• 郑云(Yun Zheng)

    博士,教授,硕士生导师

    第20届国际生物信息学会议主席(InCoB 2021);亚太地区最早的生物信息学组织亚太生物信息学网络

    (Asia Pacific Bioinformatics Network, APBioNET)执行委员会委员暨中国联络员(Liaison) ;

    Frontiers in Genetics副主编;MDPI Genes编辑

    一、受教育经历 Educational Background

       郑云,1998年毕业于北京航空航天大学,获得制造工程工学学士学位,2007年毕业于新加坡南洋理工大学,获得计算机科学哲学博士学位。他从2005年12月到2006年8月在新加坡国立大学担任Research Fellow,从2006年8月至2009年1月在美国圣路易斯华盛顿大学任Research Associate,从事博士后研究。他从2009年1月至2013年8月任复旦大学发育生物学研究所副教授,PI。郑云博士于2013年8月加入昆明理工大学,任生命科学与技术学院生物信息实验室PI。他分别在2011年3到4月,2013年4到5月以及2018年8到9月间应邀以访问学者学者身份访问了美国俄克拉荷马州立大学;在2011年7至8月和2013年11月至12月应邀以访问教授身份访问了新加坡南洋理工大学;在2015年1到2月间以访问教授身份访问了澳大利亚悉尼科技大学。2018年担任第29届国际基因组信息学会议主席。

    1. 2011年7月 – 8月 新加坡南洋理工大学Visiting Professorship
    2. 2011年3月 – 4月 美国俄克拉荷马州立大学Visiting Scholarship
    3. 2006年8月 – 2009年1月 华盛顿大学圣路易斯Postdoctoral Fellowship
    4. 2005年12月 – 2006年8月 新加坡国立大学Postdoctoral Fellowship
    5. 2002年9月 – 2005年9月 新加坡南洋理工大学Fellowship


       In 1998, Yun Zheng got his Bachelor degree in Manufacturing Engineering from Beijing University of Aeronautics and Astronautics, and PhD in computer science from Nanyang Technological University, Singapore, in 2007. He worked as a research fellow at the National University of Singapore, Singapore, from December 2005 to August 2006, and as a research associate at Washington University in St. Louis, US, from August 2006 to January 2009. From January 2009 to August 2013, he was an associate professor and PI of Institute of Developmental Biology and Molecular Medicine of Fudan University, China. In August 2013, Dr. Zheng Yun joined Kunming University of Science and Technology, China, as a PI of Bioinformatics Laboratory. He was a Visiting Faculty of Oklahoma State University, US, from March to April in 2011, April to May in 2013 and August to September in 2018. He was a Visiting Professor of Nanyang Technological University, Singapore, from July to August in 2011 and November to December in 2013, and of University of Technology Sydney, Australia, from January to February in 2015. In 2018, he was the chair of the 29th International Conference on Genome Informatics (GIW 2018). He is an Academic Editor of PLoS ONE since July, 2014. He is on the Editor Board of Frontiers in Genetics.

    1. 2011.07-08 Visiting Professorship of Nanyang Technological University in Singapore
    2. 2011.03-04 Oklahoma State University Visiting Scholarship
    3. 2006.08 - 2009.01 Washington University in St. Louis Postdoctoral Fellowship
    4. 2005.12 - 2006.08 National University of Singapore Postdoctoral Fellowship
    5. 2002.09 - 2005.09 Graduate Fellowship of Nanyang Technological University in Singapore

    二、主要研究方向 Major research

    microRNA介导的基因调控的相关计算机算法,Gene Ontology,信号通路,基因组学,转录组学,机器学习和计算学习的理论基础。

     

    Computer algorithms of microRNA-based gene regulation, miRNA editing, miRNA target, lariat RNA, intron, intron branch point, gene ontology, signaling pathway, genomics, transcriptome, data mining, machine learning and computational learning theory.

    三、科研领域描述 Description of the Research

    MicroRNA是一类最近发现的具有调控功能的重要非编码小RNA。我们目前的一些科研包括小RNA高通量测序数据分析,基于高通量测序的转录组分析,识别和鉴定microRNA在植物发育、抗逆和肝癌、结肠癌等疾病中的功能,癌症诊断新分子标记物的预测和验证,CHIP-seq数据分析,基因调控网络分析,SNP和疾病的分析,基因GO和信号通路分析,蛋白质互作网络分析。

     

    Our current research area includes transcriptome analysis, single cell transcriptomics, identification of miRNAs, identification of miRNA editing sites, identification of microRNA targets, lariat RNA, prediction of intron branch point, circular RNA, prediction of new molecular markers for cancer diagnosis, CHIP-seq data analysis, gene regulatory network analysis, SNP and disease analysis, gene ontology and pathway analysis, and protein interaction network analysis.

     

    四、承担科研项目情况 Scientific Grants

    1. 2018年 – 2021年       国家干细胞重大专项,项目编号2018YFA0108502,研究骨干,承担金额100万元人民币
    2. 2018年 – 2021年       复旦大学遗传工程重点实验室开发课题,项目编号SKLGE-18141,PI,8万元人民币
    3. 2018年 – 2021年       国家自然科学基金,项目编号31760314,PI,直接经费39万人民币
    4. 2016年 – 2018年 复旦大学遗传工程重点实验室开发课题,项目编号SKLGE-1511,PI,6万元人民币
    5. 2015年 – 2018年 国家自然科学基金,项目编号31460295, PI,50万元人民币
    6. 2013年7月 – 现在,昆明理工大学高端引进人才启动基金,150万人民币。
    7. 2009年1月 – 2012年1月,复旦大学引进人才启动基金,PI,45万人民币。
    8. 2010 年4月 – 2012年3月,上海市科学技术委员会,项目编号10ZR1403000,PI,10万元人民币。
     
    1. 2018-2021  The National Major Special Project of Stem Cell Research, No. 2018YFA0108502, Key member, 1 Million RMB
    2. 2018 – 2021    The Open Research Funds of the State Key Laboratory of Genetic Engineering, No. SKLGE-18141, Fudan University, China, PI, 80,000 RMB
    3. 2018 – 2021    National Natural Science Foundation of China, No. 31760314, PI, 390,000 RMB
    4. 2016 – 2018    The Open Research Funds of the State Key Laboratory of Genetic Engineering, No. SKLGE-1511, PI, 60,000 RMB
    5. 2015 – 2018    National Natural Science Foundation of China, No. 31460295, PI, 500,000 RMB 
    6. 2013 – now    Startup Research Grant, Kunming University of Science and Technology, PI, 1.5 million RMB.
    7. 2009 – 2012    Startup Research Grant, Fudan University, PI, 450,000 RMB.
    8. 2010 – 2012 Science and Technology Commission of Shanghai Municipality, Grant No. 10ZR1403000, PI, 100,000 RMB.

    五、获奖情况 HONORS AND AWARDS

    1. 2017年9月 第16届国际生物信息学会议BMC Genomics最佳论文奖
    2. 2013年11月-12月 新加坡南洋理工大学Visiting Professorship
    3. 2013年4月 – 5月 美国俄克拉荷马州立大学Visiting Scholarship
    4. 2012年7月 第13届人类基因组变异和复杂基因组分析(HGV2012)国际会议trainee full scholarship
    5. 2011年10月 2009-2010年度海南省自然科学优秀学术论文一等奖
    1. 2017.09 :the Best Paper Award for the 16th International Conference on Bioinformatics (InCoB 2017) BMC Genomics track
    2. 2013.11-12 Visiting Professorship of Nanyang Technological University in Singapore
    3. 2013.04-05 Oklahoma State University Visiting Scholarship
    4. 2012.07 A trainee full scholarship of the 13th International Meeting on Human Genome Variation and Complex Genome Analysis (HGV2012)
    5. 2011.10 The first prize of outstanding natural science academic papers of Hainan Province, 2009-2010

    六、发表专著与图书章节 PUBLICATIONS

    1. Yun Zheng. Computational Non-coding RNA Biology. Academic Press (Elsevier), ISBN 978-0128143650, Oct 1, 2018, Cambridge, MA.

    2. Yun Zheng#, Junqiang Guo, Ching Man Wai, Ray Ming, Ramanjulu Sunkar. MicroRNAs, tasiRNAs, phasiRNAs and their potential functions in pineapple. in R. Ming (Eds.), Genetics and Genomics of Pineapple, pp. 167-182, DOI:10.1007/978-3-030-00614-3_12. Cham, Switzerland: Springer International Publishing AG.

     

    七、代表性论文 Journal Papers

    1. Kui Duan*, Chen-Yang Si*, Shu-Mei Zhao, Zong-Yong Ai, Bao-Hua Niu, Yu Yin, Li-Feng Xiang, Hao Ding, and Yun Zheng#. The long terminal repeats of ERV6 are activated in pre-implantation embryos of cynomolgus monkeys. Cells 2021, 10(10):2710. (IF = 6.6)
    2. Lifeng Xiang*, Yu Yin*, Yun Zheng*, Yanping Ma*, Yonggang Li*, Zhigang Zhao, Junqiang Guo, Zongyong Ai, Yuyu Niu, Kui Duan, Jingjing He, Shuchao Ren, Dan Wu, Yun Bai, Weizhi Ji#, Tianqing Li#. A developmental landscape of 3D-cultured human pre-gastrulation embryos. Nature 2020, 577:537–542(2020). (IF = 43.07)
    3. Xiaotuo Zhang*, Yong Zhang*, Taiyun Wang, Ziwei Li, Jinping Cheng, Haoran Ge, Qi Tang, Kun Chen, Li Liu, Chenyu Lu, Junqiang Guo, Binglian Zheng# and Yun Zheng#. A comprehensive map of intron branchpoints and lariat RNAs in plants. The Plant Cell 2019, 31(5):956-973. (IF = 9.62)
    4. Shiyong Guo*, Jun Yang*, Bingbing Jiang*, Nan Zhou, Hao Ding, Guangchen Zhou, Shuai Wu, Angbaji Suo, Xingwang Wu, Wenping Xie, Wanran Li, Yulong Liu, Wei Deng, and Yun Zheng#. MicroRNA editing patterns in Huntington’s disease. Scientific Reports 2022, accepted.
    5. Chandra Obul Reddy Puli, Yun Zheng, Yong-Fang Li, Guru Jagadeeswaran, Angbaji Suo, Bingbing Jiang, Pradeep Sharma, Robert Mann, Govindan Ganesan, Nirmali Gogoi, Asha Srinivasan, Aparna Kakani, Vijaya Gopal Kakani, Abdelali Barakat & Ramanjulu Sunkar. MicroRNA profiles in Sorghum exposed to individual drought or heat or their combination. Journal of Plant Biochemistry and Biotechnology 2021, 30:848–861. (IF = 1.18)
    6. Menglei Wang, Chenhui Yang, Kangning Wei, Miao Zhao, Liqiang Shen, Jie Ji, Li Wang, Daijing Zhang, Junqiang Guo, Yun Zheng, Juanjuan Yu, Mo Zhu, Haiying Liu and Yong-Fang Li#. Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions. BMC Genomics 2021, 22: 793. (IF = 3.99)
    7. Angbaji Suo*, Zengquan Lan*, Chenyu Lu*, Zhigang Zhao, Dian Pu, Xingwang Wu, Bingbing Jiang, NanZhou, Hao Ding, Dongming Zhou, Peiran Liao, Ramanjulu Sunkar, and Yun Zheng#. Characterizing microRNAs and their targets in different organs of Camellia sinensis var. assamica. Genomics 2021, 113:159-170 (IF = 5.74)
    8. Dahai Liu*, Li Liu*, Kui Duan*, Junqiang Guo, Shipeng Li, Zhigang Zhao, Xiaotuo Zhang, Nan Zhou, and Yun Zheng#. Transcriptional dynamics of transposable elements when converting fibroblast cells of Macaca mulatta to neuroepithelial stem cells. BMC Genomics 2021, 22(S3):405. (IF = 3.97)
    9. Yapin Yan*, Shuchao Ren*, Yanchao Duan, Chenyu Lu, Zhengbo Wang, Briauna Inglis, Weizhi Ji#Yun Zheng#, and Wei Si#. Gut microbiota and metabolites of α-synuclein transgenic monkey models with early stage of Parkinson's disease. npj Biofilms and Microbiomes 2021, 7(1):69. (IF = 7.29)
    10. Chenyu Lu*, Shuchao Ren*, Zhigang Zhao, Xingwang Wu, Angbaji Suo, Nan Zhou, Jun Yang, Shuai Wu, Tianqing Li, Chao Peng, and Yun Zheng#. Characterizing relevant microRNA editing sites in Parkinson’s disease. medRxiv 2020, DOI:10.1101/2020.04.06.20054791
    11. Xingwang Wu, Wanran Li, and Yun Zheng#. Recent Progress on Relevant microRNAs in Autism Spectrum Disorders. International Journal of Molecular Sciences 2020, 21:5904. (IF = 5.92)
    12. Jie Zheng#, Jinyan Li# and Yun Zheng#. Guest Editorial for the 29th International Conference on Genome Informatics (GIW 2018). IEEE/ACM Transactions on Computational Biology and Bioinformatics 2019, 2020, 17(3):726-727. (IF = 2.9)
    13. Yun Zheng# and Philipp Kapranov#. Editorial: Recent progresses of non-coding RNAs in biological and medical research. Frontiers in Genetics 2020, 11:187. (IF = 4.60)
    14. Qingyi Wang*, Zhigang Zhao*, Xiaotuo Zhang, Chenyu Lu, Shuchao Ren, Shipeng Li, Junqiang Guo, Peiran Liao, Bingbing Jiang, Yun Zheng#. Identifying MicroRNAs and Their Editing Sites in Macaca mulatta. Cells 2019, 8(7). (IF = 5.65)
    15. Yong-Fang Li*, Miao Zhao, Menglei Wang, Junqiang Guo, Li Wang, Jie Ji Zongbo Qiu, Yun Zheng and Ramanjulu Sunkar*. An improved method of constructing degradome library suitable for sequencing using Illumina platform. Plant Methods 2019, 15:134. (IF = 3.17)
    16. Candace M. Seeve, Ramanjulu Sunkar, Yun Zheng, Li Liu, Zhijie Liu, Michael McMullen, Sven Nelson, Robert E. Sharp, Melvin J. Oliver. Water-deficit responsive microRNAs in the primary root growth zone of maize. BMC Plant Biology 2019, 19:447 (IF = 3.67)
    17. Xiaohong Ou*, Shipeng Li*, Peiran Liao, Xiuming Cui, Binglian Zheng, Ye Yang#, Dahui Liu#Yun Zheng#. The transcriptome variations of Panax notoginseng roots treated with different forms of nitrogen fertilizers. BMC Genomics 2019, 20(Suppl 9):965. (IF = 3.5)
    18. Yong-Fang Li#, Kangning Wei, Menglei Wang, Li Wabg, Junxia Cui, Daijing Zhang, Junqiang Guo, Miao Zhao, Yun Zheng. Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field. Frontiers in Genetics 2019, DOI: 10.3389/fgene.2019.00779. (IF = 3.52)
    19. Songxiao Zhong, Yifeng Xu, Chaoyi Yu, Xiaotuo Zhang, Lei Li, Haoran Ge, Guodong Ren, Yingxiang Wang, Jinbiao Ma, Yun Zheng, and Binglian Zheng#. Anaphase-promoting complex/cyclosome regulates RdDM activity by degrading DMS3 in Arabidopsis. Proceedings of the National Academy of Sciences 2019, 116 (9) 3899-3908 (IF = 9.5)
    20. Junqiang Guo, Qingyi Wang, Li Liu, Shuchao Ren, Shipeng Li, Peiran Liao, Zhigang Zhao, Chenyu Lu, Bingbing Jiang, Ramanjulu Sunkar and Yun Zheng#. Analysis of microRNAs, phased small interfering RNAs and their potential targets in Rosa rugosa Thunb.. BMC Genomics 2018, DOI: 10.1186/s12864-018-5325-2. (IF=3.73)
    21. Yong-Fang Li*, Yun Zheng*, Lakshminarayana R Vemireddy, Sanjib Kumar Panda, Smitha Jose, Alok Ranjan, Piyalee Panda, Ganesan Govindan, Junxia Cui, Kangning Wei, Mahmoud W Yaish, Charmain Naidoo and Ramanjulu Sunkar. Comparative transcriptome and translatome analysis in rice revealed differential mRNA translation in Pokkali compared to IR29 under salt stress. BMC Genomics 2018, 19(Suppl 10):935. (IF=3.73)
    22. Robert Pokoo, Shuchao Ren, Qingyi Wang, Christy M. Motes, Tim D. Hernández, Sayvan Ahmadi, Maria Monteros, Yun Zheng# and Ramanjulu Sunkar#. Genotype- and tissue-specific microRNA profiles and their targets in three alfalfa (Medicago sativa L.) accessions. BMC Genomics 2018, 19(Suppl 10):913. (IF=3.73)
    23. Yi-Kun Zhou#, Xiaochun Yang, Yang Gao, Heng Su, Li Liu, Zhi Liang# and Yun Zheng#. A homozygous G insertion in MPLKIP leads to TTDN1 with the hypergonadotropic hypogonadism symptom. BMC Medical Genetics 2018, 19(Suppl 1):214. (IF=1.9)
    24. Yu Kang, Zongyong Ai, Kui Duan, Chenyang Si, Yong Wang, Yun Zheng, Jingjing He, Yu Yin, Shumei Zhao, Baohua Niu, Xiaoqing Zhu, Li Liu, Lifeng Xiang, Linming Zhang, Yuyu Niu, Weizhi Ji, Tianqing Li. Improving Cell Survival in Injected Embryos Allows Primed Pluripotent Stem Cells to Generate Chimeric Cynomolgus Monkeys. Cell Reports 2018, 25(9): 2563-2576. e9.(IF = 8.03)
    25. Ye Yang, Li Ma, Hong Zeng, Lu-Yao Chen, Yun Zheng, Cai-Xia Li, Ze-Ping Yang, Nan Wu, Xi Mu, Chun-Yan Dai, Hui-Lin Guan, Xiu-Ming Cui, Ying Liu. iTRAQ-based proteomics screen for potential regulators of wheat (Triticum aestivum L.) root cell wall component response to Al stress. Gene 2018, 675:301-311.
    26. Peiran Liao, Shipeng Li, Xiuming Cui, Yun Zheng#. A comprehensive review of web-based resources of non-coding RNAs for plant science research. International Journal of Biological Sciences 2018, 14(8):819-832. (IF=4.06)
    27. Li Liu*, Shuchao Ren*, Junqiang Guo, Qingyi Wang, Xiaotuo Zhang, Peiran Liao, Shipeng Li, Ramanjulu Sunkar and Yun Zheng#. Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon. BMC Genomics 2018, 19(Suppl 2):111. (IF=3.73)
    28. Kun Chen*, Li Liu*, Xiaotuo Zhang*, Yuanyuan Yuan*, Shuchao Ren, Junqiang Guo, Qingyi Wang, Peiran Liao, Shipeng Li, Xiuming Cui#, Yong-Fang Li# and Yun Zheng#. Phased secondary small interfering RNAs in Panax notoginseng. BMC Genomics 2018, 19(Suppl 1): 41. (IF=3.73)
    29. Jessica Matts, Yun Zheng, Guru Jagadeeswaran & Ramanjulu Sunkar. MicroRNA expression profiles in the emerging tillers and inflorescence of switchgrass, a major feedstock for biofuel production. Indian Journal of Plant Physiology 2017, 22 (4), 558–565.
    30. Yun Zheng#, Li Liu, and Girish C. Shukla. A comprehensive review of web-based non-coding RNA resources for cancer research, Cancer Letters 2017, 407:1-8. (IF=6.49)
    31. Yun Zheng*,#, Kun Chen*, Zhenning Xu*, Peiran Liao, Xiaotuo Zhang, Li Liu, Kangning Wei, Diqiu Liu, Yong-Fang Li, Ramanjulu Sunkar, and Xiuming Cui#. Small RNA profiles from Panax notoginseng roots differing in sizes reveal correlation between miR156 abundances and root biomass levels. Scientific Reports 2017, 7(1):9418. (IF=4.12)
    32. Chuanbin Su, Ziwei Li, Jinping Cheng, Lei Li, Songxiao Zhong, Li Liu, Yun Zheng, and Binglian Zheng*. The Protein Phosphatase 4 and SMEK1 Complex Dephosphorylates HYL1 to PromotemiRNA Biogenesisby Antagonizing the MAPK Cascade in Arabidopsis. Developmental Cell 2017, 41:527–539 (IF=9.62)
    33. Mahmoud W Yaish, Himanshu V Patankar, Dekoum V M Assaha, Yun Zheng, Rashid Al-Yahyai, Ramanjulu Sunkar. Genome-wide expression profiling in leaves and roots of date palm (Phoenix dactylifera L.) exposed to salinity. BMC Genomics (2017) 18: 246.(IF=3.73)
    34. Vallabhi Ghorecha, Yun Zheng, Li Liu, Ramanjulu Sunkar, N S R Krishnayya. MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress. Physiology and Molecular Biology of Plants 2017, 23:291.
    35. Ziwei Li*, Shengpeng Wang*, Jinping Cheng, Chuanbin Su, Songxiao Zhong, Qi Liu, Yuda Fang, Yao Yu, Hong Lv, Yun Zheng#, and Binglian Zheng#. Intron lariat RNA inhibits microRNA biogenesis by sequestering the dicing complex in Arabidopsis. PLOS Genetics 2016, 12(11):e1006422.(IF=6.66)
    36. Yun Zheng, Vandana Hivrale, Xiaotuo Zhang, BabuValliyodan, Christine Lelandais-Brière, Andrew D. Farmer, Gregory D. May,Martin Crespi, Henry T. Nguyen, and Ramanjulu Sunkar. Small RNA profiles in soybean primary root tips under water deficit. BMC Systems Biology 2016, 10(Suppl 5):126. (IF=2.30)
    37. Dong Yang, Ruiqi Liao, Yun Zheng, Ling Sun, Tian Xu. Analysis of PBase Binding Profile Indicates An Insertion Target Selection Mechanism Dependent on TTAA, But Not Transcriptional Activity. International Journal of Biological Sciences 2016, 12(9):1074-1082. doi:10.7150/ijbs.15589. (IF=3.98)
    38. Yun Zheng#, Bo Ji, Renhua Song, Shengpeng Wang, Ting Li, Xiaotuo Zhang, Kun Chen, Tianqing Li, and Jinyan Li#. Accurate Detection for a Wide Range of Mutation and Editing Sites of MicroRNAs from Small RNA High-Throughput Sequencing Profiles, Nucleic Acids Research, 2016, 44(14): e123. DOI: 10.1093/nar/gkw471. (IF = 10.12)
    39. Yun Zheng#, Ting Li, Zhenning Xu, Kun Chen, Xiaotuo Zhang, Shengpeng Wang, Bo Ji, Ray Ming, and Ramanjulu Sunkar#. Identification of microRNAs, phasiRNAs and Their Targets in Pineapple. Tropical Plant Biology, 2016, DOI: 10.1007/s12042-016-9173-4. (IF = 1.5)
    40. Zongyong Ai, Zheng Xiang, Yuemin Li, Guoku Liu, Hong Wang, Yun Zheng, Xiaoyan Qiu, Shumei Zhao, Xiaoqing Zhu, Yanhua Li, Weizhi Ji, Tianqing Li. Conversion of Monkey Fibroblasts to Transplantable Telencephalic Neuroepithelial Stem Cells. Biomaterials 10/2015; 77. DOI:10.1016/j.biomaterials.2015.10.079 (IF=8.56)
    41. Savita Singh*, Yun Zheng*,Guru Murugashesn*, JeyEbronSabith, Kavleen Sikand, Sanjay Gupta, Ramanjulu Sunker#, and Girish C. Shukla#. Deep Sequencing of Small RNA Libraries from Human Prostate Epithelial and Stromal Cells Reveal Distinct Pattern of MicroRNAs Primarily Predicted to Target Growth Factors. Cancer Letters 2016, 371(2):262-73. doi: 10.1016/j.canlet.2015.10.038. (IF = 6.38)
    42. Mahmoud W. Yaish#, Ramanjulu Sunkar, Yun Zheng, Bo Ji, Sardar A. Farooq and Rashid Al-Yahyai. A Genome-Wide Identification of the miRNAome in Response to Salinity Stress in Date palm (Phoenix dactylifera L.). Front. Plant Sci. 2015, doi: 10.3389/fpls.2015.00946 (IF = 3.95)
    43. Ray Ming, Robert Van Buren, Ching Man Wai, Haibao Tang, Michael Schatz, John E. Bowers, Eric Lyon, Ming-Li Wang, Nancy Chen, Xiaohan Yang,Eric Biggers,Jisen Zhang, Lixian Huang, Lingmao Zhang, Wenjing Miao, Jian Zhang, Zhangrao Ye, Chenyong Miao, Henry D. Priest, Won C. Yim, Patrick P. Edger, Chunfang Zheng, Margaret Woodhouse, Hao Wang, Guangyong Zheng, Romain Guyot, Xiangjia Min, Yun Zheng, Ratnesh Singh, Hayan Lee, James Gurtowski, Fritz Sedlazeck,Hao-Bo Guo,Hong Guo, Alex Harkess, Michael McKain, Zhenyang Liao, Jingping Fang, Juan Liu, Xiaodan Zhang, Qing Zhang, Weichang Hu, Yuan Qin, Kai Wang, Liyu Chen, Neil Shirley,Yann-Rong Lin, Li-Yu Liu, Katy Heath, Francis Zee, Paul H. Moore, Ramanjulu Sunkar, Gerald A. Tuskan, James Leebens-Mack, Jeffrey L. Bennetzen, Michael Freeling, David Sankoff, Andrew H. Paterson, Todd Mockler, Xinguang Zhu, Andrew Smith, John C. Cushman, Robert E. Paull, Qingyi Yu. The pineapple genome and evolution of CAM photosynthesis. Nature Genetics 2015, doi:10.1038/ng.3435. (IF = 29.35)
    44. Vandana K Hivrale*, Yun Zheng*, Chandra Obul Reddy Puli, Guru Jagadeeswaran, Kanchana Gowdu, Gopal Kakani, Abdelali Barakat, Ramanjulu Sunkar. Characterization of drought-and heat-responsive microRNAs in switchgrass. Plant Science 07/2015; DOI:10.1016/j.plantsci.2015.07.018. (IF = 4.11)
    45. Sangeeta Srivastava*, Yun Zheng*, Himabindu Kudapa, Guru Jagadeeswaran, Vandana Hivrale, Rajeev Varshney# and Ramanjulu Sunkar#. Highthroughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea. Plant Science 2015, 235:46-57, DOI:10.1016/j.plantsci.2015.03.002. (IF = 4.11)
    46. Yun Zheng, Shengpeng Wang, Ramanjulu Sunkar. Genome-Wide Discovery and Analysis of Phased Small Interfering RNAs in Chinese Sacred Lotus. PLoS ONE 2014, 9(12): e113790, DOI:10.1371/journal.pone.0113790. (IF=3.53)
    47. Yun Zheng, Ting Li, Ren Ren, Donghua Shi, Shengpeng Wang. Revealing Editing and SNPs of MicroRNAs in Colon Tissues by Analyzing High-Throughput Sequencing Profiles of Small RNAs. BMC Genomics 2014, 15(Suppl 9):S11, DOI:10.1186/1471-2164-15-S9-S11. (IF=4.04)
    48. Xiufeng Zhang, Yun Zheng, Xiaolong Cao, Ren Ren, Xiao-Qiang Yu, Haobo Jiang. Identification and profiling of Manduca sexta microRNAs and their possible roles in regulating specific transcripts in fat body, hemocytes, and midgut. Insect Biochemistry and Molecular Biology 2014, DOI:j.ibmb.2014.08.006 (IF=3.42)
    49. Xiufeng Zhang, Yun Zheng, Guru Jagadeeswaran, Ren Ren, Ramanjulu Sunkar, Haobo Jiang. Identification of conserved and novel microRNAs in Manduca sexta and their possible roles in the expression regulation of immunity-related genes. Insect Biochemistry and Molecular Biology 2014, 47:12-22, doi:j.ibmb.2014.01.008 (IF=3.42)
    50. Chenggang Wang , Ren Ren, Haolin Hu, Changjun Tan, Miao Han, Xiaolin Wang, and Yun Zheng#. MiR-182 is Up-regulated and Targeting Cebpa in Hepatocellular Carcinoma. Chinese Journal of Cancer Research 2014. 26(1):17-29. (IF = 0.93)
    51. Rishi Aryal, Guru Jagadeeswaran, Yun Zheng, Qingyi Yu, Ramanjulu Sunkar and Ray Ming. Sex specific expression and distribution of small RNAs in papaya. BMC Genomics 2014, 15:20, doi:10.1186/1471-2164-15-20 (IF = 4.04)
    52. Yun Zheng# and Chee Keong Kwoh . Improved Time Complexities for Learning Boolean Networks. Entropy 2013, 15(9):3762-3795. (IF = 1.56)
    53. Miao Han, Yun Zheng*#. Comprehensive Analysis of Single Nucleotide Polymorphisms in Human MicroRNAs. PLoS ONE 2013. 8(11): e78028. (IF = 3.53)
    54. Yun Zheng, Guru Jagadeeswaran, Kanchana Gowdu, Nian Wang, Shaohua Li, Ray Ming, Ramanjulu Sunkar. Genome-Wide Analysis of MicroRNAs in Sacred Lotus,
    55. Nelumbo nucifera (Gaertn). Tropical Plant Biol. 2013, 6:117-130.
    56. Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell,Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, GiuseppeNarzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, YuannianJiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Jia Min, Karen AHudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer RWatling, Kikukatsu Ito, Sharon A Robinson, Matthew E Hudson, Qingyi Yu,Todd C Mockler, Andrew Carroll, Yun Zheng, Ramanjulu Sunkar, Ruizong Jia,Nancy Chen, Jie Arro, Ching Man Wai, Eric Wafula, Ashley Spence, Yanni Han,Liming Xu, Jisen Zhang, Rhiannon Peery, Miranda J Haus, Wenwei Xiong, JamesA Walsh, Jun Wu, Ming-Li Wang, Yun J Zhu, Robert E Paull, Anne B Britt,Chunguang Du, Stephen R Downie, Mary A Schuler,, Todd P Michael, Steve PLong, Donald R Ort, J William Schopf, David R Gang, Ning Jiang, MarkYandell, Claude W dePamphilis, Sabeeha S Merchant, Andrew H Paterson, Bob B Buchanan, Shaohua Li, Jane Shen-Miller. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology 2013, 14:R41. (IF = 10.3)
    57. Yong-Fang Li, Yun Zheng*, Guru Jagadeeswarana, Ramanjulu Sunkar. Characterization of small RNAs and their target genes in wheat seedlings using sequencing-based approaches. Plant Science 2013, 203-204:17-24, doi: j.plantsci.2012.12.014. (IF = 4.11)
    58. Guru Jagadeeswaran, Padma Nimmakayala, Yun Zheng*, Kanchana Gowdu, Umesh K Reddy and Ramanjulu Sunkar. Characterization of the small RNA component of leaves and fruits from four different cucurbit species. BMC Genomics 2012, 13:329, doi:10.1186/1471-2164-13-329. (IF = 4.04)
    59. Olufemi J Alabi, Yun Zheng, Guru Jagadeeswaran, Ramanjulu Sunkar, Rayapati A Naidu. High-throughput sequence analysis of small RNAs in grapevine (Vitis vinifera L.) affected by grapevine leafroll disease. Molecular Plant Pathology 2012, 13(9):1060-1076. DOI: 10.1111/j.1364-3703.2012.00815.x. (IF = 4.49)
    60. Xiufeng Zhang, Yun Zheng, Guru Jagadeeswaran, Ren Ren, Ramanjulu Sunkar, Haobo Jiang. Identification and developmental profiling of conserved and novel microRNAs in Manduca sexta. Insect Biochemistry and Molecular Biology 2012, 42:381-395 (IF=3.53)
    61. Yun Zheng , Yong-Fang Li, Ramanjulu Sunkar, Weixiong Zhang. SeqTar: An Effective Method for Identifying MicroRNA Guided Cleavage Sites from Degradome of Polyadenylated Transcripts in Plants. Nucleic Acids Research 2012, 40:e28.(IF = 8.81)
    62. Li Zhang, Yun Zheng, Guru Jagadeeswaran, Yongfang Li, Kanchana Gowdu, Ramanjulu Sunkar. Identification and temporal expression analysis of conserved and novel microRNAs in Sorghum. Genomics 2011, 98(6):460-8. (IF = 2.79)
    63. Yun Zheng# and Chee Keong Kwoh . A Feature Subset Selection Method Based On High-Dimensional Mutual Information. Entropy 2011, 13(4):860-901; doi:10.3390/e13040860. (IF=1.56)
    64. Yun Zheng and Weixiong Zhang. Animal microRNA Target Prediction Using Diverse Sequence-Specific Determinants. Journal of Bioinformatics and Computational Biology 2010, 8:763-788.(IF=0.93)
    65. Guru Jagadeeswaran, Yun Zheng, Niranji Sumathipala, Haobo Jiang, Estela L Arrese, Jose L Soulages, Weixiong Zhang, Ramanjulu Sunkar. Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC Genomics 2010, 11:52. (IF=4.04)
    66. Yong-Fang Li,Yun Zheng,Charles Addo-Quaye,Li Zhang,Ajay Saini,Guru Jagadeeswaran,Michael J. Axtell,Weixiong Zhang,Ramanjulu Sunkar. Transcriptome-wide identification of microRNA targets in rice. The Plant Journal 2010, 62:742-759. (IF=6.82)
    67. Alavala Matta Reddy, Yun Zheng, Guru Jagadeeswaran, Simone L Macmil, Wiley B Graham, Bruce A Roe, Udaya Desilva, Weixiong Zhang & Ramanjulu Sunkar. Cloning, characterization and expression analysis of porcine microRNAs. BMC Genomics 2009, 10:65. (IF=4.04)
    68. Guru Jagadeeswaran,Yun Zheng,Yong-Fang Li,Lata I. Shukla,Jessica Matts,Peter Hoyt,Simone L. Macmil,Graham B. Wiley,Bruce A. Roe,Weixiong Zhang,Ramanjulu Sunkar,. Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families. New Phytologist 2009,184:85-98. (IF=6.37)
    69. Changying Zeng, Wenquan Wang, Yun Zheng, Xin Chen, Weiping Bo, Shun Song, Weixiong Zhang, Ming Peng. Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants. Nucleic Acids Research 2009. 38:981-995. (IF=8.81)
    70. Ramanjulu Sunkar, Xuefeng Zhou, Yun Zheng, Weixiong Zhang & Jian-Kang Zhu. Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biology 2008, 8:25. (IF=3.94)
    71. Yun Zheng# and Chee Keong Kwoh. Dynamic algorithm for inferring qualitative models of gene regulatory networks. International Journal of Data Mining and Bioinformatics 2006. 1(2):111-137. (IF=0.66)
    72. Yun Zheng# and Chee Keong Kwoh. Cancer Classification With MicroRNA Expression Patterns Found By An Information Theory Approach. Journal of Computers 2006. 1(5):30-39.
    73. Yun Zheng# & Chee Keong Kwoh. Informative MicroRNA Expression Patterns for Cancer Classification. Lecture Notes in Computer Science (LNCS) 2006, 3916:143-154.
    74. Yun Zheng#,Wynne Hsu, Mong Li Lee, Limsoon Wong. Exploring Essential Attributes For Detecting MicroRNA Precursors From Background Sequences. Lecture Notes in Computer Science (LNCS) 2006, 4316:131-145.

    八、Conference Papers

    1. Zhang GL, Tong JC, Zhang ZH, Zheng Y, August JT, Kwoh CK & Brusic V. Computational models for identifying promiscuous hla-b7 binders based on information theory and support vector machine. In Proceedings of the International Conference on Biomedical and Pharmaceutical Engineering 2006 (ICBPE 2006), 319-323.
    2. Zheng Y# & Kwoh CK. Identifying simple discriminatory gene vectors with an information theory approach. in Proceedings of the 4th Computational Systems Bioinformatics Conference, CSB 2005, 12-23 (Stanford, CA, 2005, Acceptance Ratio 30/246).
    3. Zheng Y & Kwoh CK. A feature vector selection method for cancer classification. in Proceedings of International Conference of Bioinformatics, Bioinfo2005, 23-28. (Busan, Korea, 2005).
    4. Adi M, Zheng Y and Kwoh CK. Development of Correlation Based Feature Selection Method by Predicting the Markov Blanket for Gene Selection Analysis. in Proceedings of International Conference on Bioinformatics 2005, Bioinfo 2005. to appear. (Busan, Korea, 2005).
    5. Zheng Y# & Kwoh CK. Dynamic algorithm for inferring qualitative models of gene regulatory networks. in Proceedings of the 3rd Computational Systems Bioinformatics Conference, CSB 2004, 353-362 (Stanford, CA, 2004, Acceptance Ratio 30/202).
    6. Zheng Y# & Kwoh CK. Identifying decision lists with the discrete function learning algorithm. in Proceedings of the 2nd International Conference on Artificial Intelligence in Science And Technology, AISAT 2004, 30-35 (Hobart, Australia, 2004).
    7. Zheng Y# & Kwoh CK. Improved MDL score for learning of Bayesian networks. in Proceedings of the 2nd International Conference on Artificial Intelligence in Science And Technology, AISAT 2004, 98-103 (Hobart, Australia, 2004).
    8. Zheng Y# & Kwoh CK. Reconstructing Boolean networks from noisy gene expression data. in Proceedings of the 8th International Conference on Control, Automation, Robotics and Vision, ICARCV 2004, 1049-1054 (Kunming, China, 2004)
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