电子邮件: songshh@big.ac.cn
通信地址: 北京市朝阳区北辰西路1号院中科院北京基因组研究所
邮政编码: 100101
研究领域
主要研究方向 生物信息学:基因组变异及RNA转录调控
1. 生物信息算法及大数据整合与挖掘:基于二代测序技术的多组学数据生物信息分析方法研发(包括RNA转录调控分析、RNA表观修饰分析、基因组变异分析与整合),数据信息整合及数据库开发;
2. 基因组变异:基因组序列变异是重要的生物遗传资源,是物种多样性的基础。围绕基因组变异信息资源匮乏、变异知识挖掘与应用有限,系统开展大尺度基因组变异的数据整合、变异知识挖掘及变异演化研究;
3. RNA转录及表观修饰调控:RNA m6A是真核生物信使RNA上含量最多的化学修饰之一,近年来的多项研究证明m6A修饰是动态可逆的,参与RNA稳定性、出核转运、可变剪切等RNA代谢过程,且与细胞分化、发育、肥胖、植物开花时间等相关,具有广泛的重要生物意义。基因表达与RNA修饰的动态变化暗示两者间存在复杂的相互调控关系,发展RNA m6A表观修饰与基因表达调控网络研究的生物信息方法,并围绕神经系统发育及肿瘤发生发展等重要相关生物问题开展系统研究,揭示RNA转录及修饰在肿瘤发生及发展中的新调控途径,发展可应用与肿瘤诊断及治疗的新靶点。
教育背景
工作经历
2022.01--至今 中国科学院北京基因组研究所(国家生物信息中心) 研究员
2011.01--2021.12 中国科学院北京基因组研究所 副研究员
2008.04--2010.12 中国科学院北京基因组研究所 助理研究员
社会兼职
2021-05-01-2025-05-01,中国生物工程学会, 计算生物学与生物信息学专业委员
教授课程
出版信息
发表文章
1. 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. (并列第一)
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. (并列通讯,IF=7.051)
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. (并列通讯,IF=11.502)
4. 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. (并列通讯,IF=10.806)
5. Liu Q, Zhao S, Shi CM, Song S, Zhu S, Su Y, Zhao W, Li M, Bao Y, Xue Y, Chen H. Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters. Genomics Proteomics Bioinformatics,2020. (并列第一,IF=7.051)
6. 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. (并列第一,9.326)
7. 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. (第一作者和并列通讯,IF=6.615)
8. 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. (并列第一和并列通讯,IF=11.561)
9. 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 WM. RNA m(6)A methylation participates in regulation of postnatal development of the mouse cerebellum. Genome Biol,2018,19(1):68. (并列通讯,13.214)
10. Li D, Huang Z, Song S, Xin Y, Mao D, Lv Q, Zhou M, Tian D, Tang M, Wu Q, Liu X, Chen T, Song X, Fu X, Zhao B, Liang C, Li A, Liu G, Li S, Hu S, Cao X, Yu J, Yuan L, Chen C, Zhu L. 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. (并列第一和并列通讯,IF=9.423)
11. Wang XL, Song SH, Wu YS, Li YL, Chen TT, Huang ZY, Liu S, Dunwell TL, Pfeifer GP, Dunwell JM, Wamaedeesa R, Ullah I, Wang Y, Hu SN. 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. (并列第一和并列通讯,IF=5.526)
12. Li Y, Wang X, Chen T, Yao F, Li C, Tang Q, Sun M, Sun G, Hu S, Yu J, Song S. RNA-Seq Based De Novo Transcriptome Assembly and Gene Discovery of Cistanche deserticola Fleshy Stem. PLoS One,2015,10(5):e0125722. (通讯作者,IF=4.09)
13. Li YL, Yu J, Song SH. [Recent progresses in RNA N6-methyladenosine research]. Yi Chuan,2014,35(12):1340-1351. (通讯作者)
14. 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. (并列第一和并列通讯,IF=5.377)
15. Di R, He J, Song S, Tian D, Liu Q, Liang X, Ma Q, Sun M, Wang J, Zhao W, Cao G, Yang Z, Ge Y, Chu M. Characterization and comparative profiling of ovarian microRNAs during ovine anestrus and the breeding season. Bmc Genomics,2014,15(1):899. (并列第一,IF=4.041)
16. 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. (通讯作者)
17. 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. (并列通讯,IF=4.877)
18. 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. (并列第一,IF=11.502)
20. 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. (并列第一,IF=11.147)
21. 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. (并列第一,IF=11.561)
23. 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. (并列第一,IF=10.162)
专利、软件著作权
1. 指示肉苁蓉生药材总苷含量范围的快速检测方法及试剂盒, 201510648363,发明专利
2. 新冠病毒基因组序列变异鉴定及注释在线分析软件V1.0,2021SR1971135,软件著作权
3. 新冠病毒基因组序列变异自动化监测系统,2021SR2039217,软件著作权
4. 基因组变异关联知识数据库系统V1.0[简称:GWAS Atlas],2020SR0054886,软件著作权
5. 基因组变异数据库系统V2.0,2021SR1324808,软件著作权
6. 基因组变异数据库系统V1,2019SR0347243,软件著作权
7. MeRIP-PF:基于MeRIP-Seq数据鉴定RNA m6A修饰峰的分析软件,2014SR057409,软件著作权
8. wapRNA:基于高通量测序的在线RNA分析软件,2012SR0832, 软件著作权
数据库
1. GVM:Genome Variation Map (基因组序列变异数据库)http://bigd.big.ac.cn/gvm/
2. GWAS Atlas(基因组变异关联知识库)https://bigd.big.ac.cn/gwas/
3. 2019nCoVR (新冠病毒基因组信息库)https://bigd.big.ac.cn/ncov/
4. MPoxVR(猴痘病毒基因组信息库)https://ngdc.cncb.ac.cn/gwh/poxvirus/
5. SR4R (水稻不同应用变异数据集及在线分析)http://sr4r.ic4r.org/
6. SoyOmics(大豆组学数据库)https://ngdc.cncb.ac.cn/soyomics
7. CGIR(叶绿体基因组信息资源库)https://ngdc.cncb.ac.cn/cgir/
8. EpiCancer(癌症表观知识库)https://ngdc.cncb.ac.cn/epicancer/
承担项目
1. 生物大数据管理和分析关键技术与系统[2021YFF0703700], 课题负责人,科技部重点研发计划,480万,2021.12-2024.11
2. 新型冠状病毒变异监测及功能影响分析[2021YFC0863300],任务负责人,科技部重点研发计划应急攻关项目,120万,2021.01-2022.01
3. 新型冠状病毒基因组及其演化变异动态监控平台[XDA19090116],主持,中科院战略先导专项(A类)地球大数据应急开发子课题,50万,2020.1-2020.12
4. 已知遗传位点关联系统及表型鉴定软件开发[XDA24040201],任务负责人,中国科学院战略先导专项(A类)种子精准设计与创造,146万,2019.11-2024.12
5. 水稻5-羟甲基胞嘧啶表观遗传调控的研究[31271372], 主持, 国家自然基金面上项目,80万,2013.1--2016.12
7. 基于杂种优势潜在相关基因数据库的基因调控网络的构建与比较分析[30900831], 主持, 国家自然基金青年项目,20万,2010.1--2012.12