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王秀杰


王秀杰,博士,研究员,博士生导师
 
        1998年获南开大学生物学专业学士学位, 2000年获香港科技大学生物化学专业硕士学位, 2004年6月获洛克菲勒大学 (The Rockefeller University) 生物信息学专业博士学位, 同年在洛克菲勒大学从事博士后研究。2004年12月加入中国科学院遗传与发育生物学研究所。入选中科院“百人计划”。
 
        现任国家重大科学研究计划项目首席科学家。担任 RNA Biology, BMC Genomics, Journal of Genetics and Genomics 等杂志编委。兼任第十二届中华青年全国联合会科学技术界别工作委员会副主任委员、第五届中国青年科技工作者协会常务理事、中国细胞生物学学会功能基因组信息学与系统生物学分会副会长等职务。
 
        研究方向为生物信息学和系统生物学,重点关注非编码RNA和表观遗传修饰相关的功能与机制。


近期研究重点:
 
        1.非编码RNA与表观遗传修饰在哺乳动物胚胎干细胞多能性调控中的功能与机制研究
        利用新一代高通量测序技术,发现对哺乳动物胚胎干细胞多能性的获得与维持具有重要调控作用的microRNA、lncRNA等非编码RNA并研究部分非编码RNA的作用机制,研究RNA甲基化等表观遗传修饰对哺乳动物胚胎干细胞多能性的影响与机理。
 
        2.细胞分化与组织器官形成的调控机制研究
        整合各种高通量测序数据,解析哺乳动物细胞分化与主要组织器官形成的调控网络,挖掘调控哺乳动物细胞分化与主要组织器官形成的关键因子。
 
        3. 生物信息学算法和软件的开发
        已开发软件:
GOEAST (Gene Ontology Enrichment Analysis Software Toolkit)      
            psRobot (Plant Small RNA Analysis Toolbox)
            ISRNA (Integrative Short Reads NAvigator)
 
奖励与荣誉:
2016年       入选中组部“万人计划领军人才”
2016年       国家自然科学奖二等奖 (排名第四)
2016年       高等学校科学研究优秀成果自然科学奖一等奖 (排名第七)
2016年       “中源协和生命医学奖”创新突破奖
2016年       中国科学院“优秀研究生指导教师奖”
2015年      “全国五一巾帼标兵”荣誉称号
2015年      “全国三八红旗集体”荣誉称号
2014年       入选科技部“中青年科技创新领军人才”
2014 年       国家自然科学奖二等奖(排名第二)
2014年      中国科学院京区“巾帼建功”先进集体奖
2013年      “中国青年五四奖章”荣誉称号
2013 年      中国科学院“杰出科技成就奖”集体奖
2012 年     “全国青年岗位能手”荣誉称号
2012年      中央国家机关青年“五四奖章标兵”荣誉称号
2007 年      杜邦青年科学家奖
2007 年      国家杰出青年科学基金

Publications:
 
2017

1. Wang M, Wu HJ, Fang J, Chu CC and Wang XJ*. (2017) A long noncoding RNA involved in rice reproductive development by negatively regulating osa-iR160. Science Bulletin 62:470-475.

2. Chen M, Liu X, Jie D, Wang XJ* and Xia L*. (2017) Differentiated regulation of immune-response related genes between LUAD and LUSC subtypes of lung cancers. Oncotarget  8:133-144.

3. Deonovic B, Wang YH, Weirather J, Wang XJ and Au KF*. (2017) IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing. Nucleic Acids Research 45:e32.

2016

4. Feng GH, Tong M, Xia BL, Luo GZ, Wang M, Xie DF, Wan HF, Zhang Y, Zhou Q* and Wang XJ*. (2016) Ubiquitously expressed genes participate in cell-specific functions via alternative promoter usage. EMBO Reports 17: 1304-1313.

5. Zhang ZH, Liu XY, Guo XW, Wang XJ* and Zhang XR*. (2016) Arabidopsis AGO3 predominantly recruits 24-nt small RNAs to regulate epigenetic silencing. Nature Plants 2:16049. 

6. Zhang Y, Feng GH, Xu K, Wang LB, Cui P, Li YH, Wang CX, Teng F, Hao J, Wan HF, Tan YQ, Wang XJ* and Zhou Q*. (2016) A non-invasive method to determine the pluripotent status of stem cells by culture medium microRNA expression detection. Scientific Reports 6: 22380.

7. Li X, Cui XL, Wang JQ, Wang YK, Li YF, Wang LY, Wan HF, Li TD, Feng GH, Shuai L, Li ZK, Gu Q, Hao J, Wang L, Zhao XY, Liu ZH, Wang XJ, Li W* and Zhou Q*. (2016) Generation and application of mouse-rat allodiploid embryonic stem cells. Cell 164(1-2): 279-292.

8. Xiao W, Adhikari S, Dahal U, Chen YS, Hao YJ, Sun BF, Sun HY, Li A, Ping XL, Lai WY, Wang X, Ma HL, Huang CM, Yang Y, Huang N, Jiang GB, Wang HL, Zhou Q, Wang XJ, Zhao YL and Yang YG*. (2016) Nuclear m6A reader YTHCD1 regulates mRNA splicing. Molecular Cell 61(4): 507-519.

9. Li ZK, Wan HF, Feng GH, Wang LY, He ZQ, Wang YK, Wang XJ, Li W*, Zhou Q* and Hu BY*. (2016) Birth of fertile bimaternal offspring following intracytoplasmic injection of parthenogenetic haploid embryonic stem cells. Cell Research 26(1): 135-138.
 
2015
10.Chen T, Hao YJ, Zhang Y, Li MM, Wang M, Han W, Wu Y, Lv Y, Hao J, Wang L, Li A, Yang Y, Jin KX, Zhao X, Li Y, Ping XL, Lai WY, Wu LG, Jiang G, Wang HL, Sang L, Wang XJ*, Yang YG* and Zhou Q*. (2015) m6A RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency. Cell Stem Cell (Cover Story) 16:289-301. (*co-corresponding author) 

On the cover: In this issue, Chen et al. (289–301) showthat m6A modifications on mRNAs are enriched at microRNA target sites,   the formation of m6A modification is regulated by microRNAs via a sequence pairing mechanism, and increased m6A formation promotes cell reprogramming to pluripotency. The cover art depicts the formation of m6A on mRNA sequences. m6A (the fire) is formed on adenosine (the beacon towers) within the RRACH motif, with the help of microRNAs (the firewood)

11. Castillo-González C, Liu XY, Huang CJ, Zhao CJ, Ma ZY, Hu T, Sun F, Zhou YJ, Zhou XP, Wang XJ and Zhang XR*. (2015) Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense. Elife 4: e06671.

12. Shuai L, Wang YK, Dong MZ, Wang XP, Sang LS, Wang M, Wan HF, Luo GZ, Gu TT, Yuan Y, Feng CJ, Teng F, Li W, Liu XY, Li TD, Wang L, Wang XJ, Zhao XY and Zhou Q*. (2015) Durable pluripotency and haploidy in epiblast stem cells derived from haploid embryonic stem cells in vitro. Journal of Molecular Cell Biology 7(4): 326-337.

13. Liu YL, Su HD, Pang JL, Gao Z, Wang XJ, Birchler JA* and Han FP*. (2015) Sequential de novo centromere formation and inactivation on a chromosomal fragment in maize. Proc. Natl. Acad. Sci. USA 112(11): E1263-71.

14. Zhao YT, Wang M, Wang ZM, Fang RX, Wang XJ* and Jia YT*. (2015) Dynamic and coordinated expression changes of rice small RNAs in response to Xanthomonas oryzae pv. oryzae. Journal of Genetics and Genomics 42(11): 625-37. (*co-corresponding author)
 
2014
15. Luo GZ, Yang W, Ma YK and Wang XJ*. (2014) ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data. Bioinformatics 30: 434-436.

16. Liu YX, Wang M and Wang XJ*. (2014) Endogenous small RNA clusters in plants. Genomics Proteomics Bioinformatics 12: 64-71.

17. Gao W, Sun HX, Xiao HB, Cui GH, Hillwig ML, Jackson A, Wang X, Shen Y, Zhao N, Zhang LX, Wang XJ*, Peters RJ* and Huang LQ*. (2014) Combining metabolomics and transcriptomics to characterize tanshinone biosynthesis in Salvia miltiorrhiza. BMC Genomics 15: 73. (*co-corresponding author)

18. Li W, Li X, Li TD, Jiang MG, Wan HF, Luo GZ, Feng CJ, Cui XL, Teng F, Yuan Y, Zhou Q, Gu Q, Shuai L, Sha JH, Xiao YM, Wang L, Liu ZH, Wang XJ, Zhao XY and Zhou Q*. (2014) Genetic modification and screening in rat using haploid embryonic stem cells. Cell Stem Cell 14: 404-414.

19. Cui Y, Xiao Z, Chen T, Wei J, Chen L, Liu L, Chen B, Wang XJ, Li X and Dai JW*. (2014) The miR-7 identified from collagen biomaterial-based three-dimensional cultured cells regulates neural stem cell differentiation. Stem Cells and Development 23: 393-405.

2013

20. Wu HJ, Wang ZM, Wang M and Wang XJ*. (2013) Wide-spread long non-coding RNAs (lncRNAs) as endogenous target mimics (eTMs) for microRNAs in plants. Plant Physiology 161: 1875-84.

21. Zhang Y, Teng F, Luo GZ, Wang M, Tong M, Zhao XY, Wang L, Wang XJ* and     Zhou Q*. (2013) MicroRNA-323-3p regulates the activity of polycomb repressive complex 2 (PRC2) via targeting the mRNA of embryonic ectoderm development (Eed) gene in mouse embryonic stem cells. Journal of Biological Chemistry 288: 23659-23665. (*co-corresponding author)

22. Liu X, Zhang Y, Tong M, Liu XY, Luo GZ, Xie DF, Ren SF, Bai DH, Wang L, Zhou Q and Wang XJ*. (2013) Identification of a small molecule 1,4-bis-[4-(3-phenoxy-ropoxy)-but-2-ynyl]-piperazine as a novel inhibitor of the transcription factor p53. Acta Pharmacologica Sinica 34: 805–810.

23. Li W, Yang W and Wang XJ*. (2013) Pseudogenes: pseudo or real functional elements? Journal of Genetics and Genomics 40: 171-177.

24. Zhang XM, Ma YZ, Liu XY, Zhou Q* and Wang XJ*. (2013) Evolutionary and functional analysis of the key pluripotency factor Oct4 and its family proteins. Journal of Genetics and Genomics 40: 399-412. (*co-corresponding author)

25. Ling HQ*, Zhao SC, Liu DC, Wang JY, Sun H, Zhang C, Fan HJ, Li D, Dong LL, Tao Y, Gao C, Wu HL, Li YW, Cui Y, Guo XS, Zheng SS, Wang B, Yu K, Liang QS, Yang WL, Lou XY, Chen J, Feng MJ, Jian JB, Zhang XF, Luo GB, Jiang Y, Liu JJ, Wang ZB, Sha YH, Zhang BR, Wu HJ, Tang DZ, Shen QH, Xue PY, Zou SH, Wang XJ, Liu X, Wang FM, Yang YP, An XL, Dong ZY, Zhang KP, Zhang XQ, Luo MC, Dvorak J, Tong YP, Wang J, Yang HM, Li ZS*, Wang DW*, Zhang AM* and Wang J*. (2013) Draft genome of the wheat A-genome Triticum urartu. Nature 496: 87-90.

26. Zhu H, Zhou Y, Castillo-González C, Lu A, Ge C, Zhao YT, Duan L, Li Z, Axtell MJ, Wang XJ and Zhang XR* (2013). Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1. Nature Structureal & Molecular Biology 20: 1106-1115. (Cover story)

27. Li RC, Tao J, Guo YB, Wu HD, Liu RF, Bai Y, Lv ZZ, Luo GZ, Li LL, Wang M, Yang HQ, Gao W, Han QD, Zhang YY, Wang XJ, Xu M* and Wang SQ*. (2013) In vivo suppression of microRNA-24 prevents the transition toward decompensated hypertrophy in aortic-constricted mice. Circulation Research 112: 601-605.

28. Zhang B#, Lv ZL#, Pang JL#, Liu YL, Guo X, Fu SL, Li J, Dong QH, Wu HJ, Gao Z, Wang XJ* and Han FP*. (2013) Formation of a functional maize centromere after loss of centromeric sequences and gain of ectopic sequences. Plant Cell 25(6): 1979-1989. (*co-corresponding author)

29. Fu SL, Lv ZL, Gao Z, Wu HJ, Pang JL, Zhang B, Dong QH, Guo X, Wang XJ, Birchler JA* and Han F*. (2013)  De novo centromere formation on a chromosome fragment in maize. Proc. Natl. Acad. Sci. USA 110: 6033-6036.

30. Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang CM, Li CJ, Vagbo CB, Shi Y, Wang WL, Song SH, Lu Z, Bosmans RP, Dai Q, Hao YJ, Yang X, Zhao WM, Tong WM, Wang XJ, Bogdan F, Furu K, Fu Y, Jia G, Zhao X, Liu J, Krokan HE, Klungland A, Yang YG* and He C*. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Molecular Cell 10: 18-29.

31. Shi ZM, Luo GZ, Fu LJ, Fang ZD, Wang XJ and Li XC*. (2013) miR-9 and miR-140-5p target FoxP2 and are regulated by the social context of song behavior in zebra finches. Journal of Neuroscience 16: 16510-16521.

32. Niu YM, Zhao X, Wu YS, Li MM, Wang XJ and Yang YG*. (2013) N6-methyl-    adenosine (m6A) in RNA: an old modification with a novel epigenetic function. Genomics Proteomics Bioinformatics 11: 8-17.

2012

33. Xu M, Wu HD, Li RC, Zhang HB, Wang M, Tao J, Feng XH, Guo YB, Li SF, Lai ST,  Zhou P, Li LL, Yang HQ, Luo GZ, Bai Y, Xi J, Gao W, Han QD, Zhang YY, Wang XJ*, Meng X and Wang SQ*. (2012) Mir-24 regulates junctophilin-2 expression in cardiomyocytes. Circulation Research 111: 837-841. (*co-corresponding author)

34. Wu HJ, Zhang Z, Wang J, Oh DH, Dassanayake M, Liu B, Huang Q, Sun HX, Xia R,  Wu Y, Wang Y, Yang Z, Liu Y, Zhang W, Zhang H, Chu J, Yan C, Fang S, Zhang J, Wang Y, Zhang F, Wang G, Lee SY, Cheeseman JM, Yang B, Li B, Ming J, Yang L, Wang J, Chu CC*, Chen SY*, Bohert HJ, Zhu JK*, Wang XJ* and Xie Q*. (2012) Insights into salt tolerance from the genome of Thellungislla salsuginea. Proc. Natl. Acad. Sci. USA 109: 12219-12224. (*co-corresponding author)

35. Wu HJ, Ma YK, Chen T, Wang M and Wang XJ*. (2012) PsRobot: a web-based plant small RNA meta-analysis toolbox. Nucleic Acids Research 40: W22-W28.

36. Zhao YT, Wang M, Fu SX, Yang WC, Qi CK and Wang XJ*. (2012) Small RNA profiling in two Brassica napus cultivars identifies microRNAs with oil production and developmental correlated expressions and new small RNA classes. Plant Physiology 158: 813-823.

37. Luo GZ, Hafner M, Shi ZM, Brown M, Feng GH, Tuschl T, Wang XJ* and Li XC*. (2012) Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression. BMC Genomics 13: 727. (*co-corresponding author)

38. Li W, Shuai L, Wan HF, Dong MZ, Wang M, Sang LS, Feng CJ, Luo GZ, Li TD, Li X, Wang LB, Zheng QY, Sheng C, Wu HJ, Liu ZH, Liu L, Wang L, Wang XJ, Zhao XY* and Zhou Q*. (2012) Androgenetic haploid embryonic stem cells produce live transgenic mice. Nature 490: 407-411.

39. Du YY, Gao C, Liu ZY, Wang L, Liu B, He F, Zhang T, Wang Y, Wang XJ, Xu MJ, Zhu Y, Xu QB, Wang X* and Kong W*. (2012) Up-regulation of ADAMTS-7 by miR-29 expression mediates vascular smooth muscle calcification. Arteriosclerosis, Thrombosis, and Vascular Biology 32: 2580-2588.

40. Zhang C, Xu YY, Guo SY, Zhu JY, Huan Q, Liu HH, Wang L, Guo GZ, Wang XJ and Chong K*. (2012) Dynamics of brassinosteroid response modulated by negative regulator LIC in rice. PLoS Genetics 8: e1002686.

41. Woo J, MacPherson CR, Liu J, Wang H, Kiba T, Hannah MA, Wang XJ, Bajic VB and Chua NH*. (2012) The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation. BMC Plant Biology 12: 62.

42. Song XM, Li PC, Zhai JX, Zhou M, Ma LJ, Liu B, Jeong DH, Nakano M, Cao SY, Liu CY, Chu CC, Wang XJ, Green PJ, Meyers BC and Cao XF*. (2012) Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. The Plant Journal 69: 462-474

43. Xu N, Li Y, Zhao YT, Guo L, Fang YY, Zhao JH, Wang XJ, Huang L and Guo HS*. (2012) Identification and characterization of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. PLoS One 7: e35306.

44. Sheng C, Zheng QY, Wu JY, Xu Z, Wang LB, Li W, Zhang HJ, Zhao XY, Liu L, Wang ZW, Guo CL, Wu HJ, Liu ZH, Wang L, He SG, Wang XJ, Chen ZG* and Zhou Q*. (2012) Direct reprogramming of sertoli cells into multipotent neural stem cells by defiend factors. Cell Research 22: 208-218.

2011

45. Wang H, Zhang XR, Liu J, Kiba T, Woo J, Ojo T, Hafner M, Tuschl T, Chua NH* and Wang XJ*. (2011) Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions. The Plant Journal 67: 292-304. (*co-corresponding author)

46. Cui H*, Zhang ST, Yang HJ, Ji H and Wang XJ. (2011) Gene expression profile analysis of tobacco leaf trichomes. BMC Plant Biology 11: 76.

47. Lei MG, Liu YD, Zhang BC, Zhao YT, Wang XJ, Zhou YH, Raghothama KG and Liu D*. (2011) Genetic and genomic evidence that sucrose is a global regulator of plant responses to phosphate starvation in Arabidopsis. Plant Physiology 156: 1116-1130.

48. Liang H, Zhao YT, Zhang JQ, Wang XJ, Fang RX* and Jia YT*. (2011) Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae. BMC Genomics 12: 87.

49. Wong CE, Zhao YT, Wang XJ, Croft L, Wang ZH, Haerizadeh F, Mattick JS, Singh MB, Carroll BJ and Bhalla PL*. (2011) MicroRNAs in the shoot apical meristem of soybean. Journal of Experimental Botany 62: 2495-2506.

50. Wang JL, Liu DC, Guo XL, Yang WL, Wang XJ, Zhan KH and Zhang AM*.  (2011) Variability of gene expression after polyhaploidization in wheat (Triticum aestivum L.). Genes Genomics Genetics 1: 27-33.

51. Li W, Zhao XY, Wan HF, Zhang Y, Liu L, Zhuo L, Wang XJ, Wang L* and Zhou Q*. (2011)  iPS cells generated without c-Myc have active Dlk1-Dio3 region and are capable of producing full-term mice through tetraploid complementation. Cell Research 21: 550-553.

52. Tong M, Lv Z, Liu L, Zhu H, Zheng QY, Zhao XY, Li W, Wu YB, Zhang HJ, Wu HJ, Li ZK, Zeng FY, Wang L, Wang XJ, Sha JH* and Zhou Q*. (2011) Mice generated from tetraploid complementation competent iPS cells show similar developmental features as those from ES cells but are prone to tumorigenesis. Cell Research 21: 1634-1637.

2010

53. Liu L, Luo GZ, Yang W, Zhao XY, Zheng QY, Lv Z, Li W, Wu HJ, Wang L, Wang XJ* and Zhou Q*. (2010) Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells. Journal of Biological Chemistry (Cover story) 285: 19483-19490. (*co-corresponding author)

54. Zhang Y, Liu J, Jia CS, Li TT, Wu RM, Wang J, Chen Y, Zou XT, Chen RS, Wang XJ* and Zhu DH*. (2010) Systematic identification and evolutionary features of rhesus             monkey small nucleolar RNAs. BMC Genomics 11: 61. (*co-corresponding author)

55. Yang W, Zhou Q and Wang XJ*. (2010) Regulation beyond genome sequences: DNA and histone methylation in embryonic stem cells. Frontier of Biology 5: 41-47.

56. Li Y, Liu XY, Huang L, Guo HS and Wang XJ*. (2010) Potential coexistence of both bacterial and eukaryotic small RNA biogenesis and functional related protein homologs in Archaea. Journal of Genetics and Genomics 37: 493-503.

57. Xiong XH, Lu Y, Zhang LB, Wang B, Zhao YT, Wang XJ, Huo XF, Shen Y, Liang ZC* and Chen MH*. (2010) Discovery of novel cell proliferation-enhancing gene by random siRNA library based combinatorial screening. Combinatorial Chemistry & High Throughput Screening 13: 798-806.

58. Jian XY, Zhang L, Li GL, Zhang L, Wang XJ, Cao XF, Fang XH and Chen F*. (2010)  Identification of novel stress-regulated microRNAs from Oryza sativa L. Genomics 95: 47-55.

2009

59. Zheng Q, Zhang Y, Chen Y, Yang N, Wang XJ* and Zhu DH*. (2009) Systematic identification of genes involved in divergent skeletal muscle growth rates of broiler and layer chickens. BMC Genomics 10: 87. (*co-corresponding author)

60. Liu XY, Luo GZ, Bai XJ and Wang XJ*. (2009) Bioinformatic analysis of microRNA biogenesis and function related proteins in eleven animal genomes. Journal of Genetics and Genomics 36: 591-601.

61. Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, Chapman EJ, Carrington JC, Chen X, Wang XJ and Chen ZJ*. (2009) Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc. Natl. Acad. Sci. USA 106: 17835-17840.

62. Wuriyanghan H, Zhang B, Cao WH, Ma B, Lei G, Liu YF, Wei W, Wu HJ, Chen LJ, Chen HW, Cao YR, He SJ, Zhang WK, Wang XJ, Chen SY and Zhang JS*. (2009) The ethylene receptor ETR2 delays floral transition and affects starch accumulation in rice. Plant Cell 21: 1473-1494.

63. Besecker MI, Harden ME, Li G, Wang XJ and Griffiths A*. (2009) Discovery of herpes B virus-encoded microRNAs. Journal of Virology 83: 3413-3416.

64. Zhou YH, Li SB, Qian Q, Zeng DL, Zhang M, Guo LB, Liu XL, Zhang BC, Deng LW, Liu XF, Luo GZ, Wang XJ and Li JY*. (2009) BC10, a DUF266-containing and golgi-located type II membrane protein, is required for cell wall biosynthesis in rice (Oryza  sativa L.). The Plant Journal 57: 446-462.

65. Huang YH, Huang XH, Liu H, Gong J, Ouyang ZL, Cui HC, Cao JH, Zhao YT, Wang XJ, Jiang YL* and Qin QW*. (2009) Complete sequence determination of a novel reptile iridovirus isolated from soft-shelled turtle and evolutionary analysis of iridoviridae. BMC Genomics 10: 224.

66. Zhang Y, Wang J, Huang SJ, Zhu XP, Liu J, Yang N, Song DD, Wu RM, Deng W, Skogerbø G, Wang XJ, Chen RS* and Zhu DH*. (2009) Systematic identification and characterization of chicken (Gallus gallus) ncRNAs. Nucleic Acids Research 37: 6562-6574.

67. Ruan MB, Zhao YT, Meng ZH, Wang XJ* and Yang WC*. (2009) Conserved miRNA analysis in Gossypium hirsutum through small RNA sequencing. Genomics 94: 263-268.

68. Wang YW, Li PC, Cao XF, Wang XJ, Zhang AM and Li X*. (2009) Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules. Biochemical Biophysical Research Communications 378: 799-803.

2008

69. Zheng Q and Wang XJ*. (2008) GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res. 36: W358-W363. 

70. Mu JY, Tan HL, Zheng Q, Fu FY, Liang Y, Zhang J, Yang XH, Wang T, Chong K, Wang XJ and Zuo JR*. (2008) LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis thaliana. Plant Physiology 148: 1042-1054.

71. Lu FL, Li GL, Cui X, Liu CY, Wang XJ and Cao XF*. (2008) Comparative analysis of JmjC domain-containing proteins in higher plants and human reveals potential histone demethylases in Arabidopsis and rice. Journal of Integrative Plant Biology 50: 886-896.

2007

72. Zhao T, Li GL, Mi SJ, Li S, Hannon GJ, Wang XJ* and Qi YJ*. (2007) A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes & Development 21: 1190-1203. (*co-corresponding Author) 

73. Li XC*, Wang XJ*, Tannenhauser J, Podell S, Mukherjee P, Hertel, M, Biane J, Masuda S, Nottebohm F and Gaasterland T. (2007) Genomic resources for songbird research and their use in characterizing gene expression during brain development. Proc. Natl. Acad. Sci. USA 104: 6834-6839. (*co-first author)

74. Liu B, Chen ZY, Song XW, Liu CY, Cui X, Zhao XF, Fang J, Xu WY, Zhang HY, Wang XJ, Chu CC, Deng XW, Xue YB and Cao XF*. (2007) Oryza sativa Dicer-like4 reveals a key role for small interfering RNA silencing in plant development. Plant Cell 19: 2705-2718.

75. Li PJ, Wang YH, Qian Q, Fu ZM, Wang M, Zeng DL, Li BH, Wang XJ and Li JY*. (2007) LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Research 15: 402-410.

76. Liu XQ, Bai XQ, Wang XJ and Chu CC*. (2007) OsWRKY71, a rice transcription factor, is involved in rice defense response. Journal of Plant Physiology 164: 969-979. 

2006

77. Wang H, Chua NH and Wang XJ*. (2006) Prediction of trans-antisense transcripts in Arabidopsis thaliana. Genome Biology 7: R92.  

78. Qi YJ, He XY, Wang XJ, Kohany O, Jurka J and Hannon GJ*. (2006) Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443: 1008-1012.

79. Cui C, Griffiths A, Li G, Silva LM, Kramer MF, Gaasterland T, Wang XJ* and Coen DM*. (2006) Prediction and identification of herpes simplex virus 1-Encoded microRNAs. Journal of Virology 80: 5499-5508. (* co-corresponding author)

80. Li G, Tao S and Wang XJ*. (2006) Sequence and epitope analysis of surface proteins of avian influenza H5N1 viruses from Asian patients. Chinese Science Bulletin 51: 472-2481. 

81. Liu J and Wang XJ*. (2006) An integrative analysis of the effects of auxin on jasmonic acid biosynthesis in Arabidopsis thaliana. Journal of Integrative Plant Biology 48: 110-114. 

82. Luo AD, Qian Q, Yin HF, Liu XQ, Yin CX, Lan Y, Tang JY, Tang ZS, Cao SY, Wang XJ, Xia K, Fu XD, Luo D* and Chu CC*. (2006) EUI1, encoding a putative cytochrome P450 monooxygenase, regulates the internodes elongation by modulating GA responses in rice. Plant Cell Physiology 47: 181-191.

2005 and before

83. Wang XJ, Gaasterland T and Chua NH*. (2005) Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biology 6: R30.

84. Liu XQ, Bai XQ, Qian Q, Wang XJ, Chen MS and Chu CC*. (2005) OsWRKY03, a rice transcriptional activator that functions in defense signaling pathway upstream of OsNPR1. Cell Research 15: 593-603.

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