2023

Tsai Kuen‐Jin, Suen Der‐Fen, Shih Ming‐Che

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

Sugars and sucrose transporters in pollinia of <i>Phalaenopsis aphrodite</i> (<i>Orchidaceae</i>). Journal of Experimental Botany , 74(8), 2556-2571

2022

Tu Po-Wen, Chiu Jie-Siang, Lin Chih, Chien Chih-Cheng, Hsieh Feng-Chia, Shih Ming-Che , Yang Yu-Liang

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.

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.

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.

DNA-free CRISPR-Cas9 gene editing of tetraploid tomatoes using protoplast regeneration. Plant Physiology

2021

Hsu CT, Yuan YH, Lin YC, Lin S, Cheng QW, Wu FH, Sheen J, Shih MC , Lin CS

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

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.*

CaNRT2.1 is required for nitrate but not nitrite uptake in chili pepper pathogen Colletotrichum acutatum.. Frontiers in Microbiology , 11, 613674

2020

Ko S.-S., Jhong C.-M. and Shih, M.-C.

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.

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.

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

2019

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

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

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.

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

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

2018

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

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

Application of protoplast technology to CRISPR/Cas9 mutagenesis: from single-cell mutation detection to mutant plant regeneration. Plant Biotechnology Journal , 16(7), 1295-1310

2017

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

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

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

Community recommendations on terminology and procedures used in flooding and low oxygen stress research. The New phytologist , 214(4), 1403-1407

2016

Lin CS, Hsu CT, Liao DC, Chang WJ, Chou ML, Huang YT, Chen JJ, Ko SS, Chan MT, Shih MC

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

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

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

Ethylene-Regulated Glutamate Dehydrogenase Fine-Tunes Metabolism during Anoxia-Reoxygenation. Plant Physiology , 172(3), 1548-1562

2015

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

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

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

Integrating an algal beta-carotene hydroxylase gene into a designed carotenoid-biosynthesis pathway increases carotenoid production in yeast. Bioresource Technology , 184, 2-8

2014

Shih MC , Chou ML, Yue JJ, Hsu CT, Chang WJ, Ko SS, Liao DC, Huang YT, Chen JJ, Yuan JL, Gu XP, Lin CS

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

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

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

Characterization of an Insecticidal Toxin and Pathogenicity of Pseudomonas taiwanensis against Insects. PLoS pathogens , 10(8), e1004288

2013

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

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

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

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

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.

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.

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.

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

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

2012

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.

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.

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.

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.

Development of cellulosic ethanol production process vis co-culturing of artificial cellulosomal Bacillus and kefir yeast. Applied Energy , 100, 27-32

2011

Yang, C.-Y., Hsu, F.-C., Li, J.-P., Wang, N.N., and Shih, M.-C.

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.

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.

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

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

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

De novo Assembly of Expressed Transcripts and Global Analysis of Phalaenopsis aphrodite Transcriptome. Plant & Cell Physiology , 52, 1501–1514

2009

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

Roles of trans and cis variation in yeast intraspecies evolution of gene expression. Molecular biology and evolution , 26(11), 2533-2538

2008

Chang YW, Robert Liu FG, Yu N, Sung HM, Yang P, Wang D, Huang CJ, Shih MC , Li WH

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

2007

Ahn YO, Zheng M, Bevan DR, Esen A, Shiu SH, Benson J, Peng HP, Miller JT, Cheng CL, Poulton JE, Shih MC

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

Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. Genome Research , 17(8), 1161-1169

2006

Escamilla-Trevino LL, Chen W, Card ML, Shih MC , Cheng CL, Poulton JE

Arabidopsis thaliana beta-Glucosidases BGLU45 and BGLU46 hydrolyse monolignol glucosides. Phytochemistry , 67(15), 1651-60

Xu Z, Shih MC , Poulton JE

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

2005

Shiu SH, Shih MC , Li WH

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

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

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

Differential expression of genes encoding 1-aminocyclopropane-1-carboxylate synthase in Arabidopsis during hypoxia. Plant Molecular Biology , 58(1), 15-25

2004

Fan R, Wan XR, Zhang WT, Wang SF, Wang Y, Zhu LJ, Wang NN, Shih MC , Charng YY, Yang SF

[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

Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 1. Plant Molecular Biology , 55(3), 343-367

2003

Jeong MJ, Shih MC

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

2002

Chan CS, Peng HP, Shih MC

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.

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

Arabidopsis 2010: Collaborative Project on the Functional Genomics of the Arabidopsis -Glucosidase and -Galactosidase Gene Families. Plant Physiol , 129, 406-407

2001

Peng HP, Chan CS, Shih MC , Yang SF

Signaling events in the hypoxic induction of alcohol dehydrogenase gene in Arabidopsis. Plant Physiology , 126(2), 742-749

Chan CS, Guo L, Shih MC

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

1999

Conley TR, Peng HP, Shih MC

Mutations affecting induction of glycolytic and fermentative genes during germination and environmental stresses in Arabidopsis. Plant physiology , 119(2), 599-608

1993

Dewdney J, Conley TR, Shih MC , Goodman HM

Effects of blue and red light on expression of nuclear genes encoding chloroplast glyceraldehyde-3-phosphate dehydrogenase of Arabidopsis thaliana.. Plant physiology , 103(4), 1115-1121

Yang Y, Kwon HB, Peng HP, Shih MC

Stress responses and metabolic regulation of glyceraldehyde-3-phosphate dehydrogenase genes in Arabidopsis.. Plant physiology , 101(1), 209-216