X#, Chen K#, Xiong J#, Zou D#, Yang F, Ma Y, Jiang C, Gao X, Wang G, Gu S, Zhang P, Luo S, Huang K, Bao Y, Zhang Z*, Ma L*, Miao W*. The P10K Database: A Data Portal for the Protist 10 000 Genomes Project. Nucleic Acids Res 2024;52(D1):D747-D755. [PMID=37930867]

  4. Li C#, Ma L#, Zou D#, Zhang R#, Bai X, Li L, Wu G, Huang T, Zhao W, Jin E, Bao Y*, Song S*. 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. [PMID=37898309]

  5. Ma L#,*, Zhao W#, Huang T#, Jin E#, Wu G, Zhao W, and Bao Y*. On the collection and integration of SARS-CoV-2 genome data. Biosafety and Health 2023, 5(4):204-210.

  6. Ma L* and Zhang Z*. The contribution of databases towards understanding the universe of long non-coding RNAs. Nat Rev Mol Cell Biol, 2023 May 5. doi: 10.1038/s41580-023-00612-z. (invited comment) [PMID=37147495]

  7. Li Z#, Liu L#, Feng C#, Qin Y, Xiao J, Zhang Z*, Ma L*. LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations. Nucleic Acids Res 2023, 51(D1):D186-D191. [PMID=36330950]

  8. Ma L# 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. [PMID=36420893]

  9. Ma L#,*, Zou D#, Liu L#, Shireen H, Abbasi AA, Bateman A, Xiao J, Zhao W, Bao Y, Zhang Z*. 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. [PMID: 36572336]

  10. Yu D, Yang X, Tang B, Pan YH, Yang J, Duan G, Zhu J, Hao ZQ, Mu H, Dai L, Hu W, Zhang M, Cui Y, Jin T, Li CP, Ma L; Language translation team, Su X, Zhang G, Zhao W*, Li H*. Coronavirus GenBrowser for monitoring the transmission and evolution of SARS-CoV-2. Brief Bioinform. 2022 Jan 19:bbab583. doi: 10.1093/bib/bbab583. Epub ahead of print. [PMID: 35043153]

  11. Ma L# 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 Res 2022, 50(D1):D27-D38. [PMID=34718731]

  12. Liu L#, Li Z#, Liu C#, Zou D, Li Q, Feng C, Jing W, Luo S, Zhang Z*, Ma L*. LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system. Nucleic Acids Res 2022, 50(D1):D190-D195. [PMID=34751395] 

  13. Liu L#, Zhang Y#, Niu G#, Li Q, Li Z, Zhu T, Feng C, Liu X, Zhang Y, Xu T, Chen R, Teng X, Zhang R, Zou D, Ma L*, Zhang Z*. BrainBase: a curated knowledgebase for brain diseases. Nucleic Acids Res 2022,50(D1):D1131-D1138. [PMID=34718720]

  14. Jiang S#, Du Q#, Feng C#, Ma L*, Zhang Z*. CompoDynamics: a comprehensive database for characterizing sequence composition dynamics. Nucleic Acids Res 2022, 50(D1):D962-D969. [PMID=34718745]

  15. Ma L authored in The RNAcentral Consortium. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res 2021, 49(D1):D212-D220. [PMID=33106848]

  16. Ma L# as co-first author in National Genomics Data Center Members and Partners. Database Resources of the National Genomics Data Center in 2021. Nucleic Acids Res 2021, 49(D1):D18-D28. [PMID=33175170]

  17. Gong Z, Zhu J, Li C, Jiang S, Ma L, Tang B, Zou D, Chen M, Sun Y, Song S, Zhang Z, Xiao J, Xue Y, Bao Y, Du Z, Zhao W. A coronavirus online analysis platform at the National Genomics Data Center. Zoological research 2020, 1-6. [PMID=33045776]

  18. Song S#, Ma L#, Zou D#, Tian D#, Li C#, Zhu J#, Chen M, Wang A, Ma Y, Li M, Teng X, Cui Y, Duan G, Zhang M, Jin T, Shi C, Du Z, Zhang Y, Liu C, Li R, Zeng J, Hao L, Jiang S, Chen H, Han D, Xiao J, Zhang Z*, Zhao W*, Xue Y*, Bao Y*. The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR. Genomics Proteomics Bioinformatics. 2020 Dec;18(6):749-759. [PMID=33704069]

  19. Li Z#, Liu L#, Jiang S, Li Q, Feng C, Du Q, Zou D, Xiao J, Zhang Z*, Ma L*: LncExpDB: an expression database of human long non-coding RNAs. Nucleic Acids Res 2021, 49(D1):D962-D968. [PMID=33045751]

  20. Cheng Sun, Jiaxing Huang, Yun Wang, Xiaomeng Zhao, Long Su, Gregg W C Thomas, Mengya Zhao, Xingtan Zhang, Irwin Jungreis, Manolis Kellis, Saverio Vicario, Igor V Sharakhov, Semen M Bondarenko, Martin Hasselmann, Chang N Kim, Benedict Paten, Luca Penso-Dolfin, Li Wang, Yuxiao Chang, Qiang Gao, Ling Ma, Lina Ma, Yuxiao Zhang, Hongbo Zhang, Huahao Zhang, Livio Ruzzante, Hugh M Robertson, Yihui Zhu, Yanjie Liu, Huipeng Yang, Lele Ding, Quangui Wang, Dongna Ma, Weilin Xu, Cheng Liang, Michael W Itgen, Lauren Mee, Gang Cao, Ze Zhang, Ben M Sadd, Matthew Hahn, Sarah Schaack, Seth M Barribeau, Paul H Williams, Robert M Waterhouse, Rachel Lockridge Mueller: Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Molecular Biology and Evolution 2020, msaa240.doi: 10.1093/molbev/msaa240. [PMID=32946576]

  21. Li Q#, Li Z#, Feng C, Jiang S, Zhang Z*, Ma L*: Multi-omics annotation of human long non-coding RNAs. Biochemical Society Transactions 2020. [PMID=32756901]

  22. Liu L#, Wang G#, Wang L, Yu C, Li M, Song S, Hao L, Ma L*, Zhang Z*: Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling. Biology Direct volume 15, Article number: 10 (2020). [PMID=32539851]

  23. Zhao W*,#, Song S#, Chen M#, Zou D#, Ma L#, Ma Y, Li R, Hao L, Li C, Tian D, Tang B, Wang Y, Zhu J, Chen H, Zhang Z, Xue Y*, Bao Y*. The 2019 Novel Coronavirus Resource. Hereditas(Beijing) 2020, doi: 10.16288/j.yczz.20-030. (co-first author) [PMID=32102777] (Highly Cited)

  24. Ma L# as co-first author in National Genomics Data Center Members and Partners. Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Res 2020, 48(D1):D24-D33. [PMID=31702008]

  25. Ma L*,#, Cao J#, Liu L#, Li Z, Shireen H, Pervaiz N, Batool F, Raza R, Zou D, Bao Y, Abbasi A, Zhang Z*. Community curation and expert curation of human long non-coding RNAs. Current Protocols in Bioinformatics 2019.

  26. Wang G, Yin H, Li B, Yu C, Wang F, Xu X, Cao J, Bao Y, Wang L, Abbasi A, Bajic V, Ma L*, Zhang Z*. Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics 2019, doi: 10.1093/bioinformatics/btz008 (co-corresponding author). [PMID=30649200]

  27. Sang J, Zou D, Wang Z, Wang F, Zhang Y, Xia L, Li Z, Ma L, Li M, Xu B, Liu X, Wu S, Liu L, Niu G, Li M, Luo Y, Hu S, Hao L, Zhang Z. IC4R 2.0: Rice Genome Reannotation Using Massive RNA-Seq Data. Genomics Proteomics & Bioinformatics 2020, 18(2):161-172. [PMID=32683045]

  28. Ma L authored in The RNAcentral Consortium: RNAcentral. A hub of information for non-coding RNA sequences. Nucleic Acids Res 2019. [PMID=30395267]

  29. Ma L# as co-first author in BIG Data Center Members. Database Resources of the BIG Data Center in 2019. Nucleic Acids Res 2019. [PMID=30365034]

  30. Ma L*,#, Cao J#, Liu L#, Du Q, Li Z, Zou D, Bajic VB, Zhang Z*. LncBook: a curated knowledgebase of human long non-coding RNAs. Nucleic Acids Res 2019. [PMID=30329098] (Highly Cited)

  31. Ma L# as  co-first author in BIG Data Center Members: Database Resources of the BIG Data Center in 2018. Nucleic Acids Res 2018, 46(D1):D14-D20. [PMID=29036542].

  32. Salhi A, Essack M, Alam T,Bajic VP, Ma L, Radovanovic A, Marchand B, Schmeier S, Zhang Z, Bajic V. DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. RNA Biology 2017, 14(7):963-971.[PMID=28387604]

  33. Ma L# as  co-first author in BIG Data Center Members. The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res 2017, 45(D1):D18-D24. [PMID=27899658]

  34. Ma L authored in The RNAcentral Consortium: RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Res 2017, 45(D1):D128-D134. [PMID=27794554]

  35. Yin H, Wang G, Ma L, Yi S, Zhang Z. What signatures dominantly associate with gene age? Genome Biology and Evolution 2016, 8(10):3083-9. [PMID=27609935]

  36. Yin H, Ma L, Wang G, Li M, Zhang Z. Old genes experience stronger translational selection than young genes. Gene 2016, 590(1):29-34.[PMID=27259662]

  37. Ma L authored in IC4R Project Consortium. Information Commons for Rice (IC4R). Nucleic Acids Res 2016, 44(D1):D1172-1180. [PMID=26519466]

  38. Ge X and Ma L. “Nutritionomics”-Chapter3 Transcriptome(ISBN 978-7-5679-0383-8). Peking Medical Union College Press, 2015.(Book Chapter)

  39. Ma L#, Li A#, Zou D, Xu X, Xia L, Yu J, Bajic VB, Zhang Z. LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs. Nucleic Acids Res 2015, 43(Database issue):D187-192. [PMID=25399417]

  40. Zou D#, Ma L#, Yu J, Zhang Z. Biological databases for human research. Genomics Proteomics Bioinformatics 2015, 13(1):55-63. [PMID=25712261]

  41. Zhang Z, Sang J, Ma L, Wu G, Wu H, Huang D, Zou D, Liu S, Li A, Hao L, Tian M, Xu C, Wang X, Wu J, Xiao J, Dai L, Chen LL, Hu S, Yu J. RiceWiki: a wiki-based database for community curation of rice genes. Nucleic Acids Res 2014, 42(Database issue):D1222-1228. [PMID=24136999]

  42. Ma L, Cui P, Zhu J, Zhang Z, Zhang Z. Translational selection in human: more pronounced in housekeeping genes. Biol Direct 2014, 9:17. [PMID=25011537]

  43. Ma L, Bajic VB, Zhang Z. On the classification of long non-coding RNAs. RNA Biol 2013, 10(6):925-933. [PMID=23696037] (Highly Cited)

  44. Ma L, Nie L, Liu J, Zhang B, Song S, Sun M, Yang J, Yang Y, Fang X, Hu S, Zhao Y, Yu J. An RNA-seq-based gene expression profiling of radiation-induced tumorigenic mammary epithelial cells. Genomics Proteomics Bioinformatics 2013, 10(6):326-335. [PMID=23317700]

  45. Ma L, Huang Y, Zhu W, Zhou S, Zhou J, Zeng F, Liu X, Zhang Y, Yu J. An integrated analysis of miRNA and mRNA expressions in non-small cell lung cancers. PLoS One 2011, 6(10):e26502. [PMID=22046296]

  46. Ma L, Meng Q, Cheng W, Sung Y, Tang P, Hu S, Yu J. Involvement of the GP63 protease in infection of Trichomonas vaginalis. Parasitol Res 2011, 109(1):71-79.[PMID=21221643]

  47. Ma L, Chen K, Meng Q, Liu Q, Tang P, Hu S, Yu J. An evolutionary analysis of trypanosomatid GP63 proteases. Parasitol Res 2011, 109(4):1075-1084. [PMID=21503641]

  48. Meng Q, Chen K, Ma L, Hu S, Yu J. A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases. J Genet Genomics 2011, 38(2):63-70. [PMID=21356525]

  49. Liu X, Zhu W, Huang Y, Ma L, Zhou S, Wang Y, Zeng F, Zhou J, Zhang Y. High expression of serum miR-21 and tumor miR-200c associated with poor prognosis in patients with lung cancer. Med Oncol 2011, 29(2):618-626. [PMID=21516486]

  50. Zeng F, Li Y, Chen G, Zhang Y, Wang Y, Zhou S, Ma L, Zhou J, Huang Y, Zhu W, Liu X. Nicotine inhibits cisplatin-induced apoptosis in NCI-H446 cells. Med Oncol2011, 29(1):364-373. [PMID=21267677]

  51. Chen K, Meng Q, Ma L, Liu Q, Tang P, Chiu C, Hu S, Yu J. A novel DNA sequence periodicity decodes nucleosome positioning. Nucleic Acids Res 2008, 36(19):6228-6236.[PMID=18829715]