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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, Li WH, 2015, “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(19), E2477-86.
(SCI) (IF: 9.809; SCI ranking: 7.3%)
Tzeng, T.D., Pao, Y.Y., Chen, P.C., Weng, F.C.H., Wang, D.* (2015). Effects of host phylogeny and habitats on gut microbiomes of oriental river prawn (Macrobrachium nipponense). PLOS one. 10(7): e0132860.
Chuang, Y.-C., Li, W.-C., Chen, C.-L., Hsu, P. W.-C., Tung, S.-Y., Kuo, H.-C., Schmoll, S. and *Wang, T.-F. (2015) Trichoderma reesei meiosis generates segmentally aneuploidy progeny with higher xylanase-producing capability. Biotechnology for Biofuels 8, 30.
Hsu HY, Chen SH, Cha YR, Aoyama J, Miller M, Watanabe S, Tsukamoto K, Lin CY*, Han YS* (2015). “De Novo Assembly of the Whole Transcriptome of the Wild Embryo, Preleptocephalus, Leptocephalus, and Glass Eel of Anguilla japonica and Deciphering the Digestive and Absorptive Capacities during Early Development," to appear in PLoS One, Cooperation with Team in NTU. *:Corresponding author.
(IF: 3.730,Journal ranking: Multidisciplinary Sciences/Q1: 7/56, 12.5%)
Lin CH, Chen SH,Wang YB, Hsiung CA, Lin CY* (2015). “Precise Genotyping and Recombination Detection in Enterovirus," to appear in BMC Genomics, Cooperation with Team in NHRI. *:Corresponding Author.


Sasaki E, Zhang X, Sun HG, Lu MY, Liu TL, Ou A, Li JY, Chen YH, Ealick SE, Liu HW, 2014, “Co-opting sulphur-carrier proteins from primary metabolic pathways for 2-thiosugar biosynthesis.”, Nature, 510(7505), 427-431.
(SCI) (IF: 42.351; SCI ranking: 1.8%)
Ng CS, Wu P, Fan WL, Yan J, Chen CK, Lai YT, Wu SM, Mao CT, Chen JJ,Lu MY, Ho MR, Widelitz RB, Chen CF, Chuong CM, Li WH, 2014, “Genomic organization, transcriptomic analysis, and functional characterization of avian alpha- and beta-keratins in diverse feather forms.”, Genome biology and evolution, 6(9), 2258-73.
(SCI) (IF: 4.532; SCI ranking: 23.9%,20.1%)
Lu MY, Fan WL, Wang WF, Chen T, Tang YC, Chu FH, Chang TT, Wang SY, Li MY, Chen YH, Lin ZS, Yang KJ, Chen SM, Teng YC, Lin YL, Shaw JF, Wang TF, Li WH, 2014, “Genomic and transcriptomic analyses of the medicinal fungus Antrodia cinnamomea for its metabolite biosynthesis and sexual development.”, Proceedings of the National Academy of Sciences of the United States of America, 111(44), E4743-52.
(SCI) (IF: 9.809; SCI ranking: 7.3%)
Chan-Shuo Wu, Chun-Ying Yu, Ching-Yu Chuang, Michael Hsiao, Cheng-Fu Kao, Hung-Chih Kuo, and Trees-Juen Chuang. 2014. Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency. Genome Res. Jan 2014; 24(1): 25–36.
PMCID: PMC3875859 (data added during revision)
Chao, Y.-T., Su, C.-L., Chen, W-C., Jean, W.-H., Chang, Y.-C. Alex, and *Shih, M.-C. (2014). Identification, characterization, profiling and analysis of the microRNA transcriptome of moth orchid Phalaenopsis aphrodite. Plant Mol. Biol. 84:529-548.
Chang TH, Lo WS, Ku C, Chen LL, Kuo CH. 2014, Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species. Genome Biol Evol. 2014 Mar;6(3):500-9.
doi: 10.1093/gbe/evu033.
Swamy, K.B.S., Lin, C.H., Yen, M.R., Wang, C.Y., Wang, D.* (2014) Examining the condition-specific antisense transcription in S. cerevisiae and S. paradoxus. BMC Genomics.15, 521.
Lo W-S, Chen H, Chen C-Y, Kuo C-H. 2014. Complete genome sequence of Vibrio vulnificus 93U204, a bacterium isolated from diseased tilapia in Taiwan. Genome Announc. 2:e01005–14.
doi: 10.1128/genomeA.01005-14.
Chang T-H, Lo W-S, Ku C, Chen L-L, Kuo C-H. 2014. Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species. Genome Biol Evol. 6:500–509.
doi: 10.1093/gbe/evu033.
Machida RJ and Lin YY 2014 Four methods of preparing mRNA 5 ‘ end libraries using the Illumina sequencing platform. Plos One 9, e101812.


Schaefke B, Emerson JJ, Wang TY, Lu MY, Hsieh LC, Li WH, 2013, “Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast.”, Molecular biology and evolution, 30(9), 2121-2133.
(SCI) (IF: 14.308; SCI ranking: 2.1%,4.3%,3%)
Shiao MS, Fan WL, Fang S, Lu MYJ, Kondo R, Li WH, 2013, “Transcriptional profiling of chemosensory genes in adult Drosophila antennae by High Throughput Sequencing”, ZOOLOGICAL STUDIES, 52, 42.
(SCI) (IF: 1.014; SCI ranking: 50%)
Fan WL, Ng CS, Chen CF, Lu MY, Chen YH, Liu CJ, Wu SM, Chen CK, Chen JJ, Mao CT, Lai YT, Lo WS, Chang WH, Li WH, 2013, “Genome-wide patterns of genetic variation in two domestic chickens.”, Genome biology and evolution, 5(7), 1376-1392.
(SCI) (IF: 4.532; SCI ranking: 23.9%,20.1%)
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, 2013, “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(10), 3979-3984.
(SCI) (IF: 9.809; SCI ranking: 7.3%)
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 Physiol. 54(2): e11(1–11).
Lin, CH, Tsai, ZT, Wang D.* (2013). Role of antisense RNAs in evolution of yeast regulatory complexity. Genomics. 102(5-6), 484-480.
Wang, J., Wurm, Y., Nipitwattanaphon, M., Riba-Grognuz, O., Huang, Y.-C., Shoemaker, D.D., and Keller, L. (2013) A Y-like social chromosome causes alternative colony organization in fire ants. Nature 493:664-668


Shiao MS, Chang AY, Liao BY, Ching YH, Lu MY, Chen SM, Li WH, 2012, “Transcriptomes of mouse olfactory epithelium reveal sexual differences in odorant detection.”, Genome biology and evolution, 4(5), 703-712.
(SCI) (IF: 4.532; SCI ranking: 23.9%,20.1%)
Chang YM, Liu WY, Shih AC, Shen MN, Lu CH, Lu MY, Yang HW, Wang TY, Chen SC, Chen SM, Li WH, Ku MS, 2012, “Characterizing Regulatory and Functional Differentiation between Maize Mesophyll and Bundle Sheath Cells by Transcriptomic Analysis.”, Plant physiology, 160(1), 165-177.
(SCI) (IF: 7.394; SCI ranking: 3.1%)
Chen HL, Chen YC, Lu MY, Chang JJ, Wang HT, Wang TY, Ruan SK, Wang TY, Hung KY, Cho HY, Ke HM, Lin WT, Shih MC, Li WH, 2012, “A highly efficient beta-glucosidase from a buffalo rumen fungus Neocallimastix patriciarum W5.”, Biotechnology for biofuels, 5(1), 24.
(SCI) (IF: 6.221; SCI ranking: 8.5%,6.1%)


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.
(SCI) (IF: 6.221; SCI ranking: 8.5%,6.1%)
Su, C.-L., Chao, Y.-T., Chang, Y.-C. Alex, Chen,W., Chen,C.-Y., Lee, A.-Y., Kee, T. H., Shih, M.-C. (2011). De novo assembly of expressed transcripts and construction of a transcriptome database of Phalaenopsis aphrodite. Plant Cell Physiol. 52, 1501–1514.


Emerson JJ, Hsieh LC, Sung HM, Wang TY, Huang CJ, Lu HH, Lu MYJ, Wu SH, Li WH. , 2010, “Natural selection on cis and trans regulation in yeasts.”, GENOME RESEARCH, 20(6), 826-836.
(SCI) (IF: 13.852; SCI ranking: 2.7%,1.8%,3.7%)