Publications

  1. Tao, Feng; Vishwanath Sollapura; Laurian S Robert; and Chuanzhu Fan. 2023. Neofunctionalization of tandem duplicate genes encoding putative Beta-L-arabinofuranosidases in Arabidopsis. Plant Physiology: kiad169, https://doi.org/10.1093/plphys/kiad169.

  2. Chen, Jianhai; Li Zeng; Yangying Jia; Jie Zhong; Younan Chen; Yong Zhang; Shengqian Xia; Huayan Xu; Ivan Jakovlić; Hongzheng Dai; Fuping Li; Chuanzhu Fan; and Bairong Shen. 2023. Whole genome sequencing revealed a predominant role of rare variants from X-linked genes on cryptorchidism. SSRN: https://ssrn.com/abstract=4341557/http://dx.doi.org/10.2139/ssrn.4341557.

  3. Chen, Jianhai; Jie Zhong; Xuefei He; Ivan Jakovlić; Yong Zhang; Hao Yang; Younan Chen; Guang Yang; Chuanzhu Fan; and Bairong Shen. 2022. The nanopore sequencing of a Chinese rhesus macaque revealed patterns of methylation, recombination, and selection for structural variations. bioRxiv: doi: https://doi.org/10.1101/2022.10.21.513306.

  4. Tao, Feng; Chuanzhu Fan; Yimin Liu; Subashini Sivakumar; Kurt P. Kowalski; and Edward M. Golenberg. 2023. Optimization and Application of non-native Phragmites australis Transcriptome Assemblies. PLoS One 18(1): e0280354.

  5. Li, Jingjing; Jinyan Xu; Tingting Yang; Jianhai Chen; Fuping Li; Bairong Shen; and Chuanzhu Fan. 2022.Genome-wide methylation analyses of human sperm unravel novel differentially methylated regions in asthenozoospermia. Epigenomics 14: 951-964.PDF

  6. Hu, Yanting; Xiaopei Wu; Guihua Jin; Junchu Peng; Rong Leng; Ling Li; Daping Gui; Chuanzhu Fan; Chengjun Zhang. 2022. Rapid genome evolution and adaptation of Thlaspi arvense mediated by recurrent RNA-based and tandem gene duplications. Frontiers in Plant Science 12: 772655.PDF

  7. Huang, Yuan; Jiahui Chen; Chuan Dong; Dylan Sosa; Shengqian Xia; Yidan Ouyang; Chuanzhu Fan; Dezhu Li; Emily Mortola; Manyuan Long; and Joy Bergelson. 2022. Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection. Plant Cell: 34 (2): 802-817.PDF

  8. Li, Xueting; Riwen Fei; Zhijing Chen; Chuanzhu Fan; Xiaomei Sun. 2020. Plant hormones changes and differential expression profiling reveal seed dormancy removal process in double dormant plant-herbaceous peony. PLoS One: 15(4): e0231117.PDF

  9. Li, Xueting; Ping Liu; Panpan Yang; Chuanzhu Fan; and Xiaomei Sun. 2018. Characterization of glycerol-3-phosphate acyltransferase gene and its real-time expression under cold stress in Paeonia lactiflora Pall. PLoS One 13(8): e0202168.PDF

  10. Stein, Joshua C.; Yeisoo Yu; Dario Copetti; Derrick J. Zwickl; Li Zhang; Chengjun Zhang; Kapeel Chougule; Dongying Gao; Aiko Iwata; Jose Luis Goicoechea; Sharon Wei; Jun Wang; Yi Liao; Muhua Wang; Julie Jacquemin; Claude Becker; Dave Kudrna; Jianwei Zhang; Carlos E.M. Londono; Xiang Song; Seunghee Lee; Paul Sanchez; Andrea Zuccolo; Jetty S.S. Ammiraju; Jayson Talag; Ann Danowitz; Luis F. Rivera; Andrea R. Gschwend; Christos Noutsos; Cheng-chieh Wu; Shu-min Kao; Jhih-wun Zeng; Fu-jin Wei; Qiang Zhao; Qi Feng; Moaine El Baidouri; Marie-Christine Carpentier; Eric Lasserre; Richard Cooke; Daniel da Rosa Farias; Luciano Carlos da Maia; Railson S. dos Santos; Kevin G. Nyberg; Kenneth L. McNally; Ramil Mauleon; Nickolai Alexandrov; Jeremy Schmutz; Dave Flowers; Chuanzhu Fan; Detlef Weigel; Kshirod K. Jena; Thomas Wicker; Mingsheng Chen; Bin Han; Robert Henry; Yue-ie C. Hsing; Nori Kurata; Antonio Costa de Oliveira; Olivier Panaud; Scott A. Jackson; Carlos A. Machado; Michael J. Sanderson; Manyuan Long; Doreen Ware; and Rod A. Wing. 2018. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics 50: 285-296. PDF

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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