Publications

  1. Huang, Yuan*; Jun Wang*; Yongping Yang; Chuanzhu Fan; and Jiahui Chen. 2017. Phylogenomic analysis and dynamic evolution of chloroplast genomes in Salicaceae. Frontiers in Plant Science 8: 1050. (*co-first author) PDF

  2. Wang, Jun*; Feng Tao*; Nicholas C. Marowsky; and Chuanzhu Fan. 2016. Evolutionary fates and dynamic functionalization of young duplicate genes in Arabidopsis genomes. Plant Physiology 172: 427-440. (*co-first author) PDF

  3. Wang, Jun; Yeisoo Yu; Feng Tao; Jianwei Zhang; Dario Copetti; Dave Kudrna; Jayson Talag; Seunghee Lee; Rod A. Wing; and Chuanzhu Fan. 2016. DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements. Genome Biology 17: 92. PDF

  4. Copetti, Dario; Jianwei Zhang; Moaine El Baidouri; Dongying Gao; Jun Wang; Elena Barghini; Rosa M. Cossu; Angelina Angelova; Carlos E. Maldonado L.; Stefan Roffler; Hajime Ohyanagi; Thomas Wicker; Chuanzhu Fan; Andrea Zuccolo; Mingsheng Chen; Antonio Costa de Oliveira; Bin Han; Robert Henry; Yue-ie Hsing; Nori Kurata; Wen Wang; Scott A. Jackson; Olivier Panaud; and Rod A. Wing. 2015. RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics 16: 538. PDF

  5. Wang, Jun and Chuanzhu Fan. 2015. A neutrality test for detecting selection on DNA methylation using single methylation polymorphism frequency spectrum. Genome Biology and Evolution 7: 154-171. PDF

  6. Wang, Jun; Nicholas C. Marowsky; and Chuanzhu Fan. 2014. Divergence of gene body methylation and evolution of plant duplicate genes. PLoS One 9(10): e110357. PDF

  7. Wang, Muhua *; Yeisoo Yu*; Georg Haberer*; Pradeep R. Marri*; Chuanzhu Fan; Jose L. Goicoechea; Andrea Zuccolo; Xiang Song; Dave Kudrna; Jetty S.S. Ammiraju; Rosa M. Cossu; Carlos Maldonado; Jinfeng Chen; Seunghee Lee; Nick Sisneros; Kristi de Baynast; Wolfgang Golser; Marina Wissotski; Woojin Kim; Paul Sanchez; Marie-Noelle Ndjiondjop; Kayode Sanni; Manyuan Long; Judith Carney; Olivier Panaud; Thomas Wicker; Carlos A. Machado; Mingsheng Chen; Klaus F.X. Mayer; Steve Rounsley; and Rod A. Wing. 2014. The genome of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics 46: 982-988. (*co-first authors) PDF

  8. Sivaji, Manigandan; Vinoth Sadasivam; Jayabalan Narayanasamy; Selvaraj Samuel; and Chuanzhu Fan. 2014. Detection, characterization and evolution of internal repeats in Chitinases of known 3-D structure. PLoS One 9(3): e91915. PDF

  9. Wang, Jun; Nicholas C. Marowsky; and Chuanzhu Fan. 2013. Divergent evolutionary and expression patterns between lineage specific new duplicate genes and their parental paralogs in Arabidopsis thaliana. PLoS One 8(8): e72362. PDF

  10. Zhang, Chengjun*; Jun Wang*; Nicholas C. Marowsky; Manyuan Long; Rod Wing; and Chuanzhu Fan. 2013. High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences. Genome Biology and Evolution 5: 1038-1048. (*co-first authors) PDF

  11. Zhang, Chengjun*; Jun Wang*; Manyuan Long; and Chuanzhu Fan. 2013. gKaKs: the pipeline for genome-level Ka/Ks calculation. (*co-first authors). Bioinformatics 29: 645-646. (*co-first authors) PDF

  12. Fan, Chuanzhu*; Jason Walling*; Jianwei Zhang; Cory Hirsch; Jiming Jiang; and Rod Wing. 2011. Conservation and purifying selection of transcribed genes located in a rice centromere. Plant Cell 23: 2821-2830. (*co-first authors). PDF

  13. Jetty, S.S Ammiraju; Chuanzhu Fan; Yeisoo Yu; Xiang Song; Karen Cranston; Ana Clara Pontaroli; Fei Lu; Abhijit Sanyal; Ning Jiang; Teri Rambo; Jennifer Currie; Kristi Collura; Jayson Talag; Jeffrey L. Bennetzen; Mingsheng Chen; Scott Jackson and Rod Wing. 2010. Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza. Plant Journal 63: 430-442. PDF

  14. Arguello, J. R.; Yun Zhang; Tomoyuki Kado; Chuanzhu Fan; Ruoping Zhao; Hideki Innan; Wen Wang; Manyuan Long. 2010. Recombination yet inefficient selection along the D. melanogaster subgroup fourth chromosome. Molecular Biology and Evolution 27: 848-861. PDF

  15. Gao, Dongying; Navdeep Gill; HyeRan Kim; Jason Walling; Wenli Zhang; Chuanzhu Fan; Yeisoo Yu; Jianxin Ma; Phillip SanMiguel; Ning Jiang; Rod Wing; Jiming Jiang; and Scott Jackson. 2009. A lineage-specific centromere retrotransposon in oryza brachyantha. Plant Journal 60: 820-831. PDF

  16. Schnable, P. S. et al. (Chuanzhu Fan as a coauthor). 2009. The B73 maize genome: complexity; diversity and dynamics. Science 326: 1112-1115. PDF

  17. Jetty, S.S Ammiraju; Feng Lu; Abhijit Sanyal; Yeisoo Yu; Xiang Song; Ning Jiang; Ana Clara Pontaroli; Teri Rambo; Jennifer Currie; Kristi Kollura; Jayson Talag; Chuanzhu Fan; Jose Luis Goicoechea; Andrea Zuccolo; Jeffrey L. Bennetzen; Mingsheng Chen; Scott Jackson and Rod A Wing. 2008. Dynamic evolution of Oryza genomes revealed by comparative genome analysis of a genus-wide vertical dataset. Plant Cell 20: 3191-3209. PDF

  18. Fan, Chuanzhu*; Yong Zhang*; Yeisoo Yu*; Steve Rounsley; Manyuan Long; and Rod A. Wing. 2008. The subtelomere of oryza sativa chromosome 3 short arm as a hot bed of new gene origination in rice. Molecular Plant 1:839-850. (*co-first authors). PDF

  19. Fan, Chuanzhu; Ying Chen; and Manyuan Long. 2008 Recurrent tandem gene duplication gave rise to functionally divergent genes in drosophila. Molecular Biology and Evolution 25: 1451-1458. PDF

  20. Naghabushana, Nayidu K.; Gupta Madhur; Nuruzzaman M; Lei Wang; Xie Weibo; Zhang Chengjun; Chuanzhu Fan; Song Yaling; Lian Xingming; Zhang Qifa; and Xiong Lizhong. 2008. Comprehensive sequence and expression profile analysis of PEX11 gene family in rice. Gene 421:59-70. PDF

  21. Fan, Chuanzhu; J. J. Emerson; and Manyuan Long. 2008. The origin of new gene. Evolutionary Genomics and Proteomics. Mark Pagel & Andrew Pomiankowski (eds.). Sinauer Associates; Inc.; Sunderland; Massachusetts; USA. 27-44. PDF

  22. Fan, Chuanzhu; Maria Vibranovski; Ying Chen; and Manyuan Long. 2007. A microarray-based genomic hybridization method for identification of new genes in plants: case analyses of Arabidopsis and oryza. Journal of Integrative Plant Biology 49: 915-926. PDF

  23. Arguello, J. R.; Chuanzhu Fan; Wen Wang; and Manyuan Long. 2007. Origination of chimeric genes through DNA-level recombination. Genome Dynamics 3: 131-146. In: Volff J-N (ed.): Gene and Protein Evolution. Basel; Karger; Switzerland. PDF

  24. Fan, Chuanzhu and Manyuan Long. 2007. A new retroposed gene in drosophila heterochromatin detected by microarray-based comparative genomic hybridization. Journal of Molecular Evolution 64: 272-283. PDF

  25. Fan, Chuanzhu; (Jenny) Qiu-Yun Xiang; David L. Remington; Michael D. Purugganan; and Brian M. Wiegmann. 2007. Evolutionary pattern in the antr-Cor gene in the dwarf dogwood complex (Cornus; Cornaceae). Genetica 130: 19-34. PDF

  26. Wang, Wen *; Hongkun Zheng*; Chuanzhu Fan*; Jun Li; Junjie Shi; Zhengqiu Cai; Guojie Zhang; Dongyuan Liu; Jianguo Zhang; Soren Vang; Zhike Lu; Gane Ka-Shu Wong; Manyuan Long; and Jun Wang. 2006. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18: 1791-1802. (*co-first authors). PDF

  27. Modliszewski, J.; David T. Thomas; Chuanzhu Fan; Daniel Crawford; Claude Depamphilis; and Qiu-Yun (Jenny) Xiang. 2006. Ancestral chloroplast polymorphism and historical secondary contact in a broad hybrid zone of Aesculus L. (Sapindaceae). American Journal of Botany 93: 377-388. PDF

  28. Xiang, (Jenny) Qiu-Yun; Steve R. Manchester; David Thomas; Wenheng Zhang; and Chuanzhu Fan. 2005. Phylogeny; biogoegraphy; and molecular dating of cornelian cherries (Cornus; Cornaceae) tracking tertiary plant migration. Evolution 59: 1685-1700. PDF

  29. Houston, N. L.; Chuanzhu Fan; (Jenny) Qiu-Yun Xiang; Rudolf Jung; and Rebecca S. Boston. 2005. Phylogenetic analyses identify ten classes of the protein disulfide isomerase (PDI) family in plants including single-domain PDI related proteins. Plant Physiology 137: 762-788. PDF

  30. Fan, Chuanzhu; Michael D. Purugganan; David T. Thomas; Brian M. Wiegmann; and (Jenny) Qiu-Yun Xiang. 2004. Heterogeneous evolution of the Myc-like anthocyanin regulatory gene and its phylogenetic utility in Cornus L. (Cornaceae). Molecular Phylogenetics and Evolution 33: 580-594. PDF

  31. Fan, Chuanzhu and (Jenny) Qiu-Yun Xiang. 2003. Phylogenetic analyses of Cornales based on 26S rDNA and combined 26S rDNA-matK-rbcL sequence data. American Journal of Botany 90: 1357-1372. PDF

  32. Xiang, (Jenny) Qiu-Yun; M. Moody; D. E. Soltis; Chuanzhu Fan; and P. S. Soltis. 2002. Relationships within Cornales and circumscription of Cornaceae matK and rbcL sequence data and effects of outgroups and long branches. Molecular Phylogenetics and Evolution 24: 35-57. PDF

  33. Fan, Chuanzhu and (Jenny) Qiu-Yun Xiang. 2001. Phylogenetic relationships within Cornus L. (Cornaceae) based on 26S rDNA sequences. American Journal of Botany 88: 1131-1138. PDF