1. Plant genome structure and evolution, especially the evolution caused by alternative splicing evolution

　　Genome structure evolution was wildly presented in the nature, however, the role of alternative splicing in the genome structure evolution was not well presented, we try to proposed new theories to illustrated the contribution.

　　 

2. Identifying of new genes related to Gramineae and Brassicaceae

　　Since the first widely accepted new gene Jingwei gene, it has been passed twenty years, more and more scientists have been realized the important function of new genes, and more and more function researches are act on the new genes. We want to develop a way to reveal the new genes evolution mechanisms by analyzing the Gramineae and Brassicaceae families;

　　 

3. Developing new bioinformatics tools

　　Useful new tools are always welcome. We have been developed several bioinformatics tools, such as OBSM, gKaKs and GriffinDetector. More tools will coming out soon.

4. Transcriptome analysis within seeds

2001-2005 Huazhong Agriculture University, China   bachelor  degree (college of life science and technology)   

2003-2006  Wuhan University, China         the 2nd bachelor degree      (computer school of Wuhan University)      

2005-2011   Huazhong Agriculture University,  China                PHD        (college of life science and technology)

          

   

2011​ - 2014    postdoc       University of Chicago 

2014 -            Professor      Kunming Institute of Botany Chinese Academy of Sciences 

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Bioinformatics

1. Nayidu NK, Wang L, Xie W, Zhang C, Fan C, Lian X, Zhang Q, Xiong L# (2008) Comprehensive sequence and expression profile analysis of PEX11 gene family in rice. Gene 412:59-70.

2. Nuruzzaman M, Gupta M, Zhang C, Wang L, Xie W, Xiong L, Zhang Q and Lian X# (2008) Sequence and expression analysis of the thioredoxin protein gene family in rice. MGG 280:139-151.

3. Gupta M, Qiu X, Wang L, Xie W, Zhang C, Xiong L, Lian X, Zhang Q# (2008) KT/HAK/KUP potassium transporters gene family and their whole-life cycle expression profile in rice (Oryza sativa). MGG 280:437-52.

4. Xie W, Chen Y, Zhou G, Wang L, Zhang C, Zhang J, Xiao J, Zhu T, Zhang Q# (2009) Single feature polymorphisms between two rice cultivars detected using a median polish method. Theor Appl Genet 119:151-164.

5. Xia J#, Hu X, Shi F, Niu X and Zhang C (2010) Support vector machine method on predicting resistance gene against Xanthomonas oryzae pv. oryzae in rice. Expert Systems with Applications 37:5946-5950.

6. Du H, Ouyang Y, Zhang C, Zhang Q# (2011) Complex evolution of S5, a major reproductive barrier regulator, in the cultivated rice Oryza sativa and its wild relatives, New Phytologist, 2011, 191:275-287.

7. Zhang C, Wang J, Xie W, Zhou , Long M , Zhang Q# (2011) Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method, Proc Natl Acad Sci USA, 2011, 108(19):7860-7865.

8. Hu Y, Liu D, Zhong X, Zhang C, Zhang Q, Zhou DX# (2012) CHD3 protein recognizes and regulates methylated histone H3 lysines 4 and 27 over a subset of targets in the rice genome, Proc Natl Acad Sci USA, 109(15): 5773-5778.

9. Zhou G, Chen Y, Yao W, Zhang C, Xie W, Hua J, Xing Y, Xiao J, and Zhang Q# (2012) Genetic composition of yield heterosis in an elite rice hybrid, Proc Natl Acad Sci USA, 109(39):15847-15852.

10. Zhang C*, Wang J*, Long M, Fan C# (2013) gKaKs: The pipeline for genome level Ka/Ks calculation, Bioinformatics, 29(5):645-646.

11. Yan W, Liu H, Zhou X, Li Q, Zhang J, Lu L, Liu T, Liu H, Zhang C, Zhang Z, Shen G, Yao W, Chen H, Yu S, Xie W, Xing Y# (2013) Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice, Cell Research, doi: 10.1038/cr.2013.43

12. Zhang C*, Wang J*, Marowsky NC, Long M, Rod AW#, Fan C# (2013) High Occurrence of Functional New Chimeric Genes in Survey of Rice Chromosome 3 Short Arm Genome Sequences, Genome Biology and Evolution, 5(5):1038-1048.

13. Zhang C, Gschwend RA, Ouyang Y, Long M# (2014) Evolution of gene structural complexity: An alternative-splicing based model accounts for intron-containing retrogenes, Plant Physiology, 165(1):412-423.

14. Zhang C#, Yang H, Yang H (2015) Evolutionary Character of Alternative Splicing in Plants, Bioinformatics and Biology Insights, 9(S1):1-6.

15. Ouyang Y#, Li G, Mi J, Xu C, Du H, Zhang C, Xie W, Li X, Xiao J, Song H, Zhang Q (2016) Origination and Establishment of a Trigenic Reproductive Isolation System in Rice, Molecular Plant, 9:1542-1545.

16. 杜丽思，章成君，张靖，彭晟，杨静，刘林，李成云，杜云龙#（2016）两种生态型玛咖叶片的丛生芽诱导，云南农业科技，10.3969/j.issn.1000-0488.2016.02.001

17. Zhu Y, Chen L, Zhang C, Hao P, Jing X, Li X (2017) Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in non-seed vascular plant Selaginella moellendorffii, BMC genomics, 18(1):1042.

18. Zhang L^*, Xu P^*, Cai Y^*, Ma L^*, et al., Zhang C, Gao Q, Wang J (2017) The draft genome assembly of Rhododendron delavayi Franch. var. delavayi, GigaScience, 6:1-11

19. Chen J, Ni P, Li X, Han J, Jackovlic I, Zhang C and Zhao S# (2018) Population size may shape the accumulation of functional mutations following domestication, BMC Evolutionary Biology, 18(4).

20. Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K et al., Long M, Ware D, Wing RA# (2018) Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza, Nature Genetics, 50:285-296.

21. Li Y, Fang C, Fu Y et al., Zhang C, Li C# (2018) A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing, DNA Research, 25(4) 421-437.

22. Shi Y*, Su Z*, Yang H* et al., Xue R#, Zhang C# (2019) Alternative splicing coupled to nonsense-mediated mRNA decay contributes to the high-altitude adaptation of maca (Lepidium meyenii), Gene, 694:7-18.

23. Shi Y, Yan X, Yin H et al., Zhang C#, Ma X# (2019) Divergence and hybridization in the desert plant Reaumuria soongarica, Journal of Systematics and Evolution, doi: 10.1111/jse.12490.