【返回上级目录】

2024

Identification of cell‐type specificity, trans‐ and cis‐acting functions of plant lincRNAs from single‐cell transcriptomes. Jiwei Xu#, Enhui Shen#, Fu Guo, Kaiqiang Wang, Yurong Hu, Leti Shen, Hongyu Chen, Xiaohan Li, Qian-Hao Zhu, Longjiang Fan, Qinjie Chu*.New Phytologist, 2024. doi:https://doi.org/10.1111/nph.20269

The Dynamic Transcriptome Reveals Response Patterns to Black Shank Disease in Tobacco (Nicotiana tabacum L.). Zhijun Tong#, Zuoqian Fan#, Tianyu Du, Dunhuang Fang, Xueyi Sui, Chuyu Ye, Qian-Hao Zhu, Longjiang Fan, Bingguang Xiao* and Enhui Shen*.Plant Stress, 2024. doi:https://doi.org/10.1016/j.stress.2024.100676

Assembling a reference-quality genome and resequencing diverse accessions of Beckmannia syzigachne provide insights into population structure and gene family evolution. Yang Han, Jianxiang Wu, Qian-Hao Zhu, Chu-Yu Ye*, Xinxin Li*. Plant Communications, 2024. doi:https://doi.org/10.1016/j.xplc.2024.101174

Retrospect and Prospect of Nicotiana Tabacum Genome Sequencing. Zhijun Tong, Yujie Huang, Qian-Hao Zhu, Longjiang Fan, Bingguang Xiao*, Enhui Shen*. Frontiers in Plant Science, 2024. doi: 10.3389/fpls.2024.1474658

African Cultivated, Wild and Weedy Rice (Oryza spp.): Anticipating Further Genomic Studies. Kehinde, Babatunde O., Lingjuan Xie, Beng-Kah Song, Xiaoming Zheng, and Longjiang Fan*. Biology, 2024. doi: https://doi.org/10.3390/biology13090697

Single-cell landscape of long and short glandular trichomes in Nicotiana tabacum leaves. Hongyu Chen, Xiaohan Li, Qing Cheng, Nianmin Shang, Zhijun Tong, Qinjie Chu, Chuyu Ye, Xiner Shen, Qian-Hao Zhu, Bingguang Xiao*, Longjiang Fan*. iScience, 2024. doi: https://doi.org/10.1016/j.isci.2024.110650

Are miRNAs applicable for balancing crop growth and defense trade-off? Enhui Shen*, Tianlun Zhao, Qian-Hao Zhu*. New Phytologist, 2024. doi: https://doi.org/10.1111/nph.19939

Current status of community resources and priorities for weed genomics research. Montgomery J, Morran S, MacGregor DR, McElroy JS, Neve P, Neto C, Vila-Aiub MM, Sandoval MV, Menéndez AI, Kreiner JM, Fan L, Caicedo AL, Maughan PJ, Martins BAB, Mika J, Collavo A, Merotto A Jr, Subramanian NK, Bagavathiannan MV, Cutti L, Islam MM, Gill BS, Cicchillo R, Gast R, Soni N, Wright TR, Zastrow-Hayes G, May G, Malone JM, Sehgal D, Kaundun SS, Dale RP, Vorster BJ, Peters B, Lerchl J, Tranel PJ, Beffa R, Fournier-Level A, Jugulam M, Fengler K, Llaca V, Patterson EL, Gaines TA. Genome Biology, 2024.doi:10.1186/s13059-024-03274-y

High-throughput single-microbe RNA sequencing reveals adaptive state heterogeneity and host-phage activity associations in human gut microbiome. Yifei Shen, Qinghong Qian, Liguo Ding, Wenxin Qu, Tianyu Zhang, Mengdi Song, Yingjuan Huang, Mengting Wang, Ziye Xu, Jiaye Chen, Ling Dong,Hongyu Chen, Enhui Shen, Shufa Zheng, Yu Chen, Jiong Liu, Longjiang Fan*, Yongcheng Wang*. Protein & Cell, 2024.doi:https://doi.org/10.1093/procel/pwae027

Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germination. Jie Yao, Qinjie Chu, Xing Guo, Wenwen Shao, Nianmin Shang, Kang Luo, Xiaohan Li, Hongyu Chen, Qing Cheng1, Fangyu Mo, Dihuai Zheng, Fan Xu, Fu Guo, Qian-Hao Zhu, Shuiguang Deng, Chengcai Chu, Xun Xu, Huan Liu*, Longjiang Fan*. Developmental Cell, 2024. doi:https://doi.org/10.1016/j.devcel.2024.05.016

BreedingAIDB: a database integrating crop genome-to-phenotype paired data with machine learning tools applicable in breeding. Zijie Shen, Enhui Shen, Kun Yang, Zuoqian Fan, Qian-Hao Zhu, Longjiang Fan, Chu-Yu Ye* . Plant Communications, 2024.doi:https://doi.org/10.1016/j.xplc.2024.100894

Technology-enabled great leap in deciphering plant genomes. Lingjuan Xie, Xiaojiao Gong, Kun Yang, Yujie Huang, Shiyu Zhang, Leti Shen, Yanqing Sun, Dongya Wu, Chuyu Ye, Qian-Hao Zhu, Longjiang Fan*. Nature Plants, 2024.doi:https://www.nature.com/articles/s41477-024-01655-6

A reference genome of Commelinales provides insights into the commelinids evolution and global spread of water hyacinth (Pontederia crassipes). Yujie Huang, Longbiao Guo, Lingjuan Xie, Nianmin Shang, Dongya Wu, Chuyu Ye, Eduardo Carlos Rudell, Kazunori Okada, Qian-Hao Zhu, Beng-Kah Song, Daguang Cai, Aldo Merotto Junior, Lianyang Bai*, Longjiang Fan*. GigaScience, 2024.doi:doi:https://doi.org/10.1093/gigascience/giae006

Multidimensional assessment of the biological effects of electronic cigarettes on lung bronchial epithelial cells. Meng Wang, Qing Cheng, Zehong Wu, Longjiang Fan, Linghui Zeng, Hongyu Chen* Scientific Reports, 2024.doi:https://www.nature.com/articles/s41598-024-55140-3

2023

Population genomic analysis unravels the evolutionary roadmap of pericarp color in rice. Lingjuan Xie, Dongya Wu, Yu Fang, Chuyu Ye, Qianhao Zhu, Xinghua Wei, Longjiang Fan*. Plant Communications, 2023.doi:https://doi.org/10.1016/j.xplc.2023.100778

GSCtool: a novel descriptor that characterizes the genome for applying machine learning in genomics. Zijie Shen, Enhui Shen, Qianhao Zhu, Longjiang Fan, Quan Zou*, Chuyu Ye*. Advanced Intelligent Systems, 2023.doi:https://onlinelibrary.wiley.com/doi/10.1002/aisy.202300426

Editorial: The Application of Population Genomics in Crop Research. Fanjing Yang, Wei Ma, and Chuyu Ye. Agronomy, 2023.doi:https://doi.org/10.3390/agronomy13102480

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision. Marieke Vromman, Jasper Anckaert, Stefania Bortoluzzi, Alessia Buratin, Chia-Ying Chen, Qinjie Chu, Chuyu Ye, et al. Nature Methods, 2023.doi:https://www.nature.com/articles/s41592-023-01944-6

Recent progresses in plant single-cell transcriptomics. Zheng Dihuai, Jiwei Xu, Yaqian Lu, Hongyu Chen, Qinjie Chu, Longjiang Fan*. Crop Design, 2023.doi:https://doi.org/10.1016/j.cropd.2023.100041

A syntelog-based pan-genome provides insights into rice domestication and de-domestication. Dongya Wu, Lingjuan Xie, Yanqing Sun, Yujie Huang, Lei Jia, Chenfeng Dong, Enhui Shen, Chu-Yu Ye, Qian Qian*, Longjiang Fan*. Genome Biology, 2023.doi:https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03017-5

Asymmetric variation of DNA methylation during domestication and de-domestication of rice. Shuai Cao, Kai Chen, Kening Lu, Shiting Chen, Xiyu Zhang, Congcong Shen, Shuangbin Zhu, Yanan Niu, Longjiang Fan, Z. Jeffrey Chen*, Jianlong Xu*, Qingxin Song*. Plant Cell, 2023.doi:https://doi.org/10.1093/plcell/koad160

Genome-wide dissection of Quan9311A breeding and application. Qianlong Li, Qi Feng, Heqin Wang, Yunhai Kang, Conghe Zhang, Ming Du, Yunhu Zhang, Hui Wang, Jinjie Chen, Bin Han, Yu Fang, Ahong Wang.Rice Science, 2023.doi:https://doi.org/10.21203/rs.3.rs-1727782/v1

High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq. Ziye Xu, Tianyu Zhang, Hongyu Chen, Yuyi Zhu, Yuexiao Lv, Shunji Zhang, Jiaye Chen, Haide Chen, Lili Yang, Weiqin Jiang, Shengyu Ni, Fangru Lu, Zhaolun Wang, Hao Yang, Ling Dong, Feng Chen, Hong Zhang, Yu Chen, Jiong Liu, Dandan Zhang, Longjiang Fan*, Guoji Gu* and Yongcheng Wang*. Nature Communications, 2023.doi:https://www.nature.com/articles/s41467-023-38409-5

A syntelog-based pan-genome provides insights into rice domestication and de-domestication. Dongya Wu, Lingjuan Xie, Yanqing Sun, Yujie Huang, Lei Jia, Chenfeng Dong, Enhui Shen, Chuyu Ye, Qian Qian*, Longjiang Fan*. bioRxiv, 2023. doi:https://www.biorxiv.org/content/10.1101/2023.03.17.533115v1

Transcriptomic profiling reveals candidate allelopathic genes in rice responsible for interactions with barnyardgrass. Sultana Most. Humaira, Alamin Md., Jie Qiu, Longjiang Fan, Chuyu Ye*. Frontiers in Plant Science, 2023. doi:https://www.frontiersin.org/articles/10.3389/fpls.2023.1104951/full

Editorial: The roles of ncRNAs in the genome evolution and cross-kingdom regulation. Enhui Shen*, Jun Zou, Jiandong Bao, Qianhao Zhu*. Frontiers in Plant Science, 2023.doi:https://doi.org/10.3389/fpls.2023.1133096

2022

Weed genomics: Yielding insights into the genetics of weedy traits for crop improvement. Yujie Huang, Dongya Wu, Zhaofeng Huang, Xiangyu Li, Aldo Merotto Jr, Lianyang Bai*, Longjiang Fan*. aBIOTECH , 2022.doi:https://doi.org/10.1007/s42994-022-00090-5

Poaceae chloroplast genome sequencing: great leap forward in recent ten years. Yiyu Hu, Yanqing Sun, Qianhao Zhu, Longjiang Fan, Jianhua Li*. Current Genomics , 2022.doi: https://doi.org/10.2174/1389202924666221201140603

A Manually curated database and analysis platform of cell markers of scars. Yan Zheng, Jie Yao, Xiner Shen, Haijun Cheng, Yinbo Peng, Weiqiang Tan, Michael P. Timko, Longjiang Fan*. Journal of Investigative Dermatology , 2022.doi:https://www.sciencedirect.com/science/article/abs/pii/S0022202X2202663X

Identification of plant-derived microRNAs in human kidney. Xi Chen, Xishao Xie, Lu Liu, Hongyu Chen, Bo Wang, Zheng Li, Linghui Zeng, Micheal Timko, Jianhua Chen*, Weiqiang Lin*, Longjiang Fan* bioRxiv , 2022.doi:https://doi.org/10.1101/2022.10.25.513797

Single-cell transcriptome of Nepeta tenuifolia leaves reveal differentiation trajectories in glandular trichomes. Peina Zhou, Hongyu Chen, Jingjie Dang, Zunrui Shi, Yongfang Shao, Chanchan Liu, Longjiang Fan*, Qinan Wu*. Frontiers in Plant Science, 2022.doi:https://doi.org/10.3389/fpls.2022.988594

EMLI-ICC: An ensemble machine learning-based integration algorithm for metastasis prediction and risk-stratification in intrahepatic cholangiocarcinoma. Jian Ruan, Shuaishuai Xu, Ruyin Chen, Qiong Li, Chanqi Ye, Wei Wu, Qi Jiang, Feifei Yan, ..., Michael P. Timko, Peng Zhao*, Longjiang Fan*, Yifei Shen*. Briefings in Bioinformatics, 2022.doi:https://doi.org/10.1093/bib/bbac450

When domestication bottleneck meets weed. Yanqing Sun, Longbiao Guo, Qian-Hao Zhu, Longjiang Fan*. Molecular Plant, 2022.doi:https://doi.org/10.1016/j.molp.2022.08.002

Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass. Dongya Wu, Yiyu Hu, Akashi Shota, Nojiri Hideaki, Longbiao Guo, Chuyu Ye, Qianhao Zhu, Okada Kazunori, Longjiang Fan*. The Plant Journal, 2022.doi: https://doi.org/10.1111/tpj.15893

Multi-Omic Molecular Biomarkers and database of Osteoarthritis. Jianhua Li, Xiaotian Yang, Qiejie Chu, Lingjuan Xie, Yuwen Ding, Xiaoxu Xu, Michael P. Timko, Longjiang Fan*. DATABASE, 2022.doi:https://doi.org/10.1093/database/baac052

The complete chloroplast genome of weedy rye Secale cereale subsp. segetale. Tianyu Du, Yiyu Hu, Yanqing Sun, Chuyu Ye, Enhui Shen*. Mitochondrial DNA Part B, 2022.doi:https://doi.org/10.1080/23802359.2022.2080600

PlantcircBase 7.0: full-length transcripts and conservation of plant circRNAs. Xiaoxu Xu, Tianyu Du, Weihua Mao, Xiaohan Li, Chu-Yu Ye, Qian-Hao Zhu, Longjiang Fan, Qinjie Chu*. Plant Communications, 2022.doi:https://doi.org/10.1016/j.xplc.2022.100343

Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoid in plants. Dongya Wu, Bowen Jiang, Chuyu Ye, Michael P.Timko, Longjiang Fan*. Plant Communications, 2022.doi:https://doi.org/10.1016/j.xplc.2022.100320

Horizontal transfers lead to the birth of momilactone biosynthetic gene clusters in grass. Dongya Wu, Yiyu Hu, Shota Akashi, Hideaki Nojiri, ChuYu Ye, QianHao Zhu, Kazunori Okada, Longjiang Fan*. bioRxiv , 2022.doi:https://doi.org/10.1101/2022.01.11.475971

Genomic insights into the evolution of Echinochloa species as weed and orphan crop. Dongya Wu, Enhui Shen, Bowen Jiang, Yu Feng, Wei Tang, Sangting Lao, Lei Jia, HanYang Lin, Lingjuan Xie, Xifang Weng, Chenfeng Dong, Qinghong Qian, Feng Lin, Haiming Xu, Huabing Lu, Luan Cutti, Huajun Chen, Shuiguang Deng, Longbiao Guo, Tse Seng Chuah, Beng Kah Song, Laura Scarabel, Jie Qiu, Qianhao Zhu, Qin Yu, Michael Timko, Hirofumi Yamaguchi, Aldo Merotto Jr, Yingxiong Qiu, Kenneth Olsen, Longjiang Fan, and Chuyu Ye*. Nature Communications, 2022.doi:https://www.nature.com/articles/s41467-022-28359-9 [NC's Featured article]

Weedy rice, a hidden gold mine in the paddy field. Dongya Wu, Jie Qiu, Jian Sun, Beng-Kah Song, Kenneth M. Olsen, Longjiang Fan*. Mol Plant, 2022. doi:https://doi.org/10.1016/j.molp.2022.01.008

2021

植物基因组测序研究进展. 谢玲娟, 叶楚玉, 沈恩惠*. 植物科学学报, 2021. doi:http://www.plantscience.cn/CN/10.11913/PSJ.2095-0837.2021.60681

Population genomic analysis reveals domestication of cultivated rye from weedy rye. Yanqing Sun, Enhui Shen, Yiyu Hu, Dongya Wu, Yu Feng, Sangting Lao, Chenfeng Dong, Tianyu Du, Wei Hua, Chu-Yu Ye, Jinhuan Zhu, Qian-Hao Zhu, Daguang Cai, Lidia Skuza, Jie Qiu, Longjiang Fan*. Molecular Plant, 2021. doi:https://doi.org/10.1016/j.molp.2021.12.015 [MP Spotlight]

Horizontal Transfer and Evolution of the Biosynthetic Gene Cluster for Benzoxazinoid.Dongya Wu, Bowen Jiang, Chu-Yu Ye, Michael P. Timko, Longjiang Fan*. bioRxiv, 2021. doi:https://doi.org/10.1101/2021.12.07.471670

Twenty years of plant genome sequencing: achievements and challenges.Yanqing Sun, Lianguang Shang, Qian-Hao Zhu, Longjiang Fan*, Longbiao Guo*. Trends in Plant science, 2021. doi:https://doi.org/10.1016/j.tplants.2021.10.006

Effects of sample size on plant single-cell RNA profiling. Hongyu Chen, Yang Lv, Xinxin Yin, Xi Chen, Qinjie Chu, Qian-Hao Zhu, Longjiang Fan, Longbiao Guo*. Current Issues in Molecular Biology, 2021. doi: https://doi.org/10.3390/cimb43030119

Recent origination of circular RNAs in plants. Chu, Qinjie; Ding, Yuwen; Xu, Xiaoxu ; Ye, Chuyu; Zhu, Qian-Hao; Guo, Longbiao; Fan, Longjiang*. New Phytologist, 2021. doi:https://doi.org/10.1111/nph.17798

Large-scale identification of plant miRNAs in mammals implicates their dietary intake. Xi Chen, Lu Liu, Qinjie Chu, Shuo Sun, Yixuan Wu, Zhou Tong, Weijia Fang, Michael P. Timko, Weijia Fang, and Longjiang Fan*. PLOS One, 2021. doi:https://doi.org/10.1371/journal.pone.0257878

The complete chloroplast genome of Echinochloa haploclada. Bowen Jiang, Sangting Lao, Dongya Wu, Longjiang Fan, Chu-Yu Ye*. Mitochondrial DNA Part B, 2021. doi:https://doi.org/10.1080/23802359.2021.1982654

The complete chloroplast genome of weedy rice Oryza sativa f. spontanea. Chenfeng Dong, Yiyu Hu, Chuyu Ye, Longjiang Fan & Longbiao Guo*. Mitochondrial DNA Part B, 2021. doi:https://doi.org/10.1080/23802359.2021.1977197

Signaling pathway perturbation analysis for assessment of biological impact of cigarette smoke on lung cells. Hongyu Chen , Xi Chen, Yifei Shen, Xinxin Yin, Fangjie Liu, Lu Liu, Jie Yao, Qinjie Chu, Yaqin Wang, Hongyan Qi, Michael P. Timko, Weijia Fang, Longjiang Fan*. Scientific Reports, 2021. doi:https://doi.org/10.1038/s41598-021-95938-z

scDetect: A rank-based ensemble learning algorithm for cell type identification of single-cell RNA sequencing in cancer. Yifei Shen*, Qinjie Chu, Micheal Timko, Longjiang Fan*. Bioinformatics, 2021. doi:https://doi.org/10.1093/bioinformatics/btab410

PlantscRNAdb: A Database for Plant Single-cell RNA Analysis. Hongyu Chen, Xinxin Yin, Longbiao Guo, Jie Yao, Yuwen Ding, Xiaoxu Xu, Lu Liu, Zhu Qian-Hao, Qinjie Chu*, Longjiang Fan*. Molecular Plant, 2021. doi:https://doi.org/10.1016/j.molp.2021.05.002

Rice bioinformatics in the genomic era: status and perspectives. Lei Jia, Lingjuan Xie, Sangting Lao, Qian-Hao Zhu, Longjiang Fan*. The Crop Journal, 2021. doi:https://doi.org/10.1016/j.cj.2021.03.003

An ABCC-type transporter endowing glyphosate resistance in plants. Lang Pan, Qin Yu*, Junzhi Wang, Heping Han, Lingfeng Mao, Alex Nyporko, Anna Maguza, Longjiang Fan, Lianyang Bai*, Stephen Powles*. PNAS, 2021. doi:https://doi.org/10.1073/pnas.2100136118

Decoding genomes changed our understanding and approaches for plant breeding.(TrendsTalk). Longjiang Fan*. Trends in Plant Science, 2021. doi:https://doi.org/10.1016/j.tplants.2021.03.013

De-domestication: an extension of crop evolution. Dongya Wu, Sangting Lao, Longjiang Fan*. Trends in Plant Science, 2021. doi:https://doi.org/10.1016/j.tplants.2021.02.003

Orphan crops and their wild relatives in the genomic era.（Perspective） Chu-Yu Ye, Longjiang Fan*. Molecular Plant, 2021. doi:https://doi.org/10.1016/j.molp.2020.12.013 [PDF][Featured Article][Cover story]

2020

The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Chu-Yu Ye, Dongya Wu, Lingfeng Mao, Lei Jia, Jie Qiu, Sangting Lao, Meihong Chen, Bowen Jiang, Wei Tang, Qiong Peng, Lang Pan, Lifeng Wang, Xiaoxiao Feng, Longbiao Guo, Chulong Zhang, Elizabeth Kellogg, Kenneth Olsen, Lianyang Bai, Longjiang Fan*. Molecular Plant, 2020. doi:https://doi.org/10.1016/j.molp.2020.07.001 [PDF] [MP Spotlight]

Expansion of MIR482/2118 by a Class II transposable element in cotton. Enhui Shen, Tianzhi Chen, Xintian Zhu, Longjiang Fan, Jie Sun, Danny Llewellyn, Iain Wilson, Qian-Hao Zhu*. The Plant Journal, 2020. doi:https://onlinelibrary.wiley.com/doi/10.1111/tpj.14885 [PDF]

Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants. Lingfeng Mao, Hiroshi Kawaide, Sho Miyazaki, Meihong Chen, Yoshiki Hirata, Honoka Kimura, Toshiya Higuchi, Miyu Teruya, Kaoru Fujiwara, Keisuke Tomita, Koji Miyamoto, Hisakazu Yamane, Ken-ichiro Hayashi, Hideaki Nojiri, Lei Jia, Jie Qiu, Chuyu Ye, Michael P. Timko, Longjiang Fan* and Kazunori Okada*. PNAS, 2020. doi:https://doi.org/10.1073/pnas.1914373117 [PDF]

Diverse genetic mechanisms underlie worldwide convergent rice feralization. Jie Qiu, Lei Jia, Dongya Wu, Xifang Weng, Lijuan Chen, Jian Sun, Meihong Chen, Lingfeng Mao, Bowen Jiang, Chuyu Ye, Guilherme Turra, Longbiao Guo, Guoyou Ye, Qianhao Zhu, Toshiyuki Imaizumi, Beng-Kah Song, Laura Scarabel, Aldo Merotto, Kenneth Olsen*, Longjiang Fan*. Genome Biology, 2020. doi:https://doi.org/10.1186/s13059-020-01980-x [PDF]

TOD-CUP: A gene expression rank-based majority vote algorithm for tissue origin diagnosis of cancers of unknown primary. Shen Yifei, Qinjie Chu, Xinxin Yin, Yinjun He, Panpan Bai, Yunfei Wang, Weijia Fang, Michael P. Timko, Longjiang Fan*, Weiqin Jiang*. Briefings in Bioinformatics, 2020. doi:https://doi.org/10.1093/bib/bbaa031[PDF]

2019

A transcriptomic profile of topping responsive non-coding RNAs in tobacco roots (Nicotiana tabacum). Xi Chen, Shuo Sun, Fangjie Liu, Enhui Shen, Lu Liu, Chuyu Ye, Bingguang Xiao, Michael P. Timko, Qian-Hao Zhu, Longjiang Fan* & Peijian Cao*. BMC Genomics, 2019. doi: https://doi.org/10.1186/s12864-019-6236-6 [PDF]

AKR, a novel mechanism involved in glyphosate metabolism and resistance in Echinochloa colona. Pan Lang, Qin Yu*, Heping Han, Lingfeng Mao, Alex Nyporko, Longjiang Fan*, Lianyang Bai*, and Stephen Powles. Plant Physiology, 2019. doi: https://doi.org/10.1104/pp.19.00979 [PDF]

Genomic evidence of human selection on Vavilovian mimicry. Ye Chu-Yu, Wei Tang, Dongya Wu, Lei Jia, Jie Qiu, Meihong Chen, Lingfeng Mao, Feng Lin, Haiming Xu, Xiaoyue Yu, Yongliang Lu, Yonghong Wang, Kenneth M Olsen, Michael P. Timko, Longjiang Fan*. Nature Ecology & Evolution, 2019. doi: https://doi.org/10.1038/s41559-019-0976-1 [PDF] [Behind The Paper]] [Newswise Report] [F1000Prime] [Nature Plants Highlights]

RiceRelativesGD: a genomic database of rice relatives for rice research. Mao Lingfeng, Chen Meihong, Chu Qinjie, Jia Lei, Most. Humaira Sultana, Wu Dongya, Kong X, Qiu Jie, Ye Chu-Yu, Chen Xi*, and Fan Longjiang. Database, 2019. doi: https://doi.org/10.1093/database/baz110 [PDF]

Characterization and evolution of gene clusters for terpenoid phytoalexin biosynthesis in tobacco. Chen Xi, Fangjie Liu, Lu Liu, Jie Qiu, Dunhuang Fang, Weidi Wang, Xingcheng Zhang, Chuyu Ye, Michael Paul Timko, Qian-Hao Zhu, Longjiang Fan, Bingguang Xiao*. Planta, 2019. doi: https://doi.org/10.1007/s00425-019-03255-7 [PDF]

Gene modules co-regulated with biosynthetic gene clusters for allelopathy between rice and barnyardgrass. Sultana Most. Humaira, Fangjie Liu, Md. Alamin, Lingfeng Mao, Lei Jia, Hongyu Chen, Dongya Wu, Yingying Wang, Fei Fu, Sanling Wu, Weidi Wang, Chuyu Ye, Qian-hao Zhu, Jie Qiu *, Longjiang Fan. International Journal of Molecular Sciences, 2019. doi: https://www.mdpi.com/1422-0067/20/16/3846 [PDF]

Elimination of a retrotransposon for quenching genome instability in modern rice. Yu Peng#, Yingying Zhang#, Yijie Gui, Dong An, Junzhong Liu, Xun Xu, Qun Li, Junmin Wang, Wen Wang, Chunhai Shi, Longjiang Fan, Baorong Lu, Yiwen Deng*, Sheng Teng*, Zuhua He*. Molecular Plant, 2019. doi: https://doi.org/10.1016/j.molp.2019.06.004 [PDF]

Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed. Jun Zhou#, Lingfeng Mao#, Jie Qiu#, Meng Wang, Lei Jia, Dongya Wu, Zhesi He, Meihong Chen, Yifei Shen, Enhui Shen, Yongji Huang, Ruiyuan Li, Dandan Hu, Lei Shi, Kai Wang, Qian-Hao Zhu, Chuyu Ye, Ian Bancroft, Graham J King, Jinling Meng, Longjiang Fan*. Plant Biotechnology Journal, 2019. doi: https://onlinelibrary.wiley.com/doi/10.1111/pbi.13115 [PDF]

2018

Bi-directional selection in upland rice leads to its adaptive differentiation from lowland rice on drought resistance and productivity. Hui Xia, Zhi Luo, Jie Xiong, Xiaosong Ma, Qiaojun Lou, Haibin Wei, Jie Qiu, Hua Yang, Guolan Liu, Longjiang Fan, Liang Chen, Lijun Luo*. Molecular Plant, 2018. doi: https://doi.org/10.1016/j.molp.2018.12.011 [PDF]

Characteristics of Plant Circular RNAs. Chu Qinjie, Bai Panpan, Zhu Xintian, Zhang Xingchen, Mao Lingfeng, Zhu Qian-Hao, Fan Longjiang, Ye, Chuyu*. Briefings in Bioinformatics, 2018. doi: 10.1093/bib/bby111 [PDF]

Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus. Enhui Shen#, Xintian Zhu#, Shuijin Hua, Hongyu Chen, Chuyu Ye, Longhua Zhou, Qing Liu, Qian-Hao Zhu, Longjiang Fan and Xi Chen*. BMC Genomics, 2018. doi: https://doi.org/10.1186/s12864-018-5117-8 [PDF]

Genomic clues for crop-weed interactions and evolution. Guo Longbiao#, Jie Qiu#, Lin-Feng Li, Baorong Lu, Kenneth Olsen and Longjiang Fan*. Trends in Plant Science, 2018. doi: https://doi.org/10.1016/j.tplants.2018.09.009 [PDF]

Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed. Jun Zou#, Lingfeng Mao#, Jie Qiu#, Meng Wang, Zhesi He, Lei Jia, Dongya Wu, Yongji Huang, Meihong Chen, Yifei Shen, Enhui Shen, Ruiyuan Li, Dandan Hu, Kai Wang, LeiShi, Chuyu Ye, Ian Bancroft, Graham King, Jinling Meng and Longjiang Fan*. bioRxiv , 2018. doi: https://doi.org/10.1101/412551 [PDF]

The red bayberry genome and genetic basis of sex determination. Hui-Min Jia#, Hui-Juan Jia#, Qing-Le Cai#, Yan Wang, Hai-Bo Zhao, Wei-Fei Yang, Guo-Yun Wang, Ying-Hui Li, Dong-Liang Zhan, Yu-Tong Shen, Qing-Feng Niu, Le Chang, Jie Qiu, Lan Zhao, Han-Bing Xie, Wan-Yi Fu, Jing Jin, Xiong-Wei Li, Yun Jiao, Chao-Chao Zhou, Ting Tu, Chun-Yan Chai, Jing-Long Gao, Long-Jiang Fan, Eric van de Weg, Jun-Yi Wang* and Zhong-Shan Gao*. Plant Biotechnology Journal , 2018. doi: 10.1111/pbi.12985 [PDF]

The power and potential of genomics in weed biology and management. Karl Ravet, Eric L. Patterson, Hansjörg Krähmer, Kateřina Hamouzová, Longjiang Fan, Marie Jasieniuk, Amy Lawton-Rauh, Jenna M. Malone, J. Scott McElroy, Aldo Merotto Jr, Philip Westra, Christopher Preston, Martin M. Vila-Aiub, Roberto Busi, Patrick J. Tranel, Carl Reinhardt, Christopher Saski, Roland Beffa, Paul Neve* and Todd A. Gaines*. Pest Management Science, 2018. doi: 10.1002/ps.5048 [PDF]

Construction of the third-generation Zea mays haplotype map. Robert Bukowski, Xiaosen Guo, Yanli Lu, Cheng Zou, Bing He, Zhengqin Rong, Bo Wang, Dawen Xu, Bicheng Yang, Chuanxiao Xie, Longjiang Fan, Shibin Gao, Xun Xu, Gengyun Zhang, Yingrui Li, Yinping Jiao, John F Doebley, Jeffrey Ross-Ibarra, Anne Lorant, Vince Buffalo, M Cinta Romay, Edward S Buckler, Doreen Ware, Jinsheng Lai, Qi Sun* and Yunbi Xu*. Gigascience, 2018. doi: 10.1038/s41467-017-01067-5 [PDF]

The Circular RNA Profiles of Colorectal Tumor Metastatic Cells. Weiqin Jiang, Xingchen Zhang, Qinjie Chu, Sen Lu, Linfu Zhou, Xingang Lu, Chen Liu, Lingfeng Mao, Chuyu Ye, Michael P. Timko, Longjiang Fan* and Haixing Ju*. Frontiers in Genetics, 2018. doi: 10.3389/fgene.2018.00034 [PDF]

Emerging Roles of Plant Circular RNAs. Qinjie Chu, Enhui Shen, Chu-Yu Ye, Longjiang Fan, Qian-Hao Zhu*. Journal of Plant Cell, 2018. doi: coming soon [PDF]

2017

Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed. Guo Longbiao#, Jie Qiu#, Chuyu Ye, Gulei Jin, Lingfeng Mao, Haiqiang Zhang, Xuefang Yang, Qiong Peng, Yingying Wang, Lei Jia, Zhangxiang Lin, Gengmi Li, Fei Fu, Chen Liu, Li Chen, Enhui Shen, Weidi Wang, Sanling Wu, Chenyang Xia, Yongfei Zhang, Xiaomao Zhou, Lifeng Wang, Lamei Wu, Weijie Song, Yunfei Wang, Qingyao Shu, Daisuke Aoki, Emi Yumoto, Takao Yokota, Koji Miyamoto, Kazunori Okada, Do-Soon Kim, Daguang Cai, Chulong Zhang, Yonggen Lou, Qian Qian, Hirofumi Yamaguchi, Hisakazu Yamane, Chui-Hua Kong, Michael P. Timko, Lianyang Bai*, Longjiang Fan*. Nature Communications, 2017. doi: 10.1038/s41467-017-01067-5 [PDF][Media Coverage][F1000 Recommended]

A naive Bayes algorithm for tissue origin diagnosis (TOD-Bayes) of synchronous multifocal tumors in the hepatobiliary and pancreatic system. Weiqin Jiang, Yifei Shen, Yongfeng Ding, Chuyu Ye, Yi Zheng, Peng Zhao, Lulu Liu, Zhou Tong, Linfu Zhou, Shuo Sun, Xingchen Zhang, Lisong Teng, Michael P. Timko, Longjiang Fan*, Weijia Fang*. International Journal of Cancer, 2017. doi: 10.1002/ijc.31054 [PDF][Erratum]

Comparative whole-genome analysis reveals artificial selection effects on Ustilago esculenta genome. Zihong Ye, Yao Pan, Yafen Zhang, Haifeng Cui, Gulei Jin, Alice C. McHardy, Longjiang Fan*, and Xiaoping Yu*. DNA Research, 2017. doi: 10.1093/dnares/dsx031 [PDF]

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. doi: 10.1038/ncomms15323 [PDF]

Analysis of transcriptional and epigenetic changes in hybrid vigor of allopolyploid Brassica napus uncovers key roles for small RNAs. Shen, Yifei; Sun, Shuo; Hua, Shuijin; Shen, Enhui; Ye, Chuyu; Cai, Daguang; Timko, Michael; Zhu, Qian-Hao; Fan, Longjiang*. The Plant Journal, 2017. doi: 10.1111/tpj.13605 [PDF]

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]

This article was a "Hot Paper" in Web of Science. Hot Papers were published in the past two years and received enough citations to place them in the top 0.1% of papers in its academic fields.

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]