Yang X, Li L.(2012) Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data. Biology.1:297-310
Yang X, Zhang H, Li L.(2012) Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis.Plant J.70(3):421-431
Wu N, Yang X, Li L.(2011) Identification of feed forward loops composed of microRNAs and transcription factors in Arabidopsis.Journal of Biochemistry and Molecular Biology in the Post Genomic Era.1:79-86
Yang X, Li L.(2011) miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants. Bioinformatics.27(18):2614-2615
Yang X, Zhang H, Li L.(2011) Global analysis of gene-level microRNA expression in Arabidopsis using deep sequencing data. Genomics.98(1):40-46.
Zhang H, He H, Wang X, Wang X, Yang X, Li L*, Deng XW.(2011) Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulation. Plant J.65(3):346-58. *Co-corresponding authors.
He H, Zhang H, Wang X, Wu N, Yang X, Chen R, Li Y, Deng XW, Li L.(2010) Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression. Genomics.96(5):308-315
Wang X, Yu Z, Yang X, Deng XW, Li L. (2009) Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome. Bioinformatics. 25:1215-1218.
Peng ZY, Zhang H, Liu T, Dzikiewicz KM, Li S, Wang X, Hu G, Zhu Z, Wei X, Zhu QH, Sun Z, Ge S, Ma L, Li L*, Deng XW* (2009) Characterization of the genome expression trends in the heading-stage panicle of six rice lineages. Genomics.93:169-178. *Co-corresponding authors.
Zhang HY, He H, Chen LB, Li L, Liang MZ, Wang XF, Liu XG, He GM, Chen RS, Ma LG, and Deng XW (2008) A genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids. Mol Plant. 1,720-731.
Li L, He H, Zhang J, Wang X, Bai S, Stolc V, Tongprasit W, Young ND, Yu O, Deng XW (2008) Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. Genome Biol.9,R57.
Li L, Deng XW (2008) Microarray-based approaches to rice transcriptome analysis. In "Rice biology in the genomics era.".p.37-52.
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 (2007) Global identification and characterization of transcriptionally active regions in the rice genome. PLoS ONE. 2:e294.
Kikuchi S, Wang G-L, Li L. (2007) Genome-wide RNA expression profiling. In "Rice functional genomics: Challenges, progress and prospects " N Upadhyaya, Eds. Springer. p.36-63.
Su N, He K, Jiao Y, Chen C, Zhou J, Li L, Bai S, Li X, Deng XW (2007) Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice. Plant Mol Biol. 63:337-349.
Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, Deng XW (2006) Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet.38:124-129.
Wang X, He H, Li L, Chen R, Deng XW, Li S (2006) NMPP - A user-customized Nimblegen microarray data processing pipeline. Bioinformatics.22:2955-2957.
Li L, Wang X, Li X, Su N, Stolc V, Han B, Li J, Xue Y, Wang J, Deng XW (2005) Toward genome-wide transcriptional analysis in rice using MAS oligonucleotide tiling-path microarrays. In "Rice Is Life: Scientific Perspectives for the 21st Century." K Toriyama, KL Heong, B Hardy, Eds. p.80-83.
Li L, Deng XW (2005) It runs in the family: regulation of brassinosteroid signaling by the BZR1-BES1 class of transcription factors. Trends Plant Sci.10:266-268.
Zhang S, Chen C, Li L, Meng L, Singh J, Jiang N, Deng XW, He ZH, Lemaux PG (2005) Evolutionary expansion, gene structure, and expression of the rice wall-associated kinase gene family. Plant Physiol.139:1107-1124.
Stolc V, Li L, Wang X, Li X, Su N, Tongprasit W, Han B, Xue Y, Li J, Snyder M, Gerstein M, Wang J, Deng XW (2005) A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray. Plant Mol Biol.59:137-149.
Li L, Wang X, Xia M, Stolc V, Su N, Peng Z, Li S, Wang J, Wang X, Deng XW (2005) Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol.6:R52.
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 (2005) A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. Plant Cell.17:1641-1657.
Li L, Zhao Y, McCaig BC, Wingerd BA, Wang J, Whalon ME, Pichersky E, Howe GA (2004) The tomato homolog of CORONATINE-INSENSITIVE1 is required for the maternal control of seed maturation, jasmonate-signaled defense responses, and glandular trichome development. Plant Cell.16:126-143.
Li L, Deng XW (2003) The COP9 signalosome: an alternative lid for the 26S proteasome? Trend Cell Biol.13:507-509.
Howe GA, Li L, Lee GI, Li C, Shaffer D (2002) Genetic dissection of induced resistance in tomato. In "Induced resistance in plants against insects and diseases ". A Schmitt, B Mauch-Mani, Eds. p.47-52.
Li L, Li C, Lee GI, Howe GA (2002) Distinct roles for jasmonate synthesis and action in the systemic wound response of tomato. Proc Natl Acad Sci USA.99:6416-6421.
Li L, Li C, Howe GA (2001) Genetic analysis of wound signaling in tomato: Evidence for a dual role of jasmonic acid in defense and female fertility. Plant Physiol.127:1414-1417.
Li L, Howe GA (2001) Alternative splicing of prosystemin pre-mRNA produces two isoforms that are active as signals in the wound response pathway. Plant Mol Biol.46:409-419.
Howe GA, Lee GI, Itoh A, Li L, DeRocher A (2000) Cytochrome P450-dependent metabolism of oxylipins in tomato: cloning and expression of allene oxide synthase and fatty acid hydroperoxide lyase. Plant Physiol.123:711-724.
