Shuhui Song

Team Leader, Senior Bioinformatics & Biocuration Scientist

Variation Resources

Email: songshh (AT) big.ac.cn
Tel: +86 (10) 8409-7620

PROFESSIONAL EXPERIENCE

EDUCATION

RESEARCH INTERESTS

PROJECTS & RESOURCES

PUBLICATIONS

1. Members BDC: The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res 2017. [PMID=27899658]

2. 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. [PMID=27663737]

3. 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. [PMID=25938435]

4. 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. [PMID=26272901]

5. An H, Douillard FP, Wang G, Zhai Z, Yang J, Song S, Cui J, Ren F, Luo Y, Zhang B, Hao Y: 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. [PMID=24965555]

6. 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. [PMID=24445169]

7. Cui J, Liu S, Zhang B, Wang H, Sun H, Song S, Qiu X, Liu Y, Wang X, Jiang Z, Liu Z: Transciptome analysis of the gill and swimbladder of Takifugu rubripes by RNA-Seq. PLoS One 2014, 9(1):e85505. [PMID=24454879]

8. 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. [PMID=25318541]

9. Li X, Qu F, Xie W, Wang F, Liu H, Song S, Chen T, Zhang Y, Zhu S, Wang Y, Guo C, Tang TS: Transcriptomic analyses of neurotoxic effects in mouse brain after intermittent neonatal administration of thimerosal. Toxicol Sci 2014, 139(2):452-465. [PMID=24675092]

10. 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. [PMID=25483034]

11. Li YL, Yu J, Song SH: [Recent progresses in RNA N6-methyladenosine research]. Yi Chuan 2014, 35(12):1340-1351. [PMID=24645343]

12. 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. [PMID=25273267]

13. Zhao B, Yang Y, Wang X, Chong Z, Yin R, Song SH, Zhao C, Li C, Huang H, Sun BF, Wu D, Jin KX, Song M, Zhu BZ, Jiang G, Rendtlew Danielsen JM, Xu GL, Yang YG, Wang H: 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. [PMID=24214992]

14. Zhao X, Yang Y, Sun BF, Shi Y, Yang X, Xiao W, Hao YJ, Ping XL, Chen YS, Wang WJ, Jin KX, Wang X, Huang CM, Fu Y, Ge XM, Song SH, Jeong HS, Yanagisawa H, Niu Y, Jia GF, Wu W, Tong WM, Okamoto A, He C, Rendtlew Danielsen JM, Wang XJ, Yang YG: FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res 2014, 24(12):1403-1419. [PMID=25412662]

15. 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. [PMID=23434047]

16. Ma JY, Li M, Luo YB, Song S, Tian D, Yang J, Zhang B, Hou Y, Schatten H, Liu Z, Sun QY: 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. [PMID=23673344]

17. Cui P, Liu W, Zhao Y, Lin Q, Ding F, Xin C, Geng J, Song S, Sun F, Hu S, Yu J: The association between H3K4me3 and antisense transcription. Genomics Proteomics Bioinformatics 2012, 10(2):74-81. [PMID=22768981]

18. Cui P, Liu W, Zhao Y, Lin Q, Zhang D, Ding F, Xin C, Zhang Z, Song S, Sun F, Yu J, Hu S: Comparative analyses of H3K4 and H3K27 trimethylations between the mouse cerebrum and testis. Genomics Proteomics Bioinformatics 2012, 10(2):82-93. [PMID=22768982]

19. 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. [PMID=23236393]

20. 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. [PMID=22303387]

21. Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang CM, Li CJ, Vagbo CB, Shi Y, Wang WL, Song SH, Lu Z, Bosmans RP, Dai Q, Hao YJ, Yang X, Zhao WM, Tong WM, Wang XJ, Bogdan F, Furu K, Fu Y, Jia G, Zhao X, Liu J, Krokan HE, Klungland A, Yang YG, He C: ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell 2012, 49(1):18-29. [PMID=23177736]

22. Ma JY, Li M, Ge ZJ, Luo Y, Ou XH, Song S, Tian D, Yang J, Zhang B, Ou-Yang YC, Hou Y, Liu Z, Schatten H, Sun QY: Whole transcriptome analysis of the effects of type I diabetes on mouse oocytes. PLoS One 2012, 7(7):e41981. [PMID=22911868]

23. 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. [PMID=23202979]

24. 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. [PMID=21382591]

25. 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. [PMID=21441509]

26. 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. [PMID=21896507]

27. Hao Y, Huang D, Guo H, Xiao M, An H, Zhao L, Zuo F, Zhang B, Hu S, Song S, Chen S, Ren F: Complete genome sequence of Bifidobacterium longum subsp. longum BBMN68, a new strain from a healthy chinese centenarian. J Bacteriol 2010, 193(3):787-788. [PMID=21097614]

28. 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.

29. Song S, Huang Y, Wang X, Wei G, Qu H, Wang W, Ge X, Hu S, Liu G, Liang Y, Yu J: HRGD: a database for mining potential heterosis-related genes in plants. Plant Mol Biol 2009, 69(3):255-260. [PMID=19011765]

30. 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. [PMID=19468756]

31. 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.

32. 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. [PMID=19000321]

33. 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. [PMID=18850630]

34. 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. [PMID=18416810]

35. 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. [PMID=17877838]