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丁国徽博士介绍(PI)

 

DGH

个人基因组课题组长:丁国徽,博士,上海生物信息技术研究中心/上海生物医学研究院个人基因组研究组组长。2008年中国科学院上海生命科学研究院生物信息中心获得博士学位。2009年11月,破格提升为中国科学院上海生命科学研究院副研究员。曾获中国科学院院长奖(优秀奖),赛诺菲青年科学家奖等。丁国徽博士主要以分子进化,基因组学和生物医学信息作为研究方向,已发表论文50余篇,其中以第一作者或通讯作者发表SCI论文20篇,参与申请专利5项,软件著作权11项。

【科研项目】
2008.10-2010.10,中国科学院“优秀博士学位论文、院长奖获得者科研启动专项资金”一项,项目负责人
2009.1-2010.12,中国科学院信息化专项项目一项,副组长
2010.1-2012.12,国家自然科学基金青年科学基金项目一项,负责人
2011.1-2015.8,国家重点基础研究发展计划(973计划)子任务项目一项,负责人
2011-2014,欧盟框架项目(FP7)子任务项目一项,负责人
2011-2013,中国科学院优秀青年人才项目,负责人
2012.1-2015.12,国家高技术研究发展计划(863计划)子项目一项,负责人
2013.7-2014.7,中国科学院“十二五”信息化专项超级计算重点应用示范项目,负责人
 

【第一作者或通讯作者论文】
1.  X. Gou et al., Whole genome sequencing of six dog breeds from continuous altitudes reveals adaption to high-altitude hypoxia, Genome Res. (2014), doi:10.1101/gr.171876.113.
2.  C. Li et al., The 3DGD: a database of genome 3D structure, Bioinformatics (2014), doi:10.1093/bioinformatics/btu081.
3.  X. Dong et al., Evaluating coverage of exons by HapMap SNPs, Genomics 101, 20–23 (2013).
4.  S. Deng, L. Yuan, K. Feng, G. Ding, Y. Li, A New Approach for Identifying Protein-Coding Regions by Combining Chirp z and Wavelet Transform., Current Bioinformatics 8, 557–563 (2013).
5.  Y. Dai et al., The de novo sequence origin of two long non-coding genes from an inter-genic region, BMC Genomics 14 Suppl 8, S6 (2013).
6.  S. Deng, Y. Shi, L. Yuan, Y. Li, G. Ding, Detecting the borders between coding and non-coding DNA regions in prokaryotes based on recursive segmentation and nucleotide doublets statistics, BMC Genomics 13 Suppl 8, S19 (2012).
7.  Bactrian Camels Genome Sequencing and Analysis Consortium et al., Genome sequences of wild and domestic bactrian camels, Nat Commun 3, 1202 (2012).
8.  J. Jiang et al., Different developmental potential of pluripotent stem cells generated by different reprogramming strategies, J Mol Cell Biol 3, 197–199 (2011).
9.  Z. Wang et al., Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes, Mol. Biol. Evol. 28, 1131–1140 (2011).
10.  Z. Wang, X. Dong, G. Ding, Y. Li, Comparing the retention mechanisms of tandem duplicates and retrogenes in human and mouse genomes, Genet. Sel. Evol. 42, 24 (2010).
11.  X. Dong, C. Li, Y. Chen, G. Ding, Y. Li, Human transcriptional interactome of chromatin contribute to gene co-expression, BMC Genomics 11, 704 (2010).
12.  Z. Chen, S. Deng, L. Chen, G. Ding, Y. Li, An integrated strategy for functional analysis in 16S rRNA gene-based research of microbial communities by Gene Ontology, 3rd International Conference on Environmental and Computer Science (ICECS) , V2–4 (2010).
13.  G. Ding, P. Lorenz, M. Kreutzer, Y. Li, H.-J. Thiesen, SysZNF: the C2H2 zinc finger gene database, Nucleic Acids Res. 37, D267–273 (2009).
14.  袁力赟, 赵中明, 丁国徽, 哺乳动物锌指蛋白家族中 KRAB 功能域的进化, 生物信息学 7, 202–206 (2009).
15.  A. Yan et al., Subtyping of type A influenza by sequencing the variable regions of HA gene specifically amplified with RT-PCR, Chinese Science Bulletin 54, 2164–2167 (2009).
16.  G. Ding et al., EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information, Nucleic Acids Res. 36, D255–262 (2008).
17.  G. Ding et al., Tree of life based on genome context networks, PLoS ONE 3, e3357 (2008).
18.  J. Sun et al., InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes, BMC Bioinformatics 8, 414 (2007).
19.  G. Ding et al., Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families, PLoS Comput. Biol. 2, e102 (2006).
20.  W. Wei et al., Comparative analysis of whole-genome sequences of Streptococcus suis, Chinese Science Bulletin 51, 1199–1209 (2006).

【参与作者论文】
1. Zhou, S., Gao, R., Hu, W., Qian, T., Wang, N., Ding, G., Ding, F., Yu, B., and Gu, X. (2014). miR-9 inhibits Schwann cell migration by targeting Cthrc1 following sciatic nerve injury. J. Cell. Sci. 127, 967–976.
2. Zhou, D., Zhang, D., Ding, G., Shi, L., Hou, Q., Ye, Y., Xu, Y., Zhou, H., Xiong, C., Li, S., et al. (2014). Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites. BMC Genomics 15, 42.
3. Li, B.-Q., Yu, H., Wang, Z., Ding, G.-H., and Liu, L. (2013). MicroRNA mediated network and DNA methylation in colorectal cancer. Protein Pept. Lett. 20, 352–363.
4. Yu, B., Zhou, S., Hu, W., Qian, T., Gao, R., Ding, G., Ding, F., and Gu, X. (2013). Altered long noncoding RNA expressions in dorsal root ganglion after rat sciatic nerve injury. Neurosci. Lett. 534, 117–122.
5. Yang, L., Ding, G., Lin, H., Cheng, H., Kong, Y., Wei, Y., Fang, X., Liu, R., Wang, L., Chen, X., et al. (2013). Transcriptome analysis of medicinal plant Salvia miltiorrhiza and identification of genes related to tanshinone biosynthesis. PLoS ONE 8, e80464.
6. Li, S., Liu, Q., Wang, Y., Gu, Y., Liu, D., Wang, C., Ding, G., Chen, J., Liu, J., and Gu, X. (2013). Differential gene expression profiling and biological process analysis in proximal nerve segments after sciatic nerve transection. PLoS ONE 8, e57000.
7. Yu, B., Qian, T., Wang, Y., Zhou, S., Ding, G., Ding, F., and Gu, X. (2012). miR-182 inhibits Schwann cell proliferation and migration by targeting FGF9 and NTM, respectively at an early stage following sciatic nerve injury. Nucleic Acids Res. 40, 10356–10365.
8. Yu, B., Zhou, S., Wang, Y., Qian, T., Ding, G., Ding, F., and Gu, X. (2012). miR-221 and miR-222 promote Schwann cell proliferation and migration by targeting LASS2 after sciatic nerve injury. J. Cell. Sci. 125, 2675–2683.
9. Yuan, L., Ding, G., Chen, Y. E., Chen, Z., and Li, Y. (2012). A novel strategy for deciphering dynamic conservation of gene expression relationship. J Mol Cell Biol 4, 177–179.
10. Zheng, G., Liu, Q., Ding, G., Wei, C., and Li, Y. (2012). Towards biological characters of interactions between transcription factors and their DNA targets in mammals. BMC Genomics 13, 388.
11. Yu, B., Zhou, S., Wang, Y., Ding, G., Ding, F., and Gu, X. (2011). Profile of microRNAs following rat sciatic nerve injury by deep sequencing: implication for mechanisms of nerve regeneration. PLoS ONE 6, e24612.
12. Li, Y., Li, C., Ding, G., and Jin, Y. (2011). Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways. BMC Evol. Biol. 11, 122.
13. Ji, Y., Shi, Y., Ding, G., and Li, Y. (2011). A new strategy for better genome assembly from very short reads. BMC Bioinformatics 12, 493.
14. Huang, T., Liu, L., Liu, Q., Ding, G., Tan, Y., Tu, Z., Li, Y., Dai, H., and Xie, L. (2011). The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma. Int J Comput Biol Drug Des 4, 5–18.
15. Hao, P., Zheng, H., Yu, Y., Ding, G., Gu, W., Chen, S., Yu, Z., Ren, S., Oda, M., Konno, T., et al. (2011). Complete sequencing and pan-genomic analysis of Lactobacillus delbrueckii subsp. bulgaricus reveal its genetic basis for industrial yogurt production. PLoS ONE 6, e15964.
16. Li, H., He, Y., Ding, G., Wang, C., Xie, L., and Li, Y. (2010). dbDEPC: a database of differentially expressed proteins in human cancers. Nucleic Acids Res. 38, D658–664.
17. Dong, H., Zhang, Y., Xiong, H., Yan, A., Ding, G., Chen, Y., Xie, L., Chen, J., Zhang, G., Hao, P., et al. (2010). Detection of human novel influenza A (H1N1) viruses using multi-fluorescent real-time RT-PCR. Virus Res. 147, 85–90.
18. Lorenz, P., Dietmann, S., Wilhelm, T., Koczan, D., Autran, S., Gad, S., Wen, G., Ding, G., Li, Y., Rousseau-Merck, M.-F., et al. (2010). The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues. BMC Genomics 11, 206.
19. Liu, Q., Tan, Y., Huang, T., Ding, G., Tu, Z., Liu, L., Li, Y., Dai, H., and Xie, L. (2010). TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information. BMC Bioinformatics 11 Suppl 11, S5.
20. Liu, Q., Ding, G., Huang, T., Tan, Y., Dai, H., Xie, L., and Li, Y. (2010). Considering Dependencies Amongst Genes Helps to Adjust the Significance Rank of DEGs. Chinese Journal of Chemistry 28, 1284–1290.
21. Deng, S., Chen, Z., Ding, G., and Li, Y. (2010). Prediction of protein coding regions by combining Fourier and Wavelet Transform. In 2010 3rd International Congress on Image and Signal Processing (CISP), pp. 4113–4117.
22. Li, H., Xing, X., Ding, G., Li, Q., Wang, C., Xie, L., Zeng, R., and Li, Y. (2009). SysPTM: a systematic resource for proteomic research on post-translational modifications. Mol. Cell Proteomics 8, 1839–1849.
23. Li, H., Ding, G., Xie, L., and Li, Y. (2009). PAnnBuilder: an R package for assembling proteomic annotation data. Bioinformatics 25, 1094–1095.
24. Wang, Z., Ding, G., Yu, Z., Liu, L., and Li, Y. (2009). Modeling the age distribution of gene duplications in vertebrate genome using mixture density. Genomics 93, 146–151.
25. Xi, H., Park, J., Ding, G., Lee, Y.-H., and Li, Y. (2009). SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry. Nucleic Acids Res. 37, D913–920.
26. Yu, Y., Tu, K., Zheng, S., Li, Y., Ding, G., Ping, J., Hao, P., and Li, Y. (2009). GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. BMC Bioinformatics 10, 264.
27. Wu, D., Xu, T., Sun, J., Dai, J., Ding, G., He, Y., Zhou, Z., Xiong, H., Dong, H., and Jin, W. (2009). Structure modeling and spatial epitope analysis for HA protein of the novel H1N1 influenza virus. Chinese Science Bulletin 54, 2171–2173.
28. Wang, Z., Ding, G., Yu, Z., Liu, L., and Li, Y. (2009). CHSMiner: a GUI tool to identify chromosomal homologous segments. Algorithms Mol Biol 4, 2.
29. He, Y., Ding, G., Bian, C., Huang, Z., Lan, K., Sun, B., Wang, X., Li, Y., Wang, H., and Wang, X. (2009). The mutation network for the hemagglutinin gene from the novel influenza A (H1N1) virus. Chinese Science Bulletin 54, 2168–2170.
30. Li, Y., Hao, P., Zheng, S., Tu, K., Fan, H., Zhu, R., Ding, G., Dong, C., Wang, C., Li, X., et al. (2008). Gene expression module-based chemical function similarity search. Nucleic Acids Res. 36, e137.
31. Zhou, Y.-B., Cao, J.-B., Wan, B.-B., Wang, X.-R., Ding, G.-H., Zhu, H., Yang, H.-M., Wang, K.-S., Zhang, X., and Han, Z.-G. (2008). hBolA, novel non-classical secreted proteins, belonging to different BolA family with functional divergence. Mol. Cell. Biochem. 317, 61–68.
32. Zhu, Y.-Z., Li, Q.-T., Wang, L., Zhong, Y., Ding, G.-H., Li, G., Jia, P.-L., Shi, T.-L., and Guo, X.-K. (2008). Gene expression profiling-based in silico approach to identify potential vaccine candidates and drug targets against B. pertussis and B. parapertussis. OMICS 12, 161–169.
33. Zhao, J., Ding, G.-H., Tao, L., Yu, H., Yu, Z.-H., Luo, J.-H., Cao, Z.-W., and Li, Y.-X. (2007). Modular co-evolution of metabolic networks. BMC Bioinformatics 8, 311.
34. Liu, T., Zhang, Q., Wang, L., Yu, L., Leng, W., Yang, J., Chen, L., Peng, J., Ma, L., Dong, J., Ding G, et al. (2007). The use of global transcriptional analysis to reveal the biological and cellular events involved in distinct development phases of Trichophyton rubrum conidial germination. BMC Genomics 8, 100.
35. Wei, W., Cao, Z., Zhu, Y.-L., Wang, X., Ding, G., Xu, H., Jia, P., Qu, D., Danchin, A., and Li, Y. (2006). Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228. BMC Genomics 7, 112.
36. Wang, L., Ma, L., Leng, W., Liu, T., Yu, L., Yang, J., Yang, L., Zhang, W., Zhang, Q., Dong, J., et al. (2006). Analysis of the dermatophyte Trichophyton rubrum expressed sequence tags. BMC Genomics 7, 255.
37. Guanming, Q., Wei, L., Ming, Z., Zhe, L., Changhao, Y., Yourong, L., and Guohui, Ding. (2004). Review, Intelligence and Development of Rare Earths during Biological Evolution. Journal of Rare Earths 22, 1–11.

【专利申请情况】
1. 严安;丁国徽;董辉;熊慧;金维荣;赵国屏;李亦学;车小燕;吴凡;童光志. 检测人甲型流感病毒H1和/或H3亚型的引物及方法[P]. 中国, 200910303111.9.
2. 韦朝春;蔡锴晔;刘雷;高军晖;李亦学;丁国徽;李轩. 检测人乳头瘤病毒的检测试剂盒及其制备和使用[P]. 中国, 200910303111.9.
3. 董辉;熊慧;金维荣;李辉;丁国徽;谢立群;陈嘉铮;严安;车小燕;袁国勇;赵国屏. 用于检测人甲型流感病毒的核苷酸序列、方法及试剂盒[P]. 中国. 200910303328.X.
4. 严安;丁国徽;董辉;熊慧;金维荣;赵国屏;李亦学;车小燕;吴凡;童光志. 检测人甲型流感病毒H3亚型的引物及方法[P]. 中国. 201110415387.3
5. 钟庭艳;董潇;李碧清;丁国徽;李亦学. 一种检测外显子组单核苷酸覆盖率的方法[P]. 中国. 201210179369.4


【早期译著目录】

2005年 《R 导论》(An Introduction to R; ISBN 3-900051-12-7)(国内第一本全面介绍R语言的中文材料)
2006年《基于R和Bioconductor的生物信息学与计算生物学解决方案》(Bioinformatics and Computational Biology Solutions Using R and Bioconductor; ISBN-13 978-0387-25146-2)(和石铁流老师等合作编译)
2006年 《面向初学者的R》(R for Beginners)(和网友共同翻译)
2006年 《R语言定义》(The R language definition; ISBN 3-900051-13-5)
2007年 《R 内核》(R Internals; ISBN 3-900051-14-3)
2008年 《R 数据的导入和导出》(R Data Import/Export; ISBN 3-900051-10-0)