Publications
Published >5 years ago
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Notation: e: joint first/corresponding, u:undergrad, h:high school student, Bold: lab members, Rev: review.
2019
Azodi CB, Bolger Eu, McCarren A, Roantree M, de los Campos G, Shiu SH (2019) Benchmarking algorithms for genomic prediction of complex traits. G3 9(11):3691 pubmed
Uygun Se, Azodi, CBe, Shiu, SH (2019) Cis-regulatory code for predicting plant cell-type specific high salinity response. Plant Physiol. 181(4):1739 pubmed
Lloyd JP, Bowman MJ, Azodi CB, Moghe GD, Childs KL, Shiu SH. Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae (2019) Scientific Reports 9:12122 pubmed
Panchy NL, Azodi CB, Winship EFu, Shiu SH (2019) Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication. BMC Genomics 19:77 pubmed
Chang YM, Lin HH, Liu WY, Yu CP, Chen HJ, Kao YY, Wu YH, Lin JJ, Li MYJ, Tu SL, Wu SH, Shiu SH, Ku MSB, Li WH (2019) A comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes. Proc. Natl. Acad. Sci., USA 116(8):3091-3099 pubmed
Moore BM, Wang P, Fan P, Leong B, Schenck C, Lloyd J, Lehti-Shiu MD, Last R, Pichersky E, Shiu SH (2019) Robust predictions of specialized metabolism genes through machine learning. Proc. Natl. Acad. Sci., USA 116(6):2344-2353 pubmed
2018
Wang P, Moore BM, Panchy NL, Meng F, Lehti-Shiu MD, Shiu SH (2018) Factors influencing gene family size variation among related species in a plant family, Solanaceae. Genome Biol. Evol. 10(10):2596–2613 pubmed
Liu MJ, Sugimoto K, Uygun, S, Panchy NL, Campbell M, Yandell M, Howe GA, Shiu SH (2018) Regulatory Divergence In Wound-Responsive Gene Expression In Domesticated And Wild Tomato. Plant Cell 30(7):1445-1460 pubmed
Lloyd JP, Tsai ZTY, Sowers RPu, Panchy NL, Shiu SH (2018) A model-based approach for identifying functional intergenic transcribed regions and non-coding RNAs. Mol. Biol. Evol. 35(6):1422-1436 pubmed
Tsai CH, Uygun S, Roston R, Shiu SH, Benning C (2018) Recovery from N Deprivation Is a Transcriptionally and Functionally Distinct State in Chlamydomonas. Plant Physiol. 176(3):2007-2023 pubmed
2017
Huang CF, Yu CP, Wu YH, Lu MJ, Tu SL, Wu SH, Shiu SH, Ku MSB, Li WH (2017) Elevated auxin biosynthesis and transport underlie high vein density in C4 leaves. Proc. Natl. Acad. Sci., USA 114(33):E6884 pubmed
Uygun Se, Seddon AEe, Azodi C, Shiu SH (2017) Predictive models of spatial transcriptional response to high salinity. Plant Physiol. 174:450-464 pubmed
Tsai ZTY, Lloyd J, Shiu SH (2017) Defining functional, genic regions in the human genome through integration of biochemical, evolutionary, and genetic evidence. Mol. Biol. Evol. 34(7):1788-1798 pubmed
Bennett MS, Shiu SH, Triemer RE. (2017) A rare case of plastid protein-coding gene duplication in the chloroplast genome of Euglena archaeoplastidiata (Euglenophyta). J Phycol. 53(3):493-502 pubmed
Lehti-Shiu MDe, Panchy N, Wang P, Uygun S, Shiu SHe. (2017) Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families. Biochim. Biophys. Acta Gene Regul. Mech. 1860(1):3-20 [Review] pubmed
2016
Uygun S, Peng C, Lehti-Shiu MD, Last R, Shiu SH. (2016) Utility and limitations of using gene expression data to identify functional associations. PLoS Comp. Biol. 12(12):e1005244 pubmed
Panchy N, Lehti-Shiu MD, Shiu SH. (2016) Evolution of Gene Duplication in Plants. [review] Plant Physiol. 171(4):2294-316. pubmed
Kang H, Zhu D, Lin R, Opiyo SO, Jiang N, Shiu SH, Wang GL. (2016) A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads. DNA Research 23(3):241-51. pubmed
Liu T, Newton L, Liu MJ, Shiu SH, Farre EM. (2016) A G-box-like motif is necessary for transcriptional regulation by circadian pseudo-response regulators in Arabidopsis. Plant Physiol. 170(1):528-39. pubmed
2015
Lloyd JP, Seddon AE, Moghe GD, Simenc MCu, Shiu SH (2015) Characteristics of plant essential genes allow for within- and between-species prediction of lethal mutant phenotypes. Plant Cell 27:2133 pubmed
Tsai ZTY, Shiu SHe and Tsai HKe (2015) Contribution of sequence motif, chromatin state, and DNA structure features to predictive models of transcription factor binding in yeast. PLoS Comp. Biol. 11(8):e1004418 pubmed
Liu MJ, Seddon AE, Tsai ZTY, Major IT, Floer M, Howe GA, Shiu SH (2015) Determinants of nucleosome positioning and their influence on plant gene expression. Genome Res. 25(8):1182-95. pubmed
Poliner E, Panchy N, Newton L, Wu G, Lapinsky A, Bullard B, Zienkiewicz A, Benning C, Shiu SH, Farré EM. (2015) Transcriptional coordination of physiological responses in Nannochloropsis oceanica CCMP1779 under light/dark cycles. Plant J 83:1097-113. pubmed
Peng C, Uygun S, Shiu SH, Last R. (2015) The Impact of the Branched-Chain Ketoacid Dehydrogenase Complex on Amino Acid Homeostasis in Arabidopsis. Plant Physiol. 169(3):1807-20. pubmed
Lehti-Shiu MDe, Uygun S, Moghe, GD, Panchy N, Fang L, Hufnagel Du, Jasicki HLh, Feig M, Shiu SHe. (2015) Molecular evidence for functional divergence and decay of a transcription factor derived from whole genome duplication in Arabidopsis thaliana. Plant Physiol. 168(4):1717-34. pubmed
Yu CP, Chen SC, Chang YM, Liu WY, Lin HH, Lin JJ, Chen HJ, Lu YJ, Wu YH, Lu MY, Lu CH, Shih AC, Ku MS, Shiu SHe, Wu SHe, Li WHe. (2015) Transcriptome dynamics of developing maize leaves and genome-wide prediction of cis elements and their cognate transcription factors. Proc. Natl. Acad. Sci., USA 112(19):E2477-86. pubmed
Wu G, Hufnagel DEu, Denton AK, Shiu SH (2015) Retained duplicate genes in green alga Chlamydomonas reinhardtii tend to be stress response genes and experience frequent response gains. BMC Genomics 16:149. pubmed
Law M, Childs KL, Campbell MS, Stein D, Holt C, Panchy N, Lei J, Achawanantakun R, Jiao D, Andorf CM, Lawrence CJ, Ware D, Shiu SH, Sun Y, Jiang N, Yandell M (2015) Automated update, revision and quality control of the Zea mays genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. Plant Physiol. 167(1):25-39 pubmed
2014
Panchy N, Wu G, Newton L, Tsai CH, Chen J, Benning C, Farre EMe, Shiu SHe (2014) Prevalence, Evolution, and cis-Regulation of Diel Transcription in Chlamydomonas reinhardtii. G3 4(12):2461-2471 pubmed
Moghe GD, Shiu SH (2014) The causes and molecular consequences of polyploidy in flowering plants. Ann N Y Acad Sci 1320(1):16.Rev pubmed
Moghe GD, Hufnagel DEu, Tang H, Xiao Y, Dworkin I, Town CD, Conner JK, Shiu SH (2014) Consequences of whole genome triplication as revealed by comparative genomic analyses of the wild radish Raphanus raphanistrum and three other Brassicaceae species. Plant Cell 26(5):1925. pubmed Annotation
Shiu SH (2014) Evolution of plant genomes. In “Molecular Life Sciences: An Encyclopedic Reference”, eds Bell E et al. (Springer). Rev publisher
Campbell M, Law MY, Holt C, Stein J, Moghe G, Hufnagel Du, Lei J, Achawanantakun R, Jiao D, Lawrence C, Ware D, Shiu SH, Childs K, Sun Y, Jiang N, Yandell M (2014) MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol164(2):513-24 pubmed
2013
Hua Z, Pool JE, Schmitz RJ, Schultz MD, Shiu SH, Ecker JR, Vierstra RD (2013) Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis. Proc Natl Acad Sci, USA 110:16927. pubmed
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 SHe, Ku Me, Li WHe (2013) Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination. Proc Natl Acad Sci, USA 110:3979. pubmed
Moghe GD, Lehti-Shiu MD, Seddon AEu, 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. pubmed
2012
Vieler Ae, Wu Ge, Tsai CH, Bullard B, Cornish AJ, Harvey C, Reca IB, Thornburg C, Achawanantakun R, Buehl CJ, Campbell MS, Cavalier D, Childs KL, Clark TJ, Deshpande R, Erickson E, Armenia Ferguson A, Handee W, Kong Q, Li X, Liu B, Lundback S, Peng C, Roston RL, Sanjaya, Simpson JP, Terbush A, Warakanont J, Zäuner S, Farre EM, Hegg EL, Jiang N, Kuo MH, Lu Y, Niyogi KK, Ohlrogge J, Osteryoung KW, Shachar-Hill Y, Sears BB, Sun Y, Takahashi H, Yandell M, Shiu SHe, Benning Ce (2012) Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779. PLoS Genet 8(11):e1003064. pubmed
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 pubmed
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 pubmed
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. pubmed
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. pubmed
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). Rev publisher
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.Rev pubmed
2011
Joneson S, Stajich JE, Shiu SH, Rosenblum EB (2011) Genomic Transition to Pathogenicity in Chytrid Fungi. PLoS Pathogen 7(11):e1002338. pubmed
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. pubmed
Zou C, Sun K, Mackaluso JDu , Seddon AEu, 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. pubmed
Schaller GE, Shiu SH, Armitage J (2011) Two-component systems and their co-option for eukaryotic signal transduction. Current Biology 21(9):R320-30. Rev pubmed
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. pubmed
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. pubmed
2010
Miller Re, Wu Ge, 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. pubmed
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. pubmed
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. pubmed
2009
Zou C, Lehti-Shiu, MD, Thibaud-Nissen F, Prakash Th, Buell CR, and Shiu SH (2009) Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis thaliana and Rice. Plant Physiol. 151:3-15. pubmed
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. pubmed
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. pubmed
Hanada Ke, Vallejo Ve, 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. pubmed
2008
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 pubmed
Schaller GE, Kieber, JJ, and Shiu, SH (2008) Two-Component Signaling Elements and Histidyl-Aspartyl Phosphorelays. The Arabidopsis Book Rev publisher
Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL (2008) The genome of the moss Physcomitrella patens reveals evolutionary insights into the conquest of land by plants. Science 319:64-69 pubmed
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. pubmed
Shiu SH and Borevitz JO (2008). The next generation of microarray research: applications in evolutionary and ecological genomics. Heredity 100:141-9. Rev pubmed
2007
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. pubmed
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. pubmed
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. pubmed
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. pubmed
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. pubmed
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. pubmed
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 pubmed
2006
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. pubmed
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. Rev pubmed
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. pubmed
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. pubmed
Shiu postdoctoral research
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. pubmed
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. pubmed
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. pubmed
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. pubmed
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. pubmed
Shiu doctoral research
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. pubmed
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. pubmed
Shiu, S.-H., and Bleecker, A. B. (2001). Plant receptor-like kinase gene family: diversity, function, and signaling. Science STKE 2001, RE22. Rev pubmed
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. pubmed
Shiu, S.-H. (2001). Characterization of the receptor-like kinase TMK1 and molecular evolution of the receptor-like kinase gene family in Arabidopsis thaliana (Doctoral dissertation). University of Wisconsin, Madison, WI, USA.
Shiu undregraduate research
Tzean, S.-S., S.-C. Chiu, J.-L. Chen, S.-H. Hseu (my last name was spelled wrong), 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.
Tzean, S.-S., J.-L. Chen, and S.-H. Shiu. 1992. Talaromyces unicus sp-nov from Taiwan. Mycologia 84: 739-749. jstor