Monday, March 26, 2018

Publications

近五年来主要作者论文(时间逆序,*: (共同-)通讯作者)
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Handle Biological “BIG DATA” Effectively and Efficiently

1. Cheng S. J., Shi F. Y., Liu H., Ding Y., Jiang S., Liang N., Gao G. 2017. Accurately annotate compound effects of genetic variants using a context-sensitive framework. Nucleic Acids Res. (in press)
2. Hou M., Tian F., Jiang S., Kong L., Yang D., Gao G.* 2016a. LocExpress: a web server for efficiently estimating expression of novel transcripts. BMC Genomics 17(13): 175-179. (Featured as Best Paper at InCoB’16)
3. Hou M., Tang X., Tian F., Shi F., Liu F., Gao G.* 2016b. AnnoLnc: a web server for systematically annotating novel human lncRNAs. BMC Genomics 17(1): 931.
4. Hu B., Jin J., Guo A. Y., Zhang H., Luo J., Gao G.* 2015. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31(8): 1296-1297. (Featured as ESI Highly Cited (Top 1%) Paper)
5. Xiao A., Cheng Z., Kong L., Zhu Z., Lin S., Gao G.*, Zhang B.* 2014. CasOT: a genome-wide Cas9/gRNA off-target searching tool. Bioinformatics 30(8): 1180-1182. (Featured as ESI Highly Cited (Top 1%) Paper)
6. Kong L., Wang J., Zhao S., Gu X., Luo J.*, Gao G.* 2012. ABrowse – a customizable next-generation genome browser framework. BMC Bioinformatics 13: 2. (Featured as “Highly Accessed”)
7. Wang J., Kong L., Zhao S., Zhang H., Tang L., Li Z., Gu X., Luo J.*, Gao G.* 2011. Rice-Map: a new-generation rice genome browser. BMC Genomics 12: 165. (Featured as “Highly Accessed”)

Decipher the Function and Evolution of Gene Regulatory Network

8. Jin J., Tian F., Yang D. C., Meng Y. Q., Kong L., Luo J., Gao G.* 2017. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res 45(D1): D1040-D1045.
9. Jin J., He K., Tang X., Li Z., Lv L., Zhao Y., Luo J., Gao G.* 2015. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol Biol Evol 32(7): 1767-1773.
10. Zhao Y., Tang L., Li Z., Jin J., Luo J., Gao G.* 2015. Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics. BMC Evol Biol 15: 66. (Featured as “Very Good (being of special significance in its field)” by Faculty of 1000)
11. Gao G., Vibranovski M. D., Zhang L., Li Z., Liu M., Zhang Y. E., Li X., Zhang W., Fan Q., VanKuren N. W., Long M., Wei L. 2014. A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster. Genome Res 24(4): 629-638.
12. Jin J., Zhang H., Kong L., Gao G.*, Luo J.* 2014. PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Res 42(1): D1182-1187. (Featured as ESI Highly Cited (Top 1%) Paper)
13. Tang X., Hou M., Ding Y., Li Z., Ren L., Gao G.* 2013. Systematically profiling and annotating long intergenic non-coding RNAs in human embryonic stem cell. BMC Genomics 14(Suppl 5): S3. (Featured as “Highly Accessed”)
14. Chen Z. X., Zhang Y. E., Vibranovski M., Luo J., Gao G.*, Long M.* 2011. Deficiency of X-linked inverted duplicates with male-biased expression and the underlying evolutionary mechanisms in the Drosophila genome. Mol Biol Evol 28(10): 2823-2832.

Education

15. Ding Y., Wang M., He Y., Ye A. Y., Yang X., Liu F., Meng Y., Gao G.*, Wei L.* 2014. “Bioinformatics: Introduction and Methods,” a Bilingual Massive Open Online Course (MOOC) as a New Example for Global Bioinformatics Education. PLoS Computational Biology 10(12): e1003955.

近五年来合作论文
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1. Zhou Y., Wang P., Tian F., Gao G., Huang L., Wei W., Xie X. S. 2017. Painting a specific chromosome with CRISPR/Cas9 for live-cell imaging. Cell Res 27(2): 298-301.
2. Feng S., Zhao Y., Xu Y., Ning S., Huo W., Hou M., Gao G., Ji J., Guo R.*, Xu D.* 2016. Ewing Tumor-associated Antigen 1 Interacts with Replication Protein A to Promote Restart of Stalled Replication Forks. J Biol Chem 291(42): 21956-21962.
3. Xing M., Yang M., Huo W., Feng F., Wei L., Jiang W., Ning S., Yan Z., Li W., Wang Q., Hou M., Dong C., Guo R., Gao G., Ji J., Zha S., Lan L., Liang H., Xu D. 2015. Interactome analysis identifies a new paralogue of XRCC4 in non-homologous end joining DNA repair pathway. Nat Commun 6: 6233.
4. Shu J., Wu C., Wu Y., Li Z., Shao S., Zhao W., Tang X., Yang H., Shen L., Zuo X., Yang W., Shi Y., Chi X., Zhang H., Gao G., Shu Y., Yuan K., He W., Tang C.*., Zhao Y., Deng HK.*. 2013. Induction of pluripotency in mouse somatic cells with lineage specifiers. Cell 153(5): 963-975.
5. Huang Y., Xie C., Ye A. Y., Li C. Y., Gao G., Wei L.* 2013. Recent adaptive events in human brain revealed by meta-analysis of positively selected genes. PloS ONE 8(4): e61280.
6. Wang J., Kong L., Gao G., Luo J.* 2013. A brief introduction to web-based genome browsers. Brief Bioinform 14(2): 131-143.
7. Xiao A., Wu Y., Yang Z., Hu Y., Wang W., Zhang Y., Kong L., Gao G., Zhu Z., Lin S., Zhang B. 2013. EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering. Nucleic Acids Res 41(Database issue): D415-422.
8. Yue R., Li H., Liu H., Li Y., Wei B., Gao G., Jin Y., Liu T., Wei L., Du J., Pei G.* 2012. Thrombin receptor regulates hematopoiesis and endothelial-to-hematopoietic transition. Dev Cell 22(5): 1092-1100.
9. Zhang J., Gao G., Chen J. J., Taylor G., Cui KM.*, He XQ.* 2011. Molecular features of secondary vascular tissue regeneration after bark girdling in Populus. New Phytol 192(4): 869-884.
10. Du P., Wu J., Zhang J., Zhao S., Zheng H., Gao G., Wei L., Li Y.* 2011. Viral Infection Induces Expression of Novel Phased MicroRNAs from Conserved Cellular MicroRNA Precursors. PLoS Pathog 7(8): e1002176.
11. Xie C., Mao X., Huang J., Ding Y., Wu J., Dong S., Kong L., Gao G., Li C. Y., Wei L.* 2011. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 39(Web Server issue): W316-322.
12. Liu M., Liu P. P., Zhang L., Cai Q. C., Gao G., Zhang W. X., Zhu Z. Y., Liu D.*, Fan QC.* 2011. mir-35 is involved in intestine cell G1/S transition and germ cell proliferation in C. elegans. Cell Research 21(11): 1605-1618.