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Principal Investigator (Guohui Ding, Ph.D.)

 dingguohui

Guohui Ding

Email:
                gwding@sibs.ac.cn

Telephone:            86-21-54920086

Cell-phone:          13764691063

 

Education History

1999.9 - 2003.7  Bachelor of Engineering, Study of Bio-engineering and Computer Science, South China University of Technology

2003.9 – 2008.7  Ph.D of Bio-informatics, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

2006.3          Training in Center for Information Biology and DNA Data Bank of Japan

2006.5 - 2006.7     Study in Rostock University, Germany

2006.7          Visit EMBL Heidelberg

2007.8-2007.11      Study in Rostock University, Germany

2008.9-2008.11      Visit Rosetta Inpharmatics (Merck & Co. Inc.)

 

Fellowship and Honor

National Scholarship, from the MOE of China, 2002

Triple A student, from the Graduate University of the Chinese Academy of Sciences, 2006/2007

Triple A student, from the Graduate University of the Chinese Academy of Sciences, 2007/2008

Excellent graduate, from the Shanghai Municipal Government, 2008

President award of the Chinese Academy of Sciences, 2008

 

Work experience

2008.7– 2009.12  Assistant Professor in Bioinformatics Unit, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

2010.6 – 2012.3 Co-Principal investigator in next generation sequencing unit, Shanghai Center for Bioinformation Technology.

2009.12 – current Associate Professor in Bioinformatics Unit, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

2012.3- current Principal investigator in personal genomics group, Shanghai Center for Bioinformation Technology.

 

Publications

Refereed Journal Articles

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.     S. Zhou et al., miR-9 inhibits Schwann cell migration by targeting Cthrc1 following sciatic nerve injury, J. Cell. Sci. 127, 967–976 (2014).
3.     C. Li et al., The 3DGD: a database of genome 3D structure, Bioinformatics (2014), doi:10.1093/bioinformatics/btu081.
4.     D. Zhou et al., Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites, BMC Genomics 15, 42 (2014).
5.     B.-Q. Li, H. Yu, Z. Wang, G.-H. Ding, L. Liu, MicroRNA mediated network and DNA methylation in colorectal cancer, Protein Pept. Lett. 20, 352–363 (2013).
6.     B. Yu et al., Altered long noncoding RNA expressions in dorsal root ganglion after rat sciatic nerve injury, Neurosci. Lett. 534, 117–122 (2013).
7.     X. Dong et al., Evaluating coverage of exons by HapMap SNPs, Genomics 101, 20–23 (2013).
8.     L. Yang et al., Transcriptome analysis of medicinal plant Salvia miltiorrhiza and identification of genes related to tanshinone biosynthesis, PLoS ONE 8, e80464 (2013).
9.     S. Li et al., Differential gene expression profiling and biological process analysis in proximal nerve segments after sciatic nerve transection, PLoS ONE 8, e57000 (2013).
10.   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).
11.   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).
12.   B. Yu et al., 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 (2012).
13.   B. Yu et al., miR-221 and miR-222 promote Schwann cell proliferation and migration by targeting LASS2 after sciatic nerve injury, J. Cell. Sci. 125, 2675–2683 (2012).
14.   L. Yuan, G. Ding, Y. E. Chen, Z. Chen, Y. Li, A novel strategy for deciphering dynamic conservation of gene expression relationship, J Mol Cell Biol 4, 177–179 (2012).
15.   G. Zheng, Q. Liu, G. Ding, C. Wei, Y. Li, Towards biological characters of interactions between transcription factors and their DNA targets in mammals, BMC Genomics 13, 388 (2012).
16.   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).
17.   Bactrian Camels Genome Sequencing and Analysis Consortium et al., Genome sequences of wild and domestic bactrian camels, Nat Commun 3, 1202 (2012).
18.   J. Jiang et al., Different developmental potential of pluripotent stem cells generated by different reprogramming strategies, J Mol Cell Biol 3, 197–199 (2011).
19.   Z. Wang et al., Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes, Mol. Biol. Evol. 28, 1131–1140 (2011).
20.   B. Yu et al., Profile of microRNAs following rat sciatic nerve injury by deep sequencing: implication for mechanisms of nerve regeneration, PLoS ONE 6, e24612 (2011).
21.   Y. Li, C. Li, G. Ding, Y. Jin, Evolution of MIR159/319 microRNA genes and their post-transcriptional regulatory link to siRNA pathways, BMC Evol. Biol. 11, 122 (2011).
22.   Y. Ji, Y. Shi, G. Ding, Y. Li, A new strategy for better genome assembly from very short reads, BMC Bioinformatics 12, 493 (2011).
23.   T. Huang et al., 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 (2011).
24.   P. Hao et al., Complete sequencing and pan-genomic analysis of Lactobacillus delbrueckii subsp. bulgaricus reveal its genetic basis for industrial yogurt production, PLoS ONE 6, e15964 (2011).
25.   H. Li et al., dbDEPC: a database of differentially expressed proteins in human cancers, Nucleic Acids Res. 38, D658–664 (2010).
26.   H. Dong et al., Detection of human novel influenza A (H1N1) viruses using multi-fluorescent real-time RT-PCR, Virus Res. 147, 85–90 (2010).
27.   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).
28.   P. Lorenz et al., 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 (2010).
29.   Q. Liu et al., 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 (2010).
30.   Q. Liu et al., Considering Dependencies Amongst Genes Helps to Adjust the Significance Rank of DEGs, Chinese Journal of Chemistry 28, 1284–1290 (2010).
31.   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).
32.   S. Deng, Z. Chen, G. Ding, Y. Li, in 2010 3rd International Congress on Image and Signal Processing (CISP), (2010), vol. 9, pp. 4113–4117.
33.   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).
34.   H. Li et al., SysPTM: a systematic resource for proteomic research on post-translational modifications, Mol. Cell Proteomics 8, 1839–1849 (2009).
35.   H. Li, G. Ding, L. Xie, Y. Li, PAnnBuilder: an R package for assembling proteomic annotation data, Bioinformatics 25, 1094–1095 (2009).
36.   Z. Wang, G. Ding, Z. Yu, L. Liu, Y. Li, Modeling the age distribution of gene duplications in vertebrate genome using mixture density, Genomics 93, 146–151 (2009).
37.   H. Xi, J. Park, G. Ding, Y.-H. Lee, Y. Li, SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry, Nucleic Acids Res. 37, D913–920 (2009).
38.   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).
39.   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).
40.   Y. Yu et al., GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction, BMC Bioinformatics 10, 264 (2009).
41.   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).
42.   D. Wu et al., Structure modeling and spatial epitope analysis for HA protein of the novel H1N1 influenza virus, Chinese Science Bulletin 54, 2171–2173 (2009).
43. Z. Wang, G. Ding, Z. Yu, L. Liu, Y. Li, CHSMiner: a GUI tool to identify chromosomal homologous segments, Algorithms Mol Biol 4, 2 (2009).
44.   Y. He et al., The mutation network for the hemagglutinin gene from the novel influenza A (H1N1) virus, Chinese Science Bulletin 54, 2168–2170 (2009).
45.   Y. Li et al., Gene expression module-based chemical function similarity search, Nucleic Acids Res. 36, e137 (2008).
46.   Y.-B. Zhou et al., hBolA, novel non-classical secreted proteins, belonging to different BolA family with functional divergence, Mol. Cell. Biochem. 317, 61–68 (2008).
47.   Y.-Z. Zhu et al., 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 (2008).
48.   G. Ding et al., EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information, Nucleic Acids Res. 36, D255–262 (2008).
49.   G. Ding et al., Tree of life based on genome context networks, PLoS ONE 3, e3357 (2008).
50.   J. Zhao et al., Modular co-evolution of metabolic networks, BMC Bioinformatics 8, 311 (2007).
51.   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).
52.   T. Liu et al., 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 (2007).
53.   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).
54.   W. Wei et al., Comparative analysis of whole-genome sequences of Streptococcus suis, Chinese Science Bulletin 51, 1199–1209 (2006).
55.   W. Wei et al., Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228, BMC Genomics 7, 112 (2006).
56.   L. Wang et al., Analysis of the dermatophyte Trichophyton rubrum expressed sequence tags, BMC Genomics 7, 255 (2006).57.   G. Qiu et al., Review, Intelligence and Development of Rare Earths during Biological Evolution, Journal of Rare Earths 22, 1–11 (2004). 

Translations (Chinese) of several R books
2005 R 导论》(An Introduction to R; ISBN 3-900051-12-7(First Chinese book about R in China and the only Chinese document in R official website before 2008)
2006 《面向初学者的R》(R for Beginners)(Collaborate with some volunteers
2006 R语言定义》(The R language definition; ISBN 3-900051-13-5
2007 R 内核》(R Internals; ISBN 3-900051-14-3
2008 R 数据的导入和导出》(R Data Import/Export; ISBN 3-900051-10-0)

 




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