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Lili Hao
Lili Hao

Associate Professor

Team Leader,

Email: haolili (AT) big.ac.cn

Tel: +86 (10) 8409-7845

PROFESSIONAL EXPERIENCE

  • Associate Professor, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2019 - Present

  • Visiting Scholar, University of California at Los Angeles (UCLA) & Children's Hospital of Philadelphia (CHOP), USA, 2018-2019

  • Assistant Professor, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2011 - 2018

EDUCATION

  • Ph.D. in Bioinformatics, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2011

  • B.S. in Bioengineering, Harbin Institute of Technology, China, 2005

RESEARCH INTERESTS

  • Transcriptome data integration and analytics

  • Function, regulation and evolution of RNA editing in human and plants

DATA RESOURCES

  • Gene Expression Nebulas (a data portal of gene expression profiles)

  • EDK (Editome Disease Knowledge)

  • PED (A curated database of RNA editsome in plants)

  • ICG (A knowledgebase of Internal Control Genes for RT-qPCR normalization)

  • IC4R (Information Commons for Rice - platform for integrated omics data of rice)

  • BioCode (Archive Bioinformatics Codes for Open Source Projects)

GRANTS

  • National Natural Science Foundation of China (Grant No. 31100915): Transposable activity of mStoe10 and its polymorphism in cultivated and wild rice. (2012-2014)  Project leader

  • Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDA08020102): Molecular model design and breeding. (2013-2017) Participant

AWARDS

  • Member of Youth Innovation Promotion Association, Chinese Academy of Sciences (2018-2021)

ACADEMIC ACTIVITIES

  • Talk: Big data integration of rice in IC4R. The 11th International Biocuration Conference. Shanghai, China, April 08-11, 2018

  • Talk: BioCode: archiving bioinformatics codes for open source projects. The 11th International Biocuration Conference. Shanghai, China, April 08-11, 2018

  • Talk: Improving Rice Genome Annotation Based on Public RNA-Seq Data. Plant & Animal Genome Conference XXVI. Workshop: IRIC: Rice Informatics for the Global Community. San Diego, United States, Jan. 13-17, 2018

  • Talk: An improved genome annotation release (BIGD_IC4R-1.0) for Oryza Sativa Japonica Based on RNA-Seq. The 15th International Symposium on Rice Functional Genomics. Suwon Korea, Sep. 24-27, 2017

  • Talk: Rice Expression Database (RED): an integrated RNA-Seq-derived gene expression database for rice. XIX International Botanical Congress. Shenzhen, Jul. 23-29, 2017

  • Poster: The BIG Data Center: from deposition to integration to translation. The 6th National Plant Protein Research Conference. Haikou, Dec. 21-25 2016

  • Talk: Gene Expression Nebulas. 2016 Big Data Forum for Life and Health Sciences. Dec 5-8, 2016

  • Poster: The BIG Data Center: from deposition to integration to translation. The 7th National Conference on Bioinformatics and System Biology. Chengdu, Oct. 6-9, 2016

  • Poster: Rice Expression Database (RED): an integrated RNA-Seq-derived gene expression database for rice. The 7th National Conference on Bioinformatics and System Biology. Chengdu, Oct. 6-9, 2016

  • Poster: Information Commons for Rice (IC4R). International Conference of Genomics. Xi'an, Oct 2015

  • Poster: Information Commons for Rice (IC4R). The 13 th International Symposium on Rice Functional Genomics. Wuhan, Aug.19-22, 2015

  • Poster: Information Commons for Rice (IC4R). The 8th International Biocuration Conference. Beijing, Apr. 22-25, 2015

PUBLICATIONS (#First author, *Corresponding author)

  1. Wang YY, Kang H, Xu T, Hao L, Bao Y, Jia P. CeDR Atlas: a knowledgebase of cellular drug response. Nucleic Acids Research 2022, 50(D1):D1164-D1171.[PMID=34634794]  

  2. Zhang Y, Zou D, Zhu T, Xu T, Chen M, Niu G, Zong W, Pan R, Jing W, Sang J, Liu C, Xiong Y, Sun Y, Zhai S, Chen H, Zhao W, Xiao J, Bao Y, Hao L*, Zhang Z*: 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, 50(D1):D1016-D1024.[PMID=34591957]

  3. Hao 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, 50(D1):D27-D38.[PMID=34718731]

  4. Chen M, Ma Y, Wu S, Zheng X, Kang H, Sang J, Xu X, Hao L, Li Z, Gong Z, Xiao Writing J, Zhang Z, Zhao W, Bao Y: Genome Warehouse: A Public Repository Housing Genome-scale Data. Genomics Proteomics Bioinformatics 2021, S1672-0229(21)00131-5.[PMID=34175476]

  5. Park E, Jiang Y, Hao L, Hui J, Xing Y. (2021) Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes. Genome Biology, 22:77. [PMID=33685485]

  6. Song S, Ma L, Zou D, Tian D, Li C, Zhu J, Chen M, Wang A, Ma Y, Li M, Teng X, Cui Y, Duan G, Zhang M, Jin T, Shi C, Du Z, Zhang Y, Liu C, Li R, Zeng J, Hao L, Jiang S, Chen H, Han D, Xiao J, Zhang Z, Zhao W, Xue Y, Bao Y: The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR. Genomics Proteomics Bioinformatics 2020, 18(6):749-759.

  7. Hao 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 2021. Nucleic Acids Res 2021, 49(D1):D18-D28. [PMID=33175170]

  8. 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 resource. Yi Chuan 2020, 42(2):212-221. [PMID=32102777]

  9. Sang J, Zou D, Wang Z, Wang F, Zhang Y, Xia L, Li Z, Ma L, Li M, Xu B, Liu X, Wu S, Liu L, Niu G, Li M, Luo Y, Hu S, Hao L*, Zhang Z*: IC4R 2.0: Rice Genome Reannotation Using Massive RNA-Seq Data. Genomics Proteomics & Bioinformatics 2020, 18(2):161-172. [PMID=32683045]

  10. 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 profiling. Biology Direct 2020, 15(1):10. [PMID=32539851]

  11. Hao 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]

  12. Yang R, Li P, Mei H, Wang D, Sun J, Yang C, Hao L, Cao S, Chu C, Hu S, Song X, Cao X: Fine-Tuning of MiR528 Accumulation Modulates Flowering Time in Rice. Mol Plant 2019, pii: S1674-2052(19)30159-5. [PMID:31059825]

  13. Hao L# as co-first author in BIG Data Center Members: Database Resources of the BIG Data Center in 2019. Nucleic Acids Res 2019, 47(D1):D8-D14. [PMID:30365034]

  14. 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, 47(D1):D170-D174. [PMID:30364952]

  15. Niu G, Zou D, Li M, Zhang Y, Sang J, Xia L, Li M, Liu L, Cao J, Zhang Y, Wang P, Hu S, Hao L*, Zhang Z*: Editome Disease Knowledgebase (EDK): A curated knowledgebase of editome-disease associations in human. Nucleic Acids Res 2019, 47(D1):D78-D83. [PMID:30357418]

  16. Hao L# as co-first author in BIG Data Center Members: Database Resources of the BIG Data Center in 2018. Nucleic Acids Res 2018, 46:D14-20. [PMID:29036542]

  17. Sang J, Wang ZN, Li M, Cao JB, Niu GY, Xia L, Zou D, Wang F, Xu XJ, Han XJ, Fan JQ, Yang Y, Zuo WZ, Zhang Y, Zhao WM, Bao YM, Xiao JF, Hu SN, Hao L*, Zhang Z*: ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization. Nucleic Acids Res 2018, 46:D121-126. [PMID:29036693]

  18. Xia L, Zou D, Sang J, Xu X, Yin H, Li M, Wu S, Hu S, Hao L*, Zhang Z*. Rice Expression Database (RED): an integrated RNA-Seq-derived gene expression database for rice. J Genet Genomics 2017, 44(5):235-241. [PMID:28529082]

  19. Hao L# as co-first authors in BIG Data Center Members: The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res 2017, 45(D1):D18-D24. [PMID:27899658]

  20. Zhao W, Zhang S, Tang B, Chen T, Hao L, Sang J, Li R, Xiao J, Zhang Z. Constructing the international database management system for omics big data. Big Data Research 2016, 2(6):43-52. (In Chinese)

  21. 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]

  22. Liu H, Deng Z, Chen J, Wang S, Hao L, Li D. Genome-wide identification and expression analysis of the metacaspase gene family in Hevea brasiliensis. Plant Physiol Biochem 2016, 105:90-101. [PMID:27085600]

  23. Hao L# as first author in IC4R Project Consortium: Information Commons for Rice (IC4R). Nucleic Acids Research 2016, 44(D1):D1172-1180. [PMID:26519466]

  24. Luo M, Hao L#, Hu F, Dong Y, Gou L, Zhang W, Wang X, Zhao Y, Jia M, Hu S, Zhang X: MicroRNA profiles and potential regulatory pattern during the early stage of spermatogenesis in mice. Science China Life Sciences 2015, 58(5):442-450. [PMID:25266152]

  25. Liu X, Hao L#, Li D, Zhu L, Hu S: Long non-coding RNAs and their biological roles in plants. Genomics, Proteomics & Bioinformatics 2015, 13(3):137-147. [PMID:25936895]

  26. Li D, Hao L#, Liu H, Zhao M, Deng Z, Li Y, Zeng R, Tian W: Next-generation sequencing, assembly, and comparative analyses of the latex transcriptomes from two elite Hevea brasiliensis varieties. Tree Genet Genomes 2015, 11(5).

  27. 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]

  28. Yang C, Li D, Liu X, Ji C, Hao L, Zhao X, Li X, Chen C, Cheng Z, Zhu L: OsMYB103L, an R2R3-MYB transcription factor, influences leaf rolling and mechanical strength in rice (Oryza sativa L.). BMC Plant Biology 2014, 14:158. [PMID:24906444]

  29. Zhang X, Hao L#, Meng L, Liu M, Zhao L, Hu F, Ding C, Wang Y, He B, Pan Y, Fang W, Chen J, Hu S, Jia M: Digital gene expression tag profiling analysis of the gene expression patterns regulating the early stage of mouse spermatogenesis. PLoS One 2013, 8(3):e58680. [PMID:23554914]

  30. 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]

  31. Zhou T, Benda C, Duzinger S, Huang Y, Li X, Li Y, Guo X, Cao G, Chen S, Hao L, Chan YC, Ng KM, Ho JC, Wieser M, Wu J, Redl H, Tse HF, Grillari J, Grillari-Voglauer R, Pei D, Esteban MA: Generation of induced pluripotent stem cells from urine. Journal of the American Society of Nephrology : JASN 2011, 22(7):1221-1228. [PMID:21636641]

  32. Liu F, Zhang H, Wu G, Sun J, Hao L, Ge X, Yu J, Wang W: Sequence Variation and Expression Analysis of Seed Dormancy- and Germination-Associated ABA- and GA-Related Genes in Rice Cultivars. Frontiers in Plant Science 2011, 2:17. [PMID:22629259]

  33. An J, Wan H, Zhou X, Hu DN, Wang L, Hao L, Yan D, Shi F, Zhou Z, Wang J, Hu S, Yu J, Qu J: A comparative transcriptomic analysis of uveal melanoma and normal uveal melanocyte. PLoS One 2011, 6(1):e16516. [PMID:21305041]

  34. Hao L, Ge X, Wan H, Hu S, Lercher M, Yu J, Chen W: Human functional genetic studies are biased against the medically most relevant primate-specific genes. BMC Evol Biol2010, 10. [PMID:20961448]

  35. Wang L, Hao L, Li X, Hu S, Ge S, Yu J: SNP deserts of Asian cultivated rice: genomic regions under domestication. Journal of Evolutionary Biology 2009, 22(4):751-761.[PMID:19243488]