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2023

Lu CW, Huang ST, Cheng SJ, Lin CT, Hsu YC, Yao CT, Dong F, Hung CM, Kuo HC. Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird. Mol Ecol. 2023 Feb 7. doi: 10.1111/mec.16875. Epub ahead of print. PMID: 36748940.

Mattia De Vivo, Wei-Yun Chen, Jen-Pan Huang Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha) bioRxiv 2023.02.21.529467; doi: https://doi.org/10.1101/2023.02.21.529467

Negi A, Liao BY, Yeh SD. Long-read-based Genome Assembly of Drosophila gunungcola Reveals Fewer Chemosensory Genes in Flower-breeding Species. Genome Biol Evol. 2023 Mar 3;15(3):evad048. doi: 10.1093/gbe/evad048. PMID: 36930539

Wei KH, Lin IT, Chowdhury K, Lim KL, Liu KT, Ko TM, Chang YM, Yang KC, Lai SB. Comparative single-cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration. Elife. 2023 Jul 27;12:e84679. doi: 10.7554/eLife.84679. PMID: 37498060; PMCID: PMC10411971.

Shun-Ping Huang, Hsiao Jung Kao, Ting-Ying Lin, Jia-Ying Chien, Pui-Yan Kwok, Mei-Yeh Jade Lu, Shih-Hwa Chiou; Highly efficient capture approach for the identification of diverse inherited retinal disorders. Invest. Ophthalmol. Vis. Sci. 2023;64(8):4647.

Kao, HJ., Lin, TY., Hsieh, FJ. et al. Highly efficient capture approach for the identification of diverse inherited retinal disorders. npj Genom. Med. 9, 4 (2024). https://doi.org/10.1038/s41525-023-00388-3

Hao-Chih Kuo, Cheng-Te Yao, Ben-Yang Liao, Meng-Pin Weng, Feng Dong, Yu-Cheng Hsu & Chih-Ming Hung, Weak gene–gene interaction facilitates the evolution of gene expression plasticity. BMC Biol 21, 57 (2023). https://doi.org/10.1186/s12915-023-01558-6

Lee, C.-Y., Wang, J.-F., Chang, C.-H., & Tung, C.-W. (2023). Analyzing genomic variation in cultivated pumpkins and identification of candidate genes controlling seed traits. The Plant Genome, 00, e20393. https://doi.org/10.1002/tpg2.20393

Le, M.-H., Morgan, B., Lu, M.-Y., Moctezuma, V., Burgos, O., & Huang, J.-P. (2023). The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests. Molecular Ecology Resources, 00, 1–18. https://doi.org/10.1111/1755-0998.13908

Ching-Hui Tsai, Alan Chuan-Ying Lai, Yu-Cheng Lin, Po-Yu Chi, Yun-Chi Chen, Yao-Hsu Yang, Chien-Han Chen, Sheng-Yeh Shen, Tsong-Long Hwang, Ming-Wei Su, I-Ling Hsu, Yu-Chi Huang, Anke H Maitland-van der Zee, Michael J McGeachie, Kelan G Tantisira, Ya-Jen Chang, Yungling L Lee Neutrophil extracellular trap production and CCL4L2 expression influence corticosteroid response in asthma. Sci Transl Med. 2023 Jun 7;15(699):eadf3843. doi: 10.1126/scitranslmed.adf3843. Epub 2023 Jun 7. DOI: 10.1126/scitranslmed.adf3843

Mattos FMG, Dreyer N, Fong CL, Wen YV, Jain D, De Vivo M, Huang YS, Mwihaki JK, Wang TY, Ho MJ, Tsai IJ, Wang J, Chan BKK, Machida RJ. Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller-size coral reef zooplankton by metatranscriptomics. Mol Ecol Resour. 2023 Dec 8. doi: 10.1111/1755-0998.13911. Epub ahead of print.

2022

Lu CW, Yao CT, Hung CM. Domestication obscures genomic estimates of population history. Mol Ecol. 2022 Feb;31(3):752-766. doi: 10.1111/mec.16277.

Yeh SY, Lin HH, Chang YM, Chang YL, Chang CK, Huang YC, Ho YW, Lin CY, Zheng JZ, Jane WN, Ng CY, Lu MY, Lai IL, To KY, Li WH, Ku MSB. Maize Golden2-like transcription factors boost rice chloroplast development, photosynthesis, and grain yield. Plant Physiol. 2022 Jan 20;188(1):442-459. doi: 10.1093/plphys/kiab511

Huang CK, Lin WD, Wu SH. An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development. Genome Biol. 2022 Feb 9;23(1):50. doi: 10.1186/s13059-022-02620-2.

Fang-Jung Yang, Chiao-Nung Chen, Tiffany Chang, Ting-Wei Cheng, Ni-Chen Chang, Chia-Yi Kao, Chih-Chi Lee, Yu-Ching Huang, Jung-Chen Hsu, Jengyi Li, Meiyeh J. Lu, Shih-Peng Chan, John Wang phiC31 integrase for recombination mediated single copy insertion and genome manipulation in C. elegans Genetics, Volume 220, Issue 2, February 2022, iyab206. DOI: 10.1093/genetics/iyab206

Yang CL, Huang YT, Schmidt W , Klein P, Chan MT, Pan IC. Ethylene Response Factor109 Attunes Immunity, Photosynthesis, and Iron Homeostasis in Arabidopsis Leaves. Frontiers in Plant Science. 2022 Mar 2; e841366. doi: 10.3389/fpls.2022.841366

Lee TJ, Liu Y, Liu WA, Lin YF, Lee HH, Ke HM, Huang JP, Lu MJ, Hsieh CL, Chung KF, Liti G, Tsai IJ. Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages. Genome Res. 2022 Mar 31:gr.276286.121. doi: 10.1101/gr.276286.121. Epub ahead of print.

Cho HY, Chou MY, Ho HY, Chen WC, Shih MC. Ethylene modulates translation dynamics in Arabidopsis under submergence via GCN2 and EIN2. Sci Adv. 2022 Jun 3;8(22):eabm7863. doi: 10.1126/sciadv.abm7863. Epub 2022 Jun 3.

Chen Siang Ng, Cheng-Kuo Lai, Huei-Mien Ke, Hsin-Han Lee, Chih-Feng Chen, Pin-Chi Tang, Hsu-Chen Cheng, Meiyeh J. Lu, Wen-Hsiung Li, Isheng Jason Tsai. Genome assembly and evolutionary analysis of the mandarin duck Aix galericulata reveal strong genome conservation among ducks, Genome Biology and Evolution, 2022;, evac083, https://doi.org/10.1093/gbe/evac083

Chang, Yao-Jen, Zhifu Kang, Jiayuan Bei, Shu-Jen Chou, Mei-Yeh J. Lu, Yu-Lun Su, Sheng-Wei Lin, Hsin-Hui Wang, Steven Lin, and Ching-Jin Chang. Generation of TRIM28 Knockout K562 Cells by CRISPR/Cas9 Genome Editing and Characterization of TRIM28-Regulated Gene Expression in Cell Proliferation and Hemoglobin Beta Subunits International Journal of Molecular Sciences 23, no. 12: 6839. https://doi.org/10.3390/ijms23126839

Yeh, H.h., Chang, Y.M., Chang, Y.W., Lu., M.Y.J., Chen, Y.H., Lee., C.C., and (Chen, C.C)*. Multiomic analyses reveal enriched glycolytic processes in β-myosin heavy chain-expressed cardiomyocytes in early cardiac hypertrophy. Journal of Molecular and Cellular Cardiology Plus. , 2022-06. https://doi.org/10.1016/j.jmccpl.2022.100011

Lu, CW., Yao, CT., and Hung, CM. (2022). Domestication obscures genomic estimates of population history. Molecular Ecology, 31, 752-766

Wada N, Hsu M-T, Tandon K, Hsiao SS-Y, Chen H-J, Chen Y-H, Chiang P-W, Yu S-P, Lu C-Y, Chiou Y-J, Tu Y-C, Tian X, Chen B-C, Lee D-C, Yamashiro H, Bourne DG, Tang S-L (2022) High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata. Science Advances 8:eabo2431.

Lo, KL., Chen, YN., Chiang, MY. et al. Two genomic regions of a sodium azide induced rice mutant confer broad-spectrum and durable resistance to blast disease. Rice 15, 2 (2022). https://doi.org/10.1186/s12284-021-00547-z

Lee Tracy J, Liu Yuching, Liu Wei-An, Lin Yu-Fei, Lee Hsin-Han, Ke Huei-Mien, Huang Jen-Pen, Lu Mei-Yeh Jade, Hsieh Chia-Lun, Chung Kuo-Fang, Liti Gianni, Tsai Isheng J. Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages. Genome Research. _, gr.276286.121, 2022. 32(5): 864–877

Liu Wen-Yu, Yu Chun-Ping, Chang Chao-Kang, Chen Hsiang-June, Li Meng-Yun, Chen Yi-Hua, Shiu Shin-Han, Ku Maurice S. B., Tu Shih-Long*, [Lu Mei-Yeh Jade]*, Li Wen-Hsiung*. Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells. Proceedings of the National Academy of Sciences. 119(35), e2208795119.

Hsin-Yue Tsai, Hsian-Tang Cheng, Yi-Ting Tsai Biogenesis of C. elegans spermatogenesis small RNAs is initiated by a zc3h12a-like ribonuclease Sci Adv. 2022 Aug 12;8(32):eabm0699. doi: 10.1126/sciadv.abm0699. Epub 2022 Aug 10. Affiliations expand PMID: 35947655 PMCID: PMC9365287 DOI: 10.1126/sciadv.abm0699

Chuang CR, Hsieh CL, Chang CS, Wang CM, Tandang DN, Gardner EM, Audi L, Zerega NJC, Chung KF. Amis Pacilo and Yami Cipoho are not the same as the Pacific breadfruit starch crop-Target enrichment phylogenomics of a long-misidentified Artocarpus species sheds light on the northward Austronesian migration from the Philippines to Taiwan. PLoS One. 2022 Sep 30;17(9):e0272680. doi: 10.1371/journal.pone.0272680. PMID: 36178903; PMCID: PMC9524695.

Hsieh CL, Xu WB, Chung KF. Plastomes of limestone karst gesneriad genera Petrocodon and Primulina, and the comparative plastid phylogenomics of Gesneriaceae. Sci Rep. 2022 Sep 22;12(1):15800. doi: 10.1038/s41598-022-19812-2. PMID: 36138079; PMCID: PMC9500069.

Hsieh CL, Yu CC, Huang YL, Chung KF. Mahonia vs. Berberis Unloaded: Generic Delimitation and Infrafamilial Classification of Berberidaceae Based on Plastid Phylogenomics. Front Plant Sci. 2022 Jan 6;12:720171. doi: 10.3389/fpls.2021.720171. PMID: 35069611; PMCID: PMC8770955.

2021

Chan TC, Chen YT, Tan KT, Wu CL, Wu WJ, Li WM, Wang JM, Shiue YL, Li CF. Biological significance of MYC and CEBPD coamplification in urothelial carcinoma: Multilayered genomic, transcriptional and posttranscriptional positive feedback loops enhance oncogenic glycolysis. Clin Transl Med. 2021 Dec;11(12):e674. doi: 10.1002/ctm2.674.

Tsai SY, Huang F. Acetyltransferase Enok regulates transposon silencing and piRNA cluster transcription. PLoS Genet. 2021 Feb 1;17(2):e1009349. doi: 10.1371/journal.pgen.1009349.

Lin YF, Sung CM, Ke HM, Kuo CJ, Liu WA, Tsai WS, Lin CY, Cheng HT, Lu MJ, Tsai IJ, Hsieh SY. The rectal mucosal but not fecal microbiota detects subclinical ulcerative colitis. Gut Microbes. 2021 Jan-Dec;13(1):1-10. doi: 10.1080/19490976.2020.1832856.

Huang CF, Liu WY, Lu MJ, Chen YH, Ku MSB, Li WH. Whole-Genome Duplication Facilitated the Evolution of C4 Photosynthesis in Gynandropsis gynandra. Mol Biol Evol. 2021 Oct 27;38(11):4715-4731. doi: 10.1093/molbev/msab200.

Panibe JP, Wang L, Li J, Li MY, Lee YC, Wang CS, Ku MSB, Lu MJ, Li WH. Chromosomal-level genome assembly of the semi-dwarf rice Taichung Native 1, an initiator of Green Revolution. Genomics. 2021 Jul;113(4):2656-2674. doi: 10.1016/j.ygeno.2021.06.006.

Liu HH, Wang J, Wu PH, Lu MJ, Li JY, Shen YM, Tzeng MN, Kuo CH, Lin YH, Chang HX. Whole-Genome Sequence Resource of Calonectria ilicicola, the Casual Pathogen of Soybean Red Crown Rot. Mol Plant Microbe Interact. 2021 Jul;34(7):848-851. doi: 10.1094/MPMI-11-20-0315-A.

An-Ting Liou, Chih-Hsu Chang, Ping-Chang Lin, Yu-Chen Cheng, Ching-Yi Tsai, Wen-Chang Lin, Jeng-Yi Li, Mei-Yeh Jade Lu, Jer-Ming Chang, Shang-Jyh Huang, Ming-Feng Hou, Inn-Wen Chong, Yuh-Jyh Jong, Jih-Jin Tsai, and Chiaho Shih. EPI_ISL_4169856 (hCoV-19/Taiwan/KMU-1/2020; B.1.438). 2021.

Wei-Hsuan Chuang, Hsueh-Chien Cheng, Yu-Jung Chang, Pao-Yin Fu, Yi-Chen Huang, Ping-Heng Hsieha, Shu-Hwa Chen, Chung-Yen Lina, Jan-Ming Ho. GABOLA: A Reliable Gap-Filling Strategy for de novo Chromosome-Level Assembly doi: 10.1101/2021.09.07.459217 https://www.biorxiv.org/content/10.1101/2021.09.07.459217v1

Yi-Jie Li, Reuben Wang, Chung-Yen Lin, Shu-Hwa Chen, Chia-Hsien Chuang, Tzu-Ho Chou, Chi-Fang Ko, Pei-Hsin Chou, Chi-Te Liu, Yang-hsin Shih. (2021) The degradation mechanisms of Rhodopseudomonas palustris toward hexabromocyclododecane by time-course transcriptome analysis. Chemical Engineering Journal, Volume 425, 130489. ISSN 1385-8947. https://doi.org/10.1016/j.cej.2021.130489.

Hsiu-Chin Lin, Yue Him Wong, Benny K. K. Chan. Histology and transcriptomic analyses of barnacles with different base materials and habitats shed lights on the duplication and chemical diversification of barnacle cement proteins. BMC Genomics. 2021 Nov 1;22(1):783. doi: 10.1186/s12864-021-08049-4.

Huang TH, Suen DF. Iron insufficiency in floral buds impairs pollen development by disrupting tapetum function. Plant J. 2021 Oct;108(1):244-267. doi: 10.1111/tpj.15438.

Dai-Keng Hsieh, Shu-Cheng Chuang, Chun-Yi Chen, Ya-Ting Chao, Mei-Yeh Jade Lu, Ming-Che Shih, Miin-Huey Lee Comparative genomics of three Colletotrichum scovillei strains and genetic analysis revealed genes involved in fungal growth and virulence on chili pepper. bioRxiv 2021.09.06.459084. doi: https://doi.org/10.1101/2021.09.06.459084

Tracy J. Lee, Yu-Ching Liu, Wei-An Liu, Yu-Fei Lin, Hsin-Han Lee, Huei-Mien Ke, Jen-Pen Huang, Mei-Yeh Jade Lu, Chia-Lun Hsieh, Kuo-Fang Chung, Gianni Liti, Isheng Jason Tsai Deep sampling of ancestral genetic diversity reveals Saccharomyces cerevisiae pre-domestication life histories bioRxiv 2021.09.07.459046. doi: https://doi.org/10.1101/2021.09.07.459046

Lu SH, Lee KZ, Hsu PW, Su LY, Yeh YC, Pan CY, Tsai SY. Alternative Splicing Mediated by RNA-Binding Protein RBM24 Facilitates Cardiac Myofibrillogenesis in a Differentiation Stage-Specific Manner. Circ Res. 2022 Jan 7;130(1):112-129. Epub 2021 Nov 24. doi: 10.1161/CIRCRESAHA.121.320080.

Lopez MLD, Lin YY, Sato M, Hsieh CH, Shiah FK, Machida RJ. Using metatranscriptomics to estimate the diversity and composition of zooplankton communities. Mol Ecol Resour. 2022 Feb;22(2):638-652. Epub 2021 Oct 3. doi: 10.1111/1755-0998.13506.

Ryuji J Machida, Haruko Kurihara, Ryota Nakajima, Takashi Sakamaki, Ya-Ying Lin, Kazushi Furusawa. Comparative analysis of zooplankton diversities and compositions estimated from complement DNA and genomic DNA amplicons, metatranscriptomics, and morphological identifications. ICES Journal of Marine Science, Volume 78, Issue 9, November 2021, Pages 3428–3443. https://doi.org/10.1093/icesjms/fsab084

Yang FJ, Chen CN, Chang T, Cheng TW, Chang NC, Kao CY, Lee CC, Huang YC, Hsu JC, Li J, Lu MJ, Chan SP, Wang J. phiC31 integrase for recombination-mediated single-copy insertion and genome manipulation in Caenorhabditis elegans. Genetics. 2022 Feb 4;220(2):iyab206. doi: 10.1093/genetics/iyab206.

Chiu YF, Fu HY, Skotnicová P, Lin KM, Komenda J, Chu HA. Tandem gene amplification restores photosystem II accumulation in cytochrome b559 mutants of cyanobacteria. New Phytol. 2022 Jan;233(2):766-780. doi: 10.1111/nph.17785. Epub 2021 Oct 30. PMID: 34625967.

Fan WL, Yang LY, Hsieh JC, Lin TC, Lu MJ, Liao CT. Prognostic Genetic Biomarkers Based on Oncogenic Signaling Pathways for Outcome Prediction in Patients with Oral Cavity Squamous Cell Carcinoma. Cancers (Basel). 2021 May 30;13(11):2709. doi: 10.3390/cancers13112709.

Huang YS, Lin CY, Cheng WC. Investigating the Transcriptomic and Expression Presence-Absence Variation Exist in Japanese Eel (Anguilla japonica), a Primitive Teleost. Mar Biotechnol (NY). 2021 Dec;23(6):943-954. doi: 10.1007/s10126-021-10077-w.

2020

S Fontana, N-C Chang, T Chang, C-C Lee, V-D Dang, and J Wang. (2020). The fire ant social supergene is characterized by extensive gene and transposable element copy number variation. Mol Ecol, 29: 105-120. DOI: 10.1111/mec.15308

P-H Wang, Y-L Chen, T-S S Wei, K Wu, T-H Lee, T-Y Wu, and Y-R Chiang. (2020) Retroconversion of estrogens into androgens by bacteria via a cobalamin-mediated methylation. Proceedings of the National Academy of Sciences, 117(3):1395-1403; DOI: 10.1073/pnas.1914380117

Y-I Cheng, L Chou, Y-F Chiu, H-T Hsueh, C-H Kuo, H-A Chu. (2020) Comparative Genomic Analysis of a Novel Strain of Taiwan Hot-Spring Cyanobacterium hermosynechococcus Sp. CL-1. Frontiers in Microbiology, 11:82. DOI: 10.3389/fmicb.2020.00082

J-Y Leu, S-L Chang, J-C Chao, L C Woods, and M J McDonald. (2020). Sex alters molecular evolution in diploid experimental populations of S. cerevisiae. Nat Ecol Evol, 4, 453-460. DOI: 10.1038/s41559-020-1101-1

W-F Wang, M-Y J Lu, T-J Cheng, Y-C Tang, Y-C Teng, T-Y Hwa, Y-H Chen, M-Y Li, M-H Wu, P-C Chuang, R W Jou, C-H Wong, and W-H Li. (2020). Genomic Analysis of Mycobacterium tuberculosis Isolates and Construction of a Beijing Lineage Reference Genome. Genome Biology and Evolution, 12(2): 3890-3905. DOI: 10.1093/gbe/evaa009

C-Y Chang, J-H Hung, L-W Huang, J Li, K S Fung, C-F Kao, and L Y Chen. (2020). Epigenetic Regulation of WNT3A Enhancer during Regeneration of Injured Cortical Neurons. Int. J. Mol. Sci., 21(5): 1891. DOI: 10.3390/ijms21051891

T-D Vu, Y Iwasaki, S Shigenobu, A Maruko, K Oshima, E Iioka, C-L Huang, T Abe, S Tamaki, Y-W Lin, C-K Chen, M-Y Lu, M Hojo, H-V Wang, S-F Tzeng, H-J Huang, A Kanai, T Gojobori, T-Y Chiang, H. S Sun, W-H Li, and N Okada. (2020). Behavioral and brain-transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens. PLoS genetics, 16(6), e1008831. DOI: 10.1371/journal.pgen.1008831

H-M Ke, H-H Lee, C-Y I Lin, Y-C Liu, M R Lu, J-W A Hsieh, C-C Chang, P-H Wu, M-Y J Lu, J-Y Li, G Shang, R J-H Lu, L G Nagy, P-Y Chen, H-W Kao, and I J Tsai. (2020). Mycena genomes resolve the evolution of fungal bioluminescence. DOI: 10.1101/2020.05.06.079921 (in review)

K-Y Lin, W-D Wang, C-H Lin, E Rastegari, Y-H Su, Y-T Chang, Y-F Liao, Y-C Chang, H Pi, B-Y Yu, S-H Chen, C-Y Lin, M-Y Lu, T-Y Su, F-Y Tzou, C-C Chan and H-J Hsu. (2020). Piwi reduction in the aged niche eliminates germline stem cells via Toll-GSK3 signaling. Nat Commun 11, 3147. DOI: 10.1038/s41467-020-16858-6

W-Y Liu, H-H Lin, C-P Yu, C-K Chang, H-J Chen, J-J Lin, M-Y J Lu, S-L Tu, S-H Shiu, S-H Wu, M S. B. Ku, and W-H Li. (2020). Maize ANT1 modulates vascular development, chloroplast development, photosynthesis, and plant growth. Proceedings of the National Academy of Sciences, 117(35), 21747-21756. DOI: 10.1073/pnas.2012245117

F Y-H Chen, H-W Jung, C-Y Tsuei, and J C. Liao. (2020). Converting Escherichia coli to a Synthetic Methylotroph Growing Solely on Methanol. Cell, 182(4), 933-946. DOI: 10.1016/j.cell.2020.07.010

C-Y Chen, C-K Chen, Y-Y Chen, A Fang, G T-W Shaw, C-M Hung, and D Wang. (2020). Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests. Microbiome, 8(1), 1-13. DOI: 10.1186/s40168-020-00896-9

Tandon, K., Lu, C. Y., Chiang, P. W., Wada, N., Yang, S. H., Chan, Y. F., Chen, P. Y., Chang, H. Y., Chiou, Y. J., Chou, M. S., Chen, W. M., & Tang, S. L. Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP). The ISME journal, 14(5), 1290–1303 (2020). https://doi.org/10.1038/s41396-020-0610-x

Brandon-Mong, G., Shaw, G.T., Chen, W. et al. A network approach to investigating the key microbes and stability of gut microbial communities in a mouse neuropathic pain model. BMC Microbiol 20, 295 (2020). https://doi.org/10.1186/s12866-020-01981-7

Yang Hsin-Chou, Chen Chun-houh, Wang Jen-Hung, Liao Hsiao-Chi, Yang Chih-Ting, Chen Chia-Wei, Lin Yin-Chun, Kao Chiun-How, Lu Mei-Yeh Jade, Liao James C. Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations. Proceedings of the National Academy of Sciences, 117(48) 30679-30686 (2020).

Ke Huei-Mien, Lee Hsin-Han, Lin Chan-Yi Ivy, Liu Yu-Ching, Lu Min R., Hsieh Jo-Wei Allison, Chang Chiung-Chih, Wu Pei-Hsuan, Lu Meiyeh Jade, Li Jeng-Yi, Shang Gaus, Lu Rita Jui-Hsien, Nagy László G., Chen Pao-Yang, Kao Hsiao-Wei, Tsai Isheng Jason. Mycenagenomes resolve the evolution of fungal bioluminescence. Proceedings of the National Academy of Sciences, 117(49) 31267-31277 (2020).

Lin Che-Yi, Lu Mei-Yeh Jade, Yue Jia-Xing, Li Kun-Lung, Le Pétillon Yann, Yong Luok Wen, Chen Yi-Hua, Tsai Fu-Yu, Lyu Yu-Feng, Chen Cheng-Yi, Hwang Sheng-Ping L., Su Yi-Hsien, Yu Jr-Kai. Molecular asymmetry in the cephalochordate embryo revealed by single-blastomere transcriptome profiling. PLOS Genetics, 16(12) e1009294 (2020).

Le MH, Wang D. Structure and membership of gut microbial communities in multiple fish cryptic species under potential migratory effects. Scientific reports, 10(1), 7547 (2020).

Cheng, YH., Liu, CF.J., Yu, YH. et al.  Genome plasticity in Paramecium bursaria revealed by population genomics.  BMC Biol 18, 180 (2020).

Shao-Lun Liu, Yin-Ru Chiang, Hwan Su Yoon, Han-Yi Fu Comparative Genome Analysis Reveals Cyanidiococcus gen. nov., A New Extremophilic Red Algal Genus Sister to Cyanidioschyzon (Cyanidioschyzonaceae, Rhodophyta) J Phycol. 56(6):1428-1442. (2020)

Lee, C. H., Chang, H. W., Yang, C. T., Wali, N., Shie, J. J., & Hsueh, Y. P. (2020). Sensory cilia as the Achilles heel of nematodes when attacked by carnivorous mushrooms. Proceedings of the National Academy of Sciences, 117(11), 6014-6022.

Wen-Jen Chen ,Tzu-Yen Kuo, Chun-Yi Chen ,Feng-Chia Hsieh ,Yu-Liang Yang ,Je-Ruei Liu and Ming-Che Shih Whole Genome Sequencing and Tn5-Insertion Mutagenesis of Pseudomonas taiwanensis CMS to Probe Its Antagonistic Activity Against Rice Bacterial Blight Disease. Int J Mol Sci. 2020;21(22):8639. Published 2020 Nov 16. doi:10.3390/ijms21228639

2019

Chang, Y.-M., Lin, H.-H., Liu, W.-Y., Yu, C.-P., Chen, H.-J., Wartini, P. P., Kao, Y.-Y., Wu, Y.-H., Lin, J.-J., Lu, M.-Y. J., Tu, S.-L., Wu, S.-H., Shiu, S.-H., Ku, M. S. B., and Li, W.-H. (2019). Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes. Proceedings of the National Academy of Sciences, 201817621. DOI: 10.1073/pnas.1817621116

Lin, S.-S., Chen, Y., & Lu, M.-Y. J. (2019). Degradome Sequencing in Plants. Plant MicroRNAs – Methods and Protocols, pp. Vol. 1932, USA: MiMB Springer, Humana Press.

Sung, C. M., Lin, Y.-F., Chen, K.-F., Ke, H.-M., Huang, H.-Y., Gong, Y.-N., Tsai, W.-S., Lu, M. J., Cheng, H.-T., Lin, C.-Y., Kuo, C.-J., Tsai, I. J., and Hsieh, S.-Y. (2019). Predicting Clinical Outcomes of Cirrhosis Patients With Hepatic Encephalopathy From the Fecal Microbiome. Cellular and molecular gastroenterology and hepatology. DOI: 10.1016/j.jcmgh.2019.04.008

Chien, C.-C., Chou, M.-Y., Chen, C.-Y., and Shih, M.-C. (2019). Analysis of genetic diversity of Xanthomonas oryzae pv. oryzae populations in Taiwan. Scientific reports, 9(1): 316. DOI: 10.1038/s41598-018-36575-x

Lin, C.-C., Chao, Y.-T., Chen, W.-C., Ho, H.-Y., Chou, M.-Y., Li, Y.-R., Wu, Y.-L., Yang, H.-A., Hsieh, H., Lin, C.-S., Wu, F.-H., Chou, S.-J., Jen, H.-C., Huang, Y.-H., Irene, D., Wu, W.-J., Wu, J.-L., Gibbs, D. J., Ho, M.-C., and Shih, M.-C. (2019). Regulatory cascade involving transcriptional and N-end rule pathways in rice under submergence. Proceedings of the National Academy of Sciences, 116(8): 3300-3309. DOI: 10.1073/pnas.1818507116.

Lin, C.-Y. G., Chao, J.-L., Tsai, H.-K., Chalker, D., and Yao, M.-C. (2019). Setting boundaries for genome-wide heterochromatic DNA deletions through flanking inverted repeats in Tetrahymena thermophila. Nucleic acids research. DOI: 10.1093/nar/gkz209

Gómez Luciano, L. B., Tsai, I. J., Chuma, I., Tosa, Y., Chen, Y.-H., Li, J.-Y., Li, M.-Y., Lu, M.-Y. J., Nakayashiki, H., and Li, W.-H. (2019). Blast Fungal Genomes Show Frequent Chromosomal Changes, Gene Gains and Losses, and Effector Gene Turnover. Molecular biology and evolution, 36(6): 1148-1161. DOI: 10.1093/molbev/msz045

Cho, H.‐Y., Lu, M.‐Y.J. and Shih, M.‐C. (2019). The SnRK1‐eIFiso4G1 signaling relay regulates the translation of specific mRNAs in Arabidopsis under submergence. New Phytol, 222: 366-381. DOI: 10.1111/nph.15589

Chong, G.-L., Foo, M.-H., Lin, W.-D., Wong, M. M., Verslues, P.E. (2019). Highly ABA-Induced 1 (HAI1)-Interacting protein HIN1 and drought acclimation-enhanced splicing efficiency at intron retention sites. Proceedings of the National Academy of Sciences, 116(44): 22376-22385. DOI: 10.1073/pnas.1906244116

Wong, M. M., Bhaskara, G. B., Wen, T.-N., Lin, W.-D., Nguyen, T. T., Chong, G. L., Verslues, P. E. (2019). Phosphoproteomics of Arabidopsis Highly ABA-Induced1 identifies AT-Hook Like10 phosphorylation required for stress growth regulation. Proceedings of the National Academy of Sciences, 116(6): 2354-2363. DOI: 10.1073/pnas.1819971116

Yang, S.-F., Lu, C.-W., Yao, C.-T., Hung, C.-M. (2019). To Trim or Not to Trim: Effects of Read Trimming on the De Novo Genome Assembly of a Widespread East Asian Passerine, the Rufous-Capped Babbler (Cyanoderma ruficeps Blyth). Genes, 10(10), 737. DOI: 10.3390/genes10100737

Shen. Y.-C., Hsu. C.-L., Jen. Y.-M., Ho. M.-C., Ho. C.-M., Yeh. C.-P., Yeh. C.-Y., Hsu. M.-C., Hu. R.-H., Cheng. A.-L. (2019). Reliability of a Single-Region Sample to Evaluate Tumor Immune Microenvironment in Hepatocellular Carcinoma. Journal of Hepatology, 27(3): 489-497. DOI: 10.1016/j.jhep.2019.09.032

Dang, V.‐D., Cohanim, A. B., Fontana, S., Privman, E., Wang, J. (2019). Has gene expression neofunctionalization in the fire ant antennae contributed to queen discrimination behavior? Ecol Evol, 9: 12754-12766. DOI: 10.1002/ece3.5748

Lin, Y.T., Lin, Y.F., Tsai, I.J., Chang, E.H., Jien, S.H., Lin, Y.J., and Chiu, C.Y.* 2019. Structure and diversity of soil bacterial communities in offshore islands. Scientific Reports 9:4689 | https://doi.org/10.1038/s41598-019-41170-9.

2018

Wong, M. M., Bhaskara, G. B., Wen, T., Lin, W., Nguyen, T. T., Chong, G. L., and Verslues, P. (2018). Phosphoproteomics of Highly ABA-Induced1 identifies AT Hook Like10 phosphorylation required for growth regulation during stress. Doi: 10.1101/413013. T

Cho, H. Y., Lu, M. Y. J., and Shih, M. C. (2018). The Sn RK 1‐eIF iso4G1 signaling relay regulates the translation of specific mRNA s in Arabidopsis under submergence. New Phytologist. Doi: 10.1111/nph.15589

Grillet, L., P. Lan, W. Li, G. Mokkapati, and W. Schmidt (2018). IRON MAN is a ubiquitous family of peptides that control iron transport in plants. Nature Plants 4, 953-963. DOI: 10.1038/s41477-018-0266-y

Wei, S. T. S., Y. W. Wu, T. H. Lee, Y. S. Huang, C. Y. Yang, Y. L. Chen, and Y. R. Chiang (2018). Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge. mSystems, 3(5), e00113-18. DOI: 10.1128/mSystems.00113-18

Lee, C. C., and Wang, J. (2018). Rapid expansion of a highly germline-expressed mariner element acquired by horizontal transfer in the fire ant genome. Genome biology and evolution, 10(12), 3262-3278. DOI: 10.1093/gbe/evy220.

Huang, Y. C., V. Dai Dang, N. C. Chang, and J. Wang (2018). Multiple large inversions and breakpoint rewiring of gene expression in the evolution of the fire ant social supergene. Proc. R. Soc. B, 285(1878), 20180221. DOI: 10.1098/rspb.2018.0221

Lee, C. Y., P. H. Hsieh, L. M. Chiang, A. Chattopadhyay, K. Y. Li, Y. F. Lee, T. P. Lu, L. C. Lai, E. C. Lin, H. Lee, S. T. Ding, M. H. Tsai, C. Y. Chen, and Eric Y. Chuang (2018). Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant. GigaScience, 7(5), giy044. DOI: 10.1093/gigascience/giy044

Huang, C. J., M. Y. Lu, Y. W. Chang, and W. H. Li (2018). Experimental Evolution of Yeast for High Temperature Tolerance. Molecular biology and evolution, 35(8), 1823-1839. DOI: 10.1093/molbev/msy077

Chuang, T. J., Y. J. Chen, C. Y. Chen, T. L. Mai, Y. D. Wang, C. S. Yeh, M. Y. Yang, Y. T. Hsiao, T. H. Chang, T. C. Kuo, H. H. Cho, C. N. Shen, H. C. Kuo, M. Y. Lu, Y. H. Chen, S. C. Hsieh, and T. W. Chiang (2018). Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells. Nucleic acids research, 46(7), 3671-3691. DOI: 10.1093/nar/gky032

Yen Y.P., W.F. Hsieh, Y.Y. Tsai, Y.L. Lu, E.S. Liau, H.C. Hsu, Y.C. Chen, T.C. Liu, M. Chang, J. Li, S.P. Lin, J.H. Hung, J.A. Chen (2018). Dlk1-Dio3 locus-derived lncRNAs perpetuate postmitotic motor neuron cell fate and subtype identity. eLife, 7, e38080. DOI: 10.7554/eLife.38080

Dhananjaya, D., Hung, K. Y., and Tarn, W. Y. (2018). RBM4 modulates radial migration via alternative splicing of Dab1 during cortex development. Molecular and cellular biology, 38(12), e00007-18. DOI: 10.1128/MCB.00007-18

Qiu, B., Larsen, R. S., Chang, N. C., Wang, J., Boomsma, J. J., and Zhang, G. (2018). Towards reconstructing the ancestral brain gene-network regulating caste differentiation in ants. Nature Ecology & Evolution, 2(11), 1782. DOI: 10.1038/s41559-018-0689-x

Koubkova-Yu, T. C.-T., Chao, J.-C. and Leu, J.-Y.* “Heterologous Hsp90 promotes phenotypic diversity through network evolution.” PLoS Biol. 16(11): e2006450 (2018). DOI: 10.1371/journal.pbio.2006450

Chao, Y. T., W. C. Chen, C. Y. Chen, H. Y. Ho, C. H. Yeh, Y. T. Kuo, C. L. Su, S. H. Yen, H. Y. Hsueh, J. H. Yeh, H. L. Hsu, Y. H.Tsai, T. Y. Kuo, S. B. Chang, K. Y. Chen, and M. C. Shih (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. DOI: 10.1111/pbi.12936

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.

Zhou, N., K. B. Swamy, J. Y. Leu, M. J. McDonald, S. Galafassi, C. Compagno, and J. Piškur (2017). “Coevolution with bacteria drives the evolution of aerobic fermentation in Lachancea kluyveri.” PloS one, 12(3), e0173318.

Chung, C. L., T. J. Lee, M. Akiba, H. H. Lee, T. H. Kuo, D. Liu, H. M. Ke, T. Yokoi, M. B. Roa, M. J. Lu, Y. Y. Chang, P. J. Ann, J. N. Tsai, C. Y. Chen, S. S. Tzean, Y. Ota, T. Hattori, N. Sahashi, R. F. Liou, T. Kikuchi, and I. J. Tsai (2017). “Comparative and population genomic landscape of Phellinus noxius: A hypervariable fungus causing root rot in trees.” Molecular ecology, 26(22), 6301-6316.

Merret, R., M. C. Carpenier, J. J. Favory, C. Picart, J. Descombin, C. Bousquet-Antonelli, P. Tillard, L. Lejay, J. M. Deragon, and Y. Y. Charng (2017). “Heat-shock protein HSP101 affects the release of ribosomal protein mRNAs for recovery after heat shock.” Plant physiology, pp-00269.

Chen, Y. L., C. P. Yu, T. H. Lee, K. S. Goh, K. H. Chu, P. H. Wang, W. Ismail, C. J. Shih, and *Y. R. Chiang (2017). “Biochemical mechanisms and catabolic enzymes involved in bacterial estrogen degradation pathways.” Cell chemical biology, 24(6), 712-724.

Shih, C. J., Y. L. Chen, C. H. Wang, S. T. S. Wei, I. Lin, W. A. Ismail, and Y. R. Chiang (2017). “Biochemical Mechanisms and Microorganisms Involved in Anaerobic Testosterone Metabolism in Estuarine Sediments.” Frontiers in microbiology, 8, 1520.

Lin, C. S., J. J. W. Chen, C. C. Chiu, H. C. W. Hsiao, C. J. Yang, X. H. Jin, J. Leebens-Mack, C. W. de Pamphilis, Y. T. Huang, L. H. Yang, W. J. Chang, L. Kui, G. K. Wong, J. M. Hu, W. Wang, and M.C. Shih. (2017). “Concomitant loss of NDH complex‐related genes within chloroplast and nuclear genomes in some orchids.” The Plant Journal, 90(5), 994-1006.

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

“Epigenetics Chromatin. 2016; 9: 32. Published online 2016 Jul 27. doi: 10.1186/s13072-016-0082-4 GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes”

Feng YL, Wicke S, Li JW, Han Y, Lin CS, Li DZ, Zhou TT, Huang WC, Huang LQ, Jin XH. Lineage-specific reductions of plastid genomes in an orchid tribe with partially and fully mycoheterotrophic species. Genome biology and evolution. 2016 Jul 1;8(7):2164-75.

“Evolution of long centromeres in fire ants. Huang Y-C, Lee C-C, Kao C-Y, Chang N-C, Lin C-C, Shoemaker DD, and Wang J. 2016. BMC Evolutionary Biology 16:189 (DOI: 10.1186/s12862-016-0760-7)”

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.

“Identification and evolutionary analysis of long non-coding RNAs in birds. Chih-Kuan Chen; Chun-Ping Yu; Sung-Chou Li; Siao-Man Wu; Mei-Yeh Jade Lu; Yihua Chen; Chen Siang Ng; Chau-Ti Ting; Wen-Hsiung Li. 2016 BMC Genomics Editorial Office (submission ID: GICS-D-16-01257)”

“The piggyBac transposon-derived genes TPB1 and TPB6 mediate essential transposon-like excision during the developmental rearrangement of key genes in Tetrahymena thermophila Genes Dev. 2016 Dec 15;30(24):2724-2736. doi: 10.1101/gad.290460.116. Chao-Yin Cheng1,5, Janet M. Young2,5, Chih-Yi Gabriela Lin1,3, Ju-Lan Chao1, Harmit S. Malik2,4 and Meng-Chao Yao1″

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.

Fu-Chun Yang, Yi-Lung Chen, Sen-Lin Tang, Chang-Ping Yu, Po-Hsiang Wang, Wael Ismail, Chia-Hsiang Wang, Jiun-Yan Ding, Cheng-Yu Yang, Chia-Ying Yang, and (Yin-Ru Chiang*). Integrated multi-omics analyses reveal the biochemical mechanisms and phylogenetic relevance of anaerobic androgen biodegradation in the environment. ISME Journal. , 2015-12.

“The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family. Lin CS, Chen JJW, Huang YT, Chan MT, Daniell H, Chang WJ, Hsu CT, Liao DC, Wu FU, Lin SY, Liao CF, Deyholos MK, Wong GKS, Albert VA, Chou ML, Chen CY, Shih MC.Scientific Reports 5, Article number: 9040 (2015). doi:10.1038/srep09040. Published online: 12 March 2015″

“NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss. Ruhlman TA, Chang WJ, Chen JJW, Huang YT, Chan MT, Zhang J, Liao DC, Blazier JC, Jin XJ, Shih MC, Jansen RK, Lin CS.BMC Plant Biology 201515:100. doi: 10.1186/s12870-015-0484-7. Published: 11 April 2015″

“Ng, CS, Chih-Kuan Chen, Wen-Lang Fan, Ping Wu, Siao-Man Wu, Jiun-Jie Chen, Yu-Ting Lai, Chi-Tang Mao, Mei-Yeh Jade Lu, Di-Rong Chen, Ze-Shiang Lin, Kai-Jung Yang, Yuan-An Sha, Tsung-Che Tu, Chih-Feng Chen, Cheng-Ming Chuong and Wen-Hsiung Li* (2015) Transcriptomic analyses of regenerating adult feathers in chicken. BMC Genomics. 2015 Oct 6;16(1):756. PMID: 26445093 (IF: 4.041, 2013).”

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.

Shih, M-C, Chou, M-L, Yue, J-J, Hsu, C-T, Chang, W-J, Ko, S-S, Liao, D-C, Huang, Y-T, Chen J JW, Yuan, J-L, Gu, X-P, and Lin, C-S. (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(1):179. DOI: 10.1186/1471-2229-14-179

2013

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.

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.

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%)

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%)

Chou, M.-L., Shih, M.-C., Chan, M.-T., Liao, S.-Y., Hsu, C.-T., Haung, Y.-T., Chen, J.J.W., Liao, D.-C., Wu, F.-H., and Lin, C.-S. (2013). Global transcriptome analysis and identification of a CONSTANS-like gene family in the orchid Erycina pusilla . Planta 237, 1425–1441. DOI: 10.1007/s00425-013-1850-z

Wu, C.-S., Yu, C.-Y., Chuang, C.-Y., Hsiao, M., Kao, C.-F., Kuo, H.-C., and Chuang, T.-J. (2014). Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency. Genome research, 24(1), 25-36. DOI: 10.1101/gr.159483.113

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%)