基本信息

刘长宁  男  博导  中国科学院西双版纳热带植物园
电子邮件: liuchangning@xtbg.ac.cn
通信地址: 云南省西双版纳州勐腊县勐仑镇中科院植物园科研中心
邮政编码: 666303

研究领域

主要从事生物信息学相关研究工作,特别是与非编码基因以及生物复杂网络相关的研究工作。目前研究组主要研究内容围绕云南省丰富的药用植物和经济植物资源展开,利用生物信息学和系统生物学方法,从事基于高通量测序数据分析结合分子生物学实验的非模式植物功能基因组研究,包括:相关数据库、软件、算法的设计开发;非模式植物重要分子通路的解析;重要药用植物和经济植物功能基因组的研究。

招生信息

中科院西双版纳热带植物园硕士研究生考试科目(2022):

植物学:101思想政治理论、201英语一、621植物学、853遗传学

生物与医药:101思想政治理论、201英语一、338生物化学、846普通生物学


同时在中国科学技术大学招收研究生(考试科目信息见官网),欢迎报考。


招收保研学生(中科院西双版纳热带植物园和中国科学技术大学),欢迎有保研资格同学联系。

教育背景

2006-06--2007-01   哈佛大学Dana Farber癌症研究所   访问学生
2002-09--2007-07   中国科学院计算技术研究所   博士
1996-09--2000-07   武汉大学   学士

工作经历

   
工作简历
2014-11~现在, 中国科学院西双版纳热带植物园, 研究员
2011-01~2013-01,德克萨斯大学达拉斯分校, 访问学者
2010-10~2014-10,中国科学院计算技术研究所, 副研究员
2007-07~2010-09,中国科学院计算技术研究所, 助理研究员
社会兼职
2020-01-01-今,中国医药质量管理协会临床试验及大数据质量管理分会, 委员
2020-01-01-今,中国细胞生物学学会植物器官发生分会, 委员
2020-01-01-今,Frontiers in Genetics, 客座副编辑
2019-04-30-今,Scientific Reports, Editorial Board, Editorial Board Member
2013-05-01-今,中科院数学、计算机与生命科学交叉研究青年论坛, 组委会成员
2011-06-01-今,中国科学院青年创新促进会, 会员
2010-10-01-今,Asia Pacific Bioinformatics Network , 会员

教授课程

生物信息学

专利与奖励

   
奖励信息
(1) 中国科学院卢嘉锡青年人才奖, , 院级, 2008
(2) 中国科学院院长优秀奖学金, , 院级, 2007
(3) 中国科学院计算技术研究所所长奖学金, , 研究所(学校), 2006
(4) 中国科学院研究生院优秀研究生奖学金, , 院级, 2003
专利成果
[1] 刘长宁, 李菁, 胡翔, 马菊莲. 一种治疗肝损伤的滇重楼总皂苷肠溶缓释制剂及其制备方法. CN: CN110538261A, 2019-12-06.

[2] 刘长宁, 李菁, 胡翔, 黄招琴, 马菊莲. 一种诱导增强CIK细胞的滇重楼多糖组合物及其应用. CN: CN110592015A, 2019-12-20.

[3] 刘帮强, 刘长宁, 李恒. 一种长柱重楼的培育方法. CN: CN107637411A, 2018-01-30.

出版信息

   
发表论文
[1] Liangliang He, Ye Liu, Yawen Mao, Xinyuan Wu, Xiaoling Zheng, Weiyue Zhao, Xiaoyu Mo, Ruoruo Wang, Qinq Wu, Dongfa Wang, Youhan Li, Yuanfan Yang, Quanzi Bai, Xiaojia Zhang, Shaoli Zhou, Baolin Zhao, Changning Liu, Yu Liu, Million Tadege, Jianghua Chen. GRAS transcription factor PINNATE-LIKE PENTAFOLIATA2 controls compound leaf morphogenesis in Medicago truncatula. THE PLANT CELL. 2024, 第 17 作者36(5): 1755-1776, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11062474/.
[2] Zitian Yang, Zexin Zhang, Jing Li, Wen Chen, Changning Liu. CRISPRlnc: a machine learning method for lncRNA-specific single-guide RNA design of CRISPR/Cas9 system.. Briefings in Bioinformatics[J]. 2024, 第 5 作者  通讯作者  null(null): 
[3] Jiazhi Liu, Yan Li, Jing Li, Wen Chen, Bangzhen Pan, Aizhong Liu, ZengFu Xu, Wei Xu, Changning Liu. EupDB: An integrative and comprehensive functional genomics data hub for Euphorbiaceae plants. PLANT COMMUNICATIONS[J]. 2024, 第 9 作者  通讯作者  5(1): http://dx.doi.org/10.1016/j.xplc.2023.100683.
[4] Jiang, Lihui, Yao, Baolin, Zhang, Xiaoyan, Wu, Lixia, Fu, Qijing, Zhao, Yiting, Cao, Yuxin, Zhu, Ruomeng, Lu, Xinqi, Huang, Wuying, Zhao, Jianping, Li, Kuixiu, Zhao, Shuanglu, Han, Li, Zhou, Xuan, Luo, Chongyu, Zhu, Haiyan, Yang, Jing, Huang, Huichuan, Zhu, Zhengge, He, Xiahong, Friml, Jiri, Zhang, Zhongkai, Liu, Changning, Du, Yunlong. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. PLANT JOURNAL[J]. 2023, 第 24 作者  通讯作者  115(1): 155-174, http://dx.doi.org/10.1111/tpj.16218.
[5] Mao, Yawen, Shaoli Zhou, JIng Yang, Jiangqi Wen, Dongfa Wang, Xuan Zhou, Xinyuan Wu, Liangliang He, Mingli Liu, Huan Wu, Liling Yang, Baolin Zhao, Million Tadege, Yu Liu, 刘长宁, Jianghua Chen. The MIO1-MtKIX8 module regulates the organ size in Medicago truncatula.. Physiologia Plantarum[J]. 2023, 第 15 作者  通讯作者  null(null): 
[6] Wenjing Yang, Quanzi Bai, Yan Li, Jianghua Chen, Changning Liu. Epigenetic modifications: Allusive clues of lncRNA functions in plants. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL[J]. 2023, 第 5 作者  通讯作者  21(null): 1989-1994, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10025020/.
[7] 刘嘉智, 刘长宁. 橡胶树种子性状相关基因的预测与功能研究. 热带农业科技. 2023, 第 2 作者46(3): 42-48, http://lib.cqvip.com/Qikan/Article/Detail?id=7110014224.
[8] Chen, Wen, Li, Jing, Huang, Shulan, Li, Xiaodeng, Zhang, Xuan, Hu, Xiang, Xiang, Shuanglin, Liu, Changning. GCEN: An Easy-to-Use Toolkit for Gene Co-Expression Network Analysis and lncRNAs Annotation. CURRENT ISSUES IN MOLECULAR BIOLOGY[J]. 2022, 第 8 作者  通讯作者  44(4): 1479-1487, http://dx.doi.org/10.3390/cimb44040100.
[9] Bai, Quanzi, Yang, Wenjing, Qin, Guochen, Zhao, Baolin, He, Liangliang, Zhang, Xuan, Zhao, Weiyue, Zhou, Dian, Liu, Ye, Liu, Yu, He, Hua, Tadege, Million, Xiong, Yan, Liu, Changning, Chen, Jianghua. Multidimensional Gene Regulatory Landscape of Motor Organ Pulvinus in the Model Legume Medicago truncatula. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES[J]. 2022, 第 14 作者  通讯作者  23(8): http://dx.doi.org/10.3390/ijms23084439.
[10] Wang, Jie, Jiang, Xiaoke, Bai, Hanrui, Liu, Changning. Genome-wide identification, classification and expression analysis of the JmjC domain-containing histone demethylase gene family in Jatropha curcas L.. SCIENTIFIC REPORTS[J]. 2022, 第 4 作者  通讯作者  12(1): https://doaj.org/article/8fd8e565de394aeb808df66dd1476126.
[11] 蒋晓可, 刘长宁. 紫花苜蓿基因编辑数据库(AlfalfaGEDB)的应用研究--以MsHB7和MsPALM1为例. 热带农业科技[J]. 2022, 第 2 作者45(3): 49-54, http://lib.cqvip.com/Qikan/Article/Detail?id=7107583685.
[12] Gao, Xiaoyang, Su, Qixuan, Li, Jing, Yang, Wenjing, Yao, Baolin, Guo, Jiawei, Li, Shengying, Liu, Changning. RNA-Seq analysis reveals the important co-expressed genes associated with polyphyllin biosynthesis during the developmental stages of Paris polyphylla. BMC GENOMICS[J]. 2022, 第 8 作者  通讯作者  23(SUPPL 1): http://dx.doi.org/10.1186/s12864-022-08792-2.
[13] Qi Jin, Zitian Yang, Wenjing Yang, Xiaoyang Gao, Changning Liu, Noe FernandezPozo, M Gonzalo Claros. Genome-Wide Identification and Analysis of Lbd Transcription Factor Genes in Jatropha curcas and Related Species. PLANTS. 2022, 第 5 作者11(18): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9504267/.
[14] Zhao, Yiting, Wu, Lixia, Fu, Qijing, Wang, Dong, Li, Jing, Yao, Baolin, Yu, Si, Jiang, Li, Qian, Jie, Zhou, Xuan, Han, Li, Zhao, Shuanglu, Ma, Canrong, Zhang, Yanfang, Luo, Chongyu, Dong, Qian, Li, Saijie, Zhang, Lina, Jiang, Xi, Li, Youchun, Luo, Hao, Li, Kuixiu, Yang, Jing, Luo, Qiong, Li, Lichi, Peng, Sheng, Huang, Huichuan, Zuo, Zhili, Liu, Changning, Wang, Lei, Li, Chengyun, He, Xiahong, Friml, Jiri, Du, Yunlong. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. PLANT CELL AND ENVIRONMENT[J]. 2021, 第 29 作者44(6): 1846-1857, http://dx.doi.org/10.1111/pce.14029.
[15] Jin, GuiHua, Zhou, YanLi, Yang, Hong, Hu, YanTing, Shi, Yong, Li, Ling, Siddique, Abu N, Liu, ChangNing, Zhu, AnDan, Zhang, ChengJun, Li, DeZhu. Genetic innovations: Transposable element recruitment and de novo formation lead to the birth of orphan genes in the rice genome. JOURNAL OF SYSTEMATICS AND EVOLUTION[J]. 2021, 第 8 作者59(2): 341-351, http://sciencechina.cn/gw.jsp?action=detail.jsp&internal_id=6932052&detailType=1.
[16] 张頔, 高晓阳, 张轩, 刘长宁. 花发育相关基因分子进化与花发育调控网络拓扑中心性的相关性研究. 安徽农业科学[J]. 2021, 第 4 作者49(8): 1-4, http://lib.cqvip.com/Qikan/Article/Detail?id=7104450789.
[17] Sang, Shiye, Chen, Wen, Zhang, Di, Zhang, Xuan, Yang, Wenjing, Liu, Changning. Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants. BMC GENOMICS[J]. 2021, 第 6 作者  通讯作者  22(SUPPL 3): http://dx.doi.org/10.1186/s12864-021-08047-6.
[18] Xuan Zhang, Jing Li, BangZhen Pan, Wen Chen, Maosheng Chen, Mingyong Tang, ZengFu Xu, Changning Liu. Extended mining of the oil biosynthesis pathway in biofuel plant Jatropha curcas by combined analysis of transcriptome and gene interactome data. BMC BIOINFORMATICS[J]. 2021, 第 8 作者  通讯作者  22(SUPPL 6): 
[19] Chen, Lin, Li, Huimin, Xie, Longxiang, Zuo, Zhanjie, Tian, Liqing, Liu, Changning, Guo, Xiangqian. Editorial: Big Data and Machine Learning in Cancer Genomics. FRONTIERS IN GENETICS[J]. 2021, 第 6 作者  通讯作者  12: http://dx.doi.org/10.3389/fgene.2021.749584.
[20] 桑世叶, 任强, 吴霜寒, 刘长宁. 植物长非编码RNA进化相关研究进展. 安徽农业科学[J]. 2020, 第 4 作者48(22): 19-24, http://lib.cqvip.com/Qikan/Article/Detail?id=7103322916.
[21] 任强, 桑世叶, 刘长宁. 重楼属植物在线分类鉴定系统的设计与实现. 计算机时代[J]. 2020, 第 3 作者72-75, http://lib.cqvip.com/Qikan/Article/Detail?id=7102713313.
[22] Wang, Jun, Zhang, Xuan, Chen, Wen, Hu, Xiang, Li, Jing, Liu, Changning. Regulatory roles of long noncoding RNAs implicated in cancer hallmarks. INTERNATIONAL JOURNAL OF CANCER. 2020, 第 6 作者  通讯作者  146(4): 906-916, https://www.webofscience.com/wos/woscc/full-record/WOS:000578788100003.
[23] Li, Jing, Gao, Xiaoyang, Zhang, Xuan, Liu, Changning. Dynamic Expansion and Functional Evolutionary Profiles of Plant Conservative Gene Family SBP-Box in Twenty Two Flowering Plants and the Origin of miR156. BIOMOLECULES[J]. 2020, 第 4 作者  通讯作者  10(5): http://dx.doi.org/10.3390/biom10050757.
[24] Li, Jing, Zhang, Xuan, Liu, Changning. The computational approaches of lncRNA identification based on coding potential: Status quo and challenges. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL[J]. 2020, 第 3 作者  通讯作者  18: 3666-3677, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7710504/.
[25] Gao, Xiaoyang, Zhang, Xuan, Chen, Wen, Li, Jing, Yang, Wenjing, Zhang, Xingwang, Li, Shengying, Liu, Changning. Transcriptome analysis of Paris polyphylla var. yunnanensis illuminates the biosynthesis and accumulation of steroidal saponins in rhizomes and leaves. PHYTOCHEMISTRY[J]. 2020, 第 8 作者  通讯作者  178: http://dx.doi.org/10.1016/j.phytochem.2020.112460.
[26] Li, Jing, Liu, Changning. Coding or Noncoding, the Converging Concepts of RNAs. FRONTIERS IN GENETICS. 2019, 第 2 作者  通讯作者  10(X): https://doaj.org/article/91073bca590c4f94a7d3a46a418bc52b.
[27] Chen, Wen, Zhang, Guoqiang, Li, Jing, Zhang, Xuan, Huang, Shulan, Xiang, Shuanglin, Hu, Xiang, Liu, Changning. CRISPRlnc: a manually curated database of validated sgRNAs for lncRNAs. NUCLEIC ACIDS RESEARCH[J]. 2019, 第 8 作者  通讯作者  47(D1): D63-D68, http://ir.xtbg.org.cn/handle/353005/11221.
[28] Liu Zhangning. Regulatory roles of long non-coding RNAs implicated in cancer hallmarks. International Journal of Cancer. 2019, 第 1 作者  通讯作者  
[29] Zhang, Xuan, Li, Tianjun, Wang, Jun, Li, Jing, Chen, Long, Liu, Changning. Identification of Cancer-Related Long Non-Coding RNAs Using XGBoost With High Accuracy. FRONTIERS IN GENETICS[J]. 2019, 第 6 作者  通讯作者  10: https://doaj.org/article/e0b11b39233c46cea30da4bcc751c4e8.
[30] 李岸林, 刘长宁. 基于Snakemake构建非模式生物转录组分析框架. 绿色科技[J]. 2019, 第 2 作者207-210, http://lib.cqvip.com/Qikan/Article/Detail?id=7002679460.
[31] Zhang, Xuan, Pan, BangZhen, Chen, Maosheng, Chen, Wen, Li, Jing, Xu, ZengFu, Liu, Changning. JCDB: a comprehensive knowledge base for Jatropha curcas, an emerging model for woody energy plants. BMC GENOMICS[J]. 2019, 第 7 作者  通讯作者  20(Suppl 9): https://doaj.org/article/ff9e168f3f1d456fb98392b07a33d780.
[32] Jing Li, Xiaoyang Gao, Shiye Sang, Changning Liu. Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in Euphorbiaceae. BMC GENOMICS[J]. 2019, 第 11 作者20(S9): 1-15, http://dx.doi.org/10.1186/s12864-019-6319-4.
[33] Zhang, Wei, Du, Lei, Qu, Zepeng, Zhang, Xingwang, Li, Fengwei, Li, Zhong, Qi, Feifei, Wang, Xiao, Jiang, Yuanyuan, Men, Ping, Sun, Jingran, Cao, Shaona, Geng, Ce, Qi, Fengxia, Wan, Xiaobo, Liu, Changning, Li, Shengying. Compartmentalized biosynthesis of mycophenolic acid. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA[J]. 2019, 第 16 作者116(27): 13305-13310, http://ir.xtbg.org.cn/handle/353005/11335.
[34] Wang, Peipei, Li, Jing, Gao, Xiaoyang, Zhang, Di, Li, Anlin, Liu, Changning. Genome-Wide Screening and Characterization of the Dof Gene Family in Physic Nut (Jatropha curcas L.). INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES[J]. 2018, 第 6 作者  通讯作者  19(6): https://doaj.org/article/dd684dcfb5634df499eeedd529094e1b.
[35] Wang, Jun, Zhang, Xuan, Chen, Wen, Li, Jing, Liu, Changning. CRlncRNA: a manually curated database of cancer-related long non-coding RNAs with experimental proof of functions on clinicopathological and molecular features. BMC MEDICAL GENOMICS[J]. 2018, 第 5 作者  通讯作者  11(S6): https://doaj.org/article/89e78a9d6684487d83fbf91f1934ac0b.
[36] Li, Yueying, He, Liangliang, Li, Jing, Chen, Jianghua, Liu, Changning. Genome-Wide Identification, Characterization, and Expression Profiling of the Legume BZR Transcription Factor Gene Family. FRONTIERS IN PLANT SCIENCE[J]. 2018, 第 5 作者  通讯作者  9: https://doaj.org/article/363d1d7f155b40049e5a68b10015e60c.
[37] 王培培, 刘长宁. 植物基因家族全基因组分析平台构建及在Dof中的应用. 绿色科技[J]. 2018, 第 2 作者1-5, http://lib.cqvip.com/Qikan/Article/Detail?id=675731896.
[38] Gao, Xiaoyang, Zhang, Xuan, Meng, Honghu, Li, Jing, Zhang, Di, Liu, Changning. Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolutionary implications. BMC GENOMICS[J]. 2018, 第 6 作者  通讯作者  19(S10): http://ir.xtbg.org.cn/handle/353005/11243.
[39] Liu Zhangning. CRlncRC: a novel machine learning method for cancer-related long noncoding RNA identification based on integrated features. BMC Medical Genomics. 2018, 第 1 作者  通讯作者  
[40] Hu, Xiang, Chen, Wen, Li, Jing, Huang, Shulan, Xu, Xuling, Zhang, Xuan, Xiang, Shuanglin, Liu, Changning. ZFLNC: a comprehensive and well-annotated database for zebrafish lncRNA. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION[J]. 2018, 第 8 作者  通讯作者  2018(X): http://ir.xtbg.org.cn/handle/353005/11160.
[41] Chen, Wen, Zhang, Xuan, Li, Jing, Huang, Shulan, Xiang, Shuanglin, Hu, Xiang, Liu, Changning. Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish. BMC GENOMICS[J]. 2018, 第 7 作者  通讯作者  19(S2): http://www.irgrid.ac.cn/handle/1471x/1791609.
[42] Zhang, Xuan, Wang, Jun, Li, Jing, Chen, Wen, Liu, Changning. CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features. BMC MEDICAL GENOMICS[J]. 2018, 第 5 作者  通讯作者  11(S6): https://doaj.org/article/a9755ba0390449beb3ed220e71cd2640.
[43] Liu Zhangning. Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolution implications. BMC Genomics. 2018, 第 1 作者  通讯作者  
[44] 李月颖, 李菁, 刘长宁. 蒺藜苜蓿SBP-box转录因子基因家族全基因组分析. 湖南师范大学自然科学学报[J]. 2017, 第 3 作者40(6): 24-33, http://lib.cqvip.com/Qikan/Article/Detail?id=673967311.
[45] 孙靖然, 刘长宁, 李荣贵, 张伟, 李盛英. 短密青霉NRRL 864异戊烯基转移酶PbPT的克隆表达及功能分析. 青岛大学学报:工程技术版[J]. 2016, 第 2 作者31(2): 107-115, http://lib.cqvip.com/Qikan/Article/Detail?id=669493521.
[46] Changning Liu, Zhenyu Xuan. Prioritization of Cancer-Related Genomic Variants by SNP Association Network. CANCER INFORMATICS[J]. 2015, 第 1 作者57-70, https://doaj.org/article/8a8ec56e2c9a42479e1befa8d38dd2d7.
[47] Li Xu, Liang Fengji, Liu Changning, Zhang Liangcai, Li Yinghui, Li Yu, Chen Shanguang, Xiong Jianghui. Comparison of the Prognostic Utility of the Diverse Molecular Data among lncRNA, DNA Methylation, microRNA, and mRNA across Five Human Cancers. PLOS ONE[J]. 2015, 第 3 作者10(11): http://dx.doi.org/10.1371/journal.pone.0142433.
[48] Zhang, Wei, Cao, Shaona, Qiu, Li, Qi, Fengxia, Li, Zhong, Yang, Ying, Huang, Shaohua, Bai, Fali, Liu, Changning, Wan, Xiaobo, Li, Shengying. Functional Characterization of MpaG ', the O-Methyltransferase Involved in the Biosynthesis of Mycophenolic Acid. CHEMBIOCHEM[J]. 2015, 第 9 作者16(4): 565-569, http://ir.xtbg.org.cn/handle/353005/8682.
[49] Li, Jing, Xuan, Zhenyu, Liu, Changning. Long Non-Coding RNAs and Complex Human Diseases. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES[J]. 2013, 第 3 作者14(9): 18790-18808, https://doaj.org/article/92bfd770ed80422e9cae8d0f9fd5797a.
[50] Sun Liang, Luo HaiTao, Liao Qi, Bu DeChao, Zhao GuoGuang, Liu ChangNing, Liu YuanNing, Zhao Yi. Systematic study of human long intergenic non-coding RNAs and their impact on cancer. SCIENCECHINALIFESCIENCES[J]. 2013, 第 6 作者56(4): 324-334, https://www.webofscience.com/wos/woscc/full-record/WOS:000317610200005.
[51] Jing Li, Zhenyu Xuan. Long Non-Coding RNAs and Complex Human Diseases. MDPI. 2013, http://oa.las.ac.cn/oainone/service/browseall/read1?ptype=JA&workid=JA202003190033202ZK.
[52] 陈润生. CloudLCA: finding the lowest common ancestor in metagenome analysis using cloud computing. PROTEIN & CELL[J]. 2012, 3(50): 148-152, http://www.irgrid.ac.cn/handle/1471x/756738.
[53] 陈润生. NONCODE v3.0: integrative annotation of long noncoding RNAs. NUCLEIC ACIDS RESEARCH[J]. 2012, 40(51): D210-D215, http://www.irgrid.ac.cn/handle/1471x/756876.
[54] Liao, Qi, Yuan, Xiongying, Xiao, Hui, Liu, Changning, Lv, Zhiyue, Zhao, Yi, Wu, Zhongdao. Identifying Schistosoma japonicum Excretory/Secretory Proteins and Their Interactions with Host Immune System. PLOS ONE[J]. 2011, 第 4 作者6(8): https://doaj.org/article/6caabbfb1f6e45298a03c7757a61a198.
[55] 陈润生. ncFANs: a web server for functional annotation of long non-coding RNAs. NUCLEIC ACIDS RESEARCH[J]. 2011, 39(54): W118-W124, http://www.irgrid.ac.cn/handle/1471x/757406.
[56] Yuan, Xiongying, Zhao, Yi, Liu, Changning, Bu, Dongbo. LEX-SVM: EXPLORING THE POTENTIAL OF EXON EXPRESSION PROFILING FOR DISEASE CLASSIFICATION. JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY[J]. 2011, 第 3 作者9(2): 299-316, https://www.webofscience.com/wos/woscc/full-record/WOS:000297077400007.
[57] Liao, Qi, Liu, Changning, Yuan, Xiongying, Kang, Shuli, Miao, Ruoyu, Xiao, Hui, Zhao, Guoguang, Luo, Haitao, Bu, Dechao, Zhao, Haitao, Skogerbo, Geir, Wu, Zhongdao, Zhao, Yi. Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. NUCLEIC ACIDS RESEARCH[J]. 2011, 第 2 作者39(9): 3864-3878, https://www.webofscience.com/wos/woscc/full-record/WOS:000290589500037.
[58] Miao, RuoYu, Zhao, HaiTao, Yang, HuaYu, Mao, YiLei, Lu, Xin, Zhao, Yi, Liu, ChangNing, Zhong, ShouXian, Sang, XinTing, Huang, JieFu. Postoperative adjuvant antiviral therapy for hepatitis B/C virus-related hepatocellular carcinoma: A meta-analysis. WORLD JOURNAL OF GASTROENTEROLOGY[J]. 2010, 第 7 作者16(23): 2931-2942, http://lib.cqvip.com/Qikan/Article/Detail?id=1001267145.
[59] Liu, Changning, Li, Jing, Zhao, Yi. Exploring hierarchical and overlapping modular structure in the yeast protein interaction network. BMC GENOMICS[J]. 2010, 第 1 作者  通讯作者  11(Suppl 4): S17-S17, http://dx.doi.org/10.1186/1471-2164-11-S4-S17.
[60] Yang, Zhen, Ren, Fei, Liu, Changning, He, Shunmin, Sun, Gang, Gao, Qian, Yao, Lei, Zhang, Yangde, Miao, Ruoyu, Cao, Ying, Zhao, Yi, Zhong, Yang, Zhao, Haitao. dbDEMC: a database of differentially expressed miRNAs in human cancers. BMC GENOMICS[J]. 2010, 第 3 作者11(8): S5-S5, http://dx.doi.org/10.1186/1471-2164-11-S4-S5.
[61] Yuan, Xiongying, Liu, Changning, Yang, Pengcheng, He, Shunmin, Liao, Qi, Kang, Shuli, Zhao, Yi. Clustered microRNAs' coordination in regulating protein-protein interaction network. BMC SYSTEMS BIOLOGY[J]. 2009, 第 2 作者3(1): 65-65, http://www.corc.org.cn/handle/1471x/2399167.
[62] He, Shunmin, Liu, Changning, Skogerbo, Geir, Zhao, Haitao, Wang, Jie, Liu, Tao, Bai, Baoyan, Zhao, Yi, Chen, Runsheng. NONCODE v2.0: decoding the non-coding. NUCLEIC ACIDS RESEARCH[J]. 2008, 第 2 作者36(77): D170-D172, http://dx.doi.org/10.1093/nar/gkm1011.
[63] Sun, Shiwei, Yu, Chungong, Qiao, Yantao, Lin, Yu, Dong, Gongjin, Liu, Changning, Zhang, Lingfen, Zhang, Zhuo, Cai, Jinjin, Zhang, Hong, Bu, Dongbo. Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra. JOURNAL OF PROTEOME RESEARCH[J]. 2008, 第 6 作者7(1): 202-208, http://www.irgrid.ac.cn/handle/1471x/757736.
[64] 陈润生. MicroRNA-encoding long non-coding RNAs. BMC GENOMICS[J]. 2008, 9(75): https://doaj.org/article/275af1bd98194f92b73599d2a2a93c03.
[65] 陈润生. MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control. TRENDS IN GENETICS[J]. 2008, 24(72): 323-327, http://dx.doi.org/10.1016/j.tig.2008.04.004.
[66] 刘长宁. 基于系统生物学的非编码基因研究. 2007, 第 1 作者
[67] 陈润生. Dynamic changes in subgraph preference profiles of crucial transcription factors. PLOS COMPUTATIONAL BIOLOGY[J]. 2006, 2(5): 383-391, https://doaj.org/article/4a4203f05bf1482bb7c7292b26dee8fe.
[68] 陈润生. NONCODE: an integrated knowledge database of non-coding RNAs. NUCLEIC ACIDS RESEARCH[J]. 2005, 33(112): D112-D115, http://www.corc.org.cn/handle/1471x/2377672.
发表著作
(1) 生物信息学计算技术和软件导论, 科学出版社, 2017-01, 第 5 作者

科研活动

   
科研项目
( 1 ) 长非编码 RNA 数据库及应用软件平台的构建, 主持, 国家级, 2014-01--2016-12
( 2 ) 基于多组学数据整合的肿瘤相关长非编码 RNA 优化筛选和调控机, 主持, 国家级, 2015-01--2018-12
( 3 ) 人类-线虫超保守长非编码 RNA 的系统发现及其在线虫发育调控, 主持, 国家级, 2015-01--2017-12
( 4 ) 滇重楼功能基因组应用研究, 主持, 省级, 2016-01--2020-12
( 5 ) 小桐子花发育相关非编码RNA (miRNA/lncRNA) 的系统发现及功能和机制研究, 主持, 国家级, 2020-01--2023-12
( 6 ) 陕西秦岭地区特色中药材植物功能基因组研究, 主持, 国家级, 2021-01--2024-12
( 7 ) 牧草基因组编辑数据库搭建, 主持, 部委级, 2020-11--2025-10
参与会议
(1)Comparative chloroplast genomes of Paris Sect. Marmorata: insights into repeat regions and evolution implications   第29届国际基因组信息大会   2018-12-01
(2)CRlncRNA: a manually curated database of cancer-related long non-coding RNAs with experimental proof of functions on clinicopathological and molecular features   第29届国际基因组信息大会   2018-12-01
(3)CRlncRC: a novel machine learning method for cancer-related long noncoding RNA identification based on integrated features   第29届国际基因组信息大会   2018-12-01
(4)Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish   第16届亚太生物信息学国际会议   2018-01-01
(5)Exploring Hierarchical and Overlapping Modular Structure in the Yeast Protein Interaction Network   第9届国际生物信息学大会   2010-10-10

指导学生

已指导学生

王培培  硕士研究生  085238-生物工程  

张頔  硕士研究生  071001-植物学  

李月颖  硕士研究生  085238-生物工程  

李靖  博士研究生  071001-植物学  

桑世叶  硕士研究生  071001-植物学  

李岸林  硕士研究生  085238-生物工程  

任强  硕士研究生  085238-生物工程  

张国强  硕士研究生  071001-植物学  

现指导学生

张轩  博士研究生  071001-植物学  

杨文静  博士研究生  071001-植物学  

王杰  硕士研究生  071001-植物学  

蒋晓可  硕士研究生  085238-生物工程  

刘嘉智  硕士研究生  086000-生物与医药  

李雁  硕士研究生  071001-植物学  

杨子添  硕士研究生  086000-生物与医药