Shin-Han Shiu, Ph.D. - Publications

2001 University of Wisconsin, Madison, Madison, WI 
Botany Biology, Molecular Biology

68 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Moore BM, Wang P, Fan P, Leong B, Schenck CA, Lloyd JP, Lehti-Shiu MD, Last RL, Pichersky E, Shiu SH. Robust predictions of specialized metabolism genes through machine learning. Proceedings of the National Academy of Sciences of the United States of America. PMID 30674669 DOI: 10.1073/pnas.1817074116  0.48
2018 Wang P, Moore BM, Panchy NL, Meng F, Lehti-Shiu MD, Shiu SH. Factors influencing gene family size variation among related species in a plant family, Solanaceae. Genome Biology and Evolution. PMID 30239695 DOI: 10.1093/gbe/evy193  0.44
2018 Liu MJ, Sugimoto K, Uygun S, Panchy N, Campbell MS, Yandell M, Howe GA, Shiu SH. Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato. The Plant Cell. PMID 29743197 DOI: 10.1105/tpc.18.00194  0.48
2018 Lloyd JP, Tsai ZT, Sowers RP, Panchy NL, Shiu SH. A model-based approach for identifying functional intergenic transcribed regions and non-coding RNAs. Molecular Biology and Evolution. PMID 29554332 DOI: 10.1093/molbev/msy035  0.32
2017 Tsai CH, Uygun S, Roston R, Shiu SH, Benning C. Recovery from N Deprivation Is a Transcriptionally and Functionally Distinct State in Chlamydomonas. Plant Physiology. PMID 29288234 DOI: 10.1104/pp.17.01546  0.48
2017 Vieler A, Wu G, 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, ... ... Shiu SH, et al. Correction: Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779. Plos Genetics. 13: e1006802. PMID 28542203 DOI: 10.1371/journal.pgen.1006802  0.64
2017 Tsai ZT, Lloyd JP, Shiu SH. Defining Functional Genic Regions in the Human Genome through Integration of Biochemical, Evolutionary, and Genetic Evidence. Molecular Biology and Evolution. PMID 28398576 DOI: 10.1093/molbev/msx101  0.32
2017 Uygun S, Seddon AE, Azodi CB, Shiu SH. Predictive models of spatial transcriptional response to high salinity. Plant Physiology. PMID 28373393 DOI: 10.1104/pp.16.01828  0.48
2016 Uygun S, Peng C, Lehti-Shiu MD, Last RL, Shiu SH. Utility and Limitations of Using Gene Expression Data to Identify Functional Associations. Plos Computational Biology. 12: e1005244. PMID 27935950 DOI: 10.1371/journal.pcbi.1005244  0.48
2016 Lehti-Shiu M, Panchy N, Wang P, Uygun S, Shiu SH. Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families. Biochimica Et Biophysica Acta. PMID 27522016 DOI: 10.1016/j.bbagrm.2016.08.005  0.48
2016 Panchy N, Lehti-Shiu MD, Shiu SH. Gene Duplicates: from origins to implications for plant evolution. Plant Physiology. PMID 27288366 DOI: 10.1104/pp.16.00523  1
2016 Kang H, Zhu D, Lin R, Opiyo SO, Jiang N, Shiu SH, Wang GL. A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 27098848 DOI: 10.1093/dnares/dsw011  1
2015 Liu T, Newton L, Liu MJ, Shiu SH, Farre EM. A G-box-like motif is necessary for transcriptional regulation by circadian pseudo-response regulators in Arabidopsis. Plant Physiology. PMID 26586835 DOI: 10.1104/pp.15.01562  1
2015 Tsai ZT, Shiu SH, Tsai HK. Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast. Plos Computational Biology. 11: e1004418. PMID 26291518 DOI: 10.1371/journal.pcbi.1004418  1
2015 Lloyd JP, Seddon AE, Moghe GD, Simenc MC, Shiu SH. Characteristics of Plant Essential Genes Allow for within- and between-Species Prediction of Lethal Mutant Phenotypes. The Plant Cell. 27: 2133-47. PMID 26286535 DOI: 10.1105/tpc.15.00051  0.56
2015 Poliner E, Panchy N, Newton L, Wu G, Lapinsky A, Bullard B, Zienkiewicz A, Benning C, Shiu SH, Farré EM. Transcriptional coordination of physiological responses in Nannochloropsis oceanica CCMP1779 under light/dark cycles. The Plant Journal : For Cell and Molecular Biology. 83: 1097-113. PMID 26216534 DOI: 10.1111/tpj.12944  1
2015 Lehti-Shiu MD, Uygun S, Moghe G, Panchy N, Fang L, Hufnagel DE, Jasicki HL, Feig M, Shiu SH. Molecular evidence for functional divergence and decay of a transcription factor derived from whole genome duplication in Arabidopsis thaliana. Plant Physiology. PMID 26103993 DOI: 10.1104/pp.15.00689  1
2015 Liu MJ, Seddon AE, Tsai ZT, Major IT, Floer M, Howe GA, Shiu SH. Determinants of nucleosome positioning and their influence on plant gene expression. Genome Research. 25: 1182-95. PMID 26063739 DOI: 10.1101/gr.188680.114  1
2015 Peng C, Uygun S, Shiu SH, Last RL. The Impact of the Branched-Chain Ketoacid Dehydrogenase Complex on Amino Acid Homeostasis in Arabidopsis. Plant Physiology. PMID 25986129 DOI: 10.1104/pp.15.00461  1
2015 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, Wu SH, et al. Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 112: E2477-86. PMID 25918418 DOI: 10.1073/pnas.1500605112  1
2015 Wu G, Hufnagel DE, Denton AK, Shiu SH. Retained duplicate genes in green alga Chlamydomonas reinhardtii tend to be stress responsive and experience frequent response gains. Bmc Genomics. 16: 149. PMID 25880851 DOI: 10.1186/s12864-015-1335-5  1
2015 Law M, Childs KL, Campbell MS, Stein JC, Olson AJ, Holt C, Panchy N, Lei J, Jiao D, Andorf CM, Lawrence CJ, Ware D, Shiu SH, Sun Y, Jiang N, et al. Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. Plant Physiology. 167: 25-39. PMID 25384563 DOI: 10.1104/pp.114.245027  1
2014 Panchy N, Wu G, Newton L, Tsai CH, Chen J, Benning C, Farré EM, Shiu SH. Prevalence, evolution, and cis-regulation of diel transcription in Chlamydomonas reinhardtii. G3 (Bethesda, Md.). 4: 2461-71. PMID 25354782 DOI: 10.1534/g3.114.015032  1
2014 Moghe GD, Shiu SH. The causes and molecular consequences of polyploidy in flowering plants. Annals of the New York Academy of Sciences. 1320: 16-34. PMID 24903334 DOI: 10.1111/nyas.12466  1
2014 Moghe GD, Hufnagel DE, Tang H, Xiao Y, Dworkin I, Town CD, Conner JK, Shiu SH. Consequences of Whole-Genome Triplication as Revealed by Comparative Genomic Analyses of the Wild Radish Raphanus raphanistrum and Three Other Brassicaceae Species. The Plant Cell. 26: 1925-1937. PMID 24876251 DOI: 10.1105/tpc.114.124297  1
2014 Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ, Ware D, Shiu SH, Childs KL, Sun Y, Jiang N, et al. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiology. 164: 513-24. PMID 24306534 DOI: 10.1104/pp.113.230144  1
2014 Wu GJ, Shiu SM, Hsieh MC, Tsai GJ. Anti-inflammatory activity of a sulfated polysaccharide from the brown alga Sargassum cristaefolium Food Hydrocolloids. DOI: 10.1016/j.foodhyd.2015.01.019  0.48
2013 Hua Z, Pool JE, Schmitz RJ, Schultz MD, Shiu SH, Ecker JR, Vierstra RD. Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis Proceedings of the National Academy of Sciences of the United States of America. 110: 16927-16932. PMID 24082131 DOI: 10.1073/pnas.1316009110  1
2013 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 MS, Li WH. Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination. Proceedings of the National Academy of Sciences of the United States of America. 110: 3979-84. PMID 23431200 DOI: 10.1073/pnas.1301009110  1
2013 Moghe GD, Lehti-Shiu MD, Seddon AE, Yin S, Chen Y, Juntawong P, Brandizzi F, Bailey-Serres J, Shiu SH. Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis. Plant Physiology. 161: 210-24. PMID 23132786 DOI: 10.1104/pp.112.205245  1
2012 Vieler A, Wu G, 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, ... ... Shiu SH, et al. Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. Plos Genetics. 8: e1003064. PMID 23166516 DOI: 10.1371/journal.pgen.1003064  1
2012 Lehti-Shiu MD, Shiu SH. Diversity, classification and function of the plant protein kinase superfamily. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 367: 2619-39. PMID 22889912 DOI: 10.1098/rstb.2012.0003  1
2012 Savory EA, Zou C, Adhikari BN, Hamilton JP, Buell CR, Shiu SH, Day B. Alternative splicing of a multi-drug transporter from pseudoperonospora cubensis generates an rxlr effector protein that elicits a rapid cell death Plos One. 7. PMID 22496844 DOI: 10.1371/journal.pone.0034701  1
2012 Davidson RM, Gowda M, Moghe G, Lin H, Vaillancourt B, Shiu SH, Jiang N, Robin Buell C. Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution. The Plant Journal : For Cell and Molecular Biology. 71: 492-502. PMID 22443345 DOI: 10.1111/j.1365-313X.2012.05005.x  1
2012 Tsai YC, Weir NR, Hill K, Zhang W, Kim HJ, Shiu SH, Schaller GE, Kieber JJ. Characterization of genes involved in cytokinin signaling and metabolism from rice. Plant Physiology. 158: 1666-84. PMID 22383541 DOI: 10.1104/pp.111.192765  1
2011 Takahashi H, Buchner P, Yoshimoto N, Hawkesford MJ, Shiu SH. Evolutionary relationships and functional diversity of plant sulfate transporters. Frontiers in Plant Science. 2: 119. PMID 22629272 DOI: 10.3389/fpls.2011.00119  1
2011 Joneson S, Stajich JE, Shiu SH, Rosenblum EB. Genomic transition to pathogenicity in chytrid fungi. Plos Pathogens. 7: e1002338. PMID 22072962 DOI: 10.1371/journal.ppat.1002338  1
2011 Yang Y, Sage TL, Liu Y, Ahmad TR, Marshall WF, Shiu SH, Froehlich JE, Imre KM, Osteryoung KW. CLUMPED CHLOROPLASTS 1 is required for plastid separation in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 108: 18530-5. PMID 22025705 DOI: 10.1073/pnas.1106706108  1
2011 Zou C, Sun K, Mackaluso JD, Seddon AE, Jin R, Thomashow MF, Shiu SH. Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America. 108: 14992-7. PMID 21849619 DOI: 10.1073/pnas.1103202108  1
2011 Schaller GE, Shiu SH, Armitage JP. Two-component systems and their co-option for eukaryotic signal transduction. Current Biology : Cb. 21: R320-30. PMID 21549954 DOI: 10.1016/j.cub.2011.02.045  1
2011 Carvallo MA, Pino MT, Jeknic Z, Zou C, Doherty CJ, Shiu SH, Chen TH, Thomashow MF. 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. Journal of Experimental Botany. 62: 3807-19. PMID 21511909 DOI: 10.1093/jxb/err066  1
2011 Hua Z, Zou C, Shiu SH, Vierstra RD. Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift. Plos One. 6: e16219. PMID 21297981 DOI: 10.1371/journal.pone.0016219  1
2011 Lin JL, Shiu SY, Chung HL. Seeding methods of Fcm for clustering streaming data Icic Express Letters. 5: 2843-2848.  0.44
2010 Miller R, Wu G, Deshpande RR, Vieler A, Gartner K, Li X, Moellering ER, Zauner S, Cornish AJ, Liu B, Bullard B, Sears BB, Kuo MH, Hegg EL, Shachar-Hill Y, ... Shiu SH, et al. Changes in transcript abundance in chlamydomonas reinhardtii following nitrogen deprivation predict diversion of metabolism Plant Physiology. 154: 1737-1752. PMID 20935180 DOI: 10.1104/pp.110.165159  1
2010 Lin H, Moghe G, Ouyang S, Iezzoni A, Shiu SH, Gu X, Buell CR. Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana. Bmc Evolutionary Biology. 10: 41. PMID 20152032 DOI: 10.1186/1471-2148-10-41  1
2009 Zou C, Lehti-Shiu MD, Thomashow M, Shiu SH. Evolution of stress-regulated gene expression in duplicate genes of Arabidopsis thaliana. Plos Genetics. 5: e1000581. PMID 19649161 DOI: 10.1371/journal.pgen.1000581  1
2009 Zou C, Lehti-Shiu MD, Thibaud-Nissen F, Prakash T, Buell CR, Shiu SH. Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice. Plant Physiology. 151: 3-15. PMID 19641029 DOI: 10.1104/pp.109.140632  1
2009 Lehti-Shiu MD, Zou C, Hanada K, Shiu SH. Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes. Plant Physiology. 150: 12-26. PMID 19321712 DOI: 10.1104/pp.108.134353  1
2009 Hanada K, Vallejo V, Nobuta K, Slotkin RK, Lisch D, Meyers BC, Shiu SH, Jiang N. The functional role of pack-MULEs in rice inferred from purifying selection and expression profile. The Plant Cell. 21: 25-38. PMID 19136648 DOI: 10.1105/tpc.108.063206  1
2008 Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu SH. Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiology. 148: 993-1003. PMID 18715958 DOI: 10.1104/pp.108.122457  1
2008 Zhang X, Shiu SH, Shiu S, Cal A, Borevitz JO. Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays. Plos Genetics. 4: e1000032. PMID 18369451 DOI: 10.1371/journal.pgen.1000032  1
2008 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, ... ... Shiu SH, et al. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (New York, N.Y.). 319: 64-9. PMID 18079367 DOI: 10.1126/science.1150646  1
2007 Gingerich DJ, Hanada K, Shiu SH, Vierstra RD. Large-scale, lineage-specific expansion of a bric-a-brac/tramtrack/broad complex ubiquitin-ligase gene family in rice. The Plant Cell. 19: 2329-48. PMID 17720868 DOI: 10.1105/tpc.107.051300  1
2007 Hanada K, Shiu SH, Li WH. The nonsynonymous/synonymous substitution rate ratio versus the radical/conservative replacement rate ratio in the evolution of mammalian genes. Molecular Biology and Evolution. 24: 2235-41. PMID 17652332 DOI: 10.1093/molbev/msm152  1
2007 Hallen HE, Huebner M, Shiu SH, Güldener U, Trail F. Gene expression shifts during perithecium development in Gibberella zeae (anamorph Fusarium graminearum), with particular emphasis on ion transport proteins. Fungal Genetics and Biology : Fg & B. 44: 1146-56. PMID 17555994 DOI: 10.1016/j.fgb.2007.04.007  1
2007 Hanada K, Zhang X, Borevitz JO, Li WH, Shiu SH. 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: 632-40. PMID 17395691 DOI: 10.1101/gr.5836207  1
2006 Wang W, Esch JJ, Shiu SH, Agula H, Binder BM, Chang C, Patterson SE, Bleecker AB. Identification of important regions for ethylene binding and signaling in the transmembrane domain of the ETR1 ethylene receptor of Arabidopsis. The Plant Cell. 18: 3429-42. PMID 17189345 DOI: 10.1105/tpc.106.044537  1
2006 Samuel MA, Salt JN, Shiu SH, Goring DR. Multifunctional arm repeat domains in plants. International Review of Cytology. 253: 1-26. PMID 17098053 DOI: 10.1016/S0074-7696(06)53001-3  1
2006 Kim J, Shiu SH, Thoma S, Li WH, Patterson SE. Patterns of expansion and expression divergence in the plant polygalacturonase gene family. Genome Biology. 7: R87. PMID 17010199 DOI: 10.1186/gb-2006-7-9-r87  1
2006 Shiu SH, Byrnes JK, Pan R, Zhang P, Li WH. Role of positive selection in the retention of duplicate genes in mammalian genomes. Proceedings of the National Academy of Sciences of the United States of America. 103: 2232-6. PMID 16461903 DOI: 10.1073/pnas.0510388103  1
2005 Shiu SH, Shih MC, Li WH. Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiology. 139: 18-26. PMID 16166257 DOI: 10.1104/pp.105.065110  1
2004 Nakhamchik A, Zhao Z, Provart NJ, Shiu SH, Keatley SK, Cameron RK, Goring DR. A comprehensive expression analysis of the Arabidopsis proline-rich extensin-like receptor kinase gene family using bioinformatic and experimental approaches. Plant & Cell Physiology. 45: 1875-81. PMID 15653807 DOI: 10.1093/pcp/pch206  1
2004 Shiu SH, Li WH. Origins, lineage-specific expansions, and multiple losses of tyrosine kinases in eukaryotes. Molecular Biology and Evolution. 21: 828-40. PMID 14963097 DOI: 10.1093/molbev/msh077  1
2004 Mudgil Y, Shiu SH, Stone SL, Salt JN, Goring DR. A large complement of the predicted Arabidopsis ARM repeat proteins are members of the U-box E3 ubiquitin ligase family. Plant Physiology. 134: 59-66. PMID 14657406 DOI: 10.1104/pp.103.029553  1
2003 Shiu SH, Bleecker AB. Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis. Plant Physiology. 132: 530-43. PMID 12805585 DOI: 10.1104/pp.103.021964  1
2002 Gagne JM, Downes BP, Shiu SH, Durski AM, Vierstra RD. The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 99: 11519-24. PMID 12169662 DOI: 10.1073/pnas.162339999  1
2001 Shiu SH, Bleecker AB. Plant receptor-like kinase gene family: diversity, function, and signaling. Science's Stke : Signal Transduction Knowledge Environment. 2001: re22. PMID 11752632 DOI: 10.1126/stke.2001.113.re22  1
2001 Shiu SH, Bleecker AB. Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proceedings of the National Academy of Sciences of the United States of America. 98: 10763-8. PMID 11526204 DOI: 10.1073/pnas.181141598  1
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