Publications

  1. Chen, Jianhai, Yangying Jia, Jie Zhong, Kun Zhang, Hongzheng Dai, Guanglin He, Fuping Li, Li Zeng, Chuanzhu Fan, Huayan Xu. 2024. Novel mutation leading to splice donor loss in a conserved site of DMD causes cryptorchidism. Journal of Medical Genetics 61 (8):741-749.

  2. Zhang, yingbo, Shumin Ren, Jiao Wang, Chaoying Zhan, Mengqiao He, Xingyun Liu, Rongrong Wu, Jing Zhao, Cong Wu, Chuanzhu Fan, Bairong Shen. 2024. Expertise or Hallucination? A comprehensive evaluation of ChatGPT's aptitude in clinical genetics. IEEE Transactions on Big Data. In press.

  3. Jorgensen, Kelsey, Obed A. Garcia, Jesus Alcazar, Kimberly K.O. Walden, Abigail W. Bigham, Norma Mujica Moron, Clorinda Vergara Cobian, Julie J. Lesnik, Chuanzhu Fan. 2023. De novo genome assembly of four Andean potato weevil species (Premnotrypes rhigopsidius), the primary agricultural pest of the potato in South America. bioRxiv. DOI: 10.1101/2023.12.13.571405.

  4. 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: 192: 2855–2870.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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