Tsai Kuen‐Jin, Suen Der‐Fen, Shih Ming‐Che (2023) Hypoxia response protein HRM1 modulates the activity of mitochondrial electron transport chain in Arabidopsis under hypoxic stress. New Phytologist, doi: 10.1111/nph.19006. Epub ahead of print., PMID: 37301985.
Sun Wan-Ting, Cheng Sy-Chyi, Chao Ya-Ting, Lin Shu-Yao, Yang Ting-Ting, Ho Yi-Ping, Shih Ming-Che, Ko Swee-Suak (2023) Sugars and sucrose transporters in pollinia of Phalaenopsis aphrodite (Orchidaceae). Journal of Experimental Botany, 74(8), 2556-2571
Tu Po-Wen, Chiu Jie-Siang, Lin Chih, Chien Chih-Cheng, Hsieh Feng-Chia, Shih Ming-Che, Yang Yu-Liang (2022) Evaluation of the Antifungal Activities of Photorhabdus akhurstii and Its Secondary Metabolites against Phytopathogenic Colletotrichum gloeosporioides. Journal of Fungi, 8(4), 403
Cho, H.-Y., Chou, M.-Y., Ho, H.-Y., Chen, W.-C. and *Shih, M.-C. (2022) Ethylene modulates translation dynamics in Arabidopsis under submergence via GCN2 and EIN2.. Science Advances, 8:22
Hsieh, D.-K., Chuang, S.-C., Chen, C.-Y., Chao, Y.-T., Lu, M.-Y. *Lee, M.-H., *Shih, M.-C. (2022) Comparative genomics of three Colletotrichum scovillei strains and genetic analysis revealed genes involved in fungal growth and virulence on chili pepper. Frontiers in Microbiology,
Hsu, C.-T., Yuan, Y.-H., Zheng, P.-X. Wu, F.-H., Cheng, Q.-W., Wu, Y.-L., Lin, S., Yue, J.-J., Cheng, Y.-H., Lin, S.-I., Shih*, M.-C., Sheen*, J., Lin1*,+, Y.-C. and Lin*,+, C.-S. (2022) DNA-free CRISPR-Cas9 gene editing of tetraploid tomatoes using protoplast regeneration. Plant Physiology,
Hsu CT, Yuan YH, Lin YC, Lin S, Cheng QW, Wu FH, Sheen J, Shih MC, Lin CS (2021) Efficient and Economical Targeted Insertion in Plant Genomes via Protoplast Regeneration. The CRISPR journal, 4(5), 752-760
Cho HY, Loreti E, Shih MC, Perata P (2021) Energy and sugar signaling during hypoxia. The New phytologist, 229, 57-63.
Kuo, C.-C., Lin, Y.-C., Chen, L.-H., Lin, M.-Y., Shih, M.-C. and Lee, M.-H.* (2021) CaNRT2.1 is required for nitrate but not nitrite uptake in chili pepper pathogen Colletotrichum acutatum.. Frontiers in Microbiology, 11, 613674
Ko S.-S., Jhong C.-M. and Shih, M.-C. (2020) Blue Light Acclimation Reduces the Photoinhibition of Phalaenopsis aphrodite (Moth Orchid). International Journal of Molecular Sciences, 21(17), 6167
Ko, S.-S., Jhong, C.-M., Lin, Y.-J., Wei, C.-Y., Lee, J.-Y., *Shih, M.-C. (2020) Blue Light Mediates Chloroplast Avoidance and Enhances Photoprotection of Vanilla Orchid. International Journal of Molecular Sciences, 21(21), 8022
Chen W.-J., Kuo, T.-Y., Chen, C.-Y., Hsieh, F.-C., Yang, Y.-L., Liu, J.-R., *Shih, M.-C. (2020) Whole Genome Sequencing and Tn5-Insertion Mutagenesis of Pseudomonas taiwanensis CMS to Probe Its Antagonistic Activity Against Rice Bacterial Blight Disease. International Journal of Molecular Sciences, 21(22), 8639
Lin CC, Chao YT, Chen WC, Ho HY, Chou MY, Li YR, Wu YL, Yang HA, Hsieh H, Lin CS, Wu FH, Chou SJ, Jen HC, Huang YH, Irene D, Wu WJ, Wu JL, Gibbs DJ, Ho MC, Shih MC (2019) Regulatory cascade involving transcriptional and N-end rule pathways in rice under submergence. Proceedings of the National Academy of Sciences of the United States of America, 116(8), 3300-3309
Cho HY, Lu MJ, Shih MC (2019) The SnRK1-eIFiso4G1 signaling relay regulates the translation of specific mRNAs in Arabidopsis under submergence. The New phytologist, 222(1), 366-381
Ko, S.-S., Liu, Y.-C., Chung, M.-C., Shih, M.-C., Mohammadmehdi, H., Oguchi, T., Watanabe, K, Yeh, K.-W. (2019) Environmental biosafety assessment on transgenic Oncidium orchid modified by RNA interference of Phytoene Synthase genes. Plant Biotechnology, 36(3) 181-185
Kuo YT, Chao YT, Chen WC, Shih MC, Chang SB (2019) Segmental and tandem chromosome duplications led to divergent evolution of the chalcone synthase gene family in Phalaenopsis orchids. Annals of botany, 123(1), 69-77
Chao YT, Chen WC, Chen CY, Ho HY, Yeh CH, Kuo YT, Su CL, Yen SH, Hsueh HY, Yeh JH, Hsu HL, Tsai YH, Kuo TY, Chang SB, Chen KY, Shih MC (2018) Chromosome-level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding. Plant Biotechnology Journal, 16(12), 2027-2041
Lin CS, Hsu CT, Yang LH, Lee LY, Fu JY, Cheng QW, Wu FH, Hsiao HC, Zhang Y, Zhang R, Chang WJ, Yu CT, Wang W, Liao LJ, Gelvin SB, Shih MC (2018) Application of protoplast technology to CRISPR/Cas9 mutagenesis: from single-cell mutation detection to mutant plant regeneration. Plant Biotechnology Journal, 16(7), 1295-1310
Lin CS, Chen JJW, Chiu CC, Hsiao HCW, Yang CJ, Jin XH, Leebens-Mack J, de Pamphilis CW, Huang YT, Yang LH, Chang WJ, Kui L, Wong GK, Hu JM, Wang W, Shih MC (2017) Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. The Plant journal : for cell and molecular biology, 90(5), 994-1006
Chao YT, Yen SH, Yeh JH, Chen WC, Shih MC (2017) Orchidstra 2.0-A Transcriptomics Resource for the Orchid Family. Plant & Cell Physiology, 58(1), e9
Sasidharan R, Bailey-Serres J, Ashikari M, Atwell BJ, Colmer TD, Fagerstedt K, Fukao T, Geigenberger P, Hebelstrup KH, Hill RD, Holdsworth MJ, Ismail AM, Licausi F, Mustroph A, Nakazono M, Pedersen O, Perata P, Sauter M, Shih MC, Sorrell BK, Striker GG, van Dongen JT, Whelan J, Xiao S, Visser EJ, Voesenek LA (2017) Community recommendations on terminology and procedures used in flooding and low oxygen stress research. The New phytologist, 214(4), 1403-1407
Lin CS, Hsu CT, Liao DC, Chang WJ, Chou ML, Huang YT, Chen JJ, Ko SS, Chan MT, Shih MC (2016) Transcriptome-wide analysis of the MADS-box gene family in the orchid Erycina pusilla. Plant Biotechnology Journal, 14(1), 284-298
Cho HY, Wen TN, Wang YT, Shih MC (2016) Quantitative phosphoproteomics of protein kinase SnRK1 regulated protein phosphorylation in Arabidopsis under submergence. Journal of Experimental Botany, 67(9), 2745-2760
Chen WJ, Kuo TY, Hsieh FC, Chen PY, Wang CS, Shih YL, Lai YM, Liu JR, Yang YL, Shih MC (2016) Involvement of type VI secretion system in secretion of iron chelator pyoverdine in Pseudomonas taiwanensis. Scientific reports, 6, 32950
Tsai KJ, Lin CY, Ting CY, Shih MC (2016) Ethylene-Regulated Glutamate Dehydrogenase Fine-Tunes Metabolism during Anoxia-Reoxygenation. Plant Physiology, 172(3), 1548-1562
Lin CS, Chen JJ, Huang YT, Chan MT, Daniell H, Chang WJ, Hsu CT, Liao DC, Wu FH, Lin SY, Liao CF, Deyholos MK, Wong GK, Albert VA, Chou ML, Chen CY, Shih MC (2015) The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family. Scientific reports, 5, 9040
Ruhlman TA, Chang WJ, Chen JJ, Huang YT, Chan MT, Zhang J, Liao DC, Blazier JC, Jin X, Shih MC, Jansen RK, Lin CS (2015) NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss. BMC Plant Biology, 15, 100
Chang JJ, Thia C, Lin HY, Liu HL, Ho FJ, Wu JT, Shih MC, Li WH, Huang CC (2015) Integrating an algal beta-carotene hydroxylase gene into a designed carotenoid-biosynthesis pathway increases carotenoid production in yeast. Bioresource Technology, 184, 2-8
Shih MC, Chou ML, Yue JJ, Hsu CT, Chang WJ, Ko SS, Liao DC, Huang YT, Chen JJ, Yuan JL, Gu XP, Lin CS (2014) BeMADS1 is a key to delivery MADSs into nucleus in reproductive tissues-De novo characterization of Bambusa edulis transcriptome and study of MADS genes in bamboo floral development. BMC Plant Biology, 14, 179
Tsai KJ, Chou SJ, Shih MC (2014) Ethylene plays an essential role in the recovery of Arabidopsis during post-anaerobiosis reoxygenation. Plant Cell & Environment, 37(10), 2391-2405
Chao YT, Su CL, Jean WH, Chen WC, Chang YC, Shih MC (2014) Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite. Plant Molecular Biology, 84(4-5), 529-548
Chen WJ, Hsieh FC, Hsu FC, Tasy YF, Liu JR, Shih MC (2014) Characterization of an Insecticidal Toxin and Pathogenicity of Pseudomonas taiwanensis against Insects. PLoS pathogens, 10(8), e1004288
Wang TY, Huang CJ, Chen HL, Ho PC, Ke HM, Cho HY, Ruan SK, Hung KY, Wang IL, Cai YW, Sung HM, Li WH, Shih MC (2013) Systematic screening of glycosylation- and trafficking-associated gene knockouts in Saccharomyces cerevisiae identifies mutants with improved heterologous exocellulase activity and host secretion. BMC Biotechnology, 13, 71
Hsu FC, Shih MC (2013) Plant defense after flooding. Plant Signaling & Behavior, 8(11), e26922
Lin CS, Chen JJ, Huang YT, Hsu CT, Lu HC, Chou ML, Chen LC, Ou CI, Liao DC, Yeh YY, Chang SB, Shen SC, Wu FH, Shih MC, Chan MT (2013) Catalog of Erycina pusilla miRNA and categorization of reproductive phase-related miRNAs and their target gene families. Plant Molecular Biology, 82(1-2), 193-204
Chang JJ, Ho FJ, Ho CY, Wu YC, Hou YH, Huang CC, Shih MC, Li WH (2013) Assembling a cellulase cocktail and a cellodextrin transporter into a yeast host for CBP ethanol production. Biotechnology for biofuels, 6(1), 19
Su, C.-L., Chao, Y.-T., Yen, S.-H., Chen,C.-Y., Chen,W., Chang, Y.-C. Alex and *Shih, M.-C. (2013) Orchidstra: an integrated Orchid functional genomics database". Plant Cell and Physiology, 54(2), E11
Chou, M.-L., , *Shih, M.-C., Chan, M.-T., Liao, S.-Y., Hsu, C.-T., Haung, Y.-T., Chen, J.W., Liao, D.-C., Wu, F.-H., Lin, C.-S. (2013) Global transcriptome analysis and identification of a CONSTANS-like gene family in the orchid Erycina pusilla. Planta, 237(6), 1425-1441
Hsu, F-C., Chou, M.-Y., Chou, S.-J., Li, Y.-R., Peng, H.-P., and *Shih, M.-C. (2013) Submergence confers immunity mediated by the WRKY22 transcription factor in Arabidopsis. Plant Cell, 25(7), 2699-2713
Su CL, Chen WC, Lee AY, Chen CY, Chang YC, Chao YT, Shih MC (2013) A Modified ABCDE Model of Flowering in Orchids Based on Gene Expression Profiling Studies of the Moth Orchid Phalaenopsis aphrodite. PloS one, 8(11), e80462
Pan, I-C, Liao, D-C., Wu, F-H., Daniell, H., Singh, N.D., Chang, C., Shih, M-C., Chan, M.-T. and Lin, C.-S. (2012) Complete chloroplast genome sequence of an orchid model plant candidate: Erycina pusilla apply in tropical Oncidium breeding. PLoS One, 7(4), e34738
Chen, H.-L., Chen, Y.-C., Lu, M.-Y., Chang, J.-J., Wang, H.-T., Ke, H.-M., Wang, T.-Y., Ruan, S.-K., Wang, T.-Y., Hong, K.-Y., Cho, H.-Y., Lin, W.-T., *Shih, M.-C., and *Li, W.-H. (2012) A highly efficient β-glucosidase from a buffalo rumen fungus Neocallimastix patriciarum W5 Biotechnol for Biofuel . Biotechnology for Biofuels, 5, 24
Chang, J.-J., Ho, C-Y., Huang, Ho, F-J, Tsai, T-Y, Ke, H-M, Wang, C. H.-T., Chen, H-L., *Shih, M-C, *Huang, C.-C., *Li, W.-H. (2012) PGASO: A synthetic biology tool for engineering a cellulolytic yeast . Biotechnology for Biofuels, 5, 53
Ho, C-Y., Chang, J.-J., Lee, S.-C., Chin, T-.Y., Shih, M.-C. , Li, W.-H., and *Huang, C.-C. (2012) Development of cellulosic ethanol production process vis co-culturing of artificial cellulosomal Bacillus and kefir yeast. Applied Energy, 100, 27-32
Yang, C.-Y., Hsu, F.-C., Li, J.-P., Wang, N.N., and Shih, M.-C. (2011) The AP2/ERF transcription factor HIF1 modulates ethylene responses during hypoxia in Arabidopsis . Plant Physiology, 156, 202-212
Wang, T.-Y., Chen, H.-L., Lu, M.-Y., Chen, Y.-C., Sung, H.-M., Mao, W.-C., Cho, H.-Y., Ke, H.-M., Hwa, T.-Y., Ruan, S.-K., Hong, K.-Y., Wu, Y.-C., Tsai, T.-W., Li, W.-H., Shih, M.-C. (2011) Omics approach accelerates gene hunting from novel microbes: Functional characterization of cellulases identified from Neocallimastix patriciarum w5 by transcriptome and secretome. Biotechnology for Biofuels, 4, 24
Lin, C.-W.*, Wu, C-H., Tran, D.-T., Shih, M.-C., Li, W.-H., Wu, C.F. (2011) Mixed culture fermentation from lignocellulosic materials using thermophilic lignocellulose-degrading anaerobes . PROCESS BIOCHEMISTRY, 46, 489-493
Hsu FC, Chou MY, Peng HP, Chou SJ, Shih MC (2011) Insights into hypoxic systemic responses based on analyses of transcriptional regulation in Arabidopsis. PloS one, 6(12), e28888
Wang TY, Chen HL, Lu MY, Chen YC, Sung HM, Mao CT, Cho HY, Ke HM, Hwa TY, Ruan SK, Hung KY, Chen CK, Li JY, Wu YC, Chen YH, Chou SP, Tsai YW, Chu TC, Shih CC, Li WH, Shih MC (2011) Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses. Biotechnology for biofuels, 4, 24
Su CL, Chao YT, Alex Chang YC, Chen WC, Chen CY, Lee AY, Hwa KT, Shih MC (2011) De novo Assembly of Expressed Transcripts and Global Analysis of Phalaenopsis aphrodite Transcriptome. Plant & Cell Physiology, 52, 1501–1514
Sung HM, Wang TY, Wang D, Huang YS, Wu JP, Tsai HK, Tzeng J, Huang CJ, Lee YC, Yang P, Hsu J, Chang T, Cho CY, Weng LC, Lee TC, Chang TH, Li WH, Shih MC (2009) Roles of trans and cis variation in yeast intraspecies evolution of gene expression. Molecular biology and evolution, 26(11), 2533-2538
Chang YW, Robert Liu FG, Yu N, Sung HM, Yang P, Wang D, Huang CJ, Shih MC, Li WH (2008) Roles of cis- and trans-changes in the regulatory evolution of genes in the gluconeogenic pathway in yeast. Molecular biology and evolution, 25(9), 1863-1875
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(11), 1510-1520
Wang D, Sung HM, Wang TY, Huang CJ, Yang P, Chang T, Wang YC, Tseng DL, Wu JP, Lee TC, Shih MC, Li WH (2007) Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. Genome Research, 17(8), 1161-1169
Escamilla-Trevino LL, Chen W, Card ML, Shih MC, Cheng CL, Poulton JE (2006) Arabidopsis thaliana beta-Glucosidases BGLU45 and BGLU46 hydrolyse monolignol glucosides. Phytochemistry, 67(15), 1651-60
Xu Z, Shih MC, Poulton JE (2006) An extracellular exo-beta-(1,3)-glucanase from Pichia pastoris: purification, characterization, molecular cloning, and functional expression. Protein expression and purification, 47(1), 118-127
Shiu SH, Shih MC, Li WH (2005) Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiology, 139(1), 18-26
Wang NN, Shih MC, Li N (2005) The GUS reporter-aided analysis of the promoter activities of Arabidopsis ACC synthase genes AtACS4, AtACS5, and AtACS7 induced by hormones and stresses. Journal of Experimental Botany, 56(413), 909-920
Mezzari MP, Walters K, Jelinkova M, Shih MC, Just CL, Schnoor JL (2005) Gene expression and microscopic analysis of Arabidopsis exposed to chloroacetanilide herbicides and explosive compounds A phytoremediation approach. Plant Physiology, 138(2), 858-69
Peng HP, Lin TY, Wang NN, Shih MC (2005) Differential expression of genes encoding 1-aminocyclopropane-1-carboxylate synthase in Arabidopsis during hypoxia. Plant Molecular Biology, 58(1), 15-25
Fan R, Wan XR, Zhang WT, Wang SF, Wang Y, Zhu LJ, Wang NN, Shih MC, Charng YY, Yang SF (2004) [Promoter specificity of LE-ACS6 gene in LE-ACS6::GUS transgenic arabidopsis plants]. Zhi wu sheng li yu fen zi sheng wu xue xue bao = Journal of plant physiology and molecular biology, 30(3), 351-358
Xu Z, Escamilla-Trevino L, Zeng L, Lalgondar M, Bevan D, Winkel B, Mohamed A, Cheng CL, Shih MC, Poulton J, Esen A (2004) Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 1. Plant Molecular Biology, 55(3), 343-367
Jeong MJ, Shih MC (2003) Interaction of a GATA factor with cis-acting elements involved in light regulation of nuclear genes encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase in Arabidopsis. Biochemical and biophysical research communications, 300(2), 555-562
Chan CS, Peng HP, Shih MC (2002) Mutations affecting light regulation of nuclear genes encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase in Arabidopsis. Plant Physiology, 130(3), 1476-86
Wang, Q., Sjolund, R., and *Shih, M.-C. (2002) Involvement of calcium in the anoxic signaling pathways of Arabidopsis thaliana . Journal of Plant Physiology and Molecular Biology, 28, 441-448
Esen, A., Poulton, J. E., Shih, M.-C., Cheng, C.-L., Bevan, D. R., Winkel-Shirley, B., Mohamed, A., Henrissat, B. and B. L. Møller (2002) Arabidopsis 2010: Collaborative Project on the Functional Genomics of the Arabidopsis -Glucosidase and -Galactosidase Gene Families. Plant Physiol, 129, 406-407
Peng HP, Chan CS, Shih MC, Yang SF (2001) Signaling events in the hypoxic induction of alcohol dehydrogenase gene in Arabidopsis. Plant Physiology, 126(2), 742-749
Chan CS, Guo L, Shih MC (2001) Promoter analysis of the nuclear gene encoding the chloroplast glyceraldehyde-3-phosphate dehydrogenase B subunit of Arabidopsis thaliana. Plant Molecular Biology, 46(2), 131-141
Conley TR, Peng HP, Shih MC (1999) Mutations affecting induction of glycolytic and fermentative genes during germination and environmental stresses in Arabidopsis. Plant physiology, 119(2), 599-608
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