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Shuhui Song
Shuhui Song

Professor

Team Leader, Variation Resources

Email: songshh (AT) big.ac.cn

Tel: +86 (10) 8409-7620

PROFESSIONAL EXPERIENCE

  • Professor, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), China, 2022−Present

  • Associate Professor, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS), China, 2010−2021

  • 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

  • Genomic Variation and Knowledge Data Integration and Analytics

  • Cancer Bioinformatics

  • RNA-Omics and Bioinformatics

RESOURCES and TOOLs

FUNDING

  • Research and development of massive pathogene genome sequences analysis method and tracking application platform (2021YFF0703703), 480w RMB, 2021.12-2024.11

  • The Youth Innovation Promotion Association of Chinese Academy of Science (Y2021038), 200w RMB, 2022.1-2024.12

  • 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 Conference，The 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

RECENT PUBLICATIONS (ISI web of Science cited: 3984, as of 20230215; H index: 31)

1.           Liu X, Tian D, Li C, Tang B, Wang Z, Zhang R, Pan Y, Wang Y, Zou D, Zhang Z, Song S. GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals. Nucleic Acids Res,2023,51(D1):D969-D976. (并列通讯，IF=19.16)       https://www.ncbi.nlm.nih.gov/pubmed/36263826.

2.           Hua Z, Jiang C, Song S, Tian D, Chen Z, Jin Y, Zhao Y, Zhou J, Zhang Z, Huang L, Yuan Y. Accurate identification of taxon-specific molecular markers in plants based on DNA signature sequence. Mol Ecol Resour,2023,23(1):106-117. (并列第一，IF=8.678)       https://www.ncbi.nlm.nih.gov/pubmed/35951477.

3.           Zhang ZW, Teng X, Zhao F, Ma C, Zhang J, Xiao LF, Wang Y, Chang M, Tian Y, Li C, Zhang Z, Song S, Tong WM, Liu P, Niu Y. METTL3 regulates m(6)A methylation of PTCH1 and GLI2 in Sonic hedgehog signaling to promote tumor progression in SHH-medulloblastoma. Cell Rep,2022,41(4):111530. (并列通讯，IF=9.423)       https://www.ncbi.nlm.nih.gov/pubmed/36288719.

4.           Song S as co-first author in National Genomics Data Center 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. (并列第一，IF=16.971)       https://www.ncbi.nlm.nih.gov/pubmed/34718731.

5.           Ma Y, Chen M, Bao Y, Song S, Team MP. MPoxVR: A comprehensive genomic resource for monkeypox virus variant surveillance. Innovation (Camb),2022,3(5):100296. (并列通讯)       https://www.ncbi.nlm.nih.gov/pubmed/36039088.

6.           Hua Z, Tian D, Jiang C, Song S, Chen Z, Zhao Y, Jin Y, Huang L, Zhang Z, Yuan Y. Towards comprehensive integration and curation of chloroplast genomes. Plant Biotechnol J,2022,20(12):2239-2241. (并列第一，IF=13.263)       https://www.ncbi.nlm.nih.gov/pubmed/36069606.

7.           Teng X, Li Q, Li Z, Zhang Y, Niu G, Xiao J, Yu J, Zhang Z, Song S. Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades. Genomics, Proteomics & Bioinformatics,2021. (并列通讯，IF=7.051)       https://www.sciencedirect.com/science/article/pii/S1672022921000103.

8.           Song S as co-first author in National Genomics Data Center 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. (并列第一，IF=16.971)       https://www.ncbi.nlm.nih.gov/pubmed/33175170.

9.           Song S as co-first author in China-WHO Jointly team. WHO-convened global study of origins of SARS-CoV-2: China Part. 2021. (并列第一)       https://www.who.int/publications/i/item/who-convened-global-study-of-origins-of-sars-cov-2-china-part.

10.         Song S, Li C, Kang L, Tian D, Badar N, Ma W, Zhao S, Jiang X, Wang C, Sun Y, Li W, Lei M, Li S, Qi Q, Ikram A, Salman M, Umair M, Shireen H, Batool F, Zhang B, Chen H, Yang Y, Ali Abbasi A, Li M, Xue Y, Bao Y. Genomic Epidemiology of SARS-CoV-2 in Pakistan. Genomics Proteomics Bioinformatics,2021. (并列第一，IF=7.051)       https://www.ncbi.nlm.nih.gov/pubmed/34695600.

11.         Liu X, Wang P, Teng X, Zhang Z, Song S. Comprehensive Analysis of Expression Regulation for RNA m6A Regulators With Clinical Significance in Human Cancers. Front Oncol,2021,11:624395. (并列通讯，IF=6.244)       https://www.ncbi.nlm.nih.gov/pubmed/33718187.

12.         Li C, Tian D, Tang B, Liu X, Teng X, Zhao W, Zhang Z, Song S. Genome Variation Map: a worldwide collection of genome variations across multiple species. Nucleic Acids Res,2021,49(D1):D1186-D1191. (并列通讯，IF=16.971)       https://www.ncbi.nlm.nih.gov/pubmed/33170268.

13.         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)       https://www.ncbi.nlm.nih.gov/pubmed/32102777.

14.         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)       https://www.ncbi.nlm.nih.gov/pubmed/32619768.

15.         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)       https://www.ncbi.nlm.nih.gov/pubmed/31566222.

16.         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)       https://www.ncbi.nlm.nih.gov/pubmed/31702008.

17.         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. (并列第一，IF=7.051)       https://www.ncbi.nlm.nih.gov/pubmed/33704069.

18.         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)       https://www.ncbi.nlm.nih.gov/pubmed/32631406.

19.         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)       https://www.ncbi.nlm.nih.gov/pubmed/32663617.

20.         Gong Z, Zhu JW, Li CP, Jiang S, Ma LN, Tang BX, Zou D, Chen ML, Sun YB, Song SH, Zhang Z, Xiao JF, Xue YB, Bao YM, Du ZL, Zhao WM. An online coronavirus analysis platform from the National Genomics Data Center. Zool Res,2020,41(6):705-708. (IF=1.556)       https://www.ncbi.nlm.nih.gov/pubmed/33045776.

21.         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)       https://www.ncbi.nlm.nih.gov/pubmed/30365034.

22.         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)       https://www.ncbi.nlm.nih.gov/pubmed/30716410.

23.         Jiang LG, Li B, Liu SX, Wang HW, Li CP, Song SH, Beatty M, Zastrow-Hayes G, Yang XH, Qin F, He Y. Characterization of Proteome Variation During Modern Maize Breeding. Mol Cell Proteomics,2019,18(2):263-276. (IF=4.821)       https://www.ncbi.nlm.nih.gov/pubmed/30409858.

24.         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)       http://www.ncbi.nlm.nih.gov/pubmed/29036542.

25.         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)       https://www.ncbi.nlm.nih.gov/pubmed/30771506.

26.         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)       http://www.ncbi.nlm.nih.gov/pubmed/29069473.

27.         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，IF=13.214)       https://www.ncbi.nlm.nih.gov/pubmed/29855379.

28.         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)       http://www.ncbi.nlm.nih.gov/pubmed/27899658.

29.         Chang M, Lv H, Zhang W, Ma C, He X, Zhao S, Zhang ZW, Zeng YX, Song S, Niu Y, Tong WM. 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). (IF=3.481)

       http://www.ncbi.nlm.nih.gov/pubmed/28931651/.

30.         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)       http://www.ncbi.nlm.nih.gov/pubmed/27663737.

31.         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)       http://www.ncbi.nlm.nih.gov/pubmed/26272901/.

32.         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)       https://pubmed.ncbi.nlm.nih.gov/25938435/.