Rujiao Li

Professor senior engineer

Team Leader, Methylation Bank

Email: lirj (AT) big.ac.cn

Tel: +86 (10) 8409-7638

PROFESSIONAL EXPERIENCE

• Professor Senior Engineer, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), China, 2023−Present

• Senior Engineer, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), China, 2009−2023

• Engineer, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), China, 2008−2009

• Senior Engineer, Beijing Hongcam Software Technologies Co.,Ltd., China, 2005−2007

EDUCATION

• PhD in Physical Chemistry, Jilin University, China, 2005

• BS in Chemistry, Jilin University, China, 2000

RESEARCH INTERESTS

• Bioinformatics & Epigenetics

• Big Data Integration and Analytics

PROJECTS & RESOURCES

• MethBank (Methylation Bank, https://ngdc.cncb.ac.cn/methbank/)

• NucMap (A database of genome-wide nucleosome positioning map, https://ngdc.cncb.ac.cn/nucmap/)

• scMethBank (Single-cell Methylation Bank, https://ngdc.cncb.ac.cn/methbank/scm/)

• EWAS Open Platform (A comprehensive analysis suite for epigenome-wide association studies, https://ngdc.cncb.ac.cn/ewas) 

• ASCancer Atlas (A knowledge base of aberrant alternative splicing in human, https://ngdc.cncb.ac.cn/ascancer/)

• WBSA, BS-RNA, IDMP, Age Predictor, BSDMR, GMQN, wapRNA

PUBLICATIONS

1. Li R^# as co-first author in CNCB-NGDC and Partners (2023), Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023, Nucleic Acids Res, 2023, 51(D1):D18-D28.

2. Wu S^#, Huang Y^#, Zhang M, Gong Z, Wang G, Zheng X, Zong W, Zhao W, Xing P , Li R* , Liu Z*, Bao Y* ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers, Nucleic Acids Res, 2023,51(D1):D1196-D1204.

3. Zhang M^#, Zong W^#, Zou D^#, Wang G^#, Zhang X, Guo X, Ma Y, Zhao W, Yang F, Wu S, Xiong Z, Zhang Z*, Bao Y*, Li R*, MethBank 4.0: an updated database of DNA methylation across a variety of species, Nucleic Acids Res, 2023,51(D1):D208-D216.

4. Wang G^#, Xiong Z^#, Yang F, Zheng X, Zong W, Li R*, Bao Y*, Identification of COVID-19-Associated DNA Methylation Variations by Integrating Methylation Array and scRNA-Seq Data at Cell-Type Resolution, Genes, 2022, 13, 1109.

5. Zong W^#, Kang H^#, Xiong Z, Ma Y, Jin T, Gong Z, Yi L, Zhang M, Wu S, Wang G, Bao Y^*, Li R^*, scMethBank: a database for single-cell whole genome DNA methylation maps, Nucleic Acids Res, 2022, 50(D1):D380-D386.

6. Xiong Z^#, Yang F^#, Li M^#, Ma Y, Zhao W, Wang G, Li Z, Zheng X, Zou D, Zong W, Kang H, Jia Y, Li R^*, Zhang Z^*, Bao Y^*, EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study, Nucleic Acids Res, 2022, 50(D1):D1004-D1009.

7. Li R^# as co-first author in CNCB-NGDC and Partners (2022), Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022, Nucleic Acids Res, 50(D1):D27-D38.

8. Li R^# as co-first author in CNCB-NGDC and Partners (2021), Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021, Nucleic Acids Res, 2021, 49(D1):D18-D28.

9. Song S^#, Ma L^#, Zou D^#, Tian D^#, Li C^#, Zhu J, ^# …, Li R, …, Zhang Z^*, Zhao W^*, Xue Y^*, BaoY^*, The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR, Genomics Proteomics Bioinformatics, 2020, 18, 749–759. 

10. Chen M^#, Ma Y^#, Li R^*, Bao Y^*, Current status and prospects of genomics data analysis methods. Front Data Comput. 2020, 2, 1-19.

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

12.  Xiong Z, Li M, Yang F, Ma Y, Sang J, Li R, ... & Bao, Y., EWAS Data Hub: a resource of DNA methylation array data and metadata. Nucleic Acids Res, 2020, 48(D1):D890-D895. [PMID: 31584095]

13. Zhao W*, Song S*, Chen M*, Zou D*, Ma L*, Ma Y, Li R, Hao LL, Li C, Tian D et al, The 2019 novel coronavirus resource. Yi Chuan, 2020, 42(2):212-221. [PMID: 32102777]

14. Zhao Y^#, Wang J^#, Liang F, Liu Y, Wang Q, Zhang H, Jiang M, Zhang Z, Zhao W, Bao Y, Zhang Z, Wu J, Asmann Y*, Li R*, Xiao J*, NucMap: a database of genome-wide nucleosome positioning map across species. Nucleic Acids Res，2019, 47(D1):D163-D169. [PMID=30335176]

15. 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, 47(D1):D983-D988. [PMID=30364969]

16. Li R^#*, Liang F^#_, Li M^#, Zou D^#, Sun S, Zhao Y, Zhao W, Bao Y, Xiao J, Zhang Z*, MethBank 3.0: a database of DNA methylomes across a variety of species. Nucleic Acids Res，2018, 46(D1):D288-D295. [PMID=29161430]

17. Li R^# 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]

18. Li R^# 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), D18-24.

19. Jin J^#, Li R^#, Jiang C, Zhang R, Ge X, Liang F, Sheng X, Dai W, Chen M, Wu J, Xiao J*, Su W*, Transcriptome analysis reveals dynamic changes in coxsackievirus A16 infected HEK 293T cells. BMC genomics, 2017,18(Suppl 1):933. [PMID=28198671]

20. Pan Y, Liang F, Li R, Qian W*, MarR-Family Transcription Factor HpaR Controls Expression of the vgrR-vgrS Operon of Xanthomonas campestris pv. campestris. Molecular plant-microbe interactions: MPMI 2017. [PMID=29077520]

21. Peng B^#, Pan Y^#, Li R^#, Wei J, Liang F, Wang L, Wang F, Qian W*, An Essential Regulatory System Originating from Polygenic Transcriptional Rewiring of PhoP-PhoQ of Xanthomonas campestris. Genetics, 2017. [PMID=28550013]

22. Yuan L, Yu Y, Zhu Y, Li Y, Li C, Li R, Ma Q, Siu GK, Yu J, Jiang T, Xiao J, Kang Y, GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes. BMC genomics, 2017, 18(Suppl 1):952. [PMID=28198678]

23. Liu Q, Liu G, Wang T, Fu J, Li R, Song L, Wang ZG, Ding B, Chen F, Enhanced Stability of DNA Nanostructures by Incorporation of Unnatural Base Pairs. Chem phys chem: a European journal of chemical physics and physical chemistry, 2017, 18(21):2977-2980. [PMID=28856771]

24. Liang F, Hao L, Wang J, Shi S, Xiao J*, Li R*, BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data. Computational biology and chemistry, 2016, 65:173-177. [PMID=27647160]

25. 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 Res, 2015, 43(Database issue):D54-58. [PMID=25294826]

26. Li J^#, Li R^#, Wang Y, Hu X, Zhao Y, Li L, Feng C, Gu X, Liang F, Lamont SJ, Hu S, Zhou H, Li N, Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq. BMC genomics, 2015, 16(1):851.[PMID=26497311]

27. Zhang Z, Jin Z, Zhao Y, Zhang Z, Li R, Xiao J, Wu J, Systematic study on G-protein couple receptor prototypes: did they really evolve from prokaryotic genes? IET systems biology 2014, 8(4):154-161. [PMID=25075528]

28. Liang F^#, Tang B^#, Wang Y, Wang J, Yu C, Chen X, Zhu J, Yan J, Zhao W*, Li R*, WBSA: web service for bisulfite sequencing data analysis. PloS one, 2014, 9(1), e86707.[PMID=24497972]

29. Zhang R, Hao L, Wang L, Chen M, Li W, Li R, Yu J, Xiao J, Wu J, Gene expression analysis of induced pluripotent stem cells from aneuploid chromosomal syndromes. BMC genomics, 2013, 14 Suppl 5:S8. [PMID=24564826]

30. Zhao W, Liu W, Tian D, Tang B, Wang Y, Yu C,Li R, Ling Y, Wu J, Song S, Hu S, wapRNA: a web-based application for the processing of RNA sequences. Bioinformatics, 2011,27(21):3076-3077. [PMID=21896507]

31. Zhang M, Li R, Wu D, Sun XY, Li Z, Sun C, Ab initio Study on the Dipole Moments, Polarizabilities and First Hyperpolarizabilities of Fluor ide-water Clusters F-(H2O) n (n= 1-4)., Chemical Journal of Chinese Universities, 2005, 25:515-517.

32. Li R, Li Z, Di W, Hao X,Li R, Sun C, Long-range pi-type hydrogen bond in the dimers CH2O-HF, CH2O-H2O, and CH2O-NH3. Int J Quantum Chem, 2005, 103(3):299-307. [PMID=WOS:000228770900007]

33. Li R^#, Li Z, Wu D, Chen W, Li Y, Wang B, Sun C, Proton transfer of NH3-HCl catalyzed by only one molecule. J Phys Chem A, 2005, 109(4):629-634. [PMID=WOS:000226626300013]

34. Wang B, Li Z, Wu D, Hao X, Li R, Sun C, Ab initio study of the interaction hyperpolarizabilities of H-bond dimers between two pi-systems. J Phys Chem A, 2004,108(13):2464-2468. [PMID=WOS:000220524300016]

35. Li R^#, Li Z, Wu D, Hao X, Wang B, Sun C, Ab initio study of the interaction hyperpolarizabilities of HCN-HF and HNC-HF complexes. J Phys Chem A, 2003, 107(32):6306-6310. [PMID=WOS:000184664700025]

36. Li R^#, Li Z, Wu D, Hao X, Li Y, Wang B, Tao F, Sun C, Density functional study of structures and interaction hyperpolarizabilities of NH3-HCl-(H2O)_n (n=0-4) clusters. Chemical Physics Letters, 2003, 372(5-6):893-898. [PMID=WOS:000182795100047]