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. Yongbiao Xue*, Yiming Bao*, Zhang Zhang*, Wenming Zhao*, Jingfa Xiao*, Shunmin He*, Guoqing Zhang*, Yixue Li*, Guoping Zhao*, Runsheng Chen*, in CNCB-NGDC Members and Partners, Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Research. 49: D18-D28 (2021).
2. Yadong Zhang, Zhewen Zhang*, Hao Zhang, Yongbing Zhao, Zaichao Zhang, Jingfa Xiao*, PADS Arsenal: a database of prokaryotic defense systems related genes. Nucleic Acids Research. 48: D590-D598 (2020).
3. Zhang Zhang*, Wenming Zhao*, Jingfa Xiao*, Yiming Bao*, Shunmin He*, Guoqing Zhang*, Yixue Li*, Guoping Zhao*, Runsheng Chen*, in National Genomics Data Center Members and Partners, Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Research. 48: D24-D33 (2020).
4. Zhenglin Du, Liang Ma, Hongzhu Qu, et al., Xin Liu, Jingfa Xiao*, Changqing Zeng*, Whole genome analyses of Chinese population and the de novo assembly of a northern Han genome. Genomics Proteomics Bioinformatics. 17:229-247 (2019).
5. Zhang Zhang*, Wenming Zhao*, Jingfa Xiao*, Yiming Bao*, in BIG Data Center Members, Database Resources of the BIG Data Center in 2019. Nucleic Acids Research. 47: D8-D14 (2019).
6. Yongbing Zhao, Jinyue Wang, Fang Liang, et al., Wenming Zhao, Yiming Bao, Zhang Zhang, Jiayan Wu, Yan W. Asmann*, Rujiao Li*, Jingfa Xiao*, NucMap: a database of genome-wide nucleosome positioning map across species. Nucleic Acids Research. 47: D163-D169 (2019).
7. Zhang Zhang*, Wenming Zhao*, Jingfa Xiao*, Yiming Bao*, in BIG Data Center Members, Database Resources of the BIG Data Center in 2018. Nucleic Acids Research. 46: D14-D20 (2018).
8. Xin Sheng, Jiayan Wu, Qianqian Sun, Xue Li, Feng Xian, Manman Sun, Wan Fang, Meili Chen, Jun Yu*, Jingfa Xiao*, MTD: A mammalian transcriptomic database to explore gene expression regulation. Briefings in Bioinformatics. 18, 28-36 (2017).
9. Zhang Zhang*, Wenming Zhao*, Jingfa Xiao*, in BIG Data Center Members. The BIG Data Center: from deposition to integration to translation. Nucleic Acids Research. 45, D18-D24 (2017).
10. Xinpeng Tian, Zhewen Zhang, et al., 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).
11. 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).
12. 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)
13. 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).
14. 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).
15. Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jingfa Xiao*, Jun Yu*, PGAP: Pan-genomes Analysis Pipeline. Bioinformatics. 28, 416-418 (2012).
Group Members
Staff:
Dr. DU Zhenglin, Senior Engineer, duzhl@big.ac.cn
Ms. ZHANG Zhewen, Research assistant, zhangzw@big.ac.cn
Mr. BU Congfan, Assistant engineer, bucf@big.ac.cn
Dr. ZENG Jingyao Research assistant zengjy@big.ac.cn
Dr. ZHANG Yadong, Special Research Assistant, zhangyadong@big.ac.cn
Graduate Students：
SHI Shuo, 2015
LU Mingming, 2016
ZHANG Hao, 2017
JIANG Meiye, 2017
QIAN Qiheng, 2018
GAO Qianwen, 2018
SHANG Yunfei, 2019
NIE Zhi, 2020
YU Shuhuan, 2020
