Journal papers published by professors of the ITPM from 2015 to 2020

No.

Author

Paper Name

Published Jurnal

Years

Co-authors

1

Wen-Chi Chang

Weijian Zhuang, Hua Chen, Meng Yang, Jianping Wang, Manish K. Pandey, Chong Zhang, Wen-Chi Chang, ... Rajeev K. Varshney. (2019). The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nature Genetics, 51, 865–876.

GENETICS & HEREDITY

2019

2

Kai Yao Huang, Tzong Yi Lee, Hui Ju Kao, Chen Tse Ma, Chao Chun Lee, Tsai Hsuan Lin, Wen-Chi Chang, Hsien Da Huang. (2019). DbPTM in 2019: Exploring disease association and cross-Talk of post-Translational modifications. Nucleic acids research, 47(D1), D298-D308.

BIOCHEMISTRY & MOLECULAR BIOLOGY

2019

3

Chi Nga Chow, Tzong Yi Lee, Yu Cheng Hung, Guan Zhen Li, Kuan Chieh Tseng, Ya Hsin Liu, Po Li Kuo, Han Qin Zheng, Wen-Chi Chang. (2019). Plantpan3.0: A new and updated resource for reconstructing transcriptional regulatory networks from chip-seq experiments in plants. Nucleic acids research, 47(D1), D1155-D1163.

BIOCHEMISTRY & MOLECULAR BIOLOGY

2019

4

Chi Nga Chow, Yi Fan Chiang-Hsieh, Chia Hung Chien, Han Qin Zheng, Tzong Yi Lee, Nai Yun Wu, Kuan Chieh Tseng, Ping Fu Hou, Wen-Chi Chang. (2018). Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli. BMC genomics, 19, [85]

BIOTECHNOLOGY & APPLIED MICROBIOLOGY

2018

5

Mazen Alazem, Kuan Chieh Tseng, Wen-Chi Chang, Jang Kyun Seo, Kook Hyung Kim. (2018). Elements Involved in the Rsv3-Mediated Extreme Resistance against an Avirulent Strain of Soybean Mosaic Virus. Viruses, 10(11)

VIROLOGY

2018

6

Tseng, K. C., Chiang-Hsieh, Y. F., Pai, H., Chow, C. N., Lee, S. C., Zheng, H. Q., ... Chang, W-C. (2018). MicroRPM: A microRNA prediction model based only on plant small RNA sequencing data. Bioinformatics, 34(7), 1108-1115.

MATHEMATICAL & COMPUTATIONAL BIOLOGY

2018

7

Hou, P. F., Chien, C. H., Chiang-Hsieh, Y. F., Tseng, K. C., Chow, C. N., Huang, H-J., & Chang, W-C. (2018). Paddy-upland rotation for sustainable agriculture with regards to diverse soil microbial community. Scientific reports, 8(1), [7966].

MULTIDISCIPLINARY SCIENCES

2018

8

Tze Hann Ng, Chia Wei Lu, Shih Shun Lin, Che Chih Chang, Loc H. Tran, Wen-Chi Chang, Chu-Fang Lo, Han-Ching Wang. (2018). The Rho signalling pathway mediates the pathogenicity of AHPND-causing V. parahaemolyticus in shrimp. Cellular Microbiology, 20(8), [e12849].

MICROBIOLOGY

2018

9

Chung Wen Lin, Li Yao Huang, Chao-Li Huang, Yong Chuan Wang, Pei Hsuan Lai, Hao-Ven Wang, Wen-Chi Chang, Tzen-Yuh Chiang, Hao-Jen Huang. (2017). Common stress transcriptome analysis reveals functional and genomic architecture differences between early and delayed response genes. Plant and Cell Physiology, 58(3), 546-559.

PLANT SCIENCES

2017

Chao-Li Huang

Hao-Jen Huang

10

Zheng, H. Q., Wu, N. Y., Chow, C. N., Tseng, K. C., Chien, C. H., Hung, Y. C., ... Chang, W-C. (2017). EXPath tool—a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data. DNA Research, 24(4), 371-375.

GENETICS & HEREDITY

2017

11

Chang, W-C., Zheng, H. Q., & Chen, C. N. N. (2016). Comparative transcriptome analysis reveals a potential photosynthate partitioning mechanism between lipid and starch biosynthetic pathways in green microalgae. Algal Research-Biomass Biofuels and Bioproducts, 16, 54-62.

BIOTECHNOLOGY & APPLIED MICROBIOLOGY

2016

12

Chow, C. N., Zheng, H. Q., Wu, N. Y., Chien, C. H., Huang, H. D., Lee, T. Y., ... Chang, W-C. (2016). PlantPAN 2.0: An update of Plant Promoter Analysis Navigator for reconstructing transcriptional regulatory networks in plants. Nucleic Acids Research, 44(D1), D1154-D1164.

BIOCHEMISTRY & MOLECULAR BIOLOGY

2016

13

Chien, C. H., Chiang-Hsieh, Y. F., Chen, Y. A., Chow, C. N., Wu, N. Y., Hou, P. F., & Chang, W-C. (2015). AtmiRNET: A web-based resource for reconstructing regulatory networks of Arabidopsis microRNAs. Database-The Journal of Biological Databases and Curation, 2015, [bav042].

MATHEMATICAL & COMPUTATIONAL　BIOLOGY

2015

14

Chien, C. H., Chow, C. N., Wu, N. Y., Chiang-Hsieh, Y. F., Hou, P. F., & Chang, W-C. (2015). EXPath: A database of comparative expression analysis inferring metabolic pathways for plants. BMC Genomics, 16, [S6].

BIOTECHNOLOGY & APPLIED MICROBIOLOGY

2015

15

Wen-Chieh Tsai

Chuan Ming Yeh, Kwi Mi Chung, Chieh Kai Liang, Wen-Chieh Tsai. (2019). New insights into the symbiotic relationship between orchids and fungi. Applied Sciences (Switzerland), 9(3), [585].

PHYSICS, APPLIED

2019

16

Chia Chi Hsu, Pei Han Lai, Tien Chih Chen, Wen-Chieh Tsai, Jui Lin Hsu, Yu Yun Hsiao, Wen-Luan Wu, Ching Hsiu Tsai, Wen Huei Chen, Hong-Hwa Chen. (2019). PePIF1, a P-lineage of PIF-like transposable element identified in protocorm-like bodies of Phalaenopsis orchids. BMC genomics, 20(1), [25].

BIOTECHNOLOGY & APPLIED MICROBIOLOGY

2019

17

Yu Chen Chuang, Yi Chu Hung, Chi Yu Hsu, Chuan Ming Yeh, Nobutaka Mitsuda, Masaru Ohme-Takagi, Wen-Chieh Tsai, Wen Huei Chen, Hong-Hwa Chen. (2018). A dual repeat cis-element determines expression of GERANYL DIPHOSPHATE SYNTHASE for monoterpene production in phalaenopsis orchids. Frontiers in Plant Science, 9, [765].

PLANT SCIENCES

2018

18

Chuan Ming Yeh, Zhong Jian Liu, Wen-Chieh Tsai. (2018). Advanced Applications of Next-Generation Sequencing Technologies to Orchid Biology. Current Issues in Molecular Biology, 27, 51-70.

BIOCHEMISTRY & MOLECULAR BIOLOGY

2018

19

Yu Chen Chuang, Yi Chu Hung, Wen-Chieh Tsai, Wen Huei Chen, Hong-Hwa Chen. (2018). PbbHLH4 regulates floral monoterpene biosynthesis in Phalaenopsis orchids. Journal of Experimental Botany, 69(18), 4363-4377.

PLANT SCIENCES

2018

20

Wen-Chieh Tsai, Anne Dievart, Chia Chi Hsu, Yu Yun Hsiao, Shang Yi Chiou, Hsin Huang, Hong-Hwa Chen. (2017). Post genomics era for orchid research. Botanical Studies, 58(1), [61].

PLANT SCIENCES

2017

21

Zhang, G.Q., Liu, K.W., Li, Z., Lohaus, R., Hsiao, Y.Y., Niu, S.C., Wang, J.Y., Lin, Y.C., Xu, Q., Chen, L.J., Yoshida, K., Fujiwara, S., Wang, Z.W., Zhang, Y.Q., Mitsuda, N., Wang, M., Liu, G.H., Pecoraro, L., Huang, H.X., Xiao, X.J., Lin, M., Wu, X.Y., Wu, W.L., Chen, Y.Y., Chang, S.B., Sakamoto, S., Ohme-Takagi, M., Yagi, M., Zeng, S.J., Shen, C.Y., Yeh, C.M*, Luo, Y.B.*, Tsai, W.C.*, Van de Peer, Y.*, Liu, Z.J.*. (2017). The Apostasia genome and the evolution of orchids. Nature 579: 379-383.

MULTIDISCIPLINARY SCIENCES

2017

22

Shan Ce Niu, Qing Xu, Guo Qiang Zhang, Yong Qiang Zhang, Wen-Chieh Tsai, Jui Ling Hsu, Chieh Kai Liang, Yi Bo Luo, Zhong Jian Liu. (2016). De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris. Scientific Data, 3, [201683].

MULTIDISCIPLINARY SCIENCES

2016

23

Yu Fu Lin, You Yi Chen, Yu Yun Hsiao, Ching Yu Shen, Jui Ling Hsu, Chuan Ming Yeh, Nobutaka Mitsuda, Masaru Ohme-Takagi, Zhong Jian Liu, Wen-Chieh Tsai. (2016). Genome-wide identification and characterization of TCP genes involved in ovule development of Phalaenopsis equestris. Journal of Experimental Botany, 67(17), 5051-5066.

PLANT SCIENCES

2016

24

Xiaobai Li, Aaron Jackson, Ming Xie, Dianxing Wu, Wen-Chieh Tsai, Sheng Zhang. (2016). Proteomic insights into floral biology. Biochimica et Biophysica Acta-Proteins and Proteomics, 1864(8), 1050-1060.

BIOPHYSICS

2016

25

Zhang, G. Q., Xu, Q., Bian, C., Tsai, W-C., Yeh, C. M., Liu, K. W., ... Liu, Z. J. (2016). The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution. Scientific reports, 6, [19029].

MULTIDISCIPLINARY SCIENCES

2016

26

Cai, J., Liu, X., Vanneste, K., Proost, S., Tsai, W-C., Liu, K. W., ... Liu, Z. J. (2015). Erratum: The genome sequence of the orchid Phalaenopsis equestris. Nature Genetics, 47 (65-72).

GENETICS & HEREDITY

2015

27

Hsu, C. C., Chen, Y. Y., Tsai, W-C., Chen, W. H., & Chen, H-H. (2015). Three R2R3-MYB transcription factors regulate distinct floral pigmentation patterning in Phalaenopsis spp. Plant Physiology, 168(1), 175-191.

PLANT SCIENCES

2015

28

Ruey-Hua Lee

Huang, L. Y., Lin, C. W., Lee, R-H., Chiang, C. Y., Wang, Y. C., Chang, C. H., & Huang, H-J. (2017). Integrating early transcriptomic responses to rhizotoxins in rice (Oryza sativa. L.) reveals key regulators and a potential early biomarker of cadmium toxicity. Frontiers in Plant Science, 8, [1432].

PLANT SCIENCES

2017

29

B. Y. Lin, C. D. Chang, Lynn Ling-Huei Huang, Y. C. Liu, Y. Y. Su, T. C. Chen, Ruey-Hua Lee, Hao-Jen Huang, Wen-Luan Wu, Ching-Chun Chang. (2016). The mitochondrial DNA markers for distinguishing Phalaenopsis species and revealing maternal phylogeny. Biologia Plantarum, 60(1), 68-78.

PLANT SCIENCES

2016

30

Chi-Chou Chiu

Lin, C. S., Chen, J. J. W., Chiu, C-C., Hsiao, H. C. W., Yang, C. J., Jin, X. H., ... Shih, M. C. (2017). Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. Plant Journal, 90(5), 994-1006.

PLANT SCIENCES

2017

31

Chao-Li Huang, Rakesh Sarkar, Tsai-Wen Hsu, Chia-Fen Yang, Chia-Hung Chien, Wen-Chi Chang, Tzen-Yuh Chiang.  Endophytic microbiome of biofuel plant Miscanthus sinensis (Poaceae) interacts with environmental gradients. Microbial Ecology

Microbial Ecology

2020

32

Tran HT, Wang HC, Hsu TW, Sarker R, Huang CL, Chiang TY. (2019) Revegetation on abandoned salt ponds relieves the seasonal fluctuation of soil microbiomes. BMC Genomics,  20:478.

BIOTECHNOLOGY & APPLIED MICROBIOLOGY

2019

33

Zheng, Y., Chiang, T-Y., Huang, C-L., & Gong, X. (2018). Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm. Journal of Microbiology, 56(5), 337-345.

MICROBIOLOGY

2018

34

Chao-Li Huang

Chung Wen Lin, Li Yao Huang, Chao-Li Huang, Yong Chuan Wang, Pei Hsuan Lai, Hao-Ven Wang, Wen-Chi Chang, Tzen-Yuh Chiang, Hao-Jen Huang. (2017). Common stress transcriptome analysis reveals functional and genomic architecture differences between early and delayed response genes. Plant and Cell Physiology, 58(3), 546-559.

PLANT SCIENCES

2017

Wen-Chi Chang

Hao-Jen Huang

35

Xun Gong, Kuo Hsiang Hung, Yu Wei Ting, Tsai Wen Hsu, Lenka Malikova, Huyen Trang Tran, Chao-Li Huang, Shih Hui Liu, Tzen-Yuh Chiang. (2017). Frequent gene flow blurred taxonomic boundaries of sections in Lilium L. (Liliaceae). PLoS One, 12(8), [e0183209].

MULTIDISCIPLINARY SCIENCES

2017

36

Huang, C-L. (2016). Miscanthus as an example of ecological genetics and genomics for nonmodel species. Ecological Genetics and Genomics.

Ecological Genetics and Genomics

2016

37

Chi Chun Huang, Tsai Wen Hsu, Hao-Ven Wang, Zin Huang Liu, Yi Yen Chen, Chi Te Chiu, Chao-Li Huang, Kuo Hsiang Hung, Tzen-Yuh Chiang. (2016). Multilocus analyses reveal postglacial demographic shrinkage of juniperus morrisonicola (cupressaceae), a dominant alpine species in Taiwan. PLoS ONE, 11(8), [e0161713].

MULTIDISCIPLINARY SCIENCES

2016

38

Huang, C-L., Pu, P. H., Huang, H-J., Sung, H-M., Liaw, H-J., Chen, Y-M., ... Chiang, T-Y. (2015). Ecological genomics in Xanthomonas: The nature of genetic adaptation with homologous recombination and host shifts. BMC genomics, 16(1), [188].

BIOTECHNOLOGY & APPLIED MICROBIOLOGY

2015