Laboratory of Computational Biology and Bioinformatics        

Chuang Ma, Mingming Xin, Kenneth A. Feldmann, Xiangfeng Wang.  Machine Learning–Based Differential Network Analysis: A Study of Stress-Responsive Transcriptomes in Arabidopsis. The Plant Cell, 2014, doi: 10.1105/tpc.113.121913.
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Mingming Xin*, Ruolin Yang*, Guosheng Li, Hao Chen, John Laurie, Chuang Ma, Dongfang Wang, Yingyin Yao, Brian A. Larkins, Qixin Sun, Ramin Yadegari, Xiangfeng Wang#, and Zhongfu Ni. Dynamic expression of imprinted genes associates with maternally controlled nutrient allocation during maize endosperm development. The Plant Cell, 2013  25(9):3212-3227. Supplementary Data: Assembled Mo17 maize genome sequences 
Media:Plant Cell 2013.pdf  

Hao Chen, Xiangfeng Wang. CrusView: a Java-based visualization platform for comparative genomics analyses in Brassicaceae. Plant Physiology, 2013, 163(1):354-362..
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Ruolin Yang, Xiangfeng Wang. Organ evolution in angiosperms driven by correlated divergences of gene sequences and expression patterns. The Plant Cell, 2013 25(1):72-81.
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Ruolin Yang, David J. Jarvis, Hao Chen, Mark Beilstein, Jane Grimwood, Jerry Jenkins, ShengQiang Shu, Simon Prochnik,Mingming XinChuang Ma, Jeremy Schmutz, Rod A. Wing,Thomas Mitchell-Olds, Karen Schumaker and Xiangfeng Wang.  The reference genome of the halophytic plant Eutrema salsugineum.  Frontiers In Plant Genetics AND Genomics, 2013, 4:46.
Media:Frontiers In Plant Genetics AND Genomics 2012.pdf

Chuang Ma, Hao Chen, Mingming Xin, Ruolin Yang, Xiangfeng Wang. KGBassembler: A karyotype-based genome assembler for Brassicaceae species. Bioinformatics, 2012, 28(23):3141-31433.
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Chuang Ma, Xiangfeng Wang.  Application of the Gini correlation coefficient to infer regulatory relationships in transcriptome analysis.  Plant Physiology July 2012 pp.112.201962
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Mingming Xin, Xiangfeng Wang, Huiru Penga, Yingyin Yao, Chaojie Xiea, Yao Hana, Zhongfu Nia, Qixin Sun. Transcriptome Comparison of Susceptible and Resistant Wheat in Response to Powdery Mildew Infection. Genomics, Proteomics & Bioinformatics, Volume 10, Issue 2, April 2012, Pages 94–106
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Wang X and Liu XS. Systematic curation of miRBase microRNA annotation using integrated deep small RNA sequencing data for C. elegans and Drosophila. Genomics  Volume 97, Issue 4, April 2011, Pages 235–243
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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. Genomics, 97(4):235-243.
Media:Genomics 2011.pdf

Zhang H, He H, Wang X, Li L and Deng X. Genome-wide identification of Hy5 binding sites in Arabidopsis. 2011 Feb; Plant Journal. 65(3):346-58

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 Nov Genomics. 96(5):308-15

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. Plant Cell 2010 22:17-33. Published online: January 19, 2010

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. Plant Molecular Biology Volume 72, Number 6, 585-595,.

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. The Plant Cell; Epub online and highlighted “In This Issue” April 17 2009.

Wang X, Yu Z, Deng XW, Li L. Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome. Bioinformatics, 2009: 1215~1218.

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 Feb) The Plant Cell.; 20: 259-276

Wang X. Statistical Analysis of Tiling-path microarrays. A review chapter for the book Oligonucleotide Array Sequence Analysis, (2008); NOVA Science Publisher, New York, USA ISBN: 978-1-60456-542-3
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. (2008 Oct) Characterization of the genome expression trends in the heading-stage panicle of six rice lineages. Genomics 93 (2009) 169–178;

Yin BL, Guo L, Zhang DF, Terzaghi W, Wang XF, Liu TT, He H, Cheng ZK and Deng XW. Integration of Cytological Features with Molecular and Epigenetic Properties of Rice Chromosome 4. (2008 Aug) Molecular Plant 1: 816-829;

Zhang HY, He H, Chen LB, Li L, Liang MZ, Wang XF, 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 Aug) Molecular Plant; 1: 720-731;

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 Mar) Genome Biology.; 19;9(3):R57

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 Jan) PLoS ONE.; 2(3): e294

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 Mar) Plant Molecular Biology; 63(5):591-608. Epub 2007 Jan 16

Wang X, He H, Li L, Chen R, Deng XW, Li S. NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics.; (2006 Dec); 22(23): 2955-7; Epub 2006 Oct 12

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. Proceeding report, 5th International Rice Genetics Symposium; (2006 May) 65-76. 19-23; Philippines

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 Jan); Nature Genetics; 38: 124 – 129. Epub Dec 20

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 June) Genome Biology; 6(6):R52.

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 Sep) Plant Molecular Biology.; 59(1):137–14

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 Sep) Genome Research. 15(9):1274-1283

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 Jun) The Plant Cell; 17(6):1641-57. Epub 2005 Apr 29

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 Jan) In Rice Is Life: Scientific Perspectives for World Rice Research Conference held in Tokyo and Tsukuba, Japan.