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按拼音排序【正、副高职称】
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邮  箱: gaog(AT)mail.cbi.pku.edu.cn
职  称:
研究员
个人简历
工作经历
2011 - 至今 , 研究员 , 北京大学生命科学学院
2008 - 2010 , 副研究员 , 北京大学生命科学学院
荣誉奖励
北京大学教学优秀奖,2014
入选 首批青年拔尖人才支持计划 , 2012
首届绿叶生物医药杰出青年学者奖 , 2011/2016
APBioNet Service Award , 2010
学术任职
APBioNet(Asia Pacific Bioinformatics Network,亚太生物信息学网络) 教育副理事长(Vice President on Education)暨中国代表
中国遗传学会生物大数据专业委员会委员
中国人工智能学会生物信息学与人工生命专业委员会委员
中国生物工程学会计算生物学与生物信息学专业委员会委员暨共同发起人
中国细胞生物学学会功能基因组信息学与系统生物学分会委员
中国医药生物技术协会生物医学信息技术分会委员
杂志任职
Editorial board member , Genomics, Proteomics & Bioinformatics , 2012 - 至今
Editorial board member , Hereditas , 2015 - 至今
科研领域描述
  随着以深度测序为代表的高通量生物技术在生命科学领域的广泛应用,各种生物学大数据以指数增长大量涌现。这些数据之中蕴藏着大量的宝藏,即生物学的新规律、新发现。但是,这些海量的、指数增长的、并且高噪声的生物数据也带来了巨大的数据分析技术上的挑战。
  课题组以生物信息学分析技术、方法与平台开发为基础,通过综合运用大数据与统计学习(statistical learning)等计算方法,整合高通量遗传学与功能基因组学数据,探索新表达调控因子的功能与演化及其对生物体新性状和新功能的贡献。目前课题组主要研究方向包括1) 非编码RNA对干细胞命运决定过程的调控、与2) 基因组中适应性基因获得/丢失对调控网络演化的影响。
代表性论文
近五年来主要作者论文(时间逆序,*: (共同-)通讯作者)
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生物学大数据的整合与挖掘 (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”)

调控网络的功能与演化 (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.


慕课教学 (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
================

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.
执教课程
生物信息学方法,主讲教师,秋季学期,本研合上课程
基于深度测序的人类遗传学,主讲教师,秋季学期,研究生课程
遗传学小班讨论课,主讲教师,春季学期,本科生课程
现代生物学基础理论(组学与分子演化模块),主讲教师,春季学期,研究生课程
组学数据分析及其应用,主讲教师,暑期小学期,本科生课程
生物信息学:导论与方法,慕课(MOOC): https://www.coursera.org/learn/sheng-wu-xin-xi-xue
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