作物基因组与生物信息学系
2014.6 - 中国农业大学，农学与生物技术学院，教授，博导博牛彩票注册网址。
2010.8 - 2014.6. 美国亚利桑那大学博牛彩票注册网址，农业与生命科学学院博牛彩票注册网址，助理教授 (tenure-track Assistant Professor)
2008.12 - 2010.8. 美国哈佛大学，公共健康学院，博士后 (Postdoctoral associate)
2007.9 - 2008.12. 美国耶鲁大学，分子细胞发育生物学系，博士后(Postdoctoral associate)
2006.6– 2007.6. 美国耶鲁大学，分子细胞发育生物学系，交流学生(Monsanto fellowship)
2002.9 – 2007.6 北京大学，生命科学院，生物信息学，博士
1998.9 – 2002.7 中国农业大学博牛彩票注册网址，生物学院，生物科学，学士
植物基因组学
本人实验室主要从事植物基因组学博牛彩票注册网址、表观遗传学和系统生物学方面的研究，并开发了一系列生物计算模型和生物信息学软件。本人领导的研究团队在系统生物学的层面上开展了一系列的原创性研究博牛彩票注册网址。主要研究课题和已发表成果包括：1）开发了基因组拼接、可视化比较基因组分析、基因表达调控网络构建与预测等一系列生物信息学软件和算法；2）十字花科盐碱生植物基因组进化及其抗逆基因的挖掘和功能验证博牛彩票注册网址博牛彩票注册网址；3）玉米胚乳早期发育调控网络的构建和玉米胚乳中基因组印?；频难芯?；4）小麦染色体缺失系转录组测序与小麦异源多倍体中不同亲本基因组间的相互作用的研究；5）应用人工智能中机器学习方法学体系在植物中进行大规模生物数据整合博牛彩票注册网址、调控网络构建与优质抗逆基因的预测和功能筛选博牛彩票注册网址。
现发表论文38篇，包括通讯作者论文13篇，# 表明为通讯作者 *表明为第一作者
1. Ma C, Zhang H, Wang X#. Machine Learning for Big Data Analytics in Plants. Trends in Plant Science. 2014 In press. (IF: 13.479)
2. Thakare D,Yang R, Steffen J, Zhan J, Wang D, Clark R, Wang X, Yadegari R. RNA-Seq analysis of laser-capture microdissected cells of the developing central starchy endosperm of maize. Genomics Data. (2014), pp. 242-245
3. Xin M, Yang R, Yao Y, Ma C, Peng H, Sun Q, Wang X#, Ni Z#, Dynamic parent-of-origin effects on small interfering RNA expression in the developing maize endosperm. BMC Plant Biology. 2014;14(1) (IF: 3.94)
4. Zhang Y, Yu N, Huang Q, Yin G, Guo A, Wang X, Xiong Z, Liu Z. Complete genome of Hainan papaya ringspot virus using small RNA deep sequencing. Virus Genes. 2014; 48(3):502-8 (IF:1.837)
5. Li G, Wang D, Yang R, Logan K, Chen H, Zhang S, Skaggs MI, Lloyd A, Burnett WJ, Laurie JD, Hunter BG, Dannenhoffer JM, Larkins BA#, Drews GN, Wang X#, Yadegari R#. Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing. PNAS. 2014 (5-Yr IF: 10.6)
6. Ma C, Xin M, Feldmann KA, Wang X#. Machine Learning-Based Differential Network Analysis: A Study of Stress-Responsive Transcriptomes in Arabidopsis. Plant Cell. 2014 Feb 11. (5-Yr IF: 10.125)
7. Xin M, Yang R, Li G, Chen H, Laurie J, Ma C, Wang D, Yao Y, Larkins B, Sun Q, Yadegari, R, Wang X# and Ni Z. Dynamic expression of imprinted genes associates with maternally controlled nutrient allocation during maize endosperm development. (2013) 25(9):3212-27; Plant Cell (5-Yr IF: 10.125)
8. Chen, H and Wang, X#. CrusView: a Java-based visualization platform for comparative genomics analyses in Brassicaceae species. (2013) Plant Physiology; 163(1):354-62 (Five-Year Impact Factor: 7.084)
9. Wei, X and Wang, X#. A computational workflow to identify allele-specific expression and epigenetic modification in maize. (2013) Genomics Proteomics & Bioinformatics; 11(4): 247-52 (Impact Factor: Not Available Yet)
10. Yang R, Chen H, Jarvis D, Beilstein M, Grimwood J, Jenkins J, Shu S, Prochnik S, Xin M, Ma C, Schmutz J, Wing R, Mitchell-Olds T, Schumaker K#, Wang X#. The reference genome of the halophytic plant Eutrema salsugineum. (2013) Frontier in Plant Sciences; 4:46 (IF: 3.637)
11. Ma C, Chen H, Yang R, Xin M, Wang X#. KGBassembler: A karyotype-based genome assembler for Brassicaceae species. (2012) Bioinformatics; 28(23):3141-3 (Five-Year Impact Factor: 6.911)
12. Yang R and Wang X#. Organ evolution in angiosperms driven by correlated divergences of gene sequences and expression patterns. (2012) The Plant Cell; 25(1):71-82 (Five-Year Impact Factor: 10.125)
13. Ma C and Wang X#. Application of the Gini correlation coefficient to infer regulatory relationships in transcriptome analysis. (2012) Plant Physiology;160(1):192-203 (Five-Year Impact Factor: 7.084)
14. Xin M, Wang X, Peng H, Yao Y, Xie C, Han Y, Ni Z, Sun Q. Transcriptome comparison of susceptible and resistant wheat in response to powdery mildew infection. (2012) Genomics, Proteomics & Bioinformatics; 10(2):94-106 (Impact Factor: Not Available Yet)
15. Wang X# and Liu XS#. Systematic curation of miRBase microRNA annotation using integrated deep small RNA sequencing data for C. elegans and Drosophila. (2011) Frontiers in Genetics; 2:25. (Impact Factor: Not Available Yet)
16. Wang X#, Laurie J, Liu T, Wentz J, Liu XS#. Computational dissection of Arabidopsis smRNAome leads to discovery of RNA interference machinery associated with transcription start sites. (2011). Genomics; 97(4):235-43. (Cover Story) (Impact Factor: 3.010)
17. Zhang H, He H, Wang X, Li L and Deng X. Genome-wide identification of Hy5 binding sites in Arabidopsis. (2011). The Plant Journal; 65(3):346-58 (2012 Impact Factor: 6.582)
18. He H, Zhang H, Wang X, Wu N, Yang X, Chen R, Li Y, Deng XW and Li L. Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression. (2010). Genomics; 96(5):308-15 (2012 Impact Factor: 3.010)
19. He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, Liang M, He H, Zhang H, Chen F, Qi Y, Chen R and Deng XW. Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids. (2010). The Plant Cell; 22:17-33. (Five-Year Impact Factor: 10.125)
20. Zhou J, Wang X, He K, Stocl V, Tongprasit W, Elling A, Charron J, Deng XW. Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression. (2010). Plant Molecular Biology; 72:6, 585-595 (2012 Impact Factor: 3.518)
21. Wang X*, Elling A*, Li X*, Li L*, Charron J, Martinessen R, Wang J, Peng Z, Qi Y, Liu XS and Deng X. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and smRNA transcriptomes in maize. (2009). The Plant Cell; 21(4): 1053–1069 (Five-Year Impact Factor: 10.125)
22. Wang X*, Yu Z*, Deng XW, Li L. Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome. (2009). Bioinformatics; 15;25(10): 1215-1218. (Five-Year Impact Factor: 6.911)
23. Li X*, Wang X*, He K, Ma Y, Su N, He H, Stolc V, Tongprasit W, Jin W, Jiang J, Terzaghi W, Li S & Deng XW. High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. (2008). The Plant Cell; 20: 259-276 (Five-Year Impact Factor: 10.125)
24. Wang X. Statistical Analysis of Tiling-path microarrays. (2008) A Chapter for the book: Oligonucleotide Array Sequence Analysis; NOVA Science Publisher, New York, USA ISBN: 978-1-60456-542-3
25. Peng Z, Zhang H, Liu T, Dzikiewicz K, Li S, Wang X, Hu G, Zhu Z, Wei X, Zhu Q, Sun Z,Ge S, Ma L, Li L and Deng XW. Characterization of the genome expression trends in the heading-stage panicle of six rice lineages. (2008). Genomics; 93: 169-178; (Impact Factor: 3.010)
26. Yin BL, Guo L, Zhang DF, Terzaghi W, Wang X, Liu TT, He H, Cheng ZK and Deng XW. Integration of Cytological Features with Molecular and Epigenetic Properties of Rice Chromosome 4. (2008). Molecular Plant; 1: 816-829; (2012 Impact factor: 6.126)
27. Zhang HY, He H, Chen LB, Li L, Liang MZ, Wang X, Liu XG, He GM, Chen RS, Ma LG, and Deng XW. A Genome-Wide Transcription Analysis Reveals a Close Correlation of Promoter INDEL Polymorphism and Heterotic Gene Expression in Rice Hybrids. (2008) Molecular Plant; 1: 720-731; (2012 Impact factor: 6.126)
28. Li L, He H, Zhang J, Wang X, Bai S, Stolc V, Tongprasit W, Young ND, Yu O, Deng XW. Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. (2008). Genome Biology; 19;9(3):R57 (2012 Impact Factor: 10.288)
29. Li L*, Wang X*, Sasidharan R., Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Deng XW. Global identification and characterization of transcriptionally active regions in the rice genome. (2007). PLoS ONE; 2(3): e294 (Five-Year Impact Factor: 4.244)
30. Zhou J*, Wang X*, Jiao Y, Qin Y, Liu X, He K, Chen C, Ma L, Wang J, Xiong L, Zhang Q, Fan L, Deng XW. Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. (2007). Plant Molecular Biology; 63(5):591-608. (2012 Impact Factor: 3.518)
31. Wang X*, He H*, Li L, Chen R, Deng XW, Li S. NMPP: a user-customized NimbleGen microarray data processing pipeline. (2006) Bioinformatics; 22(23): 2955-2957; (Five-Year Impact Factor: 6.911)
32. Wang X*, Li L*, Chen C, Wang J, Li S, and Deng XW. Analysis of oligo hybridization properties by high-resolution tiling arrays in rice. (2006) Proceeding report, 5th International Rice Genetics Symposium; 65-76. 19-23;
33. Li L*, Wang X*, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, Deng XW. Genome-wide transcription analyses in rice using tiling microarrays. (2006) Nature Genetics; 38: 124-129. (2012 Impact Factor: 35.209)
34. Li L*, Wang X*, Xia M, Stolc V, Su N, Peng Z, Li S, Wang J, Wang X, Deng XW. Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. (2005) Genome Biology; 6(6):R52. (2012 Impact Factor: 10.288)
35. Stolc V*, Li L*, Wang X*, Li X, Su N, Tongprasit W, Han B, Xue Y, Li J, Snyder1 M, Gerstein M, Wang J, Deng XW. A pilot study of transcription unit analysis in rice using tiling-path microarray. (2005) Plant Molecular Biology; 59(1):137–14 (2012 Impact Factor: 3.518)
36. Ma L, Chen C, Liu X, Jiao Y, Su N, Li L, Wang X, Cao M, Sun N, Zhang X, Bao J, Li J, Pedersen S, Bolund L, Zhao H, Yuan L, Wong GKS, Wang J, Deng XW, Wang J. A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. (2005). Genome Research; 15(9):1274-1283 (2012 Impact Factor: 14.397)
37. Jiao Y*, Jia P*, Wang X*, Su N, Yu S, Zhang D, Ma L, Feng Q, Jin Z, Li L, Xue Y, Cheng Z, Zhao H, Han B, Deng XW. A Tiling Microarray Expression Analysis of Rice Chromosome 4 Suggests a Chromosome-Level Regulation of Transcription. (2005) The Plant Cell; 17(6):1641-57. Epub 2005 Apr 29 (Cover Story) (Five-Year Impact Factor: 10.125)
38. Li L, Wang X*, Li X, Su N, Stolc V, Han B, Li J, Xue Y, Wang J, Deng XW. Toward genome-wide transcriptional analysis in rice using MAS oligonucelotide tiling-path microarrays. (2005). Rice Is Life: Scientific Perspectives for World Rice Research.
