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学术预告：

报告题目：农业生物信息湖北省重点实验室2024学术年会

主持人：李立 教授

时间：2024年11月9日下午 14:30-18:00

报告地点：一综A102会议室

研究单元

目标

实验室研究工作的定位是以应用基础研究为主、并向基础与应用研究延伸。本实验室将以我省主要作物、畜禽及相关致病微生物的基因组、转录组、蛋白质组、代谢组和表型组为研究对象，瞄准学科前沿将各种“组学”技术与信息技术相结合，分别从多组学数据挖掘、生物系统模拟与药物发现、表型组分析与设计育种和生物信息算法开发四个方面开展全方位的研究，深入解读各种“组学”产生的海量生物学数据，为动植物育种、种质资源保护、农业病虫害监测和防治提供新理论、新技术和新方法，为确保我省乃至周边省份的粮食安全做出贡献。

研究成果

2018年科研成果

1） Mao Bangqiang#, Gao Min#, Chen Changshui, Li Zhijun, Zhang Hong-Yu, Zhang Qingye*. Design, synthesis and biological evaluation of novel N-nitrophenyl derivatives based on the structure of acetohydroxyacid synthase. Pesticide biochemistry and physiology, 2018, 14: 100-107.
2） Xie Shengsong#, Zhu Qin#, Qu Wubin#, Xu Zhong, Liu Xiangdong, Li Xinyun, Li Shijun, Ma Wubin, Miao Yiliang, Zhang Lisheng, Du Xiaoyong, Dong Wuzi, Li Haiwei, Zhao Changzhi, Wang Yunlong, Fang Yaping*, Zhao Shuhong*. sRNAPrimerDB: Comprehensive primer design and search web service for small non-coding RNAs. Bioinformatics (Oxford, England), 2018, 35(9): 1566-1572.
3） Sun Jun, Yang Ling-Li, Chen Xi, Kong De-Xin, Liu Rong*. Integrating Multifaceted Information to Predict Mycobacterium tuberculosis-Human Protein-Protein Interactions. Journal of proteome research, 2018, 17(11): 3810-3823.
4） Hu Jian, Liu Hui-Fang, Sun Jun, Wang Jia, Liu Rong. Integrating co-evolutionary signals and other properties of residue pairs to distinguish biological interfaces from crystal contacts. Protein science : a publication of the Protein Society,2018,27(9): 1723-1735.
5） Qin Xuan, Wang Shuguang , Wu Yongze, Xia Jingbo. Evaluation of the Performance of BioNLP Tools for Discovering Causal Genes in Terms with Pathway Enrichment. Journal of Physics: Conference Series, 2018, 1069: 012037.秦璇，王曙光
6） Lu Panzhong, Zhang Hanyi, Liu Ying, Wu Yongze, Qin Xuan, Xia Jingbo. Parameter Searching in Attractor Algorithm for Community Detection —an Application in Pathway Enrichment Analysis. Journal of Physics: Conference Series, 2018, 1069: 012051.秦璇
7） Fang Alex Chengyu, Liu Yemao, Lu Yaping, Cao Jing, Xia Jingbo. A corpus-oriented perspective on terminologies of side effect and adverse reaction in support of text retrieval for drug repurposing. International Journal of Data Mining and Bioinformatics, 2018, 21(3):269-286.柳叶茂，陆亚平
8） Wang Maojun, Wang Pengcheng, Lin Min*, Ye Zhengxiu, Li Guoliang, Tu Lili, Shen Chao, Li Jianying, Yang Qingyong*, Zhang Xianlong*. Evolutionary dynamics of 3D genome architecture following polyploidization in cotton. Nature plants,2018,4(2):90-97.
9） Yuan Jialan, Wang Zhao, Xing Junjie, Yang Qingyong, Chen XiaoLin*. Genome-wide Identification and characterization of circular RNAs in the rice blast fungus Magnaporthe oryzae. Scientific reports,2018, 8(1): 6757.
10） Hu Limin, Zhang Hao, Yang Qingyong, Meng Qingwei, Han Shaoqing, Nwafor Chinedu Charles, Khan Muhammad Hafeez Ullah, Fan Chuchuan*, Zhou Yongming. Promoter variations in a homeobox gene, BnA10.LMI1, determine lobed leaves in rapeseed (Brassica napus L.). TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2018, 8: 2699-2708.
11） Quan Yuan#, Liu Mengyuan#, Liu Yemao, Zhu Lida, Wu Yushan, Luo Zhihui, Zhang Xiuzhen, Xu Shizhong, Yang Qingyong*, Zhang Hongyu*. Facilitating Anti-Cancer Combinatorial Drug Discovery by Targeting Epistatic Disease Genes. Molecules, 2018, 23(4):736-749.
12）Xie Fei, Yuan Jialan, Li Yiliao, Wang Canjie, Tang Hongyu, Xia Junhui, Yang Qingyong, Wan Zhengjie*. Transcriptome Analysis Reveals Candidate Genes Associated with Leaf Etiolation of a Cytoplasmic Male Sterility Line in Chinese Cabbage (Brassica Rapa L. ssp. Pekinensis). International journal of molecular sciences, 2018, 19(4). pii: E922.
13）Jin Jianjun#, Lv Wei#, Xia Pan, Xu Zaiyan, Zheng Andai, Wang Xiaojing, Wang Shanshan, Zeng Rui, Luo Hongmei, Li Guoliang, Zuo Bo*. Long noncoding RNA SYISL regulates myogenesis by interacting with polycomb repressive complex 2. Proceedings of the National Academy of Sciences of the United States of America, 2018, 115(42): 9802-9811.
14）Xu Qinhan#, Guan Pengpeng#, Zhang Ting, Lu Chang, Li Guoliang, Liu Jingxia*. Silver nanoparticles impair zebrafish skeletal and cardiac myofibrillogenesis and sarcomere formation Aquatic Toxicology, 2018, 200:102-113.
15）Lin Da#, Hong Ping#, Zhang Siheng, Xu Weize, Muhammad Jamal, Yan Keji, Lei Yingying, Li Liang, Ruan Yijun, Li Guoliang*, Cao Gang*. Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture. Nature Genetics, 2018, 50(5): 754–763.
16）Liu Haifeng#, Luo Cheng#, Song Wu#, Shen Haitao#, Li Guoliang, He Zhigang, Chen Wengang, Cao Yanyan, Huang Fang, Tang Shouwu, Hong Ping, Zhao Enfeng, Zhu Jianbo, He Dajun, Wang Shaoming, Huo Guang-Ying, Liu Hailiang*. Flavonoid biosynthesis controls fiber color in naturally colored cotton. PeerJ, 2018, 6(10):e4537.
17） Song Jiaming, Yang Lei, Shu Chengcheng, Ding Yuduan, Xing Feng, Liu Hao, Wang Jia, Xie Weibo, Zhang Jianwei*, Chen Lingling*. Rice Information GateWay: A Comprehensive Bioinformatics Platform for Indica Rice Genomes. Molecular Plant, 2018, 11(3): 505-507.
18）Bie Lihua, Du Likai, Yuan Qiaoxia*, Gao Jun*. How a single 5-methylation of cytosine regulates the recognition of C/EBPβ transcription factor: a molecular dynamic simulation study. Journal of Molecular Modeling,2018, 24(7):159.
19）Yu Guangqiang, Li Dongzhen, Lu Yulin, Wang Yaqi, Kong Dexin*, Wang Manqun*. Deciphering the Odorant Binding, Activation, and Discrimination Mechanism of Dhelobp21 from Dastarus Helophoroides. Scientific reports, 2018, 8(1):13506.
20）Kong Dexin#*, Lv Fang#, Hu Ben, Cao Limin*. Theoretical Calculation and Experimental Verification Demonstrated the Impossibility of Finding Haptens Identifying Triphenylmethane Dyes and Their Leuco Metabolites Simultaneously. Molecules, 2018, 23(3): 633.
21）Wang Long, Guo Jing, Chang Jiwei, Muhammad Tahir ul Qamar, Chen Lingling*. Inference of Transcriptional Regulation from Expression Data Using Model Integration. Current Bioinformatics, 2018, 13(4):426-434.
22） Wen Zi, Huang Zhitao, Zhang Ran, Peng Cheng*. ZNF143 is a regulator of chromatin loop. Cell biology and toxicology, 2018, 34(6): 471-478.
23）Quan Yuan#, Wang Zhongyi#, Chu Xinyi, Zhang Hongyu*. Evolutionary and genetic features of drug targets. Medicinal Research Reviews, 2018, 38(5):1536-1549.
24）Huo Yue, Zhang Hongyu*. Genetic Mechanisms of Asthma and the Implications for Drug Repositioning. Genes, 2018, 9(5):237-.
25）Zhang Cheng, Ni Pan, Ahmad Hafiz Ishfaq, Gemingguli M, Baizilaitibei A, Gulibaheti D, Fang Yaping, Wang Haiyang, Asif Akhtar Rasool, Xiao Changyi, Chen Jianhai, Ma Yunlong, Liu Xiangdong, Du Xiaoyong*, Zhao Shuhong. Detecting the Population Structure and Scanning for Signatures of Selection in Horses ( Equus caballus ) From Whole-Genome Sequencing Data. Evolutionary bioinformatics, 2018, 14: 117693431877510.
26）Shang Jun, Hu Ben, Wang Junmei, Zhu Feng, Kang Yu, Li Dan, Sun Huiyong, Kong Dexin, Hou Tingjun. Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products. J chem inf model 2018, 58, 1182-1193.

2017年科研成果

1） Xiong Xiong#, Duan Lingfeng#,Liu Lingbo, Tu Haifu,Yang Peng, Wu Dan, Chen Guoxing, Xiong Lizhong, Yang Wanneng* Liu Qian*. Panicle-SEG: a robust image segmentation method for rice panicles in the field based on deep learning and superpixel optimization. Plant Methods. 2017, 13:104.
2） Feng Hui, Chen Guoxing, Xiong Lizhong, Liu Qian*,Yang Wanneng*. Accurate Digitization of the Chlorophyll Distribution of Individual Rice Leaves Using Hyperspectral Imaging and an Integrated Image Analysis Pipeline. Front Plant Sci. 2017, 8: 1238.
3） Feng Hui#, Guo Zilong#, Yang Wanneng, Huang Chenglong, Chen Guoxing,Fang Wei, Xiong Xiong, Zhang Hongyu, Wang Gongwei, Xiong Lizhong*, Liu Qian*. An integrated hyperspectral imaging and genome-wide association analysis platform provides spectral and genetic insights into the natural variation in rice. Sci Rep. 2017, 7(1): 4401.
4） Chu Xin-Yi , Ling-Han Jiang, Xiong-Hui Zhou*, Ze-Jia Cui, Hong-Yu Zhang. Evolutionary origins of cancer driver genes and implications for cancer prognosis. Genes, 2017, 8: 182.
5） Qing-Ye Zhang*, Xin-Yi Chu, Ling-Han Jiang, Meng-Yuan Liu, Zhi-Ling Mei, Hong-Yu Zhang*. Identification of non-electrophilic Nrf2 activators from approved drugs. Molecules, 2017, 22, 883.
6） Xuan Xu, Hong-Yu Zhang*. The immunogenetics of psoriasis and implications for drug repositioning. Int. J. Mol. Sci., 2017, 18: 2650.
7） Yang Yi, Hu Xiaopan, Ma Binguang*. Construction and simulation of the Bradyrhizobium diazoefficiens USDA110 metabolic network: a comparison between free-living and symbiotic states. Mol Biosyst.2017,13(3):607-620.
8） Fang Liu, Likai Du*, Dongju Zhang, Jun Gao*. Direct Learning Hidden Excited State Interaction Patterns from ab initio Dynamics and Its Implication as Alternative Molecular Mechanism Models. Sci Rep., 2017, 7(1):8737.
9） Yiwen Guo, Jingnan Wang, Mingfei Zhu, Rui Zeng, Zaiyan Xu, Guoliang Li, Bo Zou*. Identification of MyoD-Responsive Transcripts Reveals a Novel Long Non-coding RNA (lncRNA-AK143003) that Negatively Regulates Myoblast Differentiation. Sci Rep. 2017, 7(1):2828.
10） Akhtar Rasool Asif*, Sumayyah Qadri, Nabeel Ijaz, Ruheena Javed, Abdur Rahman Ansari, Muhammd Awais, Muhammad Younus, Hasan Riaz, Xiaoyong Du*. Genetic signature of strong recent positive selection at interleukin-32 gene in goat. Asian-Australas J Anim Sci., 2017, 30(7): 912-919.
11） Yuan Quan, Le Xiong, Jing Chen, Hong-Yu Zhang*. Genetics-directed drug discovery for combating Mycobacterium tuberculosis infection. J. Biomol. Struct. Dyn., 2017, 35: 616-621.
12）Fang Liu, Likai Du*, Zhenggang Lan, Jun Gao*. Hydrogen bond dynamics governs the effective photoprotection mechanism of plant phenolic sunscreens. Photochem Photobiol Sci. 2017, 16(2):211-219.
13）Yaru Jing, Jun Gao, Chengbu Liu, Dongju Zhang*. Theoretical Insight into the Conversion Mechanism of Glucose to Fructose Catalyzed by CrCl2 in Imidazolium Chlorine Ionic Liquids. J Phys Chem B., 2017,121(9):2171-2178.
14）Mengmeng Dong, Jun Gao, Chengbu Liu, and Dongju Zhang*. DFT Study on the Formation Mechanism of Normal and Abnormal N-Heterocyclic Carbene-Carbon Dioxide Adducts from the Reaction of an Imidazolium-Based Ionic Liquid with CO2.J Phys Chem B., 2017, 121(44): 10276-10284.
15）Wang Xiaotao, Cui Wang, Peng Cheng*. HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions. Nucleic Acids Res. 2017, 45(19): e163.
16）Jun Shang, Huiyong Sun, Hui Liu, Fu Chen, Sheng Tian, Peichen Pan, Dan Li, Dexin Kong*, Tingjun Hou*. Comparative analyses of structural features and scaffold diversity for purchasable compound libraries. J Cheminform., 2017, 9(1):25.
17） Xia Wang#, Yuantao Xu#, Siqi Zhang#, Li Cao#, Yue Huang, Junfeng Cheng, Guizhi Wu, Shilin Tian, Chunli Chen, Yan Liu, Huiwen Yu, Xiaoming Yang, Hong Lan, Nan Wang, Lun Wang, Jidi Xu, Xiaolin Jiang, Zongzhou Xie, Meilian Tan, Robert M Larkin, Ling-Ling Chen, Bin-Guang Ma, Yijun Ruan, Xiuxin Deng, Qiang Xu*. Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction.Nat Genet. 2017,49(5):765-772.
18）Jing-Fen Tao, Jin-Zhi Zhou, Ting Xie, Xiao-Tao Wang, Qing-Yong Yang*, Hong-Yu Zhang. Influence of chromatin 3D organization on structural variations of the Arabidopsis thaliana genome. Mol. Plant, 2017, 10: 340-344.
19）Maojun Wang, Lili Tu, Min Lin, Zhongxu Lin, Pengcheng Wang, Qingyong Yang, Zhengxiu Ye, Chao Shen, Jianying Li, Lin Zhang, Xiaolin Zhou, Xinhui Nie, Zhonghua Li, Kai Guo, Yizan Ma, Cong Huang, Shuangxia Jin, Longfu Zhu, Xiyan Yang, Ling Min, Daojun Yuan, Qinghua Zhang, Keith Lindsey*, Xianlong Zhang*. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat Genet. 2017, 49(4):579-587.
20）Hao Liu, Yuduan Ding, Yanqing Zhou, Wenqi Jin, Kabin Xie*, Ling-Ling Chen*. CRISPR-P 2.0: An Improved CRISPR-Cas9 Tool for Genome Editing in Plants. Mol Plant. 2017, 10(3): 530-532.
21）Xin-Yi Chu, Ye-Mao Liu, Hong-Yu Zhang*. Activating or inhibiting Nrf2? Trends Pharmacol. Sci., 2017, 38: 953-955.
22） Jiaming Song, Yang Lei, Chengcheng Shu, Yuduan Ding, Feng Xing, Hao Liu, Jia Wang, Weibo Xie, Jianwei Zhang*, Lingling Chen*. Rice Information GateWay: A Comprehensive Bioinformatics Platform for Indica Rice Genomes. Mol Plant. 2018, 11(3): 505-507.
23）Jing-Xia Liu⁎, Qin-Han Xua, Sen Lic, XueDong Yua, WenYe Liua, Gang Ouyang, Ting Zhang, Ling-Ling Chen. Transcriptional factors Eaf1/2 inhibit endoderm and mesoderm formation via suppressing TGF-β signaling. Biochim Biophys Acta Gene Regul Mech. 2017 , 1860(10):1103-1116.
24）罗开，周金枝，杨植全，杨庆勇，周永明. 甘蓝型油菜MAGIC群体结构分析. 中国油料作物学报，2017, 39(6): 746-753.

2016年科研成果

1） Wei Fang, Hui Feng, Wanneng Yang, Lingfeng Duan, Guoxing Chen, Lizhong Xiong and Qian Liu*. High-throughput volumetric reconstruction for 3D wheat plant architecture studies. J Innov Opt Heal Sci. 2016, 9(5): 1650037.
2） Xiuying Liang, Ke Wang, Chenglong Huang, Xuehai Zhang, Jianbing Yan, Wanneng Yang*. A high-throughput maize kernel traits scorer based on line-scan imaging. Measurement. 2016, 90: 453-460.
3） Fang Liu, Likai Du*, Dongju Zhang, Jun Gao*. Performance of density functional theory on the anisotropic halogen interactions and potential energy surface: Problems and possible solutions. Int J Quantum Chem. 2016, 116: 710-717.
4） Meng Xie, Lili Wang*, Fang Liu, Dongju Zhang, and Jun Gao*. Dynamic Conversion Between Se-N Covalent and Noncovalent Interactions. J Phys Chem C. 2016, 120: 9081-9088.
5） Hui Zhao, Changfeng Fang*, Jun Gao* and Chengbu Liu. Spin-state energies of heme-related models from spin-flip TDDFT calculations. Phys Chem Chem Ph. 2016, 18, 29486-29494.
6） Wei Zhu, Le Xiong, Jinming Peng, Xiangyi Deng, Jun Gao* and Chun-mei Li*. Structure-Dependent Membrane-Perturbing Potency of Four Proanthocyanidin Dimers on 3T3-L1 Preadipocytes. J Agr Food Chem. 2016, 64: 7022-7032.
7） Wei Zhu, LeXiong, Jinming Peng, Xiangyi Deng, JunGao* & Chun-mei Li*. Molecular Insight into Affinities of Gallated and Nongallated Proanthocyanidins Dimers to Lipid Bilayers. Sci Rep. 2016, 6: 37680.
8） Jing Guo, Hong Zhang, Cheng Wang, Ji-Wei Chang, Ling-Ling Chen*. Construction and analysis of a genome-scale metabolic network for Bacillus licheniformis WX-02. Res Microbiol . 2016 May;167(4):282-289.
9） Yi-Chao Han, Jia-Ming Song, Long Wang, Cheng-Cheng Shu, Jing Guo* & Ling-Ling Chen*. Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02. Sci Rep. 2016 Jan 19; 6:19486.
10） Xi-Wen Xu, Xiong-Hui Zhou, Rui-Ru Wang, Wen-Lei Peng, Yue An, and Ling-Ling Chen*. Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network. Sci Rep . 2016 Feb 10; 6:20715.
11） Jing Guo#, Xueping Jing#, Wen-Lei Peng#, Qiyu Nie#, Yile Zhai, Zongze Shao, Longyu Zheng, Minmin Cai, Guangyu Li, Huaiyu Zuo, Zhitao Zhang, Rui-Ru Wang, Dian Huang, Wanli Cheng, Ziniu Yu, Ling-Ling Chen,* and Jibin Zhang*. Comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in Pseudomonas putida strain 1A00316. Sci Rep. 2016 Jul 7; 6:29211.
12） Liuyang Cai, Huidan Chang, Yaping Fang, and Guoliang Li*. A Comprehensive Characterization of the Function of LincRNAs in Transcriptional Regulation Through Long-Range Chromatin Interactions. Sci Rep. 2016(6):36572.
13） Yaping Fang*, Yunlong Wang, Qin Zhu, Jia Wang, and Guoliang Li*. In silico identification of enhancers on the basis of a combination of transcription factor binding motif occurrences. Sci Rep. 2016(6):32476.
14） Jun Sun, Jia Wang, Dan Xiong, Jian Hu, and Rong Liu*. CRHunter: integrating multifaceted information to predict catalytic residues in enzymes. Sci Rep. 2016, 6:34044.
15） Yi-Ming He and Bin-Guang Ma*. Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution. Sci Rep. 2016; 6: 26737.
16） Hong-Rui Xu, Jun-Feng Cheng, Xiao-Pan Hu, Ying-Ying Chu, Bin-Guang Ma*. Are protein hubs faster folders? Exploration based on Escherichia coli proteome. Amino Acids. 2016, 48(12): 2747–2753.
17） Xia Wang#, Yuantao Xu#, Siqi Zhang#, Li Cao#, Yue Huang, Junfeng Cheng, Guizhi Wu, Shilin Tian, Chunli Chen, Yan Liu, Huiwen Yu, Xiaoming Yang, Hong Lan, Nan Wang, Lun Wang, Jidi Xu, Xiaolin Jiang, Zongzhou Xie, Meilian Tan, Robert M Larkin, Ling-Ling Chen, Bin-Guang Ma, Yijun Ruan, Xiuxin Deng & Qiang Xu*. Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction. Nat Genet. 2016, 49: 765- 772.
18） Ting Xie#, Qing-Yong Yang#, Xiao-Tao Wang, Aoife McLysaght*, Hong-Yu Zhang*. Spatial colocalization of human ohnolog pairs acts to maintain dosage-balance. Mol Biol Evol. 2016, 33(9):2368-75.
19） Xiaojuan Qi, Wenjie Tang, Shan Gao, Min Gao, Changshui Chen, and Qingye Zhang*. Design Synthesis and Biological Evaluation of Novel N-Nitro Acid Amide Derivatives as Lead Compounds of Herbicide. J Phys Chem. 2016, Article ID 8583765.
20） Ze-Jia Cui, Qing-Yong Yang, Hong-Yu Zhang, Qiang Zhu*and Qing-Ye Zhang*. Bioinformatics Identification of Drug Resistance-Associated Gene Pairs in Mycobacterium tuberculosis. Int J Mol Sci. 2016, 17, 1417-1425.
21） Ben Hu, Zheng-Kun Kuang, Shi-Yu Feng, Dong Wang, Song-Bing He and De-Xin Kong*. Three-Dimensional Biologically Relevant Spectrum (BRS-3D): Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors. Molecules. 2016, 21(11):1554.
22） Zheng-Kun Kuang, Shi-Yu Feng, Ben Hu, Dong Wang, Song-Bing He, De-Xin Kong*. Predicting subtype selectivity of dopamine receptor ligands with three-dimensional biologically relevant spectrum. Chem Biol Drug Des. 2016, 88(6): 859-872.
23） Song-Bing He, Ben Hu, Zheng-Kun Kuang, Dong Wang & De-Xin Kong*. Predicting Subtype Selectivity for Adenosine Receptor Ligands with Three-Dimensional Biologically Relevant Spectrum (BRS-3D). Sci Rep. 2016, 6:36595.
24） Bin Zhou#, Qi Sun#, and De-Xin Kong*. Predicting cancer-relevant proteins using an improved molecular similarity ensemble approach. Oncotarget. 2016, 7(22):32394-32407.
25） Jing Xu, Li Li, Jie Xiong, Aaron denDekker, Andrew Ye, Hacer Karatas, Liu Liu, He Wang, Zhaohui S Qin, Shaomeng Wang, and Yali Dou*. MLL1 and MLL1 fusion proteins have distinct functions in regulating leukemic transcription program. Cell Discovery. 2016, 2-16008.
26） Yuduan Ding, Hong Li, Ling-Ling Chen,* and Kabin Xie*. Recent Advances in Genome Editing Using CRISPR/Cas9. Front Plant Sci. 2016, 24;7:703.
27） Jianwei Zhang, Ling-Ling Chen, Feng Xing, David A. Kudrna, Wen Yao, Dario Copetti, Ting Mu, Weiming Li, Jia-Ming Song, Weibo Xie, Seunghee Lee, Jayson Talag, Lin Shao, Yue An, Chun-Liu Zhang, Yidan Ouyang, Shuai Sun, Wen-Biao Jiao, Fang Lv, Bogu Du, Meizhong Luo, Carlos Ernesto Maldonado, Jose Luis Goicoechea, Lizhong Xiong, Changyin Wu, Yongzhong Xing, Dao-Xiu Zhou, Sibin Yu, Yu Zhao, Gongwei Wang, Yeisoo Yu, Yijie Luo, Zhi-Wei Zhou, Beatriz Elena Padilla Hurtado, Ann Danowitz, Rod A. Wing*, and Qifa Zhang*. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proc Natl Acad Sci U S A. 2016, 113(35): E5163-71.
28） Jianwei Zhang#, Ling-Ling Chen#, Shuai Sun, Dave Kudrna, Dario Copetti, Weiming Li, Ting Mu, Wen-Biao Jiao, Feng Xing, Seunghee Lee, Jayson Talag, Jia-Ming Song, Bogu Du, Weibo Xie, Meizhong Luo, Carlos Ernesto Maldonado, Jose Luis Goicoechea, Lizhong Xiong, Changyin Wu, Yongzhong Xing, Dao-xiu Zhou, Sibin Yu, Yu Zhao, Gongwei Wang, Yeisoo Yu, Yijie Luo, Beatriz Elena Padilla Hurtado, Ann Danowitz, Rod A. Wing* & Qifa Zhang*. Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Sci Data. 2016, 3:160076.
29） Akhtar Rasool Asif, Sumayyah Qadri, Yuhua FU, MD. Abdul Alim, Zhenyang Wu, Nabeel Ijaz, Jianhua Cao, Ruheena Javed, Shakeel Ahmed, Muhammd Awais, Abdur Rahman Ansari* and Xiaoyong Du*. Single nucleotide polymorphisms in drb1, igf1 and ils associated with fecal egg count confers resistance against haemonchus contortus infection in goats. Pak J Agr Sci. 2016, Vol. 53(4), p963-970. 8p.
30） 马彬广. 蛋白折叠预测. 科学通报. 2016, 61(24): 2670-2680.
31） Jinshui Zheng, Donghai Peng, Ling Chen, Hualin Liu, Feng Chen, Mengci Xu, Shouyong Ju, Lifang Ruan, and Ming Sun*. The Ditylenchus destructor genome provides new insights into the evolution of plant parasitic nematodes. P Roy Soc B-Biol Sci. 2016, 283(1835): 20160942.
32） Xiaohui Niu#, Xuehai Hu#. Improved prediction of DNA-binding proteins using chaos game representation and random forest. Curr Bioinform. 2016, 11(2): 156-163.
33）Yuan Quan, Hongyu Zhang*. A chemical-genetic criterion for identifying disease biomarkers. Trends Mol. Med, 2016, 22: 447-448.

2015年科研成果

1） Jing Guo, Gang Cheng, Xiang-Yong Gou, Feng Xing, Sen Li, Yi-Chao Han, Long Wang, Jia-Ming Song, Cheng-Cheng Shu, Shou-Wen Chen*, Ling-Ling Chen*. Comprehensive transcriptome and improved genome annotation of Bacillus licheniformis WX-02. FEBS Lett., 2015, 589: 2372-2381.
2） Xiao-Tao Wang, Peng-Fei Dong, Hong-Yu Zhang, Cheng Peng*. Structural heterogeneity and functional diversity of topologically associating domains in mammalian genomes. Nucleic Acids Research, 2015, 43(15):7237-7246.
3） Xiaoxia Yang, Jia Wang, Jun Sun, Rong Liu*. SNBRFinder: A sequence-based hybrid algorithm for enhanced prediction of nucleic acid-binding residues. PLoS ONE. 2015, 10(7): e0133260.
4） Xiao-Pan Hu, Yi Yang, Bin-Guang Ma*, Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability. Sci Rep. 2015 Jun 9;5:11113. doi: 10.1038/srep11113.
5） Ting Xie, Jue-Fei Zheng, Sheng Liu, Cheng Peng, Yong-Ming Zhou, Qing-Yong Yang*, Hong-Yu Zhang. De novo plant genome assembly based on chromatin interactions: A case study of Arabidopsis thaliana. Mol. Plant, 2015, 8: 489-492.
6） Ting Xie, Liang-Yu Fu, Qing-Yong Yang, Heng Xiong, Hong-Rui Xu, Bin-Guang Ma*, Hong-Yu Zhang*. Spatial features for Escherichia coli genome organization. BMC Genomics, 2015, 16: 37.
7） Yao W, Li G, Zhao H, Wang G, Lian X, Xie W*. Exploring the rice dispensable genome using a metagenome-like assembly strategy. Genome Biology, 2015, doi: 10.1186/s13059-015-0757-3
8） Guoping Nie, Yong Li, Feichi Wang, Siwen Wang, Xuehai Hu*. A novel fractal approach for predicting G-protein–coupled receptors and their subfamilies with support vector machines. Bio-Medical Materials and Engineering, 26 (s1), 1829-1836, 2015.
9） Shou-Kai Kang, Bai-Xue Chen, Tian Tian, Xi-Shuai Jia, Xin-Yi Chu, Rong Liu, Peng-Fei Dong, Qing-Yong Yang, Hong-Yu Zhang*. ATP selection in a random peptide library consisting of prebiotic amino acids. Biochem. Biophys. Res. Commun., 2015, 466: 400-405.
10） Cheng Wang, Zhi-Luo Deng, Zhi-Ming Xie, Xin-Yi Chu, Ji-Wei Chang, De-Xin Kong, Bao-Ju Li, Hong-Yu Zhang, Ling-Ling Chen*. Construction of a genome-scale metabolic network of the plant pathogen Pectobacterium carotovorum provides new strategies for bactericide discovery. FEBS Lett., 2015, 589: 285-294.
11） Yaping Lu, Yemao Liu, Xiaohui Niu, Qingyong Yang, Xuehai Hu, Hong-Yu Zhang, Jingbo Xia*. Systems genetic validation of the SNP-metabolite association in rice via metabolite-pathway-based phenome-wide association scans. Front. Plant Sci., 2015, 6: 1027.
12） Xiaojuan Qi, Wenjun Deng, Min Gao, Bangqiang Mao, Shengzhen Xu, Changshui Chen, Qing Ye Zhang*. Novel lead compound optimization and synthesized based on the target structure of of Xanthomonasoryzaepv. oryzaeGlmU. Pestic. Biochem. Phys.122, 22–28, 2015(support by Nos. 30900935 and 21173092 and No. 2011PY039)
13） Wanneng Yang, Zilong Guo, Chenglong Huang, Ke Wang, Ni Jiang, Hui Feng, Guoxing Chen, Qian Liu and Lizhong Xiong*. Genome-wide association study of rice (Oryza sativa L.) leaf traits with a high-throughput leaf scorer. Journal of Experimental Botany, 2015. doi:10.1093/jxb/erv100
14） Lida Zhu, Fuxi Zhu*. Identification association of drug-disease by using functional gene module for breast cancer. BMC Medical Genomics 8. Suppl 2 (2015): S3. （会议论文）
15） Xianqin Hu, Xiaozhe Fu, Ningqiu Li, Xingxing Dong, Lijuan Zhao, Jiangfeng Lan, Wei Ji, Weidong Zhou, Taoshan Ai, Shuqin Wu, Li Lin*.Transcriptomic analysis of Mandarin fish brain cells infected with infectious spleen and kidney necrosis virus with an emphasis on retinoic acid-inducible gene 1-like receptors and apoptosis pathways. Fish & shellfish immunology (2015). 7
16） Zhi-Hu Pei, Ting Xie, Qing-Yong Yang*, Qing-Ye Zhang*,Hong-Yu Zhang, Novel Isoniazid-and Ethionamide-resistance loci in mycobacterium tuberculosis identified by phenome-wide association scans[C]//Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on. IEEE, 2015: 1129-1132.（会议论文）
17） Qiang Wang, Jun Gao, Dongju Zhang, Chengbu Liu*, A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism. Chemical Physics, 2015, 450: 1-11.
18） Feifei Zheng, Muhammad Asim, Jiangfeng Lan, Lijuan Zhao, Shun Wei, Nan Chen,Xiaoling Liu, Yang Zhou*, Li Lin*. Molecular Cloning and Functional Characterization of Mannose Receptor in Zebra Fish (Danio rerio) during Infection with Aeromonas sobria[J]. International journal of molecular sciences, 2015, 16(5): 10997-11012.
19） Jing Guo, Hong Zhang1, Cheng Wang, Ji-Wei Chang, Ling-Ling Chen*, Construction and analysis of a genome-scale metabolic network for Bacillus licheniformis WX-02[J]. Research in Microbiology, 2016.
20） Li-Da Zhu, Chang-Shou He,Ye-Mao Liu,Yuan Quan, Jing Chen,Qiang Zhu*,Qing-Ye Zhang*, Hong-Yu Zhang, Asystems chemical biology approach to identify targets of antibacterial agents: A case study of Chelerythrine and Rhein[C]//Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on. IEEE, 2015: 1047-1056.
21） Xiu-Zhe Zhang*, Yuan Quan, and Guang-Yan Tang*. Medical genetics-based drug repurposing for Alzheimer's disease[J]. Brain research bulletin, 2015, 110: 26-29.
22） Yuantao Xu, Guizhi Wu, Baohai Hao, Lingling Chen, Xiuxin Deng, Qiang Xu*. Identification, characterization and expression analysis of lineage-specific genes within sweet orange (Citrus sinensis). BMC genomics, 2015, 16(1): 995.
23） Yuduan Ding, Jiwei Chang, Qiaoli Ma, Lingling Chen, Shuzhen Liu, Shuai Jin, Jingwen Han, Rangwei Xu, Andan Zhu, Jing Guo, Yi Luo, Juan Xu, Qiang Xu, YunLiu Zeng, Xiuxin Deng and Yunjiang Cheng*. Network Analysis of Postharvest Senescence Process in Citrus Fruits Revealed by Transcriptomic and Metabolomic Profiling. Plant physiology, 2015, 168(1): 357-376.
24） Hao Zhang, Jun Sun, Jing Ye, Usama Ashraf, Zheng Chen, Bibo Zhu,WenHe, Qiuping Xu, Yanming Wei, Huanchun Chen, Zhen F. Fu, Rong Liu*,Shengbo Cao. Quantitative Label-Free Phosphoproteomics Reveals Differentially Regulated Protein Phosphorylation Involved in West Nile Virus-Induced Host Inflammatory Response. Journal of proteome research, 2015, 14(12): 5157-5168.
25） Hongchu Wang, Xuehai Hu*. Accurate prediction of nuclear receptors with conjoint triad feature，BMC bioinformatics, 2015, 16(1): 1.
26） Lingfeng Duan, Chenglong Huang, Guoxing Chen, Lizhong Xiong, Qian Liu, Wanneng Yang*. High-throughput estimation of yield for individual rice plant using multi-angle RGB imaging, 2015（EI收录, in press）
梁秀英，李小昱，杨万能*。奇异数据筛选法在玉米籽粒蛋白质近红外光谱检测中的应用。激光生物学报，2015,24（1）：38-45. （中文核心）

2014年科研成果

1. Xiao-Xia Yang, Zhi-Luo Deng, Rong Liu. (2014) RBRDetector: improved prediction of binding residues on RNA-binding protein structures using complementary feature- and template-based strategies. Proteins, 82(10): 2455-71.
2. Xiao-Hui Niu, Xue-Hai Hu*, Feng Shi, Jing-Bo Xia. (2014) Predicting DNA binding proteins using support vector machine with hybrid fractal features. J Theor Biol., 21(343): 186-92.
3. Alexander Goncearenco, Bin-Guang Ma, Igor N. Berezovsky*. (2014) Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins. Nucleic Acids Res., 42(5): 2879-92.
4. Jieli Peng, Baohai Hao, Liu Liu, Shanming Wang, Binguang Ma, Yi Yang, Fuli Xie, Youguo Li*. (2014) RNA-Seq and microarrays analyses reveal global differential transcriptomes of Mesorhizobium huakuii 7653R between bacteroids and free-living cells. PLoS One., 9(4): e93626.
5. Shanming Wang, Baohai Hao, Jiarui Li, Huilin Gu, Jieli Peng, Fuli Xie, Xinyin Zhao, Christian Frech, Nansheng Chen*,Binguang Ma*, Youguo Li*. (2014) Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics. BMC Genomics, 15:440.
6. Heng Xiong, Yi Yang, Xiao-Pan Hu, Yi-Ming He, Bin-Guang Ma*. (2014) Sequence determinants of prokaryotic gene expression level under heat stress. Gene, 551(1): 92-102.
7. 彭城, 李国亮, 张红雨, 阮一骏*.(2014) 染色质三维结构重建及其生物学意义.中国科学:生命科学, 8: 794-802.
8. Jia Wang#, Dijun Chen#, Yang Lei#, Ji-Wei Chang, Bao-Hai Hao, Feng Xing, Sen Li, Qiang Xu, Xiu-Xin Deng, Ling-Ling Chen*. (2014) Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome. PLoS One, 9(1): e87723.
9. Yang Lei, Li Lu, Hai-Yang Liu, Sen Li, Feng Xing, Ling-Ling Chen*. (2014) CRISPR-P: a web tool for synthetic single-guide RNA design of CRISPR-system in plants. Mol Plant., 7(9):1494-6.
10. Feng-Biao Guo, Yan Lin, Ling -Ling Chen*. (2014) Recognition of Protein-coding Genes Based on Z-curve Algorithms. Curr Genomics., 15(2):95-103.
11. Yu-Duan Ding, Ji-Wei Chang, Jing Guo, DiJun Chen, Sen Li, Qiang Xu, Xiu-Xin Deng, Yun-Jiang Cheng*, Ling-Ling Chen*. (2014) Prediction and functional analysis of the sweet orange protein-protein interaction network. BMC Plant Biol., 14:213.
12. Wanneng Yang#, Zilong Guo#, Chenglong Huang#, Lingfeng Duan#, Guoxing Chen#, Ni Jiang, Wei Fang, Hui Feng, Weibo Xie, Xingming Lian, Gongwei Wang, Qingming Luo, Qifa Zhang, Qian Liu*, Lizhong Xiong* (2014) Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice. Nat Commun., 5:5087.
13. 李国亮, 阮一骏, 谷瑞升, 杜生明. (2014) 起航三维基因组学研究. 科学通报, 13: 1165-1172.
14. Liang Niu, Guoliang Li, and Shili Lin*. (2014) Statistical models for detecting differential chromatin interactions mediated by a protein. PLoS One, 9(5): e97560.
15. Hui-Yong Sun, Ting-Jun Hou*, Hong-Yu Zhang*. (2014) Finding chemical drugs for genetic diseases. Drug Discov. Today, 19: 1836-1840.
16. Yuan Quan, Zhong-Yi Wang, Min Xiong, Zheng-Tao Xiao, Hong-Yu Zhang*. (2014) Dissecting traditional Chinese medicines by omics and bioinformatics. Nat. Prod. Commun., 9: 1391-1396.
17. Xiu-Zhen Zhang*, Ling Wang, Dong-Wu Liu, Guang-Yan Tang, Hong-Yu Zhang. (2014) Synergistic inhibitory effect of berberine and d-limonene on human gastric carcinoma cell line MGC803. J. Med. Food, 17: 955-962.
18. Bin Li, Min Xiong, Hong-Yu Zhang*. (2014) Elucidating polypharmacological mechanisms of polyphenols by gene module profile analysis. Int. J. Mol. Sci., 15: 11245-11254.
19. You-Min Sun, Zheng-Tao Xiao, Hong-Yu Zhang*. (2014) Structure-activity relationships of tanshinones in activating Nrf2. A DFT study and implications for multifunctional antioxidant discovery. Nat. Prod. Commun., 9: 453-454.
20. Zheng-Tao Xiao, Qiang Zhu, Hong-Yu Zhang*. (2014) Identifying antibacterial targets of flavonoids by comparative genomics and molecular modeling. Open J. Genomics, 3: 1.
21. Dijun Chen, Liang-Yu Fu, Zhao Zhang, Guoliang Li, Hang Zhang, Li Jiang, Andrew P. Harrison, Hugh P. Shanahan, Christian Klukas, Hong-Yu Zhang, Yijun Ruan*, Ling-Ling Chen*, Ming Chen*. Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Res., 2014, 42: 3028-3043.
22. Min Xiong, Bin Li, Qiang Zhu, Yun-Xing Wang, Hong-Yu Zhang*. (2014) Identification of transcription factors for drug-associated gene modules and biomedical implications. Bioinformatics, 30: 305-309.
23. Zhong-Yi Wang, Yuan Quan, Hong-Yu Zhang*. (2014) Medical genetic inspirations for anticancer drug repurposing. Trends Pharmacol. Sci., 35: 1-3.
24. Haodong Chen#, Weibo Xie#, Hang He#, Huihui Yu#, Wei Chen, Jing Li, Renbo Yu, Yue Yao, Wenhui Zhang, Yuqing He, Xiaoyan Tang*, Fasong Zhou*, Xing Wang Deng*, Qifa Zhang*. (2014) A high-density SNP genotyping array for rice biology and molecular breeding. Mol Plant.7(3): 541-53.
25. Huihui Yu#, Weibo Xie#, Jing Li, Fasong Zhou*. Qifa Zhang*. (2014) A whole-genome SNP array (RICE6K) for genomic breeding in rice. Plant Biotechnol J., 12(1): 28-37.
26. Wei Chen#, Yanqiang Gao#, Weibo Xie#, Liang Gong#, Kai Lu#, Wensheng Wang#, Yang Li, Xianqing Liu, Hongyan Zhang, Huaxia Dong, Wan Zhang, Lejing Zhang, Sibin Yu, Gongwei Wang, Xingming Lian*, Jie Luo*. (2014) Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Nat Genet., 46(7): 714-21.
27. Jingnan Jin, Xiaojuan Qi, Dandan Yao, Bangqiang Mao, Jianhong Li, Qingye Zhang*, Changshui Chen*. (2014) Rational design and screening study of novel lead compound based on acetohydroxyacid synthase structure. Chem Biol Drug Des., 84(3):316-24.
28. Xia-Li Yue, Hu Li, Shuang-Shuang Liu, Qing-Ye Zhang, Jing-Jing Yao, Fei-Yan Wang. (2014) N-Fluorinated phenyl-N′-pyrimidyl urea derivatives: Synthesis, biological evaluation and 3D-QSAR study. Chinese Chem. Lett., 25(7): 1069–1072.