宋述慧

中国科学院北京基因组研究所

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  • 宋述慧
  • 硕士生导师
  • 研究员

宋述慧 ( SONG Shuhui )

职 称: 副研究员
职 务: 硕士生导师
E-Mail: songshh@big.ac.cn
学科类别: 遗传学,生物信息学
学习经历:
1999年9月-2003年7月 山西师范大学 生物学专业 理学学士 2003年9月-2008年1月 中国科学院北京基因组研究所 生物信息学专业 遗传学博士
工作经历:

2011.01至今 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

主要研究领域:

生物信息学、RNA表观转录组

承担科研项目情况:

1、中国科学院信息化专项-科学大数据工程,大数据驱动的生物信息领域创新示范平台,2018-2020,在研,子任务负责人 2、中国科学院青年创新促进会-人才项目,RNA表观修饰,2017-2020,在研,负责人 3、中国科学院先导A,分子辞海,2014-2018,结题,参与 4、国家自然基金面上项目,水稻5-羟甲基胞嘧啶表观遗传调控的研究, 2013-2016,结题,负责人 5、北京市科技新星计划项目,超级杂交稻5羟甲基表观遗传的研究,2012-2015, 结题,主持 6、国家自然基金青年项目,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,2010-2012,结题,主持 7、973,重要热带作物木薯品种改良的基础研究,2010-2014,结题,参与 8、中国科学院,第二代高通量转录组测序数据的非编码RNA鉴定与分析方法的研究,2010-2012,结题,参与 9、中国科学院,系统生物学中多组学综合数据库,2009-2010,结题,参与

代表论著:

[1] BIG Data Center Members. Database Resources of the BIG Data Center in 2019. Nucleic Acids Res 2019;47:D8-D14.[PMID=30365034] (并列第一, IF=11.561) [2] 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;18:263-76.[PMID=30409858] (IF 5.236) [3] Song S, Tian D, Zhang Z, Hu S, Yu J. Rice Genomics: over the Past Two Decades and into the Future. Genomics Proteomics Bioinformatics 2019.[PMID=30771506] (并列第一, IF=6.615) [4] Song S, Zhang Z. Database Resources in BIG Data Center: Submission, Archive and Integration of Big Data in Plant Science. Mol Plant 2019.[PMID=30716410] (并列第一, IF=9.326) [5] BIG Data Center Members. Database Resources of the BIG Data Center in 2018. Nucleic Acids Res 2018;46:D14-D20.[PMID=29036542] (并列第一, IF=11.561) [6] 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;19:68.[PMID=29855379] (并列通讯, IF=13.214) [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;16:397-404.[PMID=30771506] (第一, IF=6.615) [8] BIG Data Center Members. The BIG Data Center: from deposition to integration to translation. Nucleic Acids Res 2017;45:D18-D24.[PMID=27899658] (并列第一, IF=10.162) [9] 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.[PMID=28931651] [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:E6026-E35.[PMID=27663737] (并列第一、并列通讯, IF=9.423) [11] 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:e0125722.[PMID=25938435] (通讯作者, IF=4.09) [12] 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;66:6651-63.[PMID=26272901] (并列第一、并列通讯, IF=5.526) [13] 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;13:2558-72.[PMID=24965555] [14] 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] [15] 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:e85505.[PMID=24454879] [16] 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;15:899.[PMID=25318541] (并列第一, IF=4.041) [17] 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;139:452-65.[PMID=24675092] [18] 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;11:1180-8.[PMID=25483034] (并列第一、并列通讯, IF=5.377) [19] Li YL, Yu J, Song SH. [Recent progresses in RNA N6-methyladenosine research]. Yi Chuan 2014;35:1340-51.[PMID=24645343] (通讯作者) [20] 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] [21] 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;42:1593-605.[PMID=24214992] [22] 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;24:1403-19.[PMID=25412662] [23] 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;11:72-5.[PMID=23434047] (并列第一、并列通讯) [24] 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;12:1928-38.[PMID=23673344] [25] 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;10:74-81.[PMID=22768981] [26] 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;10:82-93.[PMID=22768982] [27] 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:e50777.[PMID=23236393] [28] 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] (并列通讯) [29] 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:e41981.[PMID=22911868] [30] 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;13:13748-63.[PMID=23202979] [31] 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;49:18-29.[PMID=23177736] [32] 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;8:229-37.[PMID=21382591] (并列通讯) [33] 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;193:2896-7.[PMID=21441509] [34] 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;27:3076-7.[PMID=21896507] (并列通讯, IF=4.877) [35] 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;193:787-8.[PMID=21097614] [36] 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;289:111-26. [37] 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;69:255-60.[PMID=19011765] (并列第一, IF=3.518) [38] 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;282:197-203.[PMID=19468756] (并列第一, IF=2.838) [39] 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;287:297-303.(并列第一, IF=1.678) [40] 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] [41] 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;8:4808-21.[PMID=18850630] [42] 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] [43] 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] (并列第一, IF=4.354)

社会任职:
中国生物工程学会 计算生物学与生物信息学专业委员
获奖及荣誉:
2012年 北京市科技新星