Qi, Ji, Professor

E-mail: qij@fudan.edu.cn

B.A., Department of Physics, Jilin University, 1995-1999; Ph.D., Institute of Theoretical Physics, The Chinese Academy of Sciences, 1999-2004; Postdoc, Center for Comparative Genomics and Bioinformatics, Penn State University, 2005-2010; Associate Professor/Professor, School of Life Sciences, Fudan University. Research interests include detection of genomic variations, investigation of polyploidization events and development of bioinformatic methods. Dr. Qi is funded by National Natural Science Foundation of China and has published many articles in Nature Communications、PNAS、Genome Research、Nucleic Acids Research、Molecular Plant etc.

Research Interests

Genomic variations, including SNPs, indels and structural variations, provide raw materials for evolution of novel gene functions. Gene duplicates resulted from whole genome duplications further enhance organismal adaptation to environmental challenges by offering genomic novelties and complexities. A challenging task is to recognize allelic polymorphisms accurately from huge amount of biomarkers for genetic studies. Dr. Qi’s particular topics include functional divergence of gene duplicates in angiosperms, correlation of polyploidization and biodiversity or environmental changes. He is also interested in developing new computational methods, e.g. approaches for detection and visualization of SNPs and SVs from high-throughput sequencing data; investigation of large scale duplication events by modeling of phylogenomics; development of metagenomic methods for taxonomic and functional study of microorganisms.

Selected publications

1. Ren R#, Wang H #, Guo Ch #, Zhang N, Zeng L, Chen Y, Ma H *, Qi J * . (2018) Widespread whole genome duplications contribute to genome complexity and species diversity in angiosperms. Mol. Plant. 11: 414-428. DOI: https://doi.org/10.1016/j.molp.2018.01.002
2. Huang C, Zhang C, Liu M, Hu Y, Gao T, Qi J * and Ma H *. (2016) Multiple polyploidization events across Asteraceae with two nested events in the early history revealed by nuclear phylogenomics. Mol. Biol. Evol. 33: 2820-2835.
3. Ye N #*, Zhang X #, Miao M #, Fan X, Zheng Y, Xu D, Wang J, Zhou L, Gao W, Wang Y, Shi W, Ji P, Li D, Guan Z, Shao C, Zhuang Z, Gao Z, Qi J*, Zhao F *. (2015) Saccharina genomes provide novel insight into kelp biology. Nat Commun. 6:6986.
4. Yang H #, Chang F #*, You C, Cui J, Zhu G, Wang L, Zheng Y, Qi J *, Ma H *. (2015) Whole-genome DNA methylation patterns and complex associations with gene structure and expression during flower development in Arabidopsis. Plant J. 81: 268-281.
5. Qi J, Chen Y, Copenhaver G, Ma H. (2014) Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping. P Natl Acad Sci U S A. 111: 10007-10012.
6. Wang H #, You C #, Chang F, Wang Y, Wang L, Qi J * and Ma H *. (2014) Alternative splicing during Arabidopsis flower development results in constitutive and stage-regulated isoforms. Frontiers in Genetics. 5: 25.
7. Liu J #, Wang H # Yang H, Zhang Y, Wang J, Zhao F * and Qi J *. (2013) Composition based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms. Nucleic Acids Res. 41:e3
8. Lu P #, Han X #, Qi J #, Yang J, Wijeratne A, Li T and Ma H. (2012). Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by re-sequencing Landsberg erecta and all four products of a single meiosis. Genome Res. 22:508-518.  
9. Qi J * and Zhao F *. (2011) inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data. Nucleic Acids Res. 39:W567-75.
10. Qi J #, Zhao F # and Schuster S. (2010) inGAP: Integrative Next Generation Genome Analysis Pipeline. Bioinformatics. 26: 127-129.