| Zou C, Lehti-Shiu, MD, Thibaud-Nissen F, Prakash T, Buell CR, and Shiu SH (2009) Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis thaliana and Rice. Plant Physiol. 151:3-15.
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| Zou C, Lehti-Shiu, MD, Thomashow M, Shiu SH (2009) Evolution of stress-regulated gene expression in duplicate genes of Arabidopsis thaliana. PLoS Genet 5(7):e1000581.
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| Lehti-Shiu MD, Zou C, Hanada K, Shiu SH (2009) Evolutionary History and Stress Regulation of Plant Receptor-Like Kinase/Pelle Genes. Plant Physiol. 150:12-26.
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| Hanada K[e], Vallejo V[e], Nobuta, K, Slotkin K, Lisch D, Meyers BC, Shiu SH, Jiang N. (2009) Functional role of Pack-MULEs in rice inferred from purifying selection and expression profile. Plant Cell 21:25-38.
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| Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, and Shiu SH. (2008) Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Responses to Environmental Stimuli. Plant Physiol 148:993-1003
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| Schaller GE, Kieber, JJ, and Shiu, SH (2008) Two-Component Signaling Elements and Histidyl-Aspartyl Phosphorelays. The Arabidopsis Book [Review]
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| Rensing SA,...Hanada K,...Shiu SH,... Boore JL (70 co-authors). (2008) The genome of the moss Physcomitrella patens reveals evolutionary insights into the conquest of land by plants. Science 319:64-69
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| Zhang X, Shiu SH, Cal A, Borevitz JO. (2008) Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays. PLoS Genet. 4:e1000032.
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| Shiu SH and Borevitz JO (2008). The next generation of microarray research: applications in evolutionary and ecological genomics. Heredity 100:141-9. [Review]
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| Gingerich DJ, Hanada K, Shiu SH, and Vierstra RD. (2007) Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice. Plant Cell 19:2329.
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| Hanada K, Shiu SH, and Li WH. (2007) The Nonsynonymous/synonymous substitution rate ratio versus the radical/conservative replacement rate ratio in the evolution of mammalian genes. Mol Biol Evol 24:2235-4.
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| Hanada K, Zhang X, Borevitz JO, Li WH., and Shiu SH (2007) A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana Genome are transcribed and/or under purifying selection. Genome Research 17(5): 632-640.
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| Robatzek S, Bittel P, Chinchilla D, Kochner P, Felix G, Shiu SH, Boller T. (2007) Molecular identification and characterization of the tomato flagellin receptor LeFLS2, an orthologue of Arabidopsis FLS2 exhibiting characteristically different perception specificities. Plant Mol. Biol. 64:539-547.
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| Ahn YO, Zheng M, Bevan DR, Esen A, Shiu SH, Benson J, Peng HP, Miller JT, Cheng CL, Poulton JE, Shih MC (2007) Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 35. Phytochemistry 68:1510-20.
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| Hallen, HE, Huebner M, Shiu, SH, Guldener U, Trail F. (2007) Gene expression shifts during perithecium development in Gibberella zeae (anamorph Fusarium graminearum), with particular emphasis on ion transport proteins. Fungal Genet Biol 24:2235-4.
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Schaller GE, Doi K, Hwang I, Kieber JJ, Khurana JP, Kurata N, Mizuno T, Pareek A, Shiu SH, Wu P, Yip WK. (2007) Nomenclature for two-component signaling elements of rice. Plant Physiol. 143:555-7 [Letter to the Editor]
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| Wang, W., Esch, J. J., Shiu, S.-H., Agula, H., Binder, B. M., Chang, C., Patterson, S. E. and Bleecker, A. B. (2006). Identification of Important Regions for Ethylene Binding and signaling in the Transmembrane Domain of the ETR1 Ethylene Receptor of Arabidopsis. Plant Cell 18: 3429-3442.
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| Samuel, M. A., Salt, J. N., Shiu, S.-H., and Goring, D. R. (2006). Multifunctional arm repeat domains in plants. Int J Cytol 253:1-26. [Review]
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| Kim, J.[e], Shiu, S.-H.[e], Thoma, S., Li, W.-H., Patterson, S. A. (2006). Patterns of expansion and expression divergence in the plant polygalacturonase gene family. Genome Biology 7, R87.
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| Shiu, S.-H., Byrnes, J. K., Pan, R., Zhang, P., and Li, W. H. (2006). Role of positive selection in the retention of duplicate genes in mammalian genomes. Proc Natl Acad Sci U S A 103, 2232-2236.
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| Shiu, S.-H., Shih, M. C., and Li, W. H. (2005). Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiol 139, 18-26.
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| Mudgil, Y.[e], Shiu, S.-H.[e], Stone, S. L., Salt, J. N., and Goring, D. R. (2004). A large complement of the predicted Arabidopsis ARM repeat proteins are members of the U-box E3 ubiquitin ligase family. Plant Physiol 134, 59-66.
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| Shiu, S.-H., Karlowski, W. M., Pan, R., Tzeng, Y. H., Mayer, K. F., and Li, W. H. (2004). Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell 16, 1220-1234.
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| Shiu, S.-H., and Li, W. H. (2004). Origins, Lineage-Specific Expansions, and Multiple Losses of Tyrosine Kinases in Eukaryotes. Mol Biol Evol 21, 828-840.
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| Nakhamchik, A., Zhao, Z., Provart, N. J., Shiu, S.-H., Keatley, S. K., Cameron, R. K., and Goring, D. R. (2004). A comprehensive expression analysis of the Arabidopsis proline-rich extensin-like receptor kinase gene family using bioinformatic and experimental approaches. Plant Cell Physiol 45, 1875-1881.
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| Shiu, S.-H., and Bleecker, A. B. (2003). Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis. Plant Physiol 132, 530-543.
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| Gagne, J. M., Downes, B. P., Shiu, S.-H., Durski, A. M., and Vierstra, R. D. (2002). The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proc Natl Acad Sci U S A 99, 11519-11524.
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| Shiu, S.-H., and Bleecker, A. B. (2001). Plant receptor-like kinase gene family: diversity, function, and signaling. Science STKE 2001, RE22. [Review]
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| Shiu, S.-H., and Bleecker, A. B. (2001). Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc Natl Acad Sci U S A 98, 10763-10768.
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