【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.