Publications

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2017

Huang, C. F., C. P. Yu, Y. H. Wu, M. J. Lu, S. L. Tu, S. H. Wu, S. H. Shiu, M. S. B. Ku and W. H. Li (2017). "Elevated auxin biosynthesis and transport underlie high vein density in C4 leaves." Proc Natl Acad Sci U S A 114(33): E6884-e6891.

Ke, H. M., A. Prachumwat, C. P. Yu, Y. T. Yang, S. Promsri, K. F. Liu, C. F. Lo, M. J. Lu, M. C. Lai, I. J. Tsai and W. H. Li (2017). "Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade." Sci Rep 7: 41394.(SCI) (IF: 5.228; SCI ranking: 11.1%)
Chen, C. K., C. P. Yu, S. C. Li, S. M. Wu, M. J. Lu, Y. H. Chen, D. R. Chen, C. S. Ng, C. T. Ting and W. H. Li (2017). "Identification and evolutionary analysis of long non-coding RNAs in zebra finch." BMC Genomics 18(1): 117. DOI: 10.1186/s12864-017-3506-z
Weng, F. C., G. T. Shaw, C. Y. Weng, Y. J. Yang and D. Wang (2017). "Inferring Microbial Interactions in the Gut of the Hong Kong Whipping Frog (Polypedates megacephalus) and a Validation Using Probiotics." Front Microbiol 8: 525.
Chao, Y. T., S. H. Yen, J. H. Yeh, W. C. Chen and M. C. Shih (2017). "Orchidstra 2.0-A Transcriptomics Resource for the Orchid Family." Plant Cell Physiol 58(1): e9.DOI: 10.1093/pcp/pcw220"
Chen, C. Y., P. C. Chen, F. C. Weng, G. T. Shaw and D. Wang (2017). "Habitat and indigenous gut microbes contribute to the plasticity of gut microbiome in oriental river prawn during rapid environmental change." PLoS One 12(7): e0181427.
Shaw, G. T., A. C. Liu, C. Y. Weng, C. Y. Chou and D. Wang (2017). "Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste." PLoS One 12(7): e0181395.

2016

Shinde, S., J. G. Villamor, W. Lin, S. Sharma and P. E. Verslues (2016). "Proline Coordination with Fatty Acid Synthesis and Redox Metabolism of Chloroplast and Mitochondria." Plant Physiol 172(2): 1074-1088.
Weng, F. C., Y. J. Yang and D. Wang (2016). "Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation." BMC Genomics 17(Suppl 13): 1024.
Lin, W. J., C. Y. Ko, M. S. Liu, C. Y. Kuo, D. C. Wu, C. Y. Chen, R. Schafleitner, L. F. Chen and H. F. Lo (2016). "Transcriptomic and Proteomic Research To Explore Bruchid-Resistant Genes in Mungbean Isogenic Lines." J Agric Food Chem 64(34): 6648-6658. DOI: 10.1021/acs.jafc.6b03015"
Liu, M. S., T. C. Kuo, C. Y. Ko, D. C. Wu, K. Y. Li, W. J. Lin, C. P. Lin, Y. W. Wang, R. Schafleitner, H. F. Lo, C. Y. Chen and L. F. Chen (2016). "Genomic and transcriptomic comparison of nucleotide variations for insights into bruchid resistance of mungbean (Vigna radiata [L.] R. Wilczek)." BMC Plant Biol 16: 46. DOI 10.1186/s12870-016-0736-1
Lin, C. G., I. T. Lin and M. C. Yao (2016). "Programmed Minichromosome Elimination as a Mechanism for Somatic Genome Reduction in Tetrahymena thermophila." PLoS Genet 12(11): e1006403.
Chen, Y. L., C. H. Wang, F. C. Yang, W. Ismail, P. H. Wang, C. J. Shih, Y. C. Wu and Y. R. Chiang (2016). "Identification of Comamonas testosteroni as an androgen degrader in sewage." Sci Rep 6: 35386. (SCI) (IF: 5.578; SCI ranking: 8.8%)
Yang, F. C., Y. L. Chen, S. L. Tang, C. P. Yu, P. H. Wang, W. Ismail, C. H. Wang, J. Y. Ding, C. Y. Yang, C. Y. Yang and Y. R. Chiang (2016). "Integrated multi-omics analyses reveal the biochemical mechanisms and phylogenetic relevance of anaerobic androgen biodegradation in the environment." Isme j 10(8): 1967-1983.(IF: 9.302; SCI ranking: 2.8%,5.9%)
Tsai, K. J., M. J. Lu, K. J. Yang, M. Li, Y. Teng, S. Chen, M. S. Ku and W. H. Li (2016). "Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance." Sci Rep 6: 35076. DOI: 10.1038/srep35076
Chen, C. K., C. S. Ng, S. M. Wu, J. J. Chen, P. L. Cheng, P. Wu, M. Y. Lu, D. R. Chen, C. M. Chuong, H. C. Cheng, C. T. Ting and W. H. Li (2016). "Regulatory Differences in Natal Down Development between Altricial Zebra Finch and Precocial Chicken." Mol Biol Evol 33(8): 2030-2043. doi: 10.1093/molbev/msw085.
Liu, T. Y., T. K. Huang, S. Y. Yang, Y. T. Hong, S. M. Huang, F. N. Wang, S. F. Chiang, S. Y. Tsai, W. C. Lu and T. J. Chiou (2016). "Identification of plant vacuolar transporters mediating phosphate storage." Nat Commun 7: 11095.
Schafleitner, R., S.-m. Huang, S.-h. Chu, J.-y. Yen, C.-y. Lin, M.-r. Yan, B. Krishnan, M.-s. Liu, H.-f. Lo, C.-y. Chen, L.-f. O. Chen, D.-c. Wu, T.-G. T. Bui, S. Ramasamy, C.-w. Tung and R. Nair (2016). "Identification of single nucleotide polymorphism markers associated with resistance to bruchids (Callosobruchus spp.) in wild mungbean (Vigna radiata var. sublobata) and cultivated V. radiata through genotyping by sequencing and quantitative trait locus analysis." BMC Plant Biology 16(1): 159. DOI: 10.1186/s12870-016-0847-8
Lee, C.-C. and J. Wang (2016). "The complete mitochondrial genome of Histiostoma blomquisti (Acari: Histiostomatidae)." Mitochondrial DNA Part B 1(1): 671-673.DOI: 10.1080/23802359.2016.1219633

2015

Hsu, H. Y., S. H. Chen, Y. R. Cha, K. Tsukamoto, C. Y. Lin and Y. S. Han (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." PLoS One 10(9): e0139105. doi: 10.1371/journal.pone.0139105.
Shiao, M. S., J. M. Chang, W. L. Fan, M. Y. Lu, C. Notredame, S. Fang, R. Kondo and W. H. Li (2015). "Expression Divergence of Chemosensory Genes between Drosophila sechellia and Its Sibling Species and Its Implications for Host Shift." Genome Biol Evol 7(10): 2843-2858.
Yu, C. P., S. C. Chen, Y. M. Chang, W. Y. Liu, H. H. Lin, J. J. Lin, H. J. Chen, Y. J. Lu, Y. H. Wu, M. Y. Lu, C. H. Lu, A. C. Shih, M. S. Ku, S. H. Shiu, S. H. Wu and W. H. Li (2015). "Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors." Proc Natl Acad Sci U S A 112(19): E2477-2486. (SCI) (IF: 9.809; SCI ranking: 7.3%)
Tzeng, T. D., Y. Y. Pao, P. C. Chen, F. C. Weng, W. D. Jean and D. Wang (2015). "Effects of Host Phylogeny and Habitats on Gut Microbiomes of Oriental River Prawn (Macrobrachium nipponense)." PLoS One 10(7): e0132860. doi:10.1371/journal.pone.0132860
Chuang, Y. C., W. C. Li, C. L. Chen, P. W. Hsu, S. Y. Tung, H. C. Kuo, M. Schmoll and T. F. Wang (2015). "Trichoderma reesei meiosis generates segmentally aneuploid progeny with higher xylanase-producing capability." Biotechnol Biofuels 8: 30.

2014

Sasaki, E., X. Zhang, H. G. Sun, M. Y. Lu, T. L. Liu, A. Ou, J. Y. Li, Y. H. Chen, S. E. Ealick and H. W. Liu (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, C. S., P. Wu, W. L. Fan, J. Yan, C. K. Chen, Y. T. Lai, S. M. Wu, C. T. Mao, J. J. Chen, M. Y. Lu, M. R. Ho, R. B. Widelitz, C. F. Chen, C. M. Chuong and W. H. Li (2014). "Genomic organization, transcriptomic analysis, and functional characterization of avian alpha- and beta-keratins in diverse feather forms." Genome Biol Evol 6(9): 2258-2273. (SCI) (IF: 4.532; SCI ranking: 23.9%,20.1%)
Lu, M.-Y. J., W.-L. Fan, W.-F. Wang, T. Chen, Y.-C. Tang, F.-H. Chu, T.-T. Chang, S.-Y. Wang, M.-y. Li, Y.-H. Chen, Z.-S. Lin, K.-J. Yang, S.-M. Chen, Y.-C. Teng, Y.-L. Lin, J.-F. Shaw, T.-F. Wang and W.-H. Li (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-E4752.(SCI) (IF: 9.809; SCI ranking: 7.3%)
Wu, C.-S., C.-Y. Yu, C.-Y. Chuang, M. Hsiao, C.-F. Kao, H.-C. Kuo and T.-J. Chuang (2014). "Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency." Genome Research 24(1): 25-36.
Chao, Y.-T., C.-L. Su, W.-H. Jean, W.-C. Chen, Y.-C. A. Chang and M.-C. Shih (2014). "Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite." Plant Molecular Biology 84(4-5): 529-548.
Swamy, K. B., C. H. Lin, M. R. Yen, C. Y. Wang and D. Wang (2014). "Examining the condition-specific antisense transcription in S. cerevisiae and S. paradoxus." BMC Genomics 15: 521.
Lo, W. S., H. Chen, C. Y. Chen and C. H. Kuo (2014). "Complete Genome Sequence of Vibrio vulnificus 93U204, a Bacterium Isolated from Diseased Tilapia in Taiwan." Genome Announc 2(5). doi: 10.1128/genomeA.01005-14.
Chang, T. H., W. S. Lo, C. Ku, L. L. Chen and C. H. Kuo (2014). "Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species." Genome Biol Evol 6(3): 500-509. doi: 10.1093/gbe/evu033.
Machida, R. J. and Y. Y. Lin (2014). "Four methods of preparing mRNA 5' end libraries using the Illumina sequencing platform." PLoS One 9(7): e101812.

2013

Wang, J., Y. Wurm, M. Nipitwattanaphon, O. Riba-Grognuz, Y.-C. Huang, D. Shoemaker and L. Keller (2013). "A Y-like social chromosome causes alternative colony organization in fire ants." Nature 493: 664.
Lin, C.-H., Z. T.-Y. Tsai and D. Wang (2013). "Role of antisense RNAs in evolution of yeast regulatory complexity." Genomics 102(5): 484-490.
Su, C. L., Y. T. Chao, S. H. Yen, C. Y. Chen, W. C. Chen, Y. C. Chang and M. C. Shih (2013). "Orchidstra: an integrated orchid functional genomics database." Plant Cell Physiol 54(2): e11.
Liu, W. Y., Y. M. Chang, S. C. Chen, C. H. Lu, Y. H. Wu, M. Y. Lu, D. R. Chen, A. C. Shih, C. R. Sheue, H. C. Huang, C. P. Yu, H. H. Lin, S. H. Shiu, M. S. Ku and W. H. Li (2013). "Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination." Proc Natl Acad Sci U S A 110(10): 3979-3984. (SCI) (IF: 9.809; SCI ranking: 7.3%)
Fan, W. L., C. S. Ng, C. F. Chen, M. Y. Lu, Y. H. Chen, C. J. Liu, S. M. Wu, C. K. Chen, J. J. Chen, C. T. Mao, Y. T. Lai, W. S. Lo, W. H. Chang and W. H. Li (2013). "Genome-wide patterns of genetic variation in two domestic chickens." Genome Biol Evol 5(7): 1376-1392. (SCI) (IF: 4.532; SCI ranking: 23.9%,20.1%)
Fan, W. L., C. S. Ng, C. F. Chen, M. Y. Lu, Y. H. Chen, C. J. Liu, S. M. Wu, C. K. Chen, J. J. Chen, C. T. Mao, Y. T. Lai, W. S. Lo, W. H. Chang and W. H. Li (2013). "Genome-wide patterns of genetic variation in two domestic chickens." Genome Biol Evol 5(7): 1376-1392. (SCI) (IF: 4.532; SCI ranking: 23.9%,20.1%)
Shiao, M.-S., W.-L. Fan, S. Fang, M.-Y. J. Lu, R. Kondo and W.-H. Li (2013). "Transcriptional profiling of adult Drosophila antennae by high-throughput sequencing." Zoological Studies 52(1): 42. (SCI) (IF: 1.014; SCI ranking: 50%)
Schaefke, B., J. J. Emerson, T. Y. Wang, M. Y. Lu, L. C. Hsieh and W. H. Li (2013). "Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast." Mol Biol Evol 30(9): 2121-2133. (SCI) (IF: 14.308; SCI ranking: 2.1%,4.3%,3%)

2012

Shiao, M. S., A. Y. Chang, B. Y. Liao, Y. H. Ching, M. Y. Lu, S. M. Chen and W. H. Li (2012). "Transcriptomes of mouse olfactory epithelium reveal sexual differences in odorant detection." Genome Biol Evol 4(5): 703-712. (SCI) (IF: 4.532; SCI ranking: 23.9%,20.1%)
Chang, Y. M., W. Y. Liu, A. C. Shih, M. N. Shen, C. H. Lu, M. Y. Lu, H. W. Yang, T. Y. Wang, S. C. Chen, S. M. Chen, W. H. Li and M. S. Ku (2012). "Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis." Plant Physiol 160(1): 165-177. (SCI) (IF: 7.394; SCI ranking: 3.1%)
Chen, H. L., Y. C. Chen, M. J. Lu, J. J. Chang, H. C. Wang, H. M. Ke, T. Y. Wang, S. K. Ruan, T. Y. Wang, K. Y. Hung, H. Y. Cho, W. T. Lin, M. C. Shih and W. H. Li (2012). "A highly efficient beta-glucosidase from the buffalo rumen fungus Neocallimastix patriciarum W5." Biotechnol Biofuels 5(1): 24. (SCI) (IF: 6.221; SCI ranking: 8.5%,6.1%)

2011

Wang, T. Y., H. L. Chen, M. J. Lu, Y. C. Chen, H. M. Sung, C. T. Mao, H. Y. Cho, H. M. Ke, T. Y. Hwa, S. K. Ruan, K. Y. Hung, C. K. Chen, J. Y. Li, Y. C. Wu, Y. H. Chen, S. P. Chou, Y. W. Tsai, T. C. Chu, C. A. Shih, W. H. Li and M. C. Shih (2011). "Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses." Biotechnol Biofuels 4: 24. (SCI) (IF: 6.221; SCI ranking: 8.5%,6.1%)
Su, C. L., Y. T. Chao, Y. C. Alex Chang, W. C. Chen, C. Y. Chen, A. Y. Lee, K. T. Hwa and M. C. Shih (2011). "De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome." Plant Cell Physiol 52(9): 1501-1514.

2010

Emerson, J. J., L. C. Hsieh, H. M. Sung, T. Y. Wang, C. J. Huang, H. H. Lu, M. Y. Lu, S. H. Wu and W. H. Li (2010). "Natural selection on cis and trans regulation in yeasts." Genome Res 20(6): 826-836.(SCI) (IF: 13.852; SCI ranking: 2.7%,1.8%,3.7%)