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Only publications in the past five years are listed here.

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

Submitted manuscripts in bioRxiv

Uygun S[e], Azodi, CB[e], Shiu, SH. Cis-regulatory code for predicting plant cell-type specific high salinity response bioRxiv DOI: 10.1101/466326 bioRxiv
Lloyd JP, Bowman MJ, Azodi, CB, Moghe, GD, Childs KL, Shiu, SH. Evolutionary characteristics of intergenic transcribed regions indicate widespread noisy transcription in the Poaceae bioRxiv DOI: 10.1101/440933 bioRxiv
Panchy NL, Lloyd JP, Shiu, SH. Predicting cell-cycle expressed genes identifies canonical and non-canonical regulators of time-specific expression in Saccharomyces cerevisiae. bioRxiv DOI: 10.1101/387050 bioRxiv
Moore BM, Wang P, Fan P, Leong B, Schenck C, Lloyd J, Last R, Pichersky E, Shiu SH. Robust predictions of specialized metabolism genes through machine learning. bioRxiv DOI: 10.1101/304873 bioRxiv
Panchy NL, Azodi CB, Winship EF[u], 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 bioRxiv


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 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 RP[u], 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


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 S[e], Seddon AE[e], 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 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


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


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,


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 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


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,


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

Papers published >5 years ago

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