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Facilities

Core Facilities

Li Zhang Ph.D. director of Genomics Center & HPC Core

E-mail: zhangli@cibr.ac.cn

Phone:

Lab Homepage:

Education

2005.09-2011.07 Peking University, Bioinformatics, Ph.D.                                          

1999.09-2003.07  East China University of Science and Technology (ECUST)                    

  Major: Bioengineering, bachelor

  Secondary: Computer Science, bachelor



Professional Experience

2018.12-  Chinese Institute for Brain Research, Beijing , director of bioinformatics center and computational core 

2018.03-2018.11  Yale University, School of Medicine, Department of Genetics, associate research scientist      

2017.03-2017.12  The University of Chicago, Department of Ecology and Evolution, staff              

2012.04-2017.01  The University of Chicago, Department of Ecology and Evolution, postdoc         

2012.01-2012.04  Northwestern University, Feinberg School of Medicine, postdoc                


Research Description

I plan to focus on the relationship between new cell types and intelligence which is a part of a novel conceptual framework derived from my previous research. In Darwinian world, selection picks out and preserves adaptive mutations. However, selection can’t efficiently pick out adaptive mutations when they are linked with deleterious mutations. Sexual recombination breaks the linkage between adaptive and deleterious mutations and promotes new gene evolution in plants and animals. Following the same idea, adaptive immunity breaks the linkage between adaptive and deleterious cells and promotes cell evolution. Adaptive immunity originated in basal vertebrates which explains why plants still rely on de novo genes. Diverse cell types emerged during vertebrate evolution which indeed agrees with the evo-devo theory. As an important innovation of vertebrate evolution, human intelligence potentially results from cell evolution. Conceptually, my question is how new cell types contribute to intelligence. Currently, it’s more realistic to start with Drosophila species which are closely related and have a workable number of brain cells. Drosophila is invertebrate but has rare de novo genes. This study will be a strong support to build the conceptual framework of cell evolution and understand the origin of intelligence from the standing point of cell evolution. This study requires to develop high quality single cell technologies but more importantly it will define what a cell type is. The best strategy is to incorporate between-species comparison to define cell types by evolutionary conservativeness. My previous work on new gene evolution can generate a mapping list of between-species orthologous genes which can be used to quickly set up a pipeline for between-species cell type comparison.

Publications

1. Zhang, L., Ren, Y., Yang, T., Li, G., Chen, J., Gschwend, A.R., Yu, Y., Hou, G., Zi, J., Zhou, R. et al. (2019) Rapid evolution of protein diversity by de novo origination in Oryza. Nat Ecol Evol.

2. Stein, J.C., Yu, Y., Copetti, D., Zwickl, D.J., Zhang, L., Zhang, C., Chougule, K., Gao, D., Iwata, A., Goicoechea, J.L. et al. (2018) Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet, 50, 285-296.

3. Chi, W., Zhang, L., Du, W. and Zhuang, X. (2014) A nutritional conditional lethal mutant due to pyridoxine 5'-phosphate oxidase deficiency in Drosophila melanogaster. G3 (Bethesda), 4, 1147-1154.

4. Gao, G., Vibranovski, M.D., Zhang, L., Li, Z., Liu, M., Zhang, Y.E., Li, X., Zhang, W., Fan, Q., VanKuren, N.W. et al. (2014) A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster. Genome Res, 24, 629-638.

5. Long, M. and Zhang, L. (2012) Why rodent pseudogenes refuse to retire. Genome Biol, 13, 178.

6. Liu, M., Liu, P., Zhang, L., Cai, Q., Gao, G., Zhang, W., Zhu, Z., Liu, D. and Fan, Q. (2011) mir-35 is involved in intestine cell G1/S transition and germ cell proliferation in C. elegans. Cell Res, 21, 1605-1618.

7. Li, Z., Liu, M., Zhang, L., Zhang, W., Gao, G., Zhu, Z., Wei, L., Fan, Q. and Long, M. (2009) Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster. Nucleic Acids Res, 37, 4308-4314.

8. Zhao, S.Q., Wang, J., Zhang, L., Li, J.T., Gu, X., Gao, G. and Wei, L. (2009) BOAT: Basic Oligonucleotide Alignment Tool. BMC Genomics, 10 Suppl 3, S2.