Publications

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[e]:joint first/corresponding. [u]:undergrad. [h]:high school student. [v]:visiting scholar. Bold: people from the Shiu lab.

Pre-Print

Panchy NL, Azodi CB, Winship EF, O'Malley RC, Shiu SH Asymmetric evolution of the transcription profiles and cis-regulatory sites contributes to the retention of transcription factor duplicates. bioRxiv DOI:10.1101/115857 DOI

2017

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. (in press)
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. (epub ahead of print) pubmed
Lehti-Shiu MD[e], Panchy N, Wang P, Uygun S, Shiu SH[e]. (2017) Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families. Biochim Biophys Acta 1860(1):3-20 [Review] pubmed,

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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. Plant Physiology 171(4):2294-316. [Review] 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 MC[u], 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 SH[e] and Tsai HK[e] (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,

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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. 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 MD[e],Uygun S, Moghe, GD, Panchy N, Fang L, Hufnagel D[u], Jasicki HL[h], Feig M, Shiu SH[e] (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 SH[e], Wu SH[e], Li WH[e]. (2015) Transcriptome dynamics of developing maize leaves and genome-wide prediction of cis elements and their cognate transcription factors. Proc Natl Acad Sci U S A. 112(19):E2477-86. pubmed
Wu G, Hufnagel DE[u], Denton AK[v], Shiu SH (2015) Retained duplicate genes in green alga Chlamydomonas reinhardtii tend to be stress response genes and experience frequent response gains. BMC Genomics16:149. 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 EM[e], Shiu SH[e] (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.[Review] pubmed
Moghe GD, Hufnagel DE[u], 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). [Review] publisher,

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Campbell M, Law MY, Holt C, Stein J, Moghe G, Hufnagel D[u], 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 SH[e], Ku M[e], Li WH[e] (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 AE[u], 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 A[e], Wu G[e], 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 SH[e], Benning C[e] (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,

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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 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). [Review] publisher,

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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] pubmed


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