| Liu WY, Chang YM, Chen SC, Lu CH, Wu YH, Lu MY, Chen DR, Shih AC, Sheue CR, Huang HC, Yu CP, Lin HH, Shiu SH*, Ku M*, Li WH* (2013) Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination. Proc Natl Acad Sci, USA 110:3979.
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| Moghe GD, Lehti-Shiu MD, Seddon AE, Yin S, Chen Y, Juntawong P, Brandizzi F, Bailey-Serres J, Shiu SH (2013) Characteristics and significance of intergenic polyA RNA transcription in Arabidopsis thaliana. Plant Physiol 161(1):210-24.
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| Vieler A*, Wu G*, <40 co-authors>, Shiu SH*, Benning C* (2012) Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779. PLoS Genet 8(11):e1003064.
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| Lehti-Shiu MD, Shiu SH (2012) Diversity and Function of the Protein Kinase Superfamily in Plants. Philos Trans R Soc Lond B Biol Sci 367(1602):2619-2639
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| Savory EA, Zou C, Adhikari BN, Hamilton JP, Buell CR, Shiu SH, Day B (2012) Alternative Splicing of a Multi-Drug Transporter from Pseudoperonospora cubensis Generates an RXLR Effector Protein That Elicits a Rapid Cell Death. PLoS One 7(4):e34701
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| Davidson R, Gowda M, Moghe G, Lin H, Vaillancourt B, Shiu SH, Jiang N, Buell C (2012) Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. Plant J 71(3):492-502.
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| Tsai YC, Weir NR, Hill K, Zhang W, Shiu SH, Schaller GE and Kieber JJ (2012) Characterization of genes involved in cytokinin signaling and metabolism from rice. Plant Physiol 158(4):1666-84.
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| Lehti-Shiu MD, Zou C, Shiu SH (2012) Origin, Diversity, Expansion History and Functional Evolution of the Plant Receptor-Like Kinase/Pelle Family. In Signaling and Communication in Plants", eds Tax T, Kemmering B (Springer). [Review]
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| Takahashi H, Buchner P, Yoshimoto N, Hawkesford MJ, Shiu SH (2012) Evolutionary relationships and functional diversity of plant sulfate transporters. Frontier in Plant Sci 2:119.[Review]
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| Joneson S, Stajich JE, Shiu SH, Rosenblum EB (2011) Genomic Transition to Pathogenicity in Chytrid Fungi. PLoS Pathogen 7(11):e1002338.
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| Yang Y, Sage TL, Liu Y, Ahmad TR, Marshall WF, Shiu SH, Froehlich JE, Imre KM, Osteryoung KW (2011) CLUMPED CHLOROPLASTS 1 is required for plastid separation in Arabidopsis. Proc Natl Acad Sci USA 108(45):18530-5.
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| Zou C, Sun K, Mackaluso JD, Seddon AE, Jin R, Thomashow MF, Shiu SH (2011) Cis-regulatory code of stress responsive transcription in Arabidopsis thaliana. Proc Natl Acad Sci USA 108(36):14992-7.
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| Schaller GE, Shiu SH, Armitage J (2011) Two-component systems and their co-option for eukaryotic signal transduction. Current Biology 21(9):R320-30. [Review]
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| Carvallo MA, Pino MT, Jeknic Z, Zou C, Doherty CJ, Shiu SH, Chen TH, Thomashow MF (2011) A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii, Solanum tuberosum, and Arabidopsis thaliana. J Exp Bot 62(11):3807-19.
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| Hua Z, Zou C, Shiu SH, Vierstra RD (2011) Phylogenetic Comparison of F-Box (FBX) Gene Superfamily within the Plant Kingdom Reveals Divergent Evolutionary Histories Indicative of Genomic Drift. PLoS ONE 6(1):e16219.
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| Miller R*, Wu G*, Deshpande RR, Vieler A, Gaertner K, Li X, Moellering ER, Zauner S, Cornish A, Liu B, Bullard B, Sears BB, Kuo MH, Hegg EL, Shachar-Hill Y, Shiu SH, and Benning C. (2010) Changes in Transcript Abundance in Chlamydomonas reinhardtii Following Nitrogen-Deprivation Predict Diversion of Metabolism. Plant Physiology 154(4):1737-52.
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| Hanada K, Akiyama K, Sakurai T, Toyoda T, Shinozaki K, Shiu SH (2010) sORF finder: a program package to identify small open reading frames with high coding potential. Bioinformatics 26(3):399.
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| Lin H, Moghe G, Ouyang S, Iezzoni A, Shiu SH, Gu X, Buell CR (2010) Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. BMC Evol Biol 10:41.
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| 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, <34 in between> Hanada K, <16 in between> Shiu SH,<16 in between> Boore JL. (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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| Tzean, S.-S., S.-C. Chiu, J.-L. Chen, S.-H. Shiu, G.-H. Lin, G.-Y. Liou, C.-C. Chen, and W.-H. Hsu. 1994. Penicillium and related teleomorphs from Taiwan. Mycological Monograph No. 9. Food Industry Research and Development Institute, Hsinchu, Taiwan.
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| Tzean, S.-S., J.-L. Chen, and S.-H. Shiu. 1992. Talaromyces unicus sp-nov from Taiwan. Mycologia 84: 739-749.
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