General

Jingfa Xiao, PhD
Profes
sor, Beijing Institute of Genomics, Chinese Academy of Sciences

Emailxiaojingfa@big.ac.cn
Adress NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China

Research Areas

Genomics and Bioinformatics

Education

Sep. 1998 to Jul 2003 – Computational Biology and Chemistry in Institute of Theoretical Chemistry, Jilin University.

Sep. 1991 to Jul 1995 – Biology, in Department of Biology, Sichuan University.

Experience

   
Work Experience


May 2012 to Present – Professor in Beijing Institute of Genomics, Chinese Academy of Sciences.


Feb 2007 to May 2012 – Associate Professor in Beijing Institute of Genomics, Chinese Academy of Sciences. 


Nov 2005 to Feb 2007 – Computational Biology Postdoctoral Research in Department of Chemistry, University of Utah.


Aug. 2003 to Sep. 2005 – Computer-aided Drug Design Postdoctoral Research in Institute of Materia Medica of Chinese Academy of Medical Sciences and Peking Union Medical College.










Publications

   
Papers

  1. Zhang Zhang*, Wenming Zhao*, Jingfa Xiao*, et al.. The BIG Data Center: from deposition to integration to translation. Nucleic Acids Research. (2016, In press).

  2. Xin Sheng, Jiayan Wu, Qianqian Sun, Feng Xian, Xue Li, Manman Sun, Wan Fang, Meili Chen, Jun Yu*, and Jingfa Xiao*, MTD: A mammalian transcriptomic database to explore gene expression regulation. Briefings in Bioinformatics (2016, In press).

  3. Fang Liang, Jinyue Wang, Shuo Shi, Jingfa Xiao*, Rujiao Li*, BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data. Comput Biol Chem. 65:173-177 (2016).

  4. Yu Xue, Eric-Wubbo Lameijer, Kai Ye, Kunlin Zhang, Suhua Chang, Xiaoyue Wang, Jianmin Wu, Ge Gao, Fangqing Zhao, Jian Li, Chunsheng Han, Shuhua Xu, Jingfa Xiao, Xuerui Yang, Xiaomin Ying, Xuegong Zhang, Weihua Chen, Yun Liu, Zhang Zhang, Kun Huang, Jun Yu, Precision Medicine: What Challenges Are We Facing? Genomics, Proteomics & Bioinformatics. 14:253-261 (2016).

  5. Xinpeng Tian, Zhewen Zhang, Tingting Yang, Meili Chen, Jie Li, Fei Chen, Jin Yang, Wenjie Li, Bing Zhang, Zhang Zhang, Jiayan Wu, Changsheng Zhang, Lijuan Long*, Jingfa Xiao*, Comparative genomics analysis of Streptomyces species reveals their adaptation to the marine environment and their diversity at the genomic level. Frontiers in Microbiology 7: fmicb.2016.00998 (2016).

  6. Lingxiang Zhu, Jun Zhong, Xinmiao Jia, Guan Liu, Yu Kang, Mengxing Dong, Xiuli Zhang, Qian Li, Liya Yue, Cuidan Li, Jialei Xie, Bing Zhang, Meng Lei, Jingfa Xiao, Jiangwei Yan, Suting Chen, Lingna Lv, Baoli Zhu, Hairong Huang, Fei Chen, Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio Single-Molecule Real-Time (SMRT) Technology. Nucleic Acids Research. 44, 730-743 (2016).

  7. The IC4R Project Consortium*, Information Commons for Rice (IC4R). Nucleic Acids Research. 44:D1172-D1180 (2016).

  8. Meili Chen, Yibo Hu, Jingxing Liu, Qi Wu, Chenglin Zhang, Jun Yu, Jingfa Xiao*, Fuwen Wei*, Jiayan Wu*. Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome. Scientific Reports. 5:18019 (2015).

  9. Jingfa Xiao*, Zhewen Zhang, Jiayan Wu and Jun Yu. A Brief Review of Online Software Packages for Pangenomics. Genomics, Proteomics & Bioinformatics. 13:73-76 (2015).

  10. Yongbing Zhao, Jinlong Yin, Haiyan Guo, Yuyu Zhang, Wen Xiao, Chen Sun, Jiayan Wu, Xiaobo Qu, Jun Yu, Xumin Wang*, Jingfa Xiao*. The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng. Frontiers in Plant Science. 5:696 (2015).

  11. Yu Kang, Chaohao Gu, Lina Yuan,Yue Wang,Yanmin Zhu, Xinna Li, Qibin Luo, Jingfa Xiao, Daquan Jiang, Minping Qian, Aftab Ahmed Khan, Fei Chen, Zhang Zhang, Jun Yu, Flexibility and Symmetry of Prokaryotic Genome Rearrangement Reveal Lineage-Associated Core-Gene-Defined Genome Organizational Frameworks. mBio. 5, e01867-14 (2014).

  12. Peng Xu, Xiaofeng Zhang, Xumin Wang, et al., Jingfa Xiao, Jiayan Wu, Zhang Zhang, Jun Yu, Xiaowen Sun. Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nature Genetics. 46, 1212-1221 (2014).

  13. Wenquan Wang, Binxiao Feng, Jingfa Xiao, Zhiqiang Xia, et al, Ming Peng. Cassava Genome from a Wild Ancestor to Cultivated Varieties. Nature Communications. DOI:10.1038/ncomms6110 (2014)

  14. Jiayan Wu, Jingfa Xiao, Zhang Zhang, Xumin Wang, Songnian Hu, Jun Yu. Ribogenomics: the Science and Knowledge of RNA. Genomics, Proteomics & Bioinformatics. 12, 57-63 (2014).

  15. Yongbing Zhao, Xinmiao Jia, Junhui Yang, Yunchao Ling, Zhang Zhang, Jun Yu, Jiayan Wu*, Jingfa Xiao*, PanGP: A tool for quick analyzing bacterial pan-genome profile. Bioinformatics. 30, 1297-1299 (2014).

  16. Yunchao Ling, Zhong Jin, Mingming Su, Jun Zhong, Yongbing Zhao, Jun Yu, Jiayan Wu*, Jingfa Xiao*, VCGDB: a dynamic genome database of Chinese population. BMC genomics. 15:265 (2014).

  17. Siew Woh Choo, Wei Yee Wee, Yun Fong Ngeow, Wayne Mitchell, Joon Liang Tan, Guat Jah Wong, Yongbing Zhao, Jingfa Xiao. Genomic reconnaissance of multiple, clinically derived isolates of the emerging human pathogen Mycobacterium abscessus reveals high evolutionary potential. Scientific Report. 4, 4061(2014).

  18. Zhang Zhang, Jian Sang, Lina Ma, Gang Wu, Hao Wu, Dawei Huang, Dong Zou, Siqi Liu, Ang Li, Lili Hao, Ming Tian, Chao Xu, Xumin Wang, Jiayan Wu, Jingfa Xiao, Lin Dai, Ling-Ling Chen, Songnian Hu, Jun Yu. RiceWiki: a wiki-based database for community curation of rice genes. Nucleic Acids Research, 42(D1): D1222-D1228 (2014).

  19. Mingming Su, Yunchao Ling, Jun Yu, Jiayan Wu, Jingfa Xiao*, Small proteins: untapped area of potential biological importance. Frontiers in Genetics, 4:286 (2013).

  20. Ruosi Zhang, Lili Hao, Lingping Wang, Meili Chen, Wen Li, Rujiao Li, Jun Yu, Jingfa Xiao*, Jiayan Wu*, Gene expression analysis of induced pluripotent stem cells from aneuploidy chromosomal syndromes. BMC Genomics. Suppl 6, S8 (2013).

  21. Meili Chen, Jingfa Xiao, Zhang Zhang, Jingxing Liu, Jiayan Wu, Jun Yu, Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Trancsriptomics Data Analysis. PLoS one. 8, e54082 (2013).

  22. Lin Dai, Ming Tian, Jiayan Wu, Jingfa Xiao, Xumin Wang, Kei-Hoi Cheung, Jeffrey P. Townsend, Zhang Zhang. Increasing participation in biological knowledge wikis through contribution quantification and explicit authorship. Bioinformatics. 29, 1837-1839 (2013).

  23. Lin Dai, Xin Gao, Benoit Marchand, Yan Guo, Jingfa Xiao, Zhang Zhang. Bioinformatics clouds for big data manipulation. Biology Direct. 7, 143 (2012).

  24. Weili Liang, Yongbing Zhao, Chunxia Chen, Xiaoying Cui, Jun Yu, Jingfa Xiao*, Biao Kan*, Pan-genome provides insights into genome variation and evolution in Salmonella Paratyphi A. PLOS one. 7, e45346 (2012).

  25. Dongyu Zhao, Jiayan Wu, Yuanyuan Zhou, Wei Gong, Jingfa Xiao*, Jun Yu*. WikiCell: a unified resource platform for human transcriptomics research. OMICS: A Journal of Integrative Biology 16(6), 357-362 (2012).

  26. Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jingfa Xiao*, Jun Yu, PGAP: Pan-genomes Analysis Pipeline. Bioinformatics. 28, 416-418 (2012).

  27. Anding Zhang, Ming Yang, Pan Hu, Jiayan Wu, Bo Chen, Yafeng Hua, Jun Yu, Huanchun Chen, Jingfa Xiao*, Meilin Jin, Comparative genomic analysis of Streptococcus suis reveals significant genomic diversity among different serotypes . BMC Genomics. 12, 523 (2011).

  28. Ming Yang, Yan Ge, Jiayan Wu, Jingfa Xiao*, Jun Yu*. Coevolution study of mitochondria respiratory chain proteins: Toward the understanding of protein-protein interaction. Journal of Genetics and Genomics. 38, 201-207 (2011).

  29. Pan Hu, Ming Yang, Anding Zhang, Jiayan Wu, Bo Chen, Yafeng Hua, Jun Yu, Jingfa Xiao*, Meilin Jin*, Complete Genome Sequence of Streptococcus suis serotype 14 Strain JS14. Journal of Bacteriology. 193, 2375-2376 (2011).  

  30. Fengyu Wang, Jingfa Xiao*, Linlin Pan, Ming Yang, Guoqian Zhang, Jun Yu*. A Systemic Study of Mini-proteins in Bacterial and Archaea. PLOS one. 3, e4027 (2008).

  31. Jingfa Xiao, Jun Yu. A Scenario on the Stepwise Evolution of the Genetic Code. Genomics, Proteomics & Bioinformatics. 5, 1 (2007).

Patents


1.  VCGDB (http://vcg.cbi.ac.cn/index.html)


2.  MTD (http://mtd.cbi.ac.cn/)


3.  WikiCell (http://www.wikicell.org/index.php/Human)


4.  PGAP(https://sourceforge.net/projects/pgap/files/)


5.  PanGP (http://pangp.big.ac.cn/faq.html)


6.  GAAP(http://gaap.big.ac.cn/)

Research Interests

Integrate public personal omics data nationally and internationally and build precise reference genomes for different populations.

Develop the knowledge database for precision medicine based on omics data and clinical data mining.

Establish the prokaryotic microbial genome annotation and data analysis platform, and integrated pathogenic bacterium pangenome database






Conferences

  1. Xin Sheng, Jiayan Wu, Qianqian Sun, Feng Xian, Xue Li, Manman Sun, Wan Fang, Meili Chen, Jun Yu, and Jingfa Xiao*, MTD: a mammalian transcriptomic database to explore gene expression and regulation. The Seventh National Conference on Bioinformatics & System Biology,  Chengdu, China, October 5-9 (2016) (Poster presentation)

  2. Xin Sheng, Jiayan Wu, Qianqian Sun, Feng Xian, Xue Li, Manman Sun, Wan Fang, Meili Chen, Jun Yu, and Jingfa Xiao*, MTD: a mammalian transcriptomic database to explore gene expression and regulation. 2nd Annual Next Generation Sequencing (NGS) USA Congress, Boston, USA, October 3-5 (2016) (Poster presentation)

  3. Yunchao Ling, Jiayan Wu, Jun Yu, Jingfa Xiao*. VCGDB: a dynamic genome database of the Chinese population. 8th International Biocuration Conference, Beijing, China, April 23-26 (2015) (Oral presentation)

  4. JiayanWu, Lina Ma, Jingfa Xiao, Zhang Zhang, Xumin Wang, Shuangxiu Wu, Yu Kang, Songnian Hu, Jun Yu. The complexity of mammalian transcriptomes and need for a pan-mammalian transcriptome project. The sixth national conference on bioinformatics and systems biology. Nanjing, China, October 6-9 (2014).

  5. Ruosi Zhang, Lili Hao, Lingping Wang, Meili Chen, Wen Li, M Esteban, Jun Yu, Jingfa Xiao and Jiayan Wu. Gene expression analysis of induced pluripotent stem cells from aneuploid chromosomal syndromes. 12th International Conference on Bioinformatics, Taichang, China, Sep 20-22th, 2013 (InCoB 2013) (Oral presentation)

  6. Yongbing Zhao, Jingfa Xiao*, New sight for bacterial genome dynamics. The 5th Chinese conference on bioinformatics & systems biology, Haerbin, China, August 8-10, pp.181 (2012).

  7. Ming Tian, Jian Sang, Chao Xu, Dong Zhou, Jiayan Wu, Jingfa Xiao, Xuming Wang, Lin Dai, Zhang Zhang. A wiki-based English-to-Chinese scientific nomenclature dictionary. The 5th Chinese conference on bioinformatics & systems biology, Haerbin, China, August 8-10, pp.97 (2012).

  8. Ming Tian, Jingfa Xiao, Xuming Wang, Lin Dai, Zhang Zhang. Quantifying authors’ contributions in biological knowledge wikis. The 5th Chinese conference on bioinformatics & systems biology, Haerbin, China, August 8-10, pp.204 (2012).

  9. Wenquan Wang, Bin Liu, Binxiao Feng, Jingfa Xiao, Kaimian Li, Luiz C, Zhiqiang Xia, Xincheng Zhou, Gong Xiao, Chi Song, Jinxing Liu, Peng Zhang, Shuigen Zhou, Ming Peng. Cassava genome from ancestor to cultivar. Plant & Animal Genome Conference, pp.0727 (2012).

  10. Jingfa Xiao, Jinlong Yin, Guiming Liu, Yongbing Zhao, Haiyan Guo, Xiaobo Qu, Xumin Wang, Jun Yu. The Ginseng Genome Project. 2011 International conference of genomics, Changchun, China, October 22-24, pp.52 (2011).

  11. Meili Chen, Jiayan Wu, Jingfa Xiao. Human cancer signatures in gene expression. HGV2011 meeting in Berkeley, CA, USA, September 8-10 (2011) (Poster presentation)

  12. Dongyu Zhao, Jiayan Wu, Jingfa Xiao, Jun Yu. Genome-wide Identification and Evolutionary Analysis of the Gene Cluster in Mammal Species. BIT’s 2nd World DNA and Genome Day. Dalian, China, April 25-30, pp.300 (2011).

  13. Zaichao Zhang, Jiayan Wu, Jingfa Xiao*. Evolutionary analysis of the multicopy genes in Human chromosome X The first Harbin international symposium on salmone and other enteric bacteria: genomics and biology. Harbin, China, May 15-17, pp.52 (2011).

  14. Yongbing Zhao, Jingfa Xiao*. Comparative analysis with strains in Escherichia from the pan-genome sight, International Symposium on bacterial Genomics, Evolution and pathogenesis, Zhenjiang, China, November 30-December 3, pp. 121-122 (2010).

Students

已指导学生

张再超  硕士研究生  071021-生物信息学  

孙世翔  硕士研究生  071021-生物信息学  

苏明明  硕士研究生  071021-生物信息学  

杨俊辉  硕士研究生  071021-生物信息学  

杨婷婷  硕士研究生  085211-计算机技术  

方皖  硕士研究生  085238-生物工程  

李雪  硕士研究生  085211-计算机技术  

王金月  博士研究生  0710J3-生物信息学  

张亚东  博士研究生  0710J3-生物信息学  

潘梦宇  硕士研究生  0710J3-生物信息学  

盛欣  博士研究生  0710J3-生物信息学  

高晨  硕士研究生  0710J3-生物信息学  

张莉娟  硕士研究生  0710Z1-基因组学  

王琪  硕士研究生  0710J3-生物信息学  

张好  硕士研究生  085211-计算机技术  

时硕  博士研究生  0710J3-生物信息学  

路明明  博士研究生  0710J3-生物信息学  

高千雯  硕士研究生  085238-生物工程  

现指导学生

姜美叶  博士研究生  0710J3-生物信息学  

于淑欢  硕士研究生  0710J3-生物信息学  

聂致  硕士研究生  0710Z1-基因组学  

张好  博士研究生  0710J3-生物信息学  

钱启衡  博士研究生  0710J3-生物信息学  

麦嘉琳  硕士研究生  0710J3-生物信息学  

尚云飞  博士研究生  0710J3-生物信息学  

徐晨乐  硕士研究生  0710J3-生物信息学  

方哲剑  硕士研究生  0710J3-生物信息学