Lina Ma

Associate Professor

Team Leader, LncRNA Resources

Email: malina (AT) big.ac.cn

Tel: +86 (10) 8409-7845

PROFESSIONAL EXPERIENCE

  • Associate Professor, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing, China 2018.6−Present

  • Assistant Professor, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), Beijing, China 2012.3−2018.5

  • Assistant Professor, Zhoushan Hospital, Zhejiang, China 2010.6−2012.2

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

  • LncExpDB (expression database of human long non-coding RNAs)

  • LncBook (a curated knowledgebase of human long non-coding RNAs, Top ten bioinformatics databases of China in 2019)

  • LncRNAWiki 2.0 (community-curation of lncRNAs)

  • LncRNAWiki (a wiki-based database for community curation of human lncRNAs)

  • LGC (characterization and identification of long non-coding RNAs based on feature relationship)

  • CompoDynamics (sequence composition dynamics of genes and genomes)

  • BrainBase (a curated knowledgebase of brain diseases)

  • P10K (Protist 10,000 Genomes Project)

  • 2019nCoVR (2019 novel coronavirus resource)

  • Database Commons (a curated catalogue of biological databases, Highly Accessed)

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

FUNDING

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

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

  • Strategic Priority Research Program of the Chinese Academy of Sciences (XDB38030400), 2020.01-2024.12

ACADEMIC ACTIVITIES

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

  • 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.

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

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

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

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

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

  • 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.

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

  • Talk: 第一届青年生命科学论坛(乌鲁木齐,2019.0712-0716),长非编码RNA跨物种鉴定及功能研究.

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

  • 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: Multi-omics annotation of human long non-coding RNAs (第二届青年生命科学论坛,武汉,2020.0924-0926;第九届全国生物信息学与系统生物学大会,上海,2020.0926-0929)

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

  • 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)

  • 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)

  • 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: 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

SCIENCE POPULARIZATION

  • 北京基因组研究所科普水果拼盘比赛,评委,2020.11.07

  • 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

  • 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,2019.05.26

PUBLICATIONS (Google Scholar citations: 2627, as of 2021.11; H index: 23)

  1. 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, https://pubmed.ncbi.nlm.nih.gov/34718731 

  2. Lin Liu#, Zhao Li#, Chang Liu#, Dong Zou, Qianpeng Li, Changrui Feng, Wei Jing, Sicheng Luo, Zhang Zhang*, Lina Ma*: LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system. Nucleic Acids Res 2022, https://pubmed.ncbi.nlm.nih.gov/34751395 

  3. Lin Liu#, Yang Zhang#, Guangyi Niu#, Qianpeng Li, Zhao Li, Tongtong Zhu, Changrui Feng, Xiaonan Liu, Yuansheng Zhang, Tianyi Xu, Ruru Chen, Xufei Teng, Rongqin Zhang, Dong Zou, Lina Ma*, Zhang Zhang*: BrainBase: a curated knowledgebase for brain diseases. Nucleic Acids Res 2022, https://doi.org/10.1093/nar/gkab987

  4. Shuai Jiang#, Qiang Du#, Changrui Feng#, Lina Ma*, Zhang Zhang*: CompoDynamics: a comprehensive database for characterizing sequence composition dynamics. Nucleic Acids Res 2022, https://doi.org/10.1093/nar/gkab979

  5. Ma L authored in The RNAcentral ConsortiumRNAcentral 2021: secondary structure integration, improved sequence search and new member databasesNucleic Acids Res 2021, doi: 10.1093/nar/gkaa921[PMID=33106848]

  6. 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. [PMID=33175170]

  7. Zheng Gong, Junwei Zhu, Cuiping Li, Shuai Jiang, Lina Ma, Bixia Tang, Dong Zou, Meili Chen, Yubin Sun, Shuhui Song, Zhang Zhang, Jingfa Xiao, Yongbiao Xue, Yiming Bao, Zhenglin Du, Wen-Ming ZhaoA coronavirus online analysis platform at the National Genomics Data Center. Zoological research, 1-6. [33045776]

  8. Shuhui Song#Lina Ma#, Dong Zou#, Dongmei Tian#, Cuiping Li#, Junwei Zhu#, Meili Chen, Anke Wang, Yingke Ma, Mengwei Li, Xufei Teng, Ying Cui, Guangya Duan, Mochen Zhang, Tong Jin, Chengmin Shi, Zhenglin Du, Yadong Zhang, Chuandong Liu, Rujiao Li, Jingyao Zeng, Lili Hao, Shuai Jiang, Hua Chen, Dali Han, Jingfa Xiao, Zhang Zhang*, Wenming Zhao*, Yongbiao Xue*, Yiming Bao*The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVRGenomics Proteomics Bioinformatics 2020

  9. Li Z#, Liu L#, Jiang S, Li QP, Feng CR, Du Q, Zou D, Xiao JF, Zhang Z*Ma LN*LncExpDB: an expression database of human long non-coding RNAsNucleic Acids Res 2021. [PMID=33045751]

  10. 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 traitsMolecular Biology and Evolution 2020, msaa240.doi: 10.1093/molbev/msaa240. [PMID=32946576]

  11. Li QP#, Li Z#, Feng CR, Jiang S, Zhang Z*Ma LN*Multi-omics annotation of human long non-coding RNAsBiochemical Society Transactions 2020. [PMID=32756901]

  12. Liu L#, Wang GY#, Wang LG, Yu CL, Li MW, Song SH, Hao LL, Ma LN* & Zhang Z*Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profilingBiology Direct volume 15, Article number: 10 (2020). [PMID=32539851]

  13. Zhao WM*,#, Song SH#, Chen ML#, Zou D#Ma LN#, Ma YK, Li RJ, Hao LL, Li CP, Tian DM, Tang BX, Wang YQ, Zhu JW, Chen HX, Zhang Z, Xue YB*, Bao YM*The 2019 Novel Coronavirus ResourceHereditas(Beijing) 2020, doi: 10.16288/j.yczz.20-030(co-first author) [PMID=32102777] (Highly Cited)

  14. 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]

  15. Ma LN*,#, Cao J#, Liu L#, Li Z, Shireen H, Pervaiz N, Batool F, Raza R, Zou D, Bao YM, Abbasi AA, Zhang Z*Community curation and expert curation of human long non-coding RNAsCurrent Protocols in Bioinformatics 2019.

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

  17. Sang J, Zou D, Wang ZN, Wang F, Zhang YS, Xia L, Li ZH, Ma LN, Li MW, Xu BX, Liu XN, Wu SY, Liu L, Niu GY, Li M, Luo YF, Hu SN, Hao LL, Zhang Z: IC4R 2.0: Rice Genome Reannotation Using Massive RNA-Seq DataGenomics Proteomics & Bioinformatics 2020, 18(2):161-172. [PMID=32683045]

  18. Ma L authored in The RNAcentral ConsortiumRNAcentral: A hub of information for non-coding RNA sequencesNucleic Acids Res 2019. [PMID=30395267]

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

  20. 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 RNAsNucleic Acids Res 2019. [PMID=30329098(Highly Cited)

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

  22. Salhi A, Essack M, Alam T,Bajic VPMa LRadovanovic AMarchand 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]

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

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

  25. Yin HY, Wang GY, Ma LN, Yi SV, Zhang Z: What signatures dominantly associate with gene age? Genome Biology and Evolution 2016, 8(10):3083-9. [PMID=27609935]

  26. Yin HY, Ma LN, Wang GY, Li MW, Zhang Z: Old genes experience stronger translational selection than young genesGene 2016, 590(1):29-34.[PMID=27259662]

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

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

  29. 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 RNAsNucleic Acids Res 2015, 43(Database issue):D187-192. [PMID=25399417]

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

  31. 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 genesNucleic Acids Res 2014, 42(Database issue):D1222-1228. [PMID=24136999]

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

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

  34. 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 cellsGenomics Proteomics Bioinformatics 2013, 10(6):326-335. [PMID=23317700]

  35. 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 cancersPLoS One 2011, 6(10):e26502. [PMID=22046296]

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

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

  38. 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 transposasesJ Genet Genomics 2011, 38(2):63-70. [PMID=21356525]

  39. Liu XG, Zhu WY, Huang YY, Ma LN, Zhou SQ, Wang YK, Zeng F, Zhou JH, Zhang YK: High expression of serum miR-21 and tumor miR-200c associated with poor prognosis in patients with lung cancerMed Oncol 2011, 29(2):618-626. [PMID=21516486]

  40. Zeng F, Li YC, Chen G, Zhang YK, Wang YK, Zhou SQ, Ma LN, Zhou JH, Huang YY, Zhu WY, Liu XG: Nicotine inhibits cisplatin-induced apoptosis in NCI-H446 cellsMed Oncol2011, 29(1):364-373. [PMID=21267677]

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