Dong Zou

Senior Engineer

Team Leader, Software & System Development

Email: zoud (AT) big.ac.cn

Tel:

PROFESSIONAL EXPERIENCE

• Senior Engineer, National Genomics Data Center,  Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation,  2021.1 −
  

• Engineer, National Genomics Data Center,  Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation,  2020.1 − 2020-12

• Assistant Professor, BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences,  2016.3 − 2019.12

• Assistant Professor, CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 2015.1 − 2016.2
  

• Research Assistant, CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 2009.9 − 2014.12

EDUCATION

• B.S. in Computer Science, Central South University of Forestry and Technology, China, 2009

RESEARCH INTERESTS

• Biological big data integration and search

• Omics big data Software & System Development

HONORS & AWARDS

• CAS Key Technology Talent Program 2021 （中国科学院技术支撑人才 2021）
  

PROJECTS & RESOURCES

• OpenLB, Open Library of Bioscience.

• RCoV19, Resource for Coronavirus 2019.

• BIGSearch, a scalable text search engine that features cross-domain search and facilitates users to gain access to a wide range of biomedical data.

• DatabaseCommons, a catalog of worldwide biological databases.

• Gene Expression Nebulas, a data portal of gene expression profiles under various conditions derived entirely from RNA-Seq data analysis in multiple species.

• MethBank, a database that integrates genome-wide DNA methylomes across a variety of species and provides an interactive browser for visualization of high-resolution DNA methylation data.

• The P10K Database, a data portal for the protist 10,000 genomes project

ACADEMIC ACTIVITIES

• Report: The 10th National Conference on Bioinformatics and Systems Biology of China，Database Commons: a global catalog of biological databases.

• Report: The 9th National Conference on Bioinformatics and Systems Biology of China， BIG Search: a Cross-database Search System for Multi-dimensional Biological Big Data

• Poster: Biocuration 2015, MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data.

• Poster: International Conference of Genomics 2015, Rice Expression Database (RED): an Integrated RNA-Seq-derived Gene Expression Database for Rice.

PUBLICATIONS

1. Xinxin Gao^#, Kai Chen^#, Jie Xiong^#, Dong Zou^#, et al. The P10K database: a data portal for the protist 10 000 genomes project. Nucleic Acids Res 2024.

2. Cuiping Li^#, Lina Ma^#, Dong Zou^#, Rongqin Zhang^#, et al. RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variant Monitoring, and Risk Pre-warning.Genomics Proteomics Bioinformatics 2023
   

3. 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 2023
   

4. Zou D^# 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.[PMID=36420893]
   

5. Zhang M^#, Zong W^#, Zou D^#, et al. MethBank 4.0: an updated database of DNA methylation across a variety of species.Nucleic Acids Res 2022.[PMID=36318250]

6. Zou D as co-author in Cell Taxonomy: a curated repository of cell types with multifaceted characterization. Nucleic Acids Res 2023.[PMID=36161321].

7. Zou D as co-author in GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals. Nucleic Acids Res 2023, 51(D1):D969-D976. [PMID=36263826]

8. 李茹姣, 张欣, 宋述慧, 王彦青, 邹东, 肖景发, 赵文明, 章张, 鲍一明: 基因组科学数据的安全管理与应用. 大数据 2022, 8(1):37-45.

9. Zhang Y^#, Zou D^#, Zhu T^#, et al. Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. Nucleic Acids Res 2022.[PMID=34591957]

10. Zou D^# 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.[PMID=34718731]

11. Zou D as co-author in BrainBase: a curated knowledgebase for brain diseases. Nucleic Acids Res 2022.[PMID=34718720]

12. Zou D as co-author in EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study. Nucleic Acids Res 2022.[PMID=34718752]

13. Shuhui Song^#, Lina Ma^#, Dong Zou^#,  et al. The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR.Genomics Proteomics Bioinformatics. 2020
    

14. Zheng Gong, Jun-Wei Zhu, Cui-Ping Li, Shuai Jiang, Li-Na Ma, Bi-Xia Tang, Dong Zou, Mei-Li Chen, Yu-Bin Sun, Shu-Hui Song, Zhang Zhang, Jing-Fa Xiao, Yong-Biao Xue, Yi-Ming Bao, Zheng-Lin Du, Wen-Ming Zhao. An online coronavirus analysis platform from the National Genomics Data Center. Zoological research, 2020

15. Zou D^# as co-first author in Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Res 2021

16. Zhao Li, Lin Liu, Shuai Jiang, Qianpeng Li, Changrui Feng, Qiang Du, Dong Zou, Jingfa Xiao, Zhang Zhang, Lina Ma. LncExpDB: an expression database of human long non-coding RNAs. Nucleic Acids Res 2021
    

17. Zhao WM^#, Song SH^#, Chen ML^#,  Zou D^#,  et al. The 2019 novel coronavirus resource. Yi Chuan. 2020;42(2):212-221.
    

18. Sang J^#, Zou D^#, Wang ZN^#,  et al. IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data. Genomics Proteomics & Bioinformatics 2020

19. Yan J^#, Zou D^#, Li C, Zhang Z, Song S*, Wang X*. SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice. Genomics Proteomics Bioinformatics. 2020

20. Zou D^# 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

21. Li Z, Zhang Y, Zou, D, Zhao Y, Wang H, Zhang Y, Xia X, Luo J, Guo H and Zhang Z:  LSD 3.0: a comprehensive resource for the leaf senescence research community. Nucleic Acids Res 2020
    

22. Tian D, Wang P, Tang B, Teng X, Li C, Liu X, Zou D, Song S, Zhang Z: GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals. Nucleic Acids Res 2020

23. Zou D as co-author of Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome.  Genomics Proteomics & Bioinformatics 2019.
    

24. 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, 67(1):e82.
    

25. Zou D^# as co-first author in BIG Data Center Members: Database Resources of the BIG Data Center in 2019. Nucleic Acids Res 2019
    

26. Li M^#, Zou D^#, Li Z^#, Gao R, Sang J, Zhang Y, Li R, Xia L, Zhang T, Niu G, Bao Y, Zhang Z: EWAS Atlas: a curated knowledgebase of epigenome-wide association studies. Nucleic Acids Res 2019.

27. Niu G^#, Zou D^#,  et al. Editome Disease Knowledgebase (EDK): A curated knowledgebase of editome-disease associations in human. Nucleic Acids Res 2019.

28. 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.

29. Li M, Xia L, Zhang Y, Niu G, Li M, Wang P, Zhang Y, Sang J, Zou D, Hu S, Hao L, Zhang Z: Plant Editosome Database: a curated database of RNA editosome in plants. Nucleic Acids Res 2019.

30. Li RJ^#, Liang F^#, Li MW^#, Zou D^#, Sun SX, Zhao YB, Zhao WM, Bao YM, Xiao JF, Zhang Z^*: MethBank 3.0: a database of DNA methylomes across a variety of species. Nucleic Acids Res 2018. Jan 4;46(D1):D288-D295.

31. Zou D^# as co-first author in BIG Data Center Members: Database Resources of the BIG Data Center in 2018. Nucleic Acids Res 2018. Jan 4;46(D1):D14-D20. [PMID=29036542]

32. Sang J, Wang Z, Li M, Cao J, Niu G, Xia L, Zou D, Wang F, Xu X, Han X, Fan J, Yang Y, Zuo W, Zhang Y, Zhao W, Bao Y, Xiao J, Hu S, Hao L, Zhang Z: ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization. Nucleic Acids Res  2018. Jan 4;46(D1):D121-D126 [PMID=29036693] 
    

33. Xia L^#, Zou D^#, Sang J, Xu XJ, Yin HY, Li MW, Wu SY, Hu SN, Hao LL*, Zhang Z*: Rice Expression Database (RED): an integrated RNA-Seq-derived gene expression database for rice. Journal of Genetics and Genomics, 2017, 44(5):235-241. [PMID=28529082]
    

34. Zou D^# as co-first author in BIG Data Center Members: The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res 2017.
    

35. Zou D^# as co-first author in IC4R Project Consortium: Information Commons for Rice (IC4R). Nucleic Acids Research 2016, 44(D1):D1172-1180. [PMID=26519466]

36. Zou D^#, Sun S^#, Li R, Liu J, Zhang J, Zhang Z: MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data.Nucleic acids research 2015, 43(Database issue):D54-58. [PMID=25294826]

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

38. 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]

39. 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 Research 2014, 42(Database issue): D1222-1228. [PMID=24136999]

40. Dai L, Xu C, Tian M, Sang J, Zou D, Li A, Liu G, Chen F, Wu J, Xiao J, Wang X, Yu J, Zhang Z: Community intelligence in knowledge curation: an application to managing scientific nomenclature. PLoS One 2013, 8(2):e56961. [PMID=23451119]