--中国科学院遗传与发育生物学研究所

姓　　名：	王秀杰
职　　称：	研究员
职　　务：	主任
电话/传真：	86-10-64806590
电子邮件：	xjwang@genetics.ac.cn
实验室主页：	http://omicslab.genetics.ac.cn/
研究方向：	生物信息学和系统生物学

简历介绍：

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月获美国洛克菲勒大学 (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。

主要从事RNA调控相关的生物信息学与实验生物学研究，近年来也开展人类多组织拟胚胎体外模型的构建和基于3D打印的心脏组织构建研究。担任Briefings in Bioinformatics杂志亚洲区主编，Life Medicine和Genomics, Proteomics & Bioinformatics杂志副主编， Science Bulletin、Quantitative Biology、RNA Biology等杂志编委。兼任国际计算生物学会中国理事会的副主席、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、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委员等职务。曾任第十届、第十一届中华全国青年联合会委员和第十二届、第十三届中华全国青年联合会常委。2007年获得国家杰出青年科学基金支持，曾获得“中央国家机关五四奖章标兵”、“中国青年五四奖章”、“全国五一巾帼标兵”、“全国三八红旗手”等荣誉称号。获得首届“中源协和生命医学创新突破奖”、第八界“中国侨界贡献奖”一等奖和2022年度3D Pioneers Challenge MEDTECH奖。2014年和2016年分别作为第二完成人和第四完成人获得“国家自然科学奖”二等奖。

奖励荣誉

2007年国家杰出青年科学基金

2007年杜邦青年科学家奖

2012年中央国家机关青年“五四奖章标兵”荣誉称号

2012年 “全国青年岗位能手”荣誉称号

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

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

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

2016年入选国家高层次人才特殊支持计划

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”

2017年中国科学院“朱李月华”优秀教师奖

2020年 “全国三八红旗手”荣誉称号

2020年第八届“中国侨届贡献奖”一等奖

2020年中国科学院大学教育教学成果奖一等奖

2021年教育部课程思政教学名师和教学团队

2021年中国科学院大学领雁银奖振翅奖

2022年中国科学院大学领雁金奖引航奖

2022年 3D Pioneers Challenge医学技术创新奖（MedTech Prize）

2025年北京自然科学奖二等奖（排名第八）

研究领域：

研究方向：

1.生物3D打印和人类新型类器官制造

基于研究组开发的全角度新型生物3D打印装置，开展人类心肌组织等具有重要临床意义的生物组织和器官的体外3D打印研究。基于人类胚胎干细胞和诱导性多能干细胞，开发可支持各组织器官协同发育调控和功能互作研究的新型人类类器官模型，并开展相关的生理调控机制、疾病发生机理和药效评价研究。

2.RNA表观遗传修饰的功能与作用机制

结合高通量检测数据和动物模型，开展m⁶A、m⁶Am等重要RNA修饰的功能鉴定和机制解析研究，重点关注RNA修饰在人体器官发育和复杂疾病发生发展中的功能。

3.生物信息数据库和软件开发与智能模型构建

应用多种人工智能方法，针对单细胞组学、空间组学等高通量生命科学数据整合与解析需求，开发数据库、数据分析算法与软件，并开展基于人工智能技术的生命调控关键过程计算模型构建研究。

已开发数据库与软件：

DRED (Database of Repeat Expansion Diseases)

http://omicslab.genetics.ac.cn/dred/

ETCM (The Encyclopedia of Traditional Chinese Medicine)

http://www.tcmip.cn/ETCM/

COSG (COSine similarity-based marker Gene identification)

https://github.com/genecell/COSG (Python)

https://github.com/genecell/COSGR (R)

GOEAST (Gene Ontology Enrichment Analysis Software Toolkit)

http://omicslab.genetics.ac.cn/GOEAST/

ISRNA (Integrative Short Reads NAvigator)

http://omicslab.genetics.ac.cn/ISRNA/

psRobot (Plant Small RNA Analysis Toolbox)

http://omicslab.genetics.ac.cn/psRobot/

社会任职：

获奖及荣誉：

承担科研项目情况：

代表论著：

代表论著（*为通讯作者）：

2025

133. Xiangjie Zhao and Xiu-Jie Wang*. A systematic analysis of human hormone receptors. Science China Life Science (Accepted).

132. Hanxiao Sun, Bo Lu, Zeyu Zhang, Ye Xiao, Zhe Zhou, Lin Xi, Zhichao Li, Zhe Jiang, Jiayi Zhang, Meng Wang, Cong Liu, Yichen Ma, Jinying Peng, Xiu-Jie Wang* and Chengqi Yi*. (2025) Mild and ultrafast GLORI enables absolute quantification of m⁶A methylome from low-input samples. Nature Methods 22: 1226–1236.

2024

131. Qingqing Shi, Min Dai, Yingke Ma, Jun Liu, Xiuying Liu and Xiu-Jie Wang*. (2024) DRED: a comprehensive database of genes related to repeat expansion diseases.Genomics Proteomics & Bioinformatics 22(5): qzae068.

130. Lei Shi, Meng Wang and Xiu-Jie Wang*. (2024) Application of artificial intelligence in life science: historical review and future perspectives. Fundamental Research Doi.org/ /j.fmre.2024.10.014.

129. Zhan Hu, Min Dai, Yuan Chang, Xiumeng Hua, Ningning Zhang, Xiao Chen, Yixuan Sheng, Zhenyu Xu, Hang Zhang, Yu Zhang, Hao Cui, Hao Jia, Xiu-Jie Wang* and Jiangping Song*. (2024) Strategies for arterial graft optimization at the single-cell level. Nature Cardiovascular Research 3: 541–557.

128. Mingyu Liao, Xing Li, Hao Zhang, Ling Zhou, Liu Shi, Weixin Li, Rufei Shen, Guiliang Peng, Huan Zhao, Jiaqing Shao, Xiu-Jie Wang, Zheng Sun, Hongting Zheng* and Min Long*. (2024) Effects and plasma proteomic analysis of GLP-1RA versus CPA/EE, in combination with metformin, on overweight PCOS women: a randomized controlled trial. Endocrine 83(1): 227-241.

2023

127. Meng Wang, Dongfang Xie, Meng Zhang and Xiu-Jie Wang*. (2023) Multiple ingredients of a Chinese medicine formula Sheng-Mai-San coordinately attenuate doxorubicin-induced cardiotoxicity. Pharmacological Research-Modern Chinese Medicine 8: 100281.

126. Zeyu Zhang and Xiu-Jie Wang*. (2023) N6-methyladenosine mRNA modification: from modification site selectivity to neurological functions. Accounts of Chemical Research 56(21): 2992-2999.

125. Xing Luo, Min Dai, Min Wang, Xiu-Jie Wang and Weixiang Guo*. (2023) Functional heterogeneity of Wnt-responsive and hedgehog-responsive neural stem cells in the murine adult hippocampus. Developmental Cell 58(22): 2545-2562.

124. Xin Qiu, Yongbo Zhang, Hongqiu Gu, Yingyu Jiang, Yuesong Pan, Yong Jiang, Xia Meng, Yilong Wang, Xingquan Zhao, Hao Li, Xiu-Jie Wang, Yongjun Wang* and Zixiao Li*. (2023) Association between CYP2B6 polymorphisms and efficacy of clopidogrel in minor stroke or transient ischemic attack. Stroke 54(7): 1770-1776.

123. Siyuan Zhang, Jinhong Kan, Xin Liu, Yao Wu, Mingyang Zhang, Jinqing Ou, Juan Wang, Lin An, Defeng Li, Li Wang, Xiu-Jie Wang, Rongxiang Fang and Yantao Jia*. (2023) Phytopathogenic bacteria utilize host glucose as a signal to stimulate virulence through LuxR homologues.Molecular Plant Pathology 24(4): 359-373.

122. Cengfan Wei,Meng Wang and Xiu-Jie Wang*. (2023) Evolutionary conservation analysis of human arachidonic acid metabolism pathway genes. Life Medicine 2(2): lnad004.

2022

121. Zeyu Zhang, Chenming Wu, Chengkai Dai, Qingqing Shi, Guoxin Fang, Dongfang Xie, Xiangjie Zhao, Yongjin Liu*, Charlie C.L. Wang* and Xiu-Jie Wang*. (2022) A multi-axis robot-based bioprinting system supporting natural cell function preservation and cardiac tissue fabrication. Bioactive Materials 18: 138-150.

120. Min Dai, Xiaobing Pei* and Xiu-Jie Wang*. (2022) Accurate and fast cell marker gene identification with COSG. Briefings in Bioinformatics 23(2): bbab579.

119. Linshuang Zhang, Jinsheng Zhang, Yuelong Hou, Weiwei Lu, Xianqiang Ni, Fan Lin, Xiuying Liu, Xiu-Jie Wang, Yanrong Yu, Mozhi Jia,Chaoshu Tang, Ling Han*, Sanbao Chai* and Yongfen Qi*. (2022) Intermedin_1-53inhibits NLRP3 inflammasome activation by targeting IRE1α in cardiac fibrosis. Inflammation 45(4): 1568-1584.

118.Haifeng Wan, Rui Fu, Man Tong, Yukai Wang, Libin Wang, Siqi Wang, Ying Zhang, Wei Li, Xiu-Jie Wang and Guihai Feng*. (2022) Influence of feeder cells on transcriptomic analysis of pluripotent stem cells. Cell Proliferation 55(2): e13189.

2021

117. Yanliang Wang, Meng Wang and Xiu-Jie Wang*. (2021) Identification of dysregulated microRNAs involved in arachidonic acid metabolism regulation in dilated cardiomyopathy-mediated heart failure patients. Acta Physiologica Sinica 73(4): 584-596.

116. Min Zhu, Juan Gao, Xianjuan Lin, Yunyun Gong, Yanchao Qi, Yuanliang Ma, Yuanxiu Song, Wei Tan, Fangyuan Li, Min Ye, Jun Gong, Qinghua Cui, Zenghui Huang, Youyi Zhang, Xiu-Jie Wang, Feng Lan, Shiqiang Wang, Gu Yuan, Yue Feng and Ming Xu*. (2021) Novel roles of an intragenic G-quadruplex in controlling microRNA expression and cardiac function. Nucleic Acids Research 49: 2522-2536.

115. Zhimin Shi, Zeyu Zhang, Lana Schaffer, Zhi Huang, Lijuan Fu, Steven Head, Terry Gaasterland, Xiu-Jie Wang and XiaoChing Li*. (2021) Dynamic transcriptome landscape in the song nucleus HVC between juvenile and adult zebra finches. Advanced Genetics 2(1): e10035.

114. Dongfang Xie, Man Tong, Baolong Xia, Guihai Feng, Leyun Wang, Ang Li, Guanzheng Luo, Haifeng Wan, Zeyu Zhang, Hao Zhang, Yungui Yang, Qi Zhou, Meng Wang* and Xiu-Jie Wang*. (2021) Long noncoding RNA lnc-NAP sponges mmu-miR-139-5p to modulate Nanog functions in mouse ESCs and embryos. RNA Biology 18(6): 875-887.

113. Huizhen Lv, Hui Wang, Meixi Quan, Chenghu Zhang, Yi Fu, Lu Zhang, Changdong Lin, Xin Liu, Xianfu Yi, Jianfeng Chen, Xiu-Jie Wang, Tao Cheng, Ding Ai, Wei Kong* and Yi Zhu*. (2021) Cartilage oligomeric matrix protein fine-tunes disturbed flow-induced endothelial activation and atherogenesis. Matrix Biology 95: 32-51.

112. Lei Shi, Hua Qu, Hongting Zheng* and Xiu-Jie Wang*. (2021) Developmental trend analysis and perspectives on researches related to hepatic glucose and lipid metabolism. Acta Physiologica Sinica 73(5): 781-794.

2020

111. Xin Liu and Xiu-Jie Wang*. (2020) Potential inhibitors against 2019-nCoV coronavirus M protease from clinically approved medicines. Journal of Genetics and Genomics 47: 119-121.

110. Le Cui, Yingyang Xu, Xiu-Jie Wang and Kai Guan*. (2020) Stinging insect allergens. Current Protein & Peptide Science 21: 142-152.

109. Lisha Li, Hao Zhang, Meng Wang, Xiu-Jie Wang and Kai Guan*. (2020) Early transcriptomic profiling variation caused by cluster allergen immunotherapy. Chinese Medical Journal (Engl) 133: 1366-1368.

2019

108. Haiyu Xu, Yanqiong Zhang, Zhenming Liu, Tong Chen, Chuanyu Lv, Shihuan Tang, Xiaobo Zhang, Wei Zhang, Zhiyong Li, Rongrong Zhou, Hongjun Yang*, Xiu-Jie Wang* and Luqi Huang*. (2019) ETCM: an encyclopaedia of traditional Chinese medicine. Nucleic Acids Research 47(D1): D976-D982.

107. Hang Wang, Shuyu Li, Yanan Li, Yiran Xu, Yunhao Wang, Ruoxi Zhang, Wenjing Sun, Qian Chen, Xiu-Jie Wang, Chuanyou Li* and Jiuhai Zhao*. (2019) MED25 connects enhancer-promoter looping and MYC2-dependent activation ofjasmonate signalling. Nature Plants 5(6): 616-625.

106. Xiaoxi Pan, Chengchao Ruan*, Xiuying Liu, Lingran Kong, Yu Ma, Qihong Wu, Haiqing Li, Yanjun Sun, Anqing Chen, Qiang Zhao, Fang Wu, Xiu-Jie Wang, Jiguang Wang, Dingliang Zhu and Pingjin Gao. (2019) Perivascular adipose tissue-derived stromal cells contribute to vascular remodeling during aging. Aging Cell 18(4): e12969.

105. Yang Weng, Rui Zeng, Chenming Wu, Meng Wang, Xiu-Jie Wang* and Yongjin Liu*. (2019) A survey on deep-learning-basedplant phenotype research in agriculture. Scientia sinica vitae 49(6): 698-716.

104. Jinjing Zhang, Lipeng Wang, Rongchang Li, Meng Wang, Zenghui Huang, Min Zhu, Jiaxing Wang, Xiu-Jie Wang, Shiqiang Wang* and Ming Xu*. (2019) Abnormal expression of miR-331 leads to impaired heart function. Science Bulletin 64(14): 1011-1017.

2018

103. Xianqiang Ni, Weiwei Lu, Jinsheng Zhang, Qing Zhu, Jinling Ren, Yanrong Yu, Xiuying Liu, Xiu-Jie Wang, Mei Han, Qing Jing, Jie Du, Chaoshu Tang and Yongfen Qi*. (2018) Inhibition of endoplasmic reticulum stress by intermedin1-53 attenuates angiotensin II-induced abdominal aortic aneurysm in ApoE KO Mice. Endocrine 62: 90-106.

102. Chenxin Wang, Guanshen Cui, Xiuying Liu, Kai Xu, Meng Wang, Xinxin Zhang, Liyuan Jiang, Ang Li, Ying Yang, Weiyi Lai, Baofa Sun, Guibin Jiang, Hailin Wang, Weimin Tong, Wei Li, Xiu-Jie Wang*, Yungui Yang* and Qi Zhou*. (2018) METTL3-mediated m⁶A modification is required for cerebellar development. PLoS Biology 16: e2004880.

101. Jinlong He, Qiankun Bao, Yan Zhang, Mingming Liu, Huizhen Lv, Yajin Liu, Liu Yao, Bochuan Li, Chenghu Zhang, Shuang He, Guijin Zhai, Yan Zhu, Xin Liu, Kai Zhang, Xiu-Jie Wang, Minghui Zou, Yi Zhu and Ding Ai*. (2018) Yes-associated protein promotes angiogenesis via signal transducer and activator of transcription 3 in endothelial cells. Circulation Research 122: 591-605.

100. Zeyu Zhang, Meng Wang, Dongfang Xie, Zenghui Huang, Lisha Zhang, Ying Yang, Dongxue Ma, Wenguang Li, Qi Zhou, Yungui Yang* and Xiu-Jie Wang*. (2018)METTL3-mediated N6-methyladenosine mRNA modification enhances long-term memory consolidation. Cell Research 28: 1050-1061.

(Cover Story. Commented byhttps://doi.org/10.1038/s41422-018-0121-8 )

N6-methyladenosine (m⁶A) mRNA modification enhances learning efficacy, and overdosed training can compensate for the effect of m⁶A insufficiency. Cover image shows two tortoises with different levels of m⁶A modifications (shown as the numbers of hexagons on their shells) are competing in a race, which is an analogy to learning process. The tortoise with more m⁶A races more easily with less steps. However, if the one with less m⁶A pays more effort, the initial disadvantage can be overcome, and the two tortoises can finish the match at the same time.

2017

99. Meng Wang, Huajun Wu, Jun Fang, Chengcai Chu and Xiu-Jie Wang*. (2017) A long noncoding RNA involved in rice reproductive development by negatively regulating osa-miR160. Science Bulletin 62: 470-475.

98. Mengzhu Chen, Xiuying Liu, Jie Du, Xiu-Jie Wang* and Lixin Xia*. (2017) Differentiated regulation of immune-response related genes between LUAD and LUSC subtypes of lung cancers. Oncotarget 8: 133-144.

97. Zeyu Zhang and Xiu-Jie Wang*. (2017) C urrent progresses of 3D bioprinting based tissue engineering. Quantitative Biology 5: 136-142.

96. Benjamin Deonovic, Yunhao Wang, Jason Weirather, Xiu-Jie Wang and Kin Fai Au*. (2017) IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing. Nucleic Acids Research 45: e32.

95. Jason L Weirather, Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck* and Kin Fai Au*. (2017) Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis. F1000Research 6: 100.

94. Kai Xu, Ying Yang, Guihai Feng, Baofa Sun, Junqing Chen, Yufei Li, Yusheng Chen, Xinxin Zhang, Chenxin Wang, Liyuan Jiang, Chao Liu, Zeyu Zhang, Xiu-Jie Wang, Qi Zhou, Yungui Yang* and Wei Li*. (2017) Mettl3-mediated m⁶A regulates spermatogonial differentiation and meiosis initiation. Cell Research 27: 1100-1114.

93. Yingying Han, Xiao Chu, Haopeng Yu, Yingke Ma, Xiu-Jie Wang, Wenfeng Qian* and Yuling Jiao*. (2017)Single-cell transcriptome analysis reveals widespread monoallelic gene expression in individual rice mesophyll cells. Science Bulletin 62(19): 1304-1314.

2016

92. Guihai Feng, Man Tong, Baolong Xia, Guanzheng Luo, Meng Wang, Dongfang Xie, Haifeng Wan, Ying Zhang, Qi Zhou* and Xiu-Jie Wang*. (2016) Ubiquitously expressed genes participate in cell-specific functions via alternative promoter usage. EMBO Reports 17: 1304-1313.

91. Zhonghui Zhang, Xiuying Liu, Xinwei Guo, Xiu-Jie Wang* and Xiuren Zhang*. (2016) Arabidopsis AGO3 predominantly recruits 24-nt small RNAs to regulate epigenetic silencing. Nature Plants 2: 16049.

90. Ying Zhang, Guihai Feng, Kai Xu, Libin Wang, Peng Cui, Yuhuan Li, Chenxin Wang, Fei Teng, Jie Hao, Haifeng Wan, Yuanqing Tan, Xiu-Jie Wang* and Qi Zhou*. (2016) A non-invasive method to determine the pluripotent status of stem cells by culture medium microRNA expression detection. Scientific Reports 6: 22380.

89. Xin Li, Xiaolong Cui, Jiaqiang Wang, Yukai Wang, Yufei Li, Leyun Wang, Haifeng Wan, Tianda Li, Guihai Feng, Ling Shuai, Zhikun Li, Qi Gu, Jie Hao, Liu Wang, Xiaoyang Zhao, Zhonghua Liu, Xiu-Jie Wang, Wei Li* and Qi Zhou*. (2016) Generation and application of mouse-rat allodiploid embryonic stem cells. Cell 164(1-2): 279-292.

88. Wen Xiao, Samir Adhikari, Ujwal Dahal, Yusheng Chen, Yajuan Hao, Baofa Sun, Huiying Sun, Ang Li, Xiaoli Ping, Weiyi Lai, Xing Wang, Haili Ma, Chunmin Huang, Ying Yang, Niu Huang, Guibin Jiang, Hailin Wang, Qi Zhou, Xiu-Jie Wang, Yongliang Zhao and Yungui Yang*. (2016) Nuclear m⁶A reader YTHDC1 regulates mRNA splicing. Molecular Cell 61(4): 507-519.

87. Zhikun Li, Haifeng Wan, Guihai Feng, Leyun Wang, Zhengquan He, Yukai Wang, Xiu-Jie Wang, Wei Li*, Qi Zhou* and Baoyang Hu*. (2016) Birth of fertile bimaternal offspring following intracytoplasmic injection of parthenogenetic haploid embryonic stem cells. Cell Research 26(1): 135-138.

86. Yi Cui, Jin Han, Zhifeng Xiao, Tong Chen, Bin Wang, Bing Chen, Sumei Liu, Sufang Han, Yongxiang Fang, Jianshu Wei, Xiu-Jie Wang, Xu Ma* and Jianwu Dai*. (2016) The miR-20-Rest-Wnt signaling axis regulates neural progenitor cell differentiation. Scientific Reports 6: 23300.

85. Jinrui Chang, Jun Guo, Yue Wang, Yuelong Hou, Weiwei Lu, Jinsheng Zhang, Yanrong Yu, Mingjiang Xu, Xiuying Liu, Xiu-Jie Wang, Youfei Guan, Yi Zhu, Jie Du, Chaoshu Tang and Yongfen Qi*. (2016) Intermedin1-53 attenuates vascular calcification in rats with chronic kidney disease by upregulation of α-Klotho. Kidney International 89(3): 586-600.

84. Handong Su, Yalin Liu, Yongxin Liu, Zhenling Lv, Hongyao Li, Shaojun Xie, Zhi Gao, Junling Pang, Xiu-Jie Wang, Jinsheng Lai, James A. Birchler* and Fangpu Han*. (2016) Dynamic chromatin changes associated with de novo centromere formation in maize euchromatin. The Plant Journal 88(5): 854-866.

2015

83. Yingtao Zhao, Meng Wang, Zhimin Wang, Rongxiang Fang, Xiu-Jie Wang* and Yantao Jia*. (2015)Dynamic and coordinated expression changes of rice small RNAs in response to Xanthomonas oryzae pv. oryzae. Journal of Genetics and Genomics 42(11): 625-637.

82. Claudia Castillogonzalez, Xiuying Liu,Changjun Huang, Changjiang Zhao, Zeyang Ma, Tao Hu, Feng Sun, Yijun Zhou, Xueping Zhou, Xiu-Jie Wang and Xiuren Zhang*. (2015) Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense.Elife 4: e06671.

81. Ling Shuai, Yukai Wang, Mingzhu Dong, Xuepeng Wang, Lisi Sang, Mei Wang, Haifeng Wan, Guanzheng Luo, Tiantian Gu, Yan Yuan, Chunjing Feng, Fei Teng, Wei Li, Xiuying Liu, Tianda Li, Liu Wang, Xiu-Jie Wang, Xiaoyang Zhao and Qi Zhou*. (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.

80. Yalin Liu, Handong Su, Junling Pang, Zhi Gao, Xiu-Jie Wang, James A. Birchler* and Fangpu Han*. (2015) Sequential de novo centromere formation and inactivation on a chromosomal fragment in maize. Proc. Natl. Acad. Sci. USA 112(11): E1263-71.

79. Tong Chen, Yajuan Hao, Ying Zhang, Miaomiao Li, Meng Wang, Weifang Han, Yongsheng Wu, Ying Lv, Jie Hao, Libin Wang, Ang Li, Ying Yang, Kangxuan Jin, Xu Zhao, Yuhuan Li, Xiaoli Ping, Weiyi Lai, Ligang Wu, Guibin Jiang, Hailin Wang, Lisi Sang, Xiu-Jie Wang*, Yungui Yang* and Qi Zhou*. (2015) m⁶A RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency. Cell Stem Cell (Cover Story) 16: 289-301.

On the cover: In this issue, Chen et al. (289–301) show that 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).

2014

78. Chuanxi Li, Peng Chen*, Rujing Wang, Xiu-Jie Wang, Yaru Su and Jinyan Li. (2014) PPI-IRO: a two-stage method for protein-protein interaction extraction based on interaction relation ontology. International Journal of Data Mining and Bioinformatics 10(1): 98-119.

77. Xu Zhao, Ying Yang, Baofa Sun, Yue Shi, Xin Yang, Wen Xiao, Yajuan Hao, Xiaoli Ping, Yusheng Chen, Wenjia Wang, Kangxuan Jin, Xing Wang, Chunmin Huang, Yu Fu, Xiaomeng Ge, Shuhui Song, Hyun Seok Jeong, Hiroyuki Yanagisawa, Yamei Niu, Guifang Jia, Wei Wu, Weimin Tong, Akimitsu Okamoto, Chuan He, Jannie M Rendtlew Danielsen, Xiu-Jie Wang and Yungui Yang*. (2014) FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Research 24(12): 1403-19.

76. Guanzheng Luo, Wei Yang, Yingke Ma and Xiu-Jie Wang*. (2014) ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data. Bioinformatics 30: 434-436.

75. Yongxin Liu, Meng Wang and Xiu-Jie Wang*. (2014) Endogenous small RNA clusters in plants. Genomics Proteomics & Bioinformatics 12: 64-71.

74. Wei Gao, Haixi Sun, Hongbin Xiao, Guanghong Cui, Matthew L Hillwig, Alana Jackson, Xiao Wang, Ye Shen, Nan Zhao, Liangxiao Zhang, Xiu-Jie Wang*, Reuben J Peters* and Luqi Huang*. (2014) Combining metabolomics and transcriptomics to characterize tanshinone biosynthesis inSalvia miltiorrhiza. BMC Genomics 15: 73.

73. Wei Li, Xin Li, Tianda Li, Minggui Jiang, Haifeng Wan, Guanzheng Luo, Chunjing Feng, Xiaolong Cui, Fei Teng, Yan Yuan, Quan Zhou, Qi Gu, Ling Shuai, Jiahao Sha, Yamei Xiao, Liu Wang, Zhonghua Liu, Xiu-Jie Wang, Xiaoyang Zhao and Qi Zhou*. (2014)Genetic modification and screening in rat using haploid embryonic stem cells. Cell Stem Cell 14: 404-414.

72. Yi Cui, Zhifeng Xiao, Tong Chen, Jianshu Wei, Lei Chen, Lijun Liu, Bing Chen, Xiu-Jie Wang, Xiaoran Li and Jianwu Dai*. (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.

71. Lijuan Fu, Zhimin Shi, Guanzheng Luo, Weihong Tu, Xiu-Jie Wang, Zhide Fang and XiaoChing Li*. (2014) Multiple microRNAs regulate human FOXP2 gene expression by targeting sequences in its 3' untranslated region. Molecular Brain 7: 71.

2013

70. Zhicao Zhang, Yi Huang, Xiu-Jie Wang, Meng Wang and Lulin Ma*. (2013) Expression of circulating microRNAs in patients with bladder urothelial carcinoma. Journal of Peking University (Health Sciences) 45(4): 532-536.

69. Huajun Wu, Zhimin Wang, Meng Wang and Xiu-Jie Wang*. (2013) Widespread long noncoding RNAs as endogenous target mimics for microRNAs in plants. Plant Physiology 161: 1875-1884.

68. Ying Zhang, Fei Teng, Guanzheng Luo, Meng Wang, Man Tong, Xiaoyang Zhao, Liu Wang, Xiu-Jie Wang* and Qi Zhou*. (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.

67. Xin Liu, Ying Zhang, Man Tong, Xiuying Liu, Guanzheng Luo, Dongfang Xie, Shaofang Ren, Donghui Bai, Liu Wang, Qi Zhou and Xiu-Jie Wang*. (2013) Identification of a small molecule 1,4-bis-[4-(3-phenoxy-propoxy)-but-2-ynyl]-piperazine as a novel inhibitor of the transcription factor p53. Acta Pharmacologica Sinica 34: 805–810.

66. Wen Li, Wei Yang and Xiu-Jie Wang*. (2013) Pseudogenes: pseudo or real functional elements? Journal of Genetics and Genomics 40: 171-177.

65. Xinmin Zhang, Yuzhen Ma, Xiuying Liu, Qi Zhou and Xiu-Jie Wang*. (2013) Evolutionary and functional analysis of the key pluripotency factor Oct4 and its family proteins. Journal of Genetics and Genomics 40: 399-412.

64. Hongqing Ling*, Shancen Zhao, Dongcheng Liu, Junyi Wang, Hua Sun, Chi Zhang, Huajie Fan, Dong Li, Lingli Dong, Yong Tao, Chuan Gao, Huilan Wu, Yiwen Li, Yan Cui, Xiaosen Guo, Shusong Zheng, Biao Wang, Kang Yu, Qinsi Liang, Wenlong Yang, Xueyuan Lou, Jie Chen, Mingji Feng, Jianbo Jian, Xiaofei Zhang, Guangbin Luo, Ying Jiang, Junjie Liu, Zhaobao Wang, Yuhui Sha, Bairu Zhang, Huajun Wu, Dingzhong Tang, Qianhua Shen, Pengya Xue, Shenhao Zou, Xiu-Jie Wang, Xin Liu, Famin Wang, Yanping Yang, Xueli An, Zhenying Dong, Kunpu Zhang, Xiangqi Zhang, Mingcheng Luo, Jan Dvorak, Yiping Tong, Jian Wang, Huanming Yang, Zhensheng Li*, Daowen Wang*, Aimin Zhang* and Jun Wang*. (2013) Draft genome of the wheat A-genome progenitorTriticum urartu. Nature 496: 87-90.

63. Hongliang Zhu, Yuyi Zhou, Claudia Castillogonzález, Amber Lu, Chunxiao Ge, Yingtao Zhao, Liusheng Duan, Zhaohu Li, Michael J. Axtell, Xiu-Jie Wang and Xiuren Zhang*. (2013) Bidirectional processing of pri-miRNAs with branched terminal loops byArabidopsisDicer-like1. Nature Structural & Molecular Biology 20: 1106-1115. (Cover story)

62. Rongchang Li, Jin Tao, Yunbo Guo, Haodi Wu, Ruifeng Liu, Yan Bai, Zhizhen Lv, Guanzheng Luo, Linlin Li, Meng Wang, Huaqian Yang, Wei Gao, Qide Han, Youyi Zhang, Xiu-Jie Wang, Ming Xu* and Shiqiang Wang*. (2013) In vivo suppression of microRNA-24 prevents the transition toward decompensated hypertrophy in aortic-constricted mice. Circulation Research 112: 601-605.

61. Bing Zhang, Zhenling Lv, Junling Pang, Yalin Liu, Xiang Guo, Shulan Fu, Jun Li, Qianhua Dong, Huajun Wu, Zhi Gao, Xiu-Jie Wang and Fangpu Han*. (2013) Formation of a functional maize centromere after loss of centromeric sequences and gain of ectopic sequences. Plant Cell 25(6): 1979-1989.

60. Shulan Fu, Zhenling Lv, Zhi Gao, Huajun Wu, Junling Pang, Bing Zhang, Qianhua Dong, Xiang Guo, Xiu-Jie Wang, James A. Birchler* and Fangpu Han*. (2013) De novo centromere formation on a chromosome fragment in maize. Proc. Natl. Acad. Sci. USA 110: 6033-6036.

59. Guanqun Zheng, John Arne Dahl, Yamei Niu, Peter Fedorcsak, Chunmin Huang, Charles J. Li, Cathrine B. Vågbø, Yue Shi, Wenling Wang, Shuhui Song, Zhike Lu, Ralph P. G. Bosmans, Qing Dai, Yajuan Hao, Xin Yang, Wenming Zhao, Weimin Tong, Xiu-Jie Wang, Florian Bogdan, Kari Furu, Ye Fu, Guifang Jia, Xu Zhao, Jun Liu, Hans E. Krokan, Arne Klungland*, Yungui Yang* and Chuan He*. (2013)ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Molecular Cell 10: 18-29.

58. Zhimin Shi, Guanzheng Luo, Lijuan Fu, Zhide Fang, Xiu-Jie Wang and XiaoChing Li*. (2013) miR-9 and miR-140-5p target FoxP2 and are regulated as a function the social context of singing behavior in zebra finches. Journal of Neuroscience 16: 16510-16521.

57. Yamei Niu, Xu Zhao, Yongsheng Wu, Mingming Li, Xiu-Jie Wang and Yungui Yang*. (2013) N⁶-methyl-adenosine (m⁶A) in RNA: an old modification with a novel epigenetic function. Genomics Proteomics & Bioinformatics 11: 8-17.

56. Jin Han, Lei Chen, Guanzheng Luo, Bin Dai, Xiu-Jie Wang and Jianwu Dai*. (2013) Three-dimensional culture may promote cell reprogramming. Organogenesis 9: 118-120.

2012

55. Ming Xu*, Haodi Wu, Rongchang Li, Haibo Zhang, Meng Wang, Jin Tao, Xinheng Feng, Yunbo Guo, Sufang Li, Shaoting Lai, Peng Zhou, Linlin Li, Huaqian Yang, Guanzheng Luo, Yan Bai, Jianzhong J. Xi, Wei Gao, Qide Han, Youyi Zhang, Xiu-Jie Wang*, Xu Meng and Shiqiang Wang*. (2012) Mir-24 regulates junctophilin-2 expression in cardiomyocytes. Circulation Research 111: 837-841.

54. Huajun Wu, Zhonghui Zhang, Junyi Wang, Dongha Oh, Maheshi Dassanayake, Binghang Liu, Quanfei Huang, Haixi Sun, Ran Xia, Yaorong Wu, Yinan Wang, Zhao Yang, Yang Liu, Wanke Zhang, Huawei Zhang, Jinfang Chu, Cunyu Yan, Shuang Fang, Jinsong Zhang, Yiqin Wang, Fengxia Zhang, Guodong Wang, Sang Yeol Lee, John M. Cheeseman, Bicheng Yang, Bo Li, Jiumeng Min, Linfeng Yang, Jun Wang*, Chengcai Chu*, Shouyi Chen*, Hans J. Bohnert, Jiankang Zhu*, Xiu-Jie Wang* and Qi Xie*. (2012) Insights into salt tolerance from the genome ofThellungislla salsuginea. Proc. Natl. Acad. Sci. USA 109: 12219-12224.

53. Huajun Wu, Yingke Ma, Tong Chen, Meng Wang* and Xiu-Jie Wang*. (2012) PsRobot: a web-based plant small RNA meta-analysis toolbox. Nucleic Acids Research 40: W22-W28.

52. Yingtao Zhao, Meng Wang, Sanxiong Fu, Weicai Yang, Cunkou Qi and Xiu-Jie Wang*. (2012) Small RNA profiling in twoBrassica napuscultivars identifies microRNAs with oil production- and developmental-correlated expressions and new small RNA classes. Plant Physiology 158: 813-823.

51. Guanzheng Luo, Markus Hafner, Zhimin Shi, Miguel Brown, Guihai Feng, Thomas Tuschl, Xiu-Jie Wang* and XiaoChing Li*. (2012) Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression. BMC Genomics 13: 727.

50. Wei Li, Ling Shuai, Haifeng Wan, Mingzhu Dong, Meng Wang, Lisi Sang, Chunjing Feng, Guanzheng Luo, Tianda Li, Xin Li, Libin Wang, Qinyuan Zheng, Chao Sheng, Huajun Wu, Zhonghua Liu, Lei Liu, Liu Wang, Xiu-Jie Wang, Xiaoyang Zhao* and Qi Zhou*. (2012) Androgenetic haploid embryonic stem cells produce live transgenic mice. Nature 490: 407-411.

49. Yaoyao Du, Cheng Gao, Ziyi Liu, Li Wang, Bo Liu, Fan He, Tao Zhang, Yue Wang, Xiu-Jie Wang, Mingjiang Xu, Guanzheng Luo, Yi Zhu, Qingbo Xu, Xian Wang* and Wei Kong*. (2012) Upregulation of a disintegrin and metalloproteinase with thrombospondin motifs-7 by miR-29 repression mediates vascular smooth muscle calcification. Arteriosclerosis, Thrombosis, and Vascular Biology 32: 2580-2588.

48. Cui Zhang, Yunyuan Xu, Siyi Guo, Jiaying Zhu, Qing Huan, Huanhuan Liu, Lei Wang, Guanzheng Luo, Xiu-Jie Wang and Kang Chong*. (2012) Dynamics of brassinosteroid response modulated by negative regulator LIC in rice. PLoS Genetics 8: e1002686.

47. Jongchan Woo, Cameron Ross MacPherson, Jun Liu, Huan Wang, Takatoshi Kiba, Matthew A Hannah, Xiu-Jie Wang, Vladimir B Bajic and Nam-Hai Chua*. (2012) The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation. BMC Plant Biology 12: 62.

46. Xianwei Song, Pingchuan Li, Jixian Zhai, Ming Zhou, Lijia Ma, Bin Liu, Donghoon Jeong, Mayumi Nakano, Shouyun Cao, Chunyan Liu, Chengcai Chu, Xiu-Jie Wang, Pamela J. Green, Blake C. Meyers and Xiaofeng Cao*. (2012) Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. Plant Journal 69: 462-474.

45. Ning Xu, Yan Li, Yingtao Zhao, Li Guo, Yuanyuan Fang, Jianhua Zhao, Xiu-Jie Wang, Li Huang and Huishan Guo*. (2012)Identification and characterization of small RNAs in the hyperthermophilic archaeonSulfolobus solfataricus. PLoS One 7: e35306.

44. Chao Sheng, Qinyuan Zheng, Jianyu Wu, Zhen Xu, Libin Wang, Wei Li, Haijiang Zhang, Xiaoyang Zhao, Lei Liu, Ziwei Wang, Changlong Guo, Huajun Wu, Zhonghua Liu, Liu Wang, Shigang He, Xiu-Jie Wang, Zhiguo Chen* and Qi Zhou*. (2012) Direct reprogramming of sertoli cells into multipotent neural stem cells by defined factors. Cell Research 22: 208-218.

2011

43. Huan Wang, Xiuren Zhang, Jun Liu, Takatoshi Kiba, Jongchan Woo, Tolulope Ojo, Markus Hafner, Thomas Tuschl, Nam-Hai Chua* and Xiu-Jie Wang*. (2011) Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions. Plant Journal 67: 292-304.

42. Hong Cui*, Songtao Zhang, Huijuan Yang, Hao Ji and Xiu-Jie Wang. (2011) Gene expression profile analysis of tobacco leaf trichomes. BMC Plant Biology 11: 76.

41. Mingguang Lei, Yidan Liu, Baocai Zhang, Yingtao Zhao, Xiu-Jie Wang, Yihua Zhou, Kashchandra G. Raghothama and Dong Liu*. (2011) Genetic and genomic evidence that sucrose is a global regulator of plant responses to phosphate starvation in Arabidopsis. Plant Physiology 156: 1116-1130.

40. Hong Liang, Yingtao Zhao, Jieqiong Zhang, Xiu-Jie Wang, Rongxiang Fang* and Yantao Jia*. (2011) I dentification and functional characterization of small non-coding RNAs inXanthomonas oryzaepathovar oryzae. BMC Genomics 12: 87.

39. Chui E. Wong, Yingtao Zhao, Xiu-Jie Wang, Larry Croft, Zhonghua Wang, Farzad Haerizadeh, John S. Mattick, Mohan B. Singh, Bernard J. Carroll and Prem L. Bhalla*. (2011) MicroRNAs in the shoot apical meristem of soybean. Journal of Experimental Botany 62: 2495-2506.

38. Jiali Wang, Dongcheng Liu, Xiaoli Guo, Wenlong Yang, Xiu-Jie Wang, Kehui Zhan and Aimin Zhang*. (2011) Variability of gene expression after polyhaploidization in wheat (Triticum aestivum L.). Genes Genomics Genetics 1: 27-33.

37. Wei Li, Xiaoyang Zhao, Haifeng Wan, Ying Zhang, Lei Liu, Zhuo Lv, Xiu-Jie Wang, Liu Wang* and Qi Zhou*. (2011) iPS cells generated without c-Myc have activeDlk1-Dio3region and are capable of producing full-term mice through tetraploid complementation. Cell Research 21: 550-553.

36. Man Tong, Zhuo Lv, Lei Liu, Hui Zhu, Qinyuan Zheng, Xiaoyang Zhao, Wei Li, Yibo Wu, Haijiang Zhang, Huajun Wu, Zhikun Li, Fanyi Zeng, Liu Wang, Xiu-Jie Wang, Jiahao Sha* and Qi Zhou*. (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

35. Yong Zhang, Jun Liu, Chunshi Jia, Tingting Li, Rimao Wu, Jie Wang, Ying Chen, Xiaoting Zou, Runsheng Chen, Xiu-Jie Wang* and Dahai Zhu*. (2010) Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs. BMC Genomics 11: 16.

34. Lei Liu, Guanzheng Luo, Wei Yang, Xiaoyang Zhao, Qinyuan Zheng, Zhuo Lv, Wei Li, Huajun Wu, Liu Wang, Xiu-Jie Wang* and Qi Zhou*. (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.

33. Wei Yang, Qi Zhou and Xiu-Jie Wang*. (2010)Regulation beyond genome sequences: DNA and histone methylation in embryonic stem cells. Frontier of Biology 5: 41-47.

32. Yan Li, Xiuying Liu, Li Huang, Huishan Guo and Xiu-Jie Wang*. (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.

31. Xiahui Xiong, Yabin Lu, Lishu Zhang, Bo Wang, Yingtao Zhao, Xiu-Jie Wang, Xiaofang Huo, Yan Shen, Zicai Liang* and Meihong Chen*. (2010) Discovery of novel cell proliferation-enhancing gene by random siRNA library based combinatorial screening. Combinatorial Chemistry & High Throughput Screening 13: 798-806.

30. Xinyu Jian, Lin Zhang, Guanglin Li, Liang Zhang, Xiu-Jie Wang, Xiaofeng Cao, Xiaohua Fang and Fan Chen*. (2010) Identification of novel stress-regulated microRNAs fromOryza sativaL. Genomics 95: 47-55.

2009

29. Qi Zheng, Yong Zhang, Ying Chen, Ning Yang, Xiu-Jie Wang* and Dahai Zhu*. (2009) Systematic identification of genes involved in divergent skeletal muscle growth rates of broiler and layer chickens. BMC Genomics 10: 87.

28. Xiuying Liu, Guanzheng Luo, Xiujuan Bai* and Xiu-Jie Wang*. (2009) Bioinformatic analysis of microRNA biogenesis and function related proteins in eleven animal genomes. Journal of Genetics and Genomics 36: 591-601.

27. Misook Ha, Jie Lu, Lu Tian, Vanitharani Ramachandran, Kristin D. Kasschau, Elisabeth J. Chapman, James C. Carrington, Xuemei Chen, Xiu-Jie Wang and Z. Jeffrey Chen*. (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.

26. Hada Wuriyanghan, Bo Zhang, Wanhong Cao, Biao Ma, Gang Lei, Yunfeng Liu, Wei Wei, Huajun Wu, Lijuan Chen, Haowei Chen, Yangrong Cao, Sijie He, Wanke Zhang, Xiu-Jie Wang, Shouyi Chen and Jinsong Zhang*. (2009) The ethylene receptor ETR2 delays floral transition and affects starch accumulation in rice. Plant Cell 21: 1473-1494.

25. Michael I. Besecker, Mallory E. Harden, Guanglin Li, Xiu-Jie Wang and Anthony Griffiths*. (2009) Discovery ofherpes B virus-encoded microRNAs. Journal of Virology 83: 3413-3416.

24. Yihua Zhou, Shengben Li, Qian Qian, Dali Zeng, Mu Zhang, Longbiao Guo, Xiangling Liu, Baocai Zhang, Lingwei Deng, Xinfang Liu, Guanzheng Luo, Xiu-Jie Wang and Jiayang Li*. (2009) BC10, a DUF266-containing and golgi-located type II membrane protein, is required for cell-wall biosynthesis in rice(Oryza sativa L.). Plant Journal 57: 446-462.

23. Youhua Huang, Xiaohong Huang, Hong Liu, Jie Gong, Zhengliang Ouyang, Huachun Cui, Jianhao Cao, Yingtao Zhao, Xiu-Jie Wang, Yulin Jiang* and Qiwei Qin*. (2009) Complete sequence determination of a novel reptile iridovirus isolated from soft-shelled turtle and evolutionary analysis of iridoviridae. BMC Genomics 10: 224.

22. Yong Zhang, Jie Wang, Shoujun Huang, Xiaopeng Zhu, Jun Liu, Ning Yang, Dandan Song, Rimao Wu, Wei Deng, Geir Skogerbø, Xiu-Jie Wang, Runsheng Chen* and Dahai Zhu*. (2009) Systematic identification and characterization of chicken (Gallus gallus) ncRNAs. Nucleic Acids Research 37: 6562-6574.

21. Mengbin Ruan, Yingtao Zhao, Zhaohong Meng, Xiu-Jie Wang and Weicai Yang*. (2009) Conserved miRNA analysis inGossypium hirsutumthrough small RNA sequencing. Genomics 94: 263-268.

20. Yanwei Wang, Pingchuan Li, Xiaofeng Cao, Xiu-Jie Wang, Aimin Zhang and Xia Li*. (2009) Identification and expression analysis of miRNAs from nitrogen-fixing soybean nodules. Biochemical Biophysical Research Communications378: 799-803.

2008

19. Qi Zheng and Xiu-Jie Wang*. (2008) GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Research 36: W358-W363.

18. Jinye Mu, Helin Tan, Qi Zheng, Fuyou Fu, Yan Liang, Jian Zhang, Xiaohui Yang, Tai Wang, Kang Chong, Xiu-Jie Wang and Jianru Zuo*. (2008) LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis inArabidopsis. Plant Physiology 148: 1042-1054.

17. Falong Lu, Guanglin Li, Xia Cui, Chunyan Liu, Xiu-Jie Wang and Xiaofeng Cao*. (2008) Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice. Journal of Integrative Plant Biology 50: 886-896.

2007

16. Tao Zhao, Guanglin Li, Shijun Mi, Shan Li, Gregory J. Hannon, Xiu-Jie Wang and Yijun Qi*. (2007) A complex system of small RNAs in the unicellular green algaChlamydomonas reinhardtii. Genes & Development 21: 1190-1203. (*co-corresponding Author)

15. XiaoChing Li*, Xiu-Jie Wang, Jonathan Tannenhauser, Sheila Podell, Piali Mukherjee, Moritz Hertel, Jeremy Biane, Shoko Masuda, Fernando Nottebohm and Terry Gaasterland. (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)

14. Bin Liu, Zhiyu Chen, Xianwei Song, Chunyan Liu, Xia Cui, Xianfeng Zhao, Jun Fang, Wenying Xu, Huiyong Zhang, Xiu-Jie Wang, Chengcai Chu, Xingwang Deng, Yongbiao Xue and Xiaofeng Cao*. (2007) Oryza sativa Dicer-like4reveals a key role for small interfering RNA silencing in plant development. Plant Cell 19: 2705-2718.

13. Peijin Li, Yonghong Wang, Qian Qian, Zhiming Fu, Mei Wang, Dali Zeng, Baohua Li, Xiu-Jie Wang and Jiayang Li*. (2007)LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Research 15: 402-410.

12. Xiaoqiang Liu, Xianquan Bai, Xiu-Jie Wang and Chengcai Chu*. (2007) OsWRKY71, a rice transcription factor, is involved in rice defense response. Journal of Plant Physiology164: 969-979.

2006

11. Huan Wang, Nam-Hai Chua and Xiu-Jie Wang*. (2006)Prediction of trans-antisense transcripts inArabidopsis thaliana. Genome Biology 7: R92.

10. Yijun Qi, Xingyue He, Xiu-Jie Wang, Oleksiy Kohany, Jerzy Jurka and Gregory J. Hannon*. (2006) Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation. Nature 443: 1008-1012.

9. Can Cui, Anthony Griffiths, Guanglin Li, Lindsey M. Silva, Martha F. Kramer, Terry Gaasterland, Xiu-Jie Wang* and Donald M. Coen*. (2006) P rediction and identification of herpes simplex virus 1-encoded microRNAs. Journal of Virology 80: 5499-5508.

8. Guanglin Li, Shiheng Tao and Xiu-Jie Wang*. (2006) Sequence and epitope analysis of surface proteins of avian influenza H5N1 viruses from Asian patients. Chinese Science Bulletin 51: 472-2481.

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

6. Anding Luo, Qian Qian, Hengfu Yin, Xiaoqiang Liu, Changxi Yin, Ying Lan, Jiuyou Tang, Zuoshun Tang, Shouyun Cao, Xiu-Jie Wang, Kai Xia, Xiangdong Fu, Da Luo* and Chengcai Chu*. (2006) EUI1, encoding a putative cytochrome P450 monooxygenase, regulates internode elongation by modulating gibberellin responses in rice. Plant and Cell Physiology 47: 181-191.

2005 and before

5. Xiu-Jie Wang, Terry Gaasterland and Nam-Hai Chua*. (2005) Genome-wide prediction and identification ofcis-natural antisense transcripts inArabidopsis thaliana. Genome Biology 6: R30.

4. Xiaoqiang Liu, Xianquan Bai, Qianqian, Xiu-Jie Wang, Mingsheng Chen and Chengcai Chu*. (2005) OsWRKY03, a rice transcriptional activator that functions in defense signaling pathway upstream of OsNPR1. Cell Research 15: 593-603.

3. Xiu-Jie Wang, José L Reyes, Nam-Hai Chua and Terry Gaasterland*. (2004) Prediction andidentification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biology 5: R65.

2. Stefan Hoth*, Yoshihisa Ikeda, Michele Morgante, Xiu-Jie Wang, Jianru Zuo, Michael K. Hanafey, Terry Gaasterland, Scott V. Tingey and Nam-Hai Chua. (2003) Monitoring genome-wide changes in gene expression in response to endogenous cytokinin reveals targets inArabidopsisthaliana. FEBS Letters 554: 373-380.

1. Xiu-Jie Wang, Yickpang Ching, Wingho Lam, Zhong Qi, Mingjie Zhang and Jerry H. Wang*. (2000) Identification of a common protein association region in the neuronal Cdk5 activator. Journal of Biological Chemistry 275: 31763-31769.

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19. ZL 201822199624.7；专利名称：一种生物3D打印培养一体化装置；发明人：刘永进，吴陈铭，王秀杰，王昌凌，戴澄恺，方国鑫，史庆庆，张泽宇。（国内专利）

20. ZL 201880096673.8；专利名称：评估或改善脑功能、学习能力或记忆力的组合物和方法；发明人：王秀杰，张泽宇，王猛，谢冬芳，黄增辉。（国内专利）

21. ZL 201820044372.8；专利名称：一种生物3D打印装置；发明人：刘永进，吴陈铭，李彦余，王秀杰，张泽宇，史庆庆。（国内专利）

22. ZL 201580074289.4；专利名称：miRNA对m6A修饰水平的调控方法及其应用；发明人：周琪，杨运桂，王秀杰，陈同，张映，郝亚娟，李苗苗，王猛。（国内专利）

23. ZL 201410394740.8；专利名称：一种诱导多能干细胞的培养基及其用途；发明人：周琪，王秀杰，顾奇，郝捷，韩伟方，刘鑫，王磊，王柳。（国内专利）

24. ZL 201310217064.2；专利名称：哌嗪衍生物作为p53分子调节剂的用途；发明人：王秀杰，周琪，刘鑫，张映，佟曼，郝捷，王柳，顾奇，谢冬芳，白冬辉，任少芳。（国内专利）

25. ZL 201210348202.6；专利名称：ath-eTM160在抑制microRNA160功能中的应用；发明人：王秀杰，王猛，吴华君，王志敏。（国内专利）

26. ZL 201210347712.1；专利名称：一种RNA及产生该RNA的基因在调控水稻根系发育中的应用；发明人：王秀杰，王猛，储成才，曹守云。（国内专利）

27. ZL 201110129687.2；专利名称：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；发明人：王秀杰，徐明，王世强，王猛，李素芳，骆观正。（国内专利）

28. ZL 201110416562.0；专利名称：启动子miR390及其应用；发明人：王秀杰，王猛，储成才，曹守云。（国内专利）

29. HK1163162；专利名称：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；发明人：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。（中国香港专利）

30. ZL 201010142746.8；专利名称：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；发明人：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。（国内专利）

31. ZL 201110416562.0；专利名称：启动子miR390及其应用；发明人：王秀杰，王猛，储成才，曹守云。（国内专利）

32. ZL 201010183227.6；专利名称：启动子miR172c及其应用；发明人：王秀杰，王猛，储成才，曹守云。（国内专利）

33. ZL 201010183307.1；专利名称：启动子AFB4及其应用；发明人：王秀杰，王猛，储成才，曹守云。（国内专利）

授权软著：

1. 2023SR0244931；软件名称：单细胞组学数据标记基因鉴定软件[简称：COSG] V1.0；完成人：王秀杰，裴小兵，戴敏。

2. 2023SR0406563；软件名称：中药复方功效解析挖掘工具软件V1.0；完成人：王秀杰，王猛，石磊，史庆庆。

3. 2013SR064503；软件名称：高通量测序数据分析的生物信息学在线科研软件；完成人：王秀杰，骆观正。