2017
Genomic variation associated with local adaptation of weedy rice during de-domestication. Jie Qiu, Yongjun Zhou, Lingfeng Mao, Chuyu Ye, Weidi Wang, Jianping Zhang, Yongyi Yu, Fei Fu, Yunfei Wang, Feijian Qian, Ting Qi, Sanling Wu, Most. Sultana, Ya-Nan Cao, Yu Wang, Michael Timko, Song Ge, Longjiang Fan*, and Yongliang Lu*. Nature Communications, 2017. In press
PlantcircBase: a database for plant circular RNAs. Qinjie Chu, Xingchen Zhang, Xintian Zhu, Chen Liu, Lingfeng Mao, Chuyu Ye, Qian-Hao Zhu, Longjiang Fan*. Molecular Plant, 2017. doi: http://dx.doi.org/10.1016/j.molp.2017.03.003 [PDF]
Accumulation of high OPDA level correlates with reduced ROS and elevated GSH benefiting white cell survival in variegated leaves. Ying-Hsuan Sun, Chiu-Yueh Hung, Jie Qiu, Jianjun Chen, Farooqahmed S. Kittur, Carla E. Oldham, Richard J. Henny, Kent O. Burkey, Longjiang Fan & Jiahua Xie. Scientific Reports, 2017. doi: 10.1038/srep44158 [PDF]
 
2016
Full length sequence assembly reveals circular RNAs with diverse non GT AG splicing signals in rice. Chu-Yu Ye*, Xingchen Zhang, Qinjie Chu, Chen Liu, Yongyi Yu, Weiqin Jiang, Qian-Hao Zhu, Longjiang Fan, Longbiao Guo*. RNA Biology, 2016. doi: 10.1080/15476286.2016.1245268 [PDF]
PcircRNA_finder: a software for circRNA prediction in plants. Li Chen, Yongyi Yu, Xinchen Zhang, Chen Liu, Chuyu Ye, Longjiang Fan*. Bioinformatics, 2016. doi: 10.1093/bioinformatics/btw496 [PDF]
Nicotine biosynthesis is regulated by two more layers: small and long non-protein-coding RNAs. Jiahua Xie and Longjiang Fan. Plant Signal and Behavior, 2016. doi: 10.1080/15592324.2016.1184811 [PDF]
Gibberellin deficiency is responsible for shy-flowering nature of Epipremnum aureum. Chiu-Yueh Hung, Jie Qiu, Ying-Hsuan Sun, Jianjun Chen, Farooqahmed Kittur, Richard Henny, Gulei Jin, Longjiang Fan*, Jiahua Xie*. Scientific Reports, 2016. doi: 10.1038/srep28598 [PDF]
Transcriptome sequencing reveals e-cigarette vapor and mainstream-smoke from tobacco cigarettes activate different gene expression profiles in human bronchial epithelial cells. Yifei Shen, Michael Wolkowitz, Tatyana Kotova, Longjiang Fan, Michael Timko*. Scientific Reports, 2016. doi: 10.1038/srep23984[PDF]
作物育种相关数据及大数据技术育种利用.樊龙江,王卫娣,王斌,叶楚玉,舒庆尧,张辉. 浙江大学学报(农业与生命科学版), 2016, 42(1). [PDF]
 
2015
Identification, evolution and expression partitioning of miRNAs in allopolyploid Brassica napus. Enhui Shen, Jun Zou, Falk Behrens, Li Chen, Chuyu Ye, Shutao Dai, Ruiyan Li, Meng Ni, Xiaoxue Jiang, Jie Qiu, Yang Liu, Weidi Wang, Qian-Hao Zhu, Boulos Chalhoub, Ian Bancroft, Jinling Meng, Daguang Cai*, Longjiang Fan*. Journal of Experimental Botany, 2015. doi: 10.1093/jxb/erv420[PDF]
Regulation of nicotine biosynthesis by an endogenous target mimicry of miRNA in tobacco. Fangfang Li, Weidi Wang, Nan Zhao, Bingguang Xiao, Peijian Cao, Xingfu Wu, Chuyu Ye, Enhui Shen, Jie Qiu, Qian-Hao Zhu, Jiahua Xie, Xueping Zhou*, Longjiang Fan*. Plant Physiology, 2015. doi: 10.1111/pp.15.00649[PDF]
Widespread non-coding circular RNAs in plants. Chuyu Ye, Li Chen, Chen Liu, Qian-Hao Zhu, Longjiang Fan*. New Phytologist, 2015. doi: 10.1111/nph.13585[PDF]
A host plant genome (Zizania latifolia) after a century-long endophyte infection. Longbiao Guo, Jie Qiu, Zujing Han, Zihong Ye, Chao Chen, Chuanjun Liu, Xiufang Xin, Chuyu Ye, Yingying Wang, Hongqing Xie, Yu Wang, Jiandong Bao, She Tang, Jie Xu, Yijie Gui, Fei Fu, Weidi Wang, Xingchen Zhang, Qianhua Zhu, Xuanmin Guang, Chongzhi Wang, Haifeng Cui, Daguang Cai, Song Ge, Gerald Tuskan, Xiaohan Yang, Qian Qian, Shengyang He, Jun Wang*, Xueping Zhou*, Longjiang Fan*. Plant Journal, 2015. doi: 10.1111/tpj.12912online[PDF]
 
2014
Genome-wide identification of non-coding RNAs interacted with microRNAs in soybean. Chuyu Ye, Hao Xu, Enhui Shen, Yang Liu, Yu Wang, Yifei Shen, Jie Qiu, Qian-Hao Zhu and Longjiang Fan*. Frontiers in Plant Science, 2014, 12, 5. doi: 10.3389/fpls.2014.00743[PDF]
Echinochloa Chloroplast Genomes: Insights into the Evolution and Taxonomic Identification of Two Weedy Species. Chuyu Ye, Zhangxiang Lin, Gengmi Li, Yingying Wang, Jie Qiu, Fei Fu, Haiqiang Zhang, Li Chen, Sisi Ye, Weijie Song, Gulei Jin, Jinwen Zhu, Yongliang Lu, Longjiang Fan*. Plos One, 2014, 11, 26. doi: 10.1371/journal.pone.0113657[PDF]
Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression. Jie Qiu, Yu Wang, Sanling Wu, Ying-Ying Wang, Chu-Yu Ye, Xuefei Bai, Zefeng Li, Chenghai Yan, Weidi Wang, Ziqiang Wang, Qingyao Shu, Jiahua Xie, Suk-Ha Lee, Longjiang Fan*. Plos One, 2014, 9, 29. doi: 10.1371/journal.pone.0108479[PDF]
Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization: A case study from southern China. Jie Qiu, Jinwen Zhu, Fei Fu, Chu-Yu Ye, Weidi Wang, Linfeng Mao, Zhangxiang Lin, Li Chen, Haiqiang Zhang, Longbiao Guo, Shen Qiang, Yongliang Lu, Longjiang Fan*. Planta, 2014, 9, 4. doi: 10.1007/s00425-014-2159-2[PDF]
茶树“龙井43”叶绿体基因组测序及其系统进化(英文).叶晓倩, 赵忠辉, 朱全武等. 浙江大学学报(农业与生命科学版), 2014, 40(4): 404-412. [PDF]
东乡野生稻叶绿体基因组拼接及系统进化分析(英文). 林张翔, 王营营, 付菲等. 浙江大学学报(农业与生命科学版), 2014, 40(4): 397-403. [PDF]
植物非编码小RNA研究进展(英文). 沈恩惠, 刘扬, 叶楚玉等. 浙江大学学报(农业与生命科学版), 2014, 40(4): 370-378. [PDF]
Identification and characterization of microRNAs in oilseed rape (Brassica napus) responsive to infection with the pathogenic fungus Verticillium longisporum using Brassica AA (Brassica rapa) and CC (Brassica oleracea) as reference genomes. Dan Shen, Ina Suhrkamp, Yu Wang, Shenyi Liu, Jan Menkhaus, Joseph-Alexander Verreet, Longjiang Fan*, Daguang Cai*. New Phytologist, 2014, 31(6). doi: 10.1111/nph.12934[PDF]
东乡野生稻叶绿体基因组拼接及系统进化分析. 林张翔,王营营,付菲,叶楚玉,樊龙江. 中国科技论文在线, 2014, 01, 02. [PDF]
植物非编码小RNA研究进展. 沈恩惠,刘杨,樊龙江. 中国科技论文在线, 2014, 01, 03. [PDF]
A diverse set of miRNAs responsive to begomovirus-associated betasatellite in Nicotiana benthamiana. Bingguang Xiao, Xiuling Yang, Chuyu Ye, Yang Liu, Chenhai Yan, Yu Wang, Xiuping Lu, Yongping Li, Longjiang Fan. BMC Plant Biology, 2014, 14(60). doi: 10.1186/1471-2229-14-60[PDF]
 
2013
Identification of phasiRNAs in wild rice (Oryza rufipogon). Yang Liu, Yu Wang, Qianhao Zhu, Longjiang Fan. Plant Signaling & Behavior, 2013, 8(8).doi: e25079[PDF]
Impact of maternal nicotine exposure on expression of myelin-related genes in Zebrafish Larvae. Shufang Zhao, Wenyan Cui, Junran Cao, Chen Luo, Longjiang Fan, and Ming D. Li. Zebrafish, 2013, 0889. doi: 10.1089/zeb[PDF]
MiR482 regulation of NBS-LRR defense genes during fungal pathogen infection in cotton. Qianhao Zhu, Longjiang Fan, Yang Liu, Hao Xu, Danny Llewellyn, Iain Wilson. Plos One, 2013, 12(8). doi: 10.1371/journal.pone.0084390[PDF]
菰(Zizania latifolia)主要农艺性状及其驯化育种. 王营营,黄璐, 樊龙江. 浙江大学学报(农业与生命科学版), 2013, 39(6):629-635. [PDF]
 
2012
A Tourist-like MITE insertion in the upstream region of the BnFLC.A10 gene is associated with vernalization requirement in rapeseed (Brassica napus L.). Hou Jinna, Yan Long, Harsh Raman, Xiaoxiao Zou, Jing Wang, Shutao Dai, Qinqin Xiao, Cong Li, Longjiang Fan, Bin Liu and Jinling Meng. BMC Plant Biology, 2012, 12:238. doi: 10.1186/1471-2229-12-238 [PDF]
Alteration of the alkaloid profile in genetically modified tobacco reveals a role of methylenetetrahydrofolate reductase in nicotine N-demethylation. Hung Chiu-Yueh, Longjiang Fan, Farooqahmed S Kittur, Bronwyn M Holliday, Bingguang Xiao, She Tang, Jie Qiu, Lowell P Bush, Mark A Conkling and Jiahua Xie. Plant Physiology, 2012, 161(2):1049-1060. doi: http:/​/​dx.​doi.​org/​10.​1104/​pp.​112.​209247 [PDF]
Characterization of the defense transcriptome responsive to Fusarium oxysporum-infection in Arabidopsis using RNA-seq. Zhu Qian-Hao, Stuart Stephen, Kemal Kazan, Gulei Jin, Longjiang Fan, Jennifer Taylor, Elizabeth S. Dennis, Chris A. Helliwell, Ming-Bo Wang. Gene, 2012, 512(2):259-266. doi: 10.1016/j.gene.2012.10.036 [PDF]

Diversity arrays technology (DArT) for studying the genetic polymorphism of flue-cured tobacco (Nicotiana tabacum). Lu Xiu-ping, Bing-guang Xiao, Yong-ping Li, Yi-jie Gui, Yu Wang, Longjiang Fan. Journal of Zhejiang University-SCIENCE B, 2012, 1862-1783. doi: 10.1631/jzus.B1200227 [PDF]
Genomic dissection of small RNAs in wild rice (O. rufipogon): lessons for rice domestication. Yu Wang, Xuefiebai, Chenghai Yan, Yiejie Gui, Xinghua Wei, Qianhao Zhu, Longbiao Guo, Longjiang Fan. New Phytologist, 2012, 196: 914. doi: 10.1111/j.1469-8137.2012.04304.x [PDF]
Development of DArT markers for linkage map of flue-cured tobacco. Xiuping Lu, Gui Yijie, Bingguang Xiao, Yongping Li, Zhijun Tong, Yun Liu, Xuefei Bai, Weiren Wu, Ling Xia, Eric Huttner, Adrzej Kilian, Longjiang Fan. Chinese Science Bulletin, 2012, 58(6):648 . [PDF]
Identification of glutinous maize landraces and inbred lines with altered transcription of waxy gene. Bao Jiandong, Jianqiang Yao, Jinqing Zhu, Weimin Hu, Daguang Cai, Yu Li, Qingyao Shu, Longjiang Fan. Molecular Breeding, 2012, 30(4):1707-1714. doi: 10.1007/s11032-012-9754-3 [PDF]
中国糯玉米wx基因种质资源遗传多样性的调查与分析. 姚坚强, 鲍坚东, 朱金庆, 桂毅杰, 胡伟民, 樊龙江. 作物学报, 2012, 39(1):43-49. [PDF]
烟草MITE位点间多态性(IMP)标记开发及其遗传作图应用. 高玉龙, 桂毅杰, 肖炳光, 薄世平, 严广号, 樊龙江. 浙江大学学报(农业与生命科学版), 2012, 38(6):655-661. [PDF]
Identification of wounding and topping responsive small RNAs in tobacco (Nicotiana tabacum). She Tang*, Yu Wang*, Zefeng Li, Yijie Gui, Bingguang Xiao, Jiahua Xie, Qian-Hao Zhu, Longjiang Fan. BMC Plant Biology, 2012, 12:28. doi: 10.1186/1471-2229-12-28 [PDF]

This article is featured highly accessed paper in BMC Plant Biology.

 
2011
Genome Sequence of the Tobacco Bacterial Wilt Pathogen Ralstonia solanacearum. Zefeng Li, Sanling Wu, Xuefei Bai, Yun Liu, Jianfei Lu, Yong Liu, Bingguang Xiao, Xiuping Lu, Longjiang Fan. Journal of Bacteriology, 2011, 193:6088. doi: 10.1128/JB.06009-11 [PDF]

河姆渡古稻DNA序列分析发现明显基因型分化. 樊龙江, 桂毅杰, 郑云飞, 王煜, 蔡大广, 游修龄. 科学通报. 2011, 56(28):2398. [PDF]

Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence. Fan Longjiang, Yijie Gui, Yunfei Zheng, Yu Wang, Daguang Cai, Xiuling You. Chinese Science Bulletin, 2011, 56:3108. doi: 10.1007/s11434-011-4691-9 [PDF]

DNA methylation polymorphism in flue-cured tobacco and candidate markers for TMV resistance. Zhao Jiehong, Zhang Jishun, Wang Yi, Wang Rengang, Wu Chun, Fan Longjiang, Ren Xueliang. Journal of Zhejiang University SCIENCE B, 2011, 6:1862. doi: 10.1631/jzus.B1000417 [PDF]
Draft Genome Sequence of Marine Streptomyces sp. Strain PP-C42, Isolated from the Baltic Sea. Longjiang Fan, Yun Liu, Zefeng Li, Heike I. Baumann, Katrin Kleinschmidt, Wanzhi Ye, Johannes F. Imhoff, Michael Kleine, and Daguang Cai. Journal of Bacteriology, 2011, on line. doi: 10.1128/JB.05097-11 [PDF]
iSNAP: a small RNA-based molecular marker technique. Yijie Gui, Guanghao Yan, Shiping Bo, Zhijun Tong, Yu Wang,Bingguang Xiao, Xiuping Lu, Yongping Li, Weiren Wu, Longjiang Fan. Plant Breeding, 2011, 130:no. doi: 10.1111/j.1439-0523.2011.01872.x [PDF]
Characterization of Small Interfering RNAs Derived from the Geminivirus/Betasatellite Complex Using Deep Sequencing. Xiuling Yang, Yu Wang, Wei Guo, Yan Xie, Qi Xie, Longjiang Fan, Xueping Zhou. PLoS ONE, 2011, 6(2):e16928. doi: 10.1371/journal.pone.0016928 [PDF]
 
2010
Genome sequence of Bacillus subtilis subsp. spizizenii gtP20b isolated from the Indian Ocean. Longjiang Fan, Shiping Bo, Huan Chen, Wanzhi Ye, Katrin Kleinschmidt, Heike I. Baumann, Johannes F. Imhoff, Michael Kleine, and Daguang Cai. J. Bacteriol., 2010, doi: 10.1128/JB.01351-10 [PDF]
Sequence variation and selection of small RNAs in domesticated rice. Yu Wang*, Dan Shen*, Shiping Bo, Jian Zheng, Qianhao Zhu, Chris Helliwell, Longjiang Fan. BMC Evolutionary Biology, 2010, 10: 119. doi: 10.1186/1471-2148-10-119 [PDF]
Insights into the bamboo genome: Syntenic relationships to rice and sorghum. Yijie Gui*, Yan Zhou*, Yu Wang*, Sheng Wang, Shengyue Wang, Yan Hu, Shiping Bo, Huan Chen, Changping Zhou, Naixun Ma, Tianzhen Zhang, Longjiang Fan. Journal of Integrative Plant Biology, 2010, 52(11): 1008. doi: 10.1111/j.1744-7909.2010.00965.x [PDF]
Identification of NBS-type Resistance Gene Homologs in Tobacco Genome. Xiaodong Leng, Bingguang Xiao, Sheng Wang, Yijie Gui, Yu Wang, Xiuping Lu, Jiahua Xie, Yongping Li, Longjiang Fan. Plant Molecular Biology Reporter, 2010, 28: 152. doi: 10.1007/s11105-009-0134-z [PDF]
 
2009
Post-domestication selection in the maize starch pathway. Longjian Fan, Jiandong Bao, Yu Wang, Jianqiang Yao, Yijie Gui, Weiming Hu, Jinqing Zhu, Mengqian Zeng, Yu Li, Yunbi Xu. PLoS ONE, 2009, On line. doi: 10.1371/journal.pone.0007612 [PDF]
Molecular phylogeny analysis of miR390-guided trans-acting siRNA genes (TAS3) in the grass family. Shen Dan, Sheng Wang, Huan Chen, Qian-Hao Zhu, Chris Helliwell, Longjiang Fan. Plant Systematics and Evolution, 2009, On line. doi: 10.1007/s00606-009-0221-5 [PDF]
 
2008
Assessment of codivergence of Mastreviruses with their plant hosts. Beilei Wu, Ulrich Melcher, Xingyi Guo, Xifeng Wang, Longjiang Fan, Guanghe Zhou. BMC Evolutionary Biology, 2008, 8:335. [PDF]
Selection and mutation on microRNA target sequences during rice evolution. Xingyi Guo, Yijie Gui, Yu Wang, Qian-Hao Zhu, Chris Helliwell and Longjiang Fan. BMC Genomics, 2008, 9:454. [PDF]

This article is featured highly accessed paper in BMC Genomics.

A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Qian-Hao Zhu, Andrew Spriggs, Louisa Matthew, Longjiang Fan, Gavin Kennedy, Frank Gubler, and Chris Helliwell. Genome Research, 2008, 18:1456-1465. [PDF]
Molecular evidence for post-domestication selection in the Waxy gene of Chinese waxy maize. Longjiang Fan, Liyan Quan, Xiaodong Leng, Xingyi Guo, Weiming Hu, Songlin Ruan, Huasheng Ma, Mengqian Zeng. Molecular Breeding, 2008, 22:329–338. [PDF]
Chloroplast DNA insertions into the nuclear genome of rice: the genes, sites and ages of insertion involved. Xingyi Guo, Songlin Ruan, Weimin Hu, Daguang Cai, Longjiang Fan. Functional & Integrative Genomics, 2008, 8:101–108. [PDF]
 

2007

Patterns of selective constraints in noncoding DNA of rice. Xingyi Guo, Yu Wang, Peter D. Keightley and Longjiang Fan*. BMC Evolutionary Biology, 2007, 7:208. [PDF]
Molecular evolution and selection of a gene encoding two tandem microRNAs in rice. Sheng Wang, Qianhao Zhu, Xingyi Guo, Yijie Gui, Jiandong Bao, Chris Helliwell, Longjiang Fan*. FEBS Letters, 2007, 581:4789-4793. [PDF]
Comparative study on the moso bamboo genome size and sequence composition. Yijie Gui, Sheng Wang, Liyan Quan, Changping Zhou, Shibao Long, Huajun Zheng, Liang Jin, Xianyin Zhang, Naixun Ma, Longjiang Fan. Science in China, 2007, 50(5): 1-6. [PDF]
Evidence of selectively driven codon usage in rice: Implications for GC content evolution of Gramineae Genes. Xingyi Guo, Jiandong Bao, Longjiang Fan. FEBS Letters, 2007, 581(5): 1015-1021. [PDF]

 

2006

Incongruent evolution of chromosome size in rice. Xingyi Guo, Guohua Xu, Yang Zhang, Xiao Wen, Weimin Hu, Longjiang Fan. Genetics and Molecular Research, 2006, 5(2): 373-389. [PDF]
Complete physical map of a wild beet (Beta procumbens) translocation in sugar beet. Daniela Schulte, Daguang Cai, Micheal Keline, Longjiang Fan, Sheng Wang, Christian Jung. Molecular Genetics and Genomics (MGG), 2006, 275:504-511. [PDF]
竹类植物与水稻等其它禾本科作物的系统进化关系及基因序列组成的比较. 樊龙江, 郭兴益, 马乃训. 林业科学研究, 2006, 19(2):165-169. [PDF]
植物基因转录起始频率分析. 张扬, 徐国华, 樊龙江. 浙江大学学报 (农业与生命科学版), 2006, 32(2): 119-122. [PDF]

植物基因转录起始频率数据库: (PIFdb)(Release 2)

利用基因组数据分析水稻基因顺式作用元件. 张扬, 徐国华, 徐飞, 樊龙江. 生物数学学报, 2006, 21(1) : 81-8 [PDF]

 

2005

Maximal sequence length of exact match between members from a gene family during early evolution. Wen Xiao, Guo Xingyi, Fan Longjiang. Journal of Zhejiang University SCIENCE, 2005, 6B(6): 470-476 [PDF]

Complementary Materials: Inter-chromosome alignment...

Small-scale duplications play a significant role in  rice genome evolution. GUO Xing-yi, XU Guo-hua, ZHANG Yang, HU Wei-min, FAN Long-jiang. Rice Science, 2005, 12(3): 173-178 [PDF]

Supplementary Information: Figure S1 Selected dot-plots ...

Two ancient rounds of polyploidy in rice genome. Zhang Yang, Xu Guohua, Guo Xingyi, Fan Longjiang. Journal of Zhejiang University SCIENCE, 2005, 6B(2): 87-90  [PDF] Program:  reciprocal BLASTN best-hit ...

This paper is one of top 10 SCI cited articles published in JZUS-B from 2005 to 2008.

从水稻基因组序列中挖掘生物信息. 樊龙江, 郭兴益. 浙江大学学报(农业与生命科学版), 2005, 31(4): 355-361 [PDF]

 

2000-2004

The absence of TIR-type resistance gene analogues in sugar beet (Beta vulgaris L.) genome. Tian Yanyan, Longjiang Fan (Co-First Author), Tim Thurau, Cristian Jung, Daguang Cai. Journal Molecular Evolution, 2004, 58(1): 40-53. [PDF]
A method of choosing location based on genotype-environment interaction for regional trial of rice. Fan LJ*, BM Hu, CH Shi, JG Wu. Plant Breeding, 2001, 120(2):139-142. [PDF]
Genetic and genotype×environment interaction effects from embryo, endosperm, cytoplasm and maternal plant for rice shape traits of indica rice. Shi CH, J Zhu, JG Wu, LJ Fan. Field Crops Research, 2000, 68(3):191-198. [PDF]