Faculty and Staff

XIAO Jingfa

Group leader
Dr. XIAO Jingfa is currently a professor of Beijing Institute of Genomics, Chinese Academy of Sciences (CAS) since 2012. Dr. Xiao received his B.S. degree in biology from Sichuan University in 1995 and Ph.D. degree in computational biology and chemistry from Jilin University in 2003. From 2003 to 2007, he performed his postdoctoral research in Dr. Zongru Guo's Lab of Institute of Materia Medica, Chinese Academy of Medical Sciences and Dr. Thanh N Truong’s Lab of Department of Chemistry, University of Utah. From 2007 to 2012, he worked as an associate professor in Beijing Institute of Genomics, Chinese Academy of Sciences. 

 Introduction 
Biological data are generated at a massive scale and continue to grow at unprecedentedly exponential rates, thus posing considerable challenges worldwide in biological data deposition, integration and translation. Currently there are two major directions in our group: 1) Integrate public personal omics data nationally and internationally to build precision reference genomes and genetic variation map for different populations; Associate omics data with clinical data with the goal to develop knowledge network for precision medicine. 2) Establish the prokaryotic microbial genome annotation and data analysis platform; Analysis of pathogenic mechanisms and host-microbe interactions for pathogenic bacterium from pangenomic insights. Recent Progress
Recently we present a mammalian transcriptomic database (MTD) that is focused on mammalian transcriptomes, and the current version contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features. To elucidate the dynamics of gene expression regulation, the MTD also enables comparative transcriptomic analysis in both intraspecies and interspecies manner. The MTD is freely accessible at http://mtd.cbi.ac.cn.

 Selected Publications
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 regulation. Briefings in Bioinformatics doi:10.1093/bib/bbv117 (2016).
2. 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).
3. The IC4R Project Consortium*, Information Commons for Rice (IC4R). Nucleic Acids Research. 44:D1172-D1180 (2016).
4. Meili Chen, Yibo Hu, Jingxing Liu, Qi Wu, Chenglin Zhang, Jun Yu, Jingfa Xiao*, Fuwen Wei*, Jiayan Wu*. Improvement of genome completeness and identification of novel full-length transcripts by RNA-seq in giant panda. Scientific Reports. 5:18019 (2015).
5. 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).
6. 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).
7. 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).
8. 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).
9. 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).
10. 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).
11. 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).
12. Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jingfa Xiao*, Jun Yu*, PGAP: Pan-genomes Analysis Pipeline. Bioinformatics. 28, 416-418 (2012).
13. 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).

Group Members
Dr. DU Zhenglin Research Senior Engineer duzhl@big.ac.cn
Dr. CHEN Meili Research assistant chenml@big.ac.cn
Dr. ZENG Jingyao Research assistant zengjy@big.ac.cn
Ms. ZHANG Zhewen Research assistant zhangzw@big.ac.cn
Ms. YUAN Na Engineer yuann@big.ac.cn

Graduate Students:
SHENG Xin, 2012
WANG Jinyue, 2013
ZHANG Yadong, 2014
FAN Wan, 2014
GAO Chen, 2014
SHI Shuo, 2015
ZHANG Lijuan, 2015
LU Mingming, 2016
PAN Mengyu, 2016