National Genomics Data Center
Shuhui Song

Associate Professor

Team Leader, Variation Resources

Email: songshh (AT) big.ac.cn

Tel: +86 (10) 8409-7620

PROFESSIONAL EXPERIENCE

  • Associate Professor, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), China, 2010−Present

  • Assistant Professor, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), China, 2008−2010

EDUCATION

  • PhD in Genetics, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), China, 2008

  • BS in Biology Science, Shanxi Normal University, China, 2003

RESEARCH INTERESTS

  • RNA-Omics and Bioinformatics

  • Genomic Variation and Knowledge Data Integration and Analytics

RESOURCES and TOOLs

FUNDING

  • 2019 novel coronavirus genome and its dynamic monitoring platform for evolution and variation, The Strategic Priority Research Program of the Chinese Academy of Sciences of China (XDA19090116), 50w RMB, 2019.1-2019.12

  • Association system of known genetic loci and development of phenotype identification software, The Strategic Priority Research Program of the Chinese Academy of Sciences of China (XDA24040201), 146w RMB, 2019.11-2024.12

  • The Youth Innovation Promotion Association of Chinese Academy of Science (2017141), 80w RMB, 2017.1-2020.12

  • Gene library establishment and rapid detection system of Cistanche deserticola based on high-throughput transcriptome sequencing technology, Cooperation project of Chinese Academy of Sciences, 50w RMB, 2013.6-2015.6

  • Epigenetic regulation Study of 5-hydroxymethylcytosine in rice, National Natural Science Foundation of China (31271372), 80w RMB, 2013.1-2016.12 

  • Epigenetic regulation Study of 5-hydroxymethylcytosine in rice, Beijing Nova Program (Z121105002512060),  28w RMB, 2012.12-2015.127

  • Construction and comparative analysis of gene regulatory networks based on heterosis potential related gene databases, National Natural Science Foundation of China, Young Scholar’s Program (30900831), 20w RMB, 2010.1-2012.12

  • Molecular module dictionary, Strategic Priority Research Program of the Chinese Academy of Sciences (XDA08020102), 250w, 2016.1-2018.12

ACADEMIC ACTIVITIES(Recent 3 years)

  • 新冠病毒基因组信息资源整合与序列变异分析,中国科学院青年创新促进会2020年学术年会(分会报告),武汉,27 Oct,2020

  • 新冠病毒基因组信息资源整合与序列变异比较分析,第九届全国生物信息学与系统生物学学术大会(分会邀请报告)上海,26 Sep,2020

  •  资源物种基因组变异整合及知识挖掘应用,第二届青年生命科学论坛(分会报告),武汉,24 Sep,2020

  • The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR, International Forum of Biodiversity, Biomedicine, Biotechnology, Biosecurity (4BIO)(分会邀请报告)温州,11 Sep,2020

  • 新型冠状病毒信息库及变异动态演化监测追踪,生物安全与生物多样性科学研究主题沙龙,青岛,16 Aug, 2020

  • Building the national genomics data center,ANSO“一带一路”国际青年科学家科技发展论坛(分论坛报告),杭州,11 Sep,2019

  • 生命与健康大数据系统建设及挖掘应用,中国科学院青年创新促进会2019年学术年会(分会报告),沈阳,16 Oct,2019

  • 生命与健康大数据系统,大科学装置交叉学科论坛(大会报告),稻城,23 Sep,2019

  • 生命组学大数据管理与资源体系建设,第二届IGDB前沿生物技术学术会议(大会报告),北京,23 Aug,2019

  • 基因组序列及知识库系统,第一届青年生命科学论坛(分会报告),新疆,12 Jul,2019

  • Improving Rice Genome Annotation Based on Public RNA-seq and the updated IC4R2.0,PAG Asia(分会报告),深圳,6 Jun,2019

  • The 11th International Biocuration ConferenceThe 11th International Biocuration Conference(分会报告),上海,8 April,2018

  • 面向精准医学的组学大数据,第一届青促会北京地区生命科学交叉论坛(大会报告),北京, Jul, 07, 2018

  • Genome variation map: a repository of genome variations for global animals and plants, 第五届全国计算生物学与生物信息学学术会议(分会报告),唐山, Apr. 21, 2018

PUBLICATIONS (Google Scholar citations: 3081, as of 202011; H index: 24)

1.  Zhao WM*, Song SH*, Chen ML*, Zou D*, Ma LN*, Ma YK, Li RJ, Hao LL, Li CP, Tian DM et al: The 2019 novel coronavirus resource. Yi Chuan 2020, 42(2):212-221. [32102777]

2.  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, 18    (2):173-185. [32619768]

3.  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, 48(D1):D927-D932. [31566222]

4.  Song S  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. [31702008]

5.  Liu S, Li C, Wang H, Wang S, Yang S, Liu X, Yan J, Li B, Beatty M, Zastrow-Hayes G, Song S#, Qin F#: Mapping regulatory variants controlling gene expression in drought response and tolerance in maize. Genome Biol 2020, 21(1):163. [32631406]

6.  Liu L, Wang G, Wang L, Yu C, Li M, Song S, Hao L, Ma L, Zhang Z: Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative  profiling. Biol Direct 2020, 15(1):10. [32539851]

7.  Gong Z, Zhu JW, Li CP, Jiang S, Ma LN, Tang BX, Zou D, Chen ML, Sun YB, Song SH et al: An online coronavirus analysis platform from the National Genomics Data Center. Zool Res 2020, 41(6):705-708. [33045776]

8.  Song S*, Zhang Z: Database Resources in BIG Data Center: Submission, Archiving, and Integration of Big Data in Plant Science. Mol Plant 2019, 12(3):279-281. [30716410]

9.  Song S  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. [30365034]

10.  Jiang LG, Li B, Liu SX, Wang HW, Li CP, Song SH, Beatty M, Zastrow-Hayes G, Yang XH, Qin F et al: Characterization of Proteome Variation During Modern Maize Breeding. Mol Cell Proteomics 2019, 18(2):263-276. [30409858]

11.  Song S *, Tian D, Zhang Z, Hu S, Yu J: Rice Genomics: over the Past Two Decades and into the Future. Genomics Proteomics Bioinformatics 2018, 16(6):397-404. [30771506]

12.  Song S*, Tian D*, Li C*, Tang B*, Dong L*, Xiao J, Bao Y, Zhao W, He H, Zhang Z: Genome Variation Map: a data repository of genome variations in BIG Data Center. Nucleic Acids  Res 2018, 46(D1):D944-D949. [29069473]

13.  Song S  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. [29036542]

14.  Ma C, Chang M, Lv H, Zhang ZW, Zhang W, He X, Wu G, Zhao S, Zhang Y, Wang D, Teng X, Liu C, Li Q, Klungland A, Niu Y#, Song S#, Tong W#: RNA m(6)A methylation participates in regulation of postnatal development of the mouse cerebellum. Genome Biol 2018, 19(1):68. [29855379]

15.  Song S  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-D24. [27899658]

16.  Chang M, Lv H, Zhang W, Ma C, He X, Zhao S, Zhang ZW, Zeng YX, Song S, Niu Y et al: Region-specific RNA m6A methylation represents a new layer of control in the gene regulatory network in the mouse brain. Open Biol 2017, 7(9). 

17.  Li D, Huang Z, Song S*, Xin Y, Mao D, Lv Q, Zhou M, Tian D, Tang M, Wu Q et al: Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase. Proc Natl Acad Sci U S A 2016, 113(41):E6026-E6035. [27663737/]

18.  Wang XL, Song SH*, Wu YS, Li YL, Chen TT, Huang ZY, Liu S, Dunwell TL, Pfeifer GP, Dunwell JM et al: Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes. J Exp Bot 2015, 66(21):6651-6663. [26272901/]

19.  Li Y, Wang X, Chen T, Yao F, Li C, Tang Q, Sun M, Sun G, Hu S, Yu J et al: RNA-Seq Based De Novo Transcriptome Assembly and Gene Discovery of Cistanche deserticola Fleshy Stem. PLoS One 2015, 10(5):e0125722.

20.  Zhao X, Yang Y, Sun BF, Shi Y, Yang X, Xiao W, Hao YJ, Ping XL, Chen YS, Wang WJ et al: FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res 2014, 24(12):1403-1419.

21.  Zhao B, Yang Y, Wang X, Chong Z, Yin R, Song SH, Zhao C, Li C, Huang H, Sun BF et al: Redox-active quinones induces genome-wide DNA methylation changes by an iron-mediated and Tet-dependent mechanism. Nucleic Acids Res 2014, 42(3):1593-1605.

22.  Tang M, Mao D, Xu L, Li D, Song S, Chen C: Integrated analysis of miRNA and mRNA expression profiles in response to Cd exposure in rice seedlings. Bmc Genomics 2014, 15:835.

23.  Li YL, Yu J, Song SH: [Recent progresses in RNA N6-methyladenosine research]. Yi Chuan 2014, 35(12):1340-1351.

24.  Li Y, Wang X, Li C, Hu S, Yu J, Song S: Transcriptome-wide N(6)-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification. RNA Biol 2014, 11(9):1180-1188.

25.  Li X, Qu F, Xie W, Wang F, Liu H, Song S, Chen T, Zhang Y, Zhu S, Wang Y et al: Transcriptomic analyses of neurotoxic effects in mouse brain after intermittent neonatal administration of thimerosal. Toxicol Sci 2014, 139(2):452-465.

26.  Di R, He J, Song S, Tian D, Liu Q, Liang X, Ma Q, Sun M, Wang J, Zhao W et al: Characterization and comparative profiling of ovarian microRNAs during ovine anestrus and the breeding season. Bmc Genomics 2014, 15(1):899.

27.  Cui J, Liu S, Zhang B, Wang H, Sun H, Song S, Qiu X, Liu Y, Wang X, Jiang Z et al: Transciptome analysis of the gill and swimbladder of Takifugu rubripes by RNA-Seq. PLoS One 2014, 9(1):e85505.

28.  Chen X, Luo Y, Yu H, Sun Y, Wu H, Song S, Hu S, Dong Z: Transcriptional profiling of biomass degradation-related genes during Trichoderma reesei growth on different carbon sources. J Biotechnol 2014, 173:59-64.

29.  An H, Douillard FP, Wang G, Zhai Z, Yang J, Song S, Cui J, Ren F, Luo Y, Zhang B et al: Integrated transcriptomic and proteomic analysis of the bile stress response in a centenarian-originated probiotic Bifidobacterium longum BBMN68. Mol Cell Proteomics 2014, 13(10):2558-2572.

30.  Ma JY, Li M, Luo YB, Song S, Tian D, Yang J, Zhang B, Hou Y, Schatten H, Liu Z et al: Maternal factors required for oocyte developmental competence in mice: transcriptome analysis of non-surrounded nucleolus (NSN) and surrounded nucleolus (SN) oocytes. Cell Cycle 2013, 12(12):1928-1938.

31.  Li Y, Song S, Li C, Yu J: MeRIP-PF: an easy-to-use pipeline for high-resolution peak-finding in MeRIP-Seq data. Genomics Proteomics Bioinformatics 2013, 11(1):72-75.

32.  Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang CM, Li CJ, Vagbo CB, Shi Y, Wang WL, Song SH et al: ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell 2012, 49(1):18-29.

33.  Sun P, Song S, Zhou L, Zhang B, Qi J, Li X: Transcriptome analysis reveals putative genes involved in iridoid biosynthesis in Rehmannia glutinosa. Int J Mol Sci 2012, 13(10):13748-13763.

34.  Ma JY, Li M, Ge ZJ, Luo Y, Ou XH, Song S, Tian D, Yang J, Zhang B, Ou-Yang YC et al: Whole transcriptome analysis of the effects of type I diabetes on mouse oocytes. PLoS One 2012, 7(7):e41981.

35.  Liu W, Zhao Y, Cui P, Lin Q, Ding F, Xin C, Tan X, Song S, Yu J, Hu S: Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing. Front Genet 2012, 2:93.

36.  Jin J, Zhang B, Guo H, Cui J, Jiang L, Song S, Sun M, Ren F: Mechanism analysis of acid tolerance response of bifidobacterium longum subsp. longum BBMN 68 by gene expression profile using RNA-sequencing. PLoS One 2012, 7(12):e50777.

37.  Cui P, Liu W, Zhao Y, Lin Q, Zhang D, Ding F, Xin C, Zhang Z, Song S, Sun F et al: Comparative analyses of H3K4 and H3K27 trimethylations between the mouse cerebrum and testis. Genomics Proteomics Bioinformatics 2012, 10(2):82-93.

38.  Cui P, Liu W, Zhao Y, Lin Q, Ding F, Xin C, Geng J, Song S, Sun F, Hu S et al: The association between H3K4me3 and antisense transcription. Genomics Proteomics Bioinformatics 2012, 10(2):74-81.

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

40.  Yuan J, Liu W, Sun M, Song S, Cai J, Hu S: Complete genome sequence of the pathogenic bacterium Riemerella anatipestifer strain RA-GD. J Bacteriol 2011, 193(11):2896-2897.

41.  Liu W, Huang D, Liu K, Hu S, Yu J, Gao G, Song S: Discovery, identification and comparative analysis of non-specific lipid transfer protein (nsLtp) family in Solanaceae. Genomics Proteomics Bioinformatics 2011, 8(4):229-237.

42.  Yang M, Song S, Liu G, Chen K, Tian X, Zhao Z, Hu S, Yu J: A comprehensive analysis of protein phosphatases in rice and Arabidopsis. Plant Systematics and Evolution 2010, 289(3):111-126.

43.  Hao Y, Huang D, Guo H, Xiao M, An H, Zhao L, Zuo F, Zhang B, Hu S, Song S et al: Complete genome sequence of Bifidobacterium longum subsp. longum BBMN68, a new strain from a healthy chinese centenarian. J Bacteriol 2010, 193(3):787-788.

44.  Zhao D, Song S, Wang Q, Zhang X, Hu S, Chen L: Discovery of immune-related genes in Chinese mitten crab (Eriocheir sinensis) by expressed sequence tag analysis of haemocytes. Aquaculture 2009, 287(3-4):297-303.

45.  Xu X, Song S, Wang Q, Qin F, Liu K, Zhang X, Hu S, Zhao Y: Analysis and comparison of a set of expressed sequence tags of the parthenogenetic water flea Daphnia carinata. Mol Genet Genomics 2009, 282(2):197-203.

46.  Song S, Huang Y, Wang X, Wei G, Qu H, Wang W, Ge X, Hu S, Liu G, Liang Y et al: HRGD: a database for mining potential heterosis-related genes in plants. Plant Mol Biol 2009, 69(3):255-260.

47.  Zhu J, He F, Song S, Wang J, Yu J: How many human genes can be defined as housekeeping with current expression data? Bmc Genomics 2008, 9:172.

48.  Wang W, Meng B, Ge X, Song S, Yang Y, Yu X, Wang L, Hu S, Liu S, Yu J: Proteomic profiling of rice embryos from a hybrid rice cultivar and its parental lines. Proteomics 2008, 8(22):4808-4821.

49.  Ge X, Chen W, Song S, Wang W, Hu S, Yu J: Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines. BMC Plant Biol 2008, 8:114.

50.  Song S, Qu H, Chen C, Hu S, Yu J: Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data. BMC Plant Biol 2007, 7:49.