• 郑云(Yun Zheng)

    博士,副教授,硕士生导师

    一、受教育经历

    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月和2013年4到5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。

    二、主要研究方向

    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。

     

    三、科研领域描述

    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。

     

    四、承担科研项目情况

    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。
    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。
    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。
    2010年1月 – 2014年1月,国家重大科学研究计划(973)项目“组织干细胞识别、谱系重编程和示踪研究”,项目编号:2010CB945500,研究骨干,40万元人民币。
    2011年4月– 2013年3月,局部化栓塞治疗对癌症组织microRNA转录组的影响,上海中山医院,项目编号:2008ZX10002-018,PI,14万元人民币。

    五、获奖情况

    2013年11月-12月 新加坡南洋理工大学Visiting Professorship
    2013年4月 – 5月 美国俄克拉荷马州立大学Visiting Scholarship
    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
    2011年10月 2009-2010年度海南省自然科学优秀学术论文一等奖
    2011年7月 – 8月 新加坡南洋理工大学Visiting Professorship
    2011年3月 – 4月 美国俄克拉荷马州立大学Visiting Scholarship
    2006年8月 – 2009年1月 华盛顿大学圣路易斯Postdoctoral Fellowship
    2005年12月 – 2006年8月 新加坡国立大学Postdoctoral Fellowship
    2002年9月 – 2005年9月 新加坡南洋理工大学Fellowship

    六、代表性论文

    1.Yaish M.W., Patankar H.V., Assaha D.V.M.,Zheng Y., Al-Yahyai R., Sunkar R. Genome-wide expression profiling in leaves and roots of date palm (Phoenix dactylifera L.) exposed to salinity. BMC Genomics (2017) 18: 246.

    2. Ghorecha, V., Zheng, Y., Liu, L., Sunkar, R., & Krishnayya, N. S. R. MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress. Physiology and Molecular Biology of Plants 2017, 23: 291.

    3. 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.

    4. 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.

    5. 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)

    6. 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 = 9.2)

    7. 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)

    8. 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)

    9. 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 = 5.62)

    10. 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)

    11. 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)

    12. 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)

    13. 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)

    14. Zheng Y#, Wang S, Sunkar R. 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)

    15. Zheng Y#, Li T, Ren R, Shi D, Wang S. 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)

    16. 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)

    17. Zhang X, Zheng Y, Jagadeeswaran G, Ren R, Sunkar R and Jiang H. Identification of conserved and novel microRNAs in Manduca sextaand 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)

    18. 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)

    19. 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)

    20. Zheng Y# and Kwoh CK. Improved Time Complexities for Learning Boolean Networks. Entropy 2013, 15(9):3762-3795. (IF = 1.56)

    21. Han M and Zheng Y*#. Comprehensive Analysis of Single Nucleotide Polymorphisms in Human MicroRNAs. PLoS ONE 2013. 8(11): e78028. (IF = 3.53)

    22. Yun Zheng, Guru Jagadeeswaran, Kanchana Gowdu, Nian Wang, Shaohua Li, Ray Ming, Ramanjulu Sunkar. Genome-Wide Analysis of MicroRNAs in Sacred Lotus,

    Nelumbo nucifera (Gaertn). Tropical Plant Biol. 2013, 6:117-130.

    23. 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)

    24. 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)

    25. 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)

    26. Alabi OJ, Zheng Y*, Jagadeeswaran G, Sunkar R and Naidu RA. 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)

    27. Zhang X, Zheng Y, Jagadeeswaran G, Ren R, Sunkar R and Jiang H. Identification and developmental profiling of conserved and novel microRNAs in Manduca sexta. Insect Biochemistry and Molecular Biology 2012, 42:381-395 (IF=3.53)

    28. Zheng Y#, Li Y-F, Sunkar R, Zhang W. SeqTar: An Effective Method for Identifying MicroRNA Guided Cleavage Sites from Degradome of Polyadenylated Transcripts in Plants. Nucleic Acids Research 2011, 40:e28.(IF = 8.81)

    29. Zhang L, Zheng Y*, Jagadeeswaran G, Li Y, Gowdu K, Sunkar R. Identification and temporal expression analysis of conserved and novel microRNAs in Sorghum. Genomics 2011, 98(6):460-8. (IF = 2.79)

    30. Zheng Y# and Kwoh CK. A Feature Subset Selection Method Based On High-Dimensional Mutual Information. Entropy 2011, 13(4):860-901; doi:10.3390/e13040860. (IF=1.56)

    31. Zheng Y# and Zhang W. Animal microRNA Target Prediction Using Diverse Sequence-Specific Determinants. Journal of Bioinformatics and Computational Biology 2010, 8:763-788.(IF=0.93)

    32. Jagadeeswaran G, Zheng Y*, Sumathipala N, Jiang H, Arrese E, Soulages J, Zhang W, Sunkar R. 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)

    33. Li Y-F, Zheng Y, Addo-Quaye C, Zhang L, Saini A, Jagadeeswaran G, Axtell MJ, Zhang W, Sunkar R. Transcriptome-wide identification of microRNA targets in rice. The Plant Journal 2010, 62:742-759. (IF=6.82)

    34. Reddy A, Zheng Y*, Jagadeeswaran G, Macmil SL, Graham WB, Roe BA, Desilva U, Zhang W, Sunkar R. Cloning, characterization and expression analysis of porcine microRNAs. BMC Genomics 2009, 10:65. (IF=4.04)

    35. Jagadeeswaran G, Zheng Y*, Li Y-F, Shukla LI, Matts J, Hoyt P, Macmil SL, Wiley GB, Roe BA, Zhang W, Sunkar R. 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)

    36. Zeng C, Wang W, Zheng Y*, Chen X, Bo W, Song S, Zhang W, Peng M. Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants. Nucleic Acids Research 2009. 38:981-995. (IF=8.81)

    37. Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu J-K. Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biology 2008, 8:25. (IF=3.94)

    38. Zheng Y# and Kwoh CK. 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)

    39. Zheng Y# and Kwoh CK. Cancer Classification With MicroRNA Expression Patterns Found By An Information Theory Approach. Journal of Computers 2006. 1(5):30-39.

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