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。

   

071021-生物信息学

基因组学
系统生物学和生物信息学

   

2023-11-01-2027-10-30,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, 会长
2023-01-01-2028-12-31,中国生物工程学会计算生物学与生物信息学专业委员会, 副主任
2022-08-06-2027-08-05,中国医药教育协会医学基因组学与生物信息学专业委员会, 主任委员
2022-01-01-今,Science Bulletin, 编委
2022-01-01-今,Life Medicine, 副主编
2021-07-01-今,RSC Chemical Biology, Advisory
2021-01-01-今,Frontiers in Bioinformatics, 副主编
2021-01-01-今,Genomics, Proteomics and Bioinformatics, 编委
2020-11-01-2025-11-30,中国侨联特聘专家委员会青年委员会, 委员
2020-01-01-今,第八届ISHR中国分会执委会, 委员
2020-01-01-今,中国病理生理学会心血管专业委员会, 委员
2020-01-01-2025-12-31,第十三届中华全国青年联合会, 常委
2019-01-01-2024-12-31,中国遗传学会青年委员会, 副主任
2009-01-01-今,RNA Biology, 编委
2009-01-01-今,Quantitative Biology, 编委

干细胞研究进展系列讲座、 生物信息学应用、 生物信息学、 人类基因组学研究-进展与应用、 遗传发育学系列讲座

2007年获得国家自然科学基金委杰出青年科学基金和美国杜邦公司青年科学家奖。2012年获得“中央国家机关五四青年奖章标兵”和“全国青年岗位能手”荣誉称号。2013年获得“中国青年五四奖章”荣誉称号，作为共同完成人获得“中国科学院杰出科技成就奖集体奖”。2014年作为第二完成人，获得国家自然科学奖二等奖。2015年获得“全国五一巾帼标兵”荣誉称号，入选科技部“中青年科技创新领军人才”。

曾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。

（1） 3D Pioneers Challenge 医学技术创新奖, 其他, 2022
（2） 中国科学院大学领雁银奖振翅奖, 部委级, 2021
（3） 教育部课程思政教学名师和教学团队, , 部委级, 2021
（4） 中国科学院教育教学成果奖, 一等奖, 院级, 2020
（5） 中国侨联第八届“中国侨届贡献奖”, 一等奖, 国家级, 2020
（6） 中国科学院大学教育教学成果奖, 一等奖, 研究所（学校）, 2020
（7） 中国科学院大学2019年校级“研究生优秀课程”, , 研究所（学校）, 2019
（8） 中国科学院朱李月华优秀教师奖, 院级, 2017
（9） 中组部“万人计划领军人才”, 国家级, 2016
（10） 中源协和生命医学奖创新突破奖, 其他, 2016
（11） “植物小RNA的功能及作用机理”获得国家自然科学奖, 二等奖, 国家级, 2016
（12） 教育部自然科学奖, 一等奖, 部委级, 2016
（13） 中国科学院大学生命科学学院“精品课程”, 院级, 2016
（14） 非编码RNA重大研究计划指导专家组, 国家级, 2016
（15） 中国科学院“优秀研究生指导教师”奖, 院级, 2016
（16） “全国三八红旗集体”荣誉称号, 国家级, 2015
（17） “全国五一巾帼标兵”荣誉称号, 国家级, 2015
（18） 科技部“中青年科技创新领军人才”, 国家级, 2014
（19） “哺乳动物多能性干细胞的建立与调控机制研究”获得国家自然科学奖, 二等奖, 国家级, 2014
（20） 中国科学院京区“巾帼建功”先进集体, , 院级, 2014
（21） 第十七届“中国青年五四奖章”荣誉称号, , 国家级, 2013
（22） “血管稳态与重构的调控机制”指导专家组, 国家级, 2013
（23） “干细胞多能性机理与转化研究”获得中国科学院杰出科技成就奖, 院级, 2013
（24） “全国青年岗位能手”荣誉称号, 部委级, 2012
（25） 第二届“中央国家机关青年五四奖章标兵”荣誉称号, , 国家级, 2012
（26） 国家杰出青年基金, , 国家级, 2007
（27） 杜邦青年科学家奖, , 其他, 2007

[1] 一种类器官模型及其构建方法和应用. 2024-01-05.
[2] 一种人参根瘤菌及其应用. 2023-11-10.
[3] 王秀杰, 王猛, 谢冬芳, 张猛. 麦冬皂苷 D’在治疗抗肿瘤药物引起的心肌损伤中应用. CN115607562B, 2024-03-19.
[4] 王秀杰, 王猛, 谢冬芳, 张猛. 人参皂苷 Rh2、麦冬皂苷 D 联合五味子乙素在治疗心肌损伤中的应用. CN115778967B, 2023-11-14.
[5] 王秀杰, 王猛, 谢冬芳, 张猛. 异绿原酸C在治疗抗肿瘤药物引起的心肌损伤中的应用. CN115590845B, 2023-10-27.
[6] 王秀杰, 周一新, 刘鑫, 宋洋, 王猛, 张豪. 一种侵蚀性蛋白酶抑制剂及其应用. CN: CN116687925A, 2023-09-05.
[7] 肖晗, 张幼仪, 王秀杰, 冯姗. 一种用于抑制纤维化的小分子药物及其应用. CN114533726B, 2022-09-09.
[8] 肖晗, 张幼仪, 王秀杰, 冯姗, 刘鑫. 一种用于抑制纤维化的小分子药物及其应用. CN114560817B, 2022-10-25.
[9] 王秀杰, 王猛, 郭庆华, 刘永进, 史庆庆, 庞树鑫, 吴陈铭, 韩义恒. 一种植物表型组学信息获取系统. CN: CN212364582U, 2021-01-15.
[10] 王秀杰, 叶岷, 王猛, 史庆庆. 一种自动移液系统及其控制方法. CN111398613B, 2021-11-09.
[11] 王秀杰, 叶岷, 王猛, 史庆庆. 一种枪头自动整理装置. CN: CN212149447U, 2020-12-15.
[12] 王秀杰, 叶岷, 王猛, 史庆庆. 一种自动移液系统. CN: CN212142666U, 2020-12-15.
[13] 刘永进, 吴陈铭, 韩义恒, 王秀杰, 王猛. 植物表型采集系统. CN: CN209820401U, 2019-12-20.
[14] 刘永进, 吴陈铭, 王秀杰, 王昌凌, 史庆庆, 张泽宇. 一种生物3D打印温控系统. CN: CN209813097U, 2019-12-20.
[15] 王秀杰, 王昌凌, 刘永进, 张泽宇, 史庆庆. 三维生物打印系统和方法. CN: CN113677505B, 2023-08-18.
[16] 刘永进, 吴陈铭, 王秀杰, 王昌凌, 戴澄恺, 方国鑫, 史庆庆, 张泽宇. 一种生物3D打印培养一体化装置. CN: CN209778889U, 2019-12-13.
[17] 王秀杰, 张泽宇, 王猛, 谢冬芳, 黄增辉. 评估或改善脑功能、学习能力或记忆力的组合物和方法. CN112585270B, 2023-12-05.
[18] 王秀杰, 王猛, 储成才, 方军, 曹守云. miR1432在水稻干旱胁迫中的应用. CN: CN105274113B, 2018-05-04.
[19] 王秀杰, 叶岷, 王猛, 史庆庆. 一种立体库. CN: CN211972364U, 2020-11-20.
[20] 王秀杰, 叶岷, 王猛, 史庆庆. 一种枪头自动整理方法. CN: CN111348387B, 2021-09-24.
[21] 周琪, 杨运桂, 王秀杰, 陈同, 张映, 郝亚娟, 李苗苗, 王猛. miRNA对m6A修饰水平的调控方法及其应用. CN: CN107207557B, 2020-07-10.
[22] 周琪, 王秀杰, 顾奇, 郝捷, 韩伟方, 刘鑫, 王磊, 王柳. 一种诱导多能干细胞的培养基及其用途. CN: CN104195103B, 2017-05-31.
[23] 王秀杰, 周琪, 刘鑫, 张映, 佟曼, 郝捷, 王柳, 顾奇, 谢东芳, 白冬辉, 任少芳. 哌嗪衍生物作为p53分子调节剂的用途. CN: CN104208066B, 2016-06-15.
[24] 王秀杰, 王猛, 吴华君, 王志敏. ath-eTM160在抑制microRNA160功能中的应用. CN: CN102864146B, 2014-05-14.
[25] 王秀杰, 王猛, 储成才, 曹守云. 一种RNA及产生该RNA的基因在调控水稻根系发育中的应用. CN: CN102851280B, 2014-12-31.
[26] 周琪, 王秀杰, 张映. 无损检测细胞miRNA的表达量及确定细胞类型与状态的方法. CN: CN103571929B, 2016-05-11.
[27] 王秀杰, 徐明, 王世强, 王猛, 李素芳, 骆观正. miR-24用于治疗或诊断心衰或患心衰倾向或者改善心肌细胞功能的方法. CN: CN102242080B, 2014-03-05.
[28] 周琪, 王秀杰, 王柳, 刘蕾, 赵小阳, 杨维, 骆观正, 吕卓, 郑钦元, 吴华君, 李伟. 用于鉴定或调控细胞多能性的关键基因、microRNA、其它非编码RNA或其组合. CN: CN102212517B, 2015-01-07.

   

（ 1 ） 遗传学, 主持, 国家级, 2008-01--2011-12
（ 2 ） 非编码RNA研究的新理论、新技术的发展及神经和肌肉早期发育过程中非编码RNA的系统发现, 主持, 国家级, 2007-07--2011-08
（ 3 ） 影响水稻幼苗生长的激素互作网络研究和职务激素相关数据整合平台的建立, 主持, 国家级, 2010-01--2012-12
（ 4 ） 高通量测序数据中新类型小分子非编码RNA的鉴定和相关生物信息学方法的开发, 主持, 部委级, 2010-11--2013-11
（ 5 ） RNA介导的体细胞重编程技术, 主持, 部委级, 2011-01--2015-12
（ 6 ） 细胞命运维持与转化的表观遗传调控作用与机制研究, 主持, 国家级, 2014-01--2018-08
（ 7 ） microRNA或microRNA基因簇在干细胞多能性维持与分化过程中的作用与调控机制, 参与, 国家级, 2011-01--2015-12
（ 8 ） 真核生物基因保守性的系统分析与功能研究, 主持, 国家级, 2013-01--2016-12
（ 9 ） DNA与RNA甲基化表观修饰对单倍体胚胎干细胞多能性与所产生个体发育能力的影响和作用机制研究, 参与, 国家级, 2014-01--2016-12
（ 10 ） 真核生物编码蛋白中未知重复序列的发现与功能研究, 主持, 国家级, 2015-01--2018-12
（ 11 ） 真核生物非编码RNA自动鉴定、分类和功能预测系统的建立, 主持, 部委级, 2007-10--2011-12
（ 12 ） MicroRNA介导mRNA中m6A甲基化形成的机制研究, 主持, 国家级, 2016-01--2019-12
（ 13 ） 人类神经系统疾病相关重复序列的系统发现与调控机制研究, 主持, 部委级, 2016-08--2020-12
（ 14 ） 主动脉瘤/夹层分子分型和诊治的精准医学研究, 参与, 国家级, 2016-07--2019-06
（ 15 ） 植物调节功能lincRNA的发现及功能研究, 参与, 国家级, 2011-05--2012-12
（ 16 ） RNA沉默技术的机理及其在转基因植物的应用, 主持, 国家级, 2008-07--2010-12

（1） 无，第十届世界生物技术工业国际年会，2013-06，无
（2） 无，国际干细胞协会第十一届年会，2013-06，无
（3） 无，国际干细胞协会第十届年会，2012-06，无
（4） 无，国际干细胞协会第九届年会，2011-06，无

已指导学生

吴旭东  博士研究生  071021-生物信息学  

郑淇  博士研究生  071021-生物信息学  

刘君  博士研究生  071021-生物信息学  

王欢  博士研究生  071021-生物信息学  

骆观正  博士研究生  071021-生物信息学  

赵营涛  博士研究生  071021-生物信息学  

王亦男  博士研究生  071021-生物信息学  

刘修营  博士研究生  071021-生物信息学  

吴华君  博士研究生  071021-生物信息学  

李玲玲  硕士研究生  430139-生物工程  

冯桂海  博士研究生  071021-生物信息学  

马英克  博士研究生  071021-生物信息学  

杨维  博士研究生  071021-生物信息学  

孙海汐  博士研究生  071021-生物信息学  

刘永鑫  博士研究生  071021-生物信息学  

陈同  博士研究生  071021-生物信息学  

徐阳  硕士研究生  085238-生物工程  

庞军玲  博士研究生  0710J3-生物信息学  

现指导学生

李稳  博士研究生  071021-生物信息学  

王志敏  博士研究生  071021-生物信息学  

苑宝文  硕士研究生  0710J3-生物信息学  

王运浩  博士研究生  0710J3-生物信息学  

陈斌  硕士研究生  085238-生物工程  

张泽宇  硕士研究生  0710J3-生物信息学  

黄增辉  博士研究生  0710J3-生物信息学  

刘勇杰  博士研究生  071009-细胞生物学  

李长昊  博士研究生  0710J3-生物信息学  

1. 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 2:16049-16055. (*co-corresponding author)

2. 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.

3. 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.

4. 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.

5. 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. (*co-corresponding author)

6. 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 GB, Wang HL, Sang LS, 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)

7. 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.

8. 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.

9. 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.

10. 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)

11. 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.

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

13. 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)

14. 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.

15. 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.

16. 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.

17. 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)

18. 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.

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

20. 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)

21. 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.

22. 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)

23. 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.

24. 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)

25. 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.

26. 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.

27. 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.

28. 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.

29. 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.

30. 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)

31. 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)

32. 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.

33. 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.

34. 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)

35. 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.

36. 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.

37. 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.

38. 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.

39. 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.

40. 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.

41. 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)

42. 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.

43. 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.

44. 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.

45. 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.

46. 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.

47. 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.

48. 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.

49. 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)

50. 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)

51. 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.

52. 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.

53. 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.

54. 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.

55. 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)

56. 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.

57. 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.

58. 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.

59. 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.

60. 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.

61. 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.

62. 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.

63. 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.

64. 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.

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

　

66. 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.

67. 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.

68. 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)　

69. 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)

70. 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.

71. 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.

72. 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. 

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

74. 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.

75. 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)

76. 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.　

77. 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.

　

78. 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.

79. 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.

80. 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.

81. Wang XJ, Reyes JL, Chua NH and Gaasterland T*. (2004) Prediction and identification of Arabidopsis thaliana microRNA genes and their mRNA targets. Genome Biology 5: R65.

82. Hoth S*, Ikeda Y, Morganteb M, Wang XJ, Zuo JR, Hanafey MK, Gaasterland T, Tingey SV and Chua NH. (2003) Monitoring genome-wide changes in gene expression in response to endogenous cytokinin reveals targets in Arabidopsis thaliana. FEBS Letters 554: 373-380.

83. Wang XJ, Ching YP, Lam WH, Qi Z, Zhang M and Wang JH*. (2000) Identification of a common protein association region in the neuronal Cdk5 activator. Journal of Biological Chemistry 275: 31763-31769.