National Genomics Data Center

Lina Ma

Associate Professor

Team Leader,

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

  • LncBook (a curated knowledgebase of human long non-coding RNAs)

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

  • Database Commons (a curated catalogue of biological databases)

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

  • 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, 2013-2015.

  • Member of Youth Innovation Promotion Association of CAS, 2019.

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

  • 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: 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, LncBook: a curated knowledgebase of human long non-coding RNAs.

  • Talk: RNA Informatics 2019, 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), Annotation of human lncRNAs based on multi-omics data integration and analysis.,

PUBLICATIONS (Google Scholar citations: 1063, as of 201905 )

  1. 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, in press.

  2. 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 RNAs. Current Protocols in Bioinformatics 2019.

  3. 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]

  4. 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*: Rice Genome Reannotation Using Massive RNA-Seq Data in IC4RGenomics Proteomics & Bioinformatics 2019, in press.

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

  6. 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]

  7. 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]

  8. 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].

  9. 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]

  10. 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]

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

  12. 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]

  13. 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]

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

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

  16. 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]

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

  18. 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]

  19. 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]

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

  21. 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]

  22. 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]

  23. 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]

  24. 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]

  25. 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]

  26. 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]

  27. 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]

  28. 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]