National Genomics Data Center
Rujiao Li

Associate Senior Engineer

Team Leader,

Email: lirj (AT) big.ac.cn

Tel: +86 (10) 8409-7638

PROFESSIONAL EXPERIENCE

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

  • 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

  • Epigenome Data Integration and Analytics

PROJECTS & RESOURCES

  • MethBank

  • NucMap

  • WBSA

  • BS-RNA

  • wapRNA

  • IDMP

  • Age Predictor

PUBLICATIONS

  1. Li R#as co-first author in National Genomics Data Center Members and Partners (2020), Database Resources of the National Genomics Data Center in 2020Nucleic Acids Research. 2019 doi: 10.1093/nar/gkz913 [PMID: 31702008]

  2. 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 metadataNucleic acids research. 2019 doi.org/10.1093/nar/gkz840 [PMID: 31584095]

  3. 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 Res2019, 47(D1):D163-D169. [PMID=30335176]

  4. 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 Jan 8;47(D1):D983-D988. [PMID=30364969]

  5. 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 Res2018, 46(D1):D288-D295. [PMID=29161430]

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

  7. 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.

  8. 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 cellsBMC genomics 2017, 18(Suppl 1):933. [PMID=28198671]

  9. 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]

  10. 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]

  11. 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]

  12. 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. Chemphyschem : a European journal of chemical physics and physical chemistry 2017, 18(21):2977-2980. [PMID=28856771]

  13. 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]

  14. 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]

  15. 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-seqBMC genomics 2015, 16(1):851.[PMID=26497311]

  16. 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]

  17. 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 analysisPloS one 2014, 9(1):e86707.[PMID=24497972]

  18. 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 syndromesBMC genomics 2013, 14 Suppl 5:S8. [PMID=24564826]

  19. 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 sequencesBioinformatics 2011,27(21):3076-3077. [PMID=21896507]

  20. Zhang M, Li R, Wu D, Sun XY, Li ZR, Sun CC: Ab initio Study on the Dipole Moments, Polar izabil ities and First Hyperpolar izabil ities of Fluor ide-water Clusters F-(H2O) n (n= 1_ 4)Chemical Journal of Chinese Universities 2005, 25:515-517.

  21. 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-NH3Int J Quantum Chem 2005, 103(3):299-307. [PMID=WOS:000228770900007]

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

  23. 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-systemsJ Phys Chem A 2004,108(13):2464-2468. [PMID=WOS:000220524300016]

  24. 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 complexesJ Phys Chem A 2003, 107(32):6306-6310. [PMID=WOS:000184664700025]

  25. 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) clustersChemical Physics Letters 2003, 372(5-6):893-898. [PMID=WOS:000182795100047]