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Chiung-Wen Hu, Yuan-Jhe Chang, Wei-Hung Chang, Marcus S. Cooke, Yet-Ran Chen*, and Mu-Rong Chao* (2024) A Novel Adductomics Workflow Incorporating FeatureHunter Software: Rapid Detection of Nucleic Acid Modifications for Studying the Exposome. Environ. Sci. Technol./ES&T, 58(1), 75-79
C. W. Hu, Y. J. Chang, W. H. Chang, M. S. Cooke, (Y. R, Chen)*, M. R. Chao* (2023) A Novel Adductomics Workflow Incorporating FeatureHunter Software: Rapid Detection of Nucleic Acid Modifications for Studying the Exposome. ENVIRONMENTAL SCIENCE & TECHNOLOGY, Article ASAP, acs.est.3c04674
Y. L. Chen, F. W. Lin, K. T. Cheng, C. H. Chang, S. C. Hung, T. Efferth, (Y. R. Chen)* (2023) XCP1 cleaves Pathogenesis-related protein 1 into CAPE9 for systemic immunity in Arabidopsis. NATURE COMMUNICATIONS, 14, 4697
MS Cooke, Y. J. Chang, Y. R. Chen, C. W. Hu, M. R. Chao* (2023) Nucleic acid adductomics – The next generation of adductomics towardsassessing environmental health risks. SCIENCE OF THE TOTAL ENVIRONMENT, 856, 159192
K. T. Fan, C. W. Hsu and Y. R. Chen* (2022) Mass spectrometry in the discovery of peptides involved in intercellular communication: From targeted to untargeted peptidomics approaches. MASS SPECTROMETRY REVIEWS, 2022, e21789
K. T. Fan, Y. Hsu, C. F. Yeh, C. H. Chang, W. H. Chang and Y. R. Chen* (2021) Quantitative Proteomics Reveals the Dynamic Regulation of the Tomato Proteome in Response to Phytophthora infestans. International Journal of Molecular Sciences, 22(8), 4174
M. T. Yang, W. H. Chang, T. F. Kuo, M. Y. Shen, C. W. Tien, Y. J. Yang, B. Y. Lai, Y. R. Chen, Y. C. Chang, W. C. Yang* (2021) Identification of Novel Biomarkers for Pre-diabetic Diagnosis Using a Combinational Approach. FRONTIERS IN ENDOCRINOLOGY, 12, E641336
J. Y. Mao, Unnikrishnan, B. Unnikrishnan, H. W. Chu, S. G. Harroun, Y. R. Chen, A. T. Wu, H. T. Chang, H. J. Lin, C. C. Huang* (2021) Thermally driven formation of polyphenolic carbonized nanogels with high anticoagulant activity from polysaccharides. BIOMATERIALS SCIENCE, 9(13), 4679-4690
Y. J. Chang, M. S. Cooke, Y. R. Chen, S. F. Yang, P. S. Li, C. W. Hu*, M. R. Chao* (2021) Is high resolution a strict requirement for mass spectrometry-based cellular DNA adductomics?. CHEMOSPHERE, 274, E129991
Y. C. Y. Yu, T. Z. K. Hui, T. H. Kao, H. F. Liao, C. Y. Yang, C. C. Hou, H. T. Hsieh, J. Y. Chang, Y. T. Tsai, M. Pinskaya, K. C. Yang, Y. R. Chen, A. Morillon, M. H. Tsai, S. P. Lin* (2020) Transient DNMT3L Expression Reinforces Chromatin Surveillance to Halt Senescence Progression in Mouse Embryonic Fibroblast. Frontiers In Cell And Developmental Biology, 8, E103
Y. J. Chen, T. I Roumeliotis, Y. H. Chang, C. T. Chen, C. L. Han*, M. H. Lin, H. W. Chen, G. C. Chang, Y. L. Chang, C. T. Wu, M. W. Lin, M. S. Hsieh, Y. T. Wang, Y. R. Chen, I. Jonassen, F. Z. Ghavidel, Z. S. Lin, K. T. Lin, C. W. Chen, P. Y. Sheu, C. T. Hung, K. C. Huang, H. C. Yang, P. Y. Lin, T. C. Yen, Y. W. Lin, J. H. Wang, L. Raghav, C. Y. Lin, Y. S. Chen, P. S. Wu, C. T. Lai, S. H. Weng, K. Y. Su, W. H. Chang, Tsai, P. Y. Tsai, A. I. Robles, H. Rodriguez, Y. J. Hsiao, W. H. Chang, T. Y. Sung*, J. S. Chen*, S. L. Yu*, J. S. Choudhary*, H. Y. Chen*, P. C. Yang*, Y. J. Chen* (2020) Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression. Cell, 182(1), 226-244.e17
Y. C. Lin, C. Y. Wu, C. H. Hu, T. W. Pai, Y. R. Chen, W. D. Wang* (2020) Integrated Hypoxia Signaling and Oxidative Stress in Developmental Neurotoxicity of Benzo[a]Pyrene in Zebrafish Embryos. Antioxidants, 9(8), E731
K. T. Fan, K. H. Wang, W. H. Chang, J. C, Yang, C. F. Yeh, K. T. Cheng, S. C. Hung, Y. R. Chen* (2019) Application of data-independent acquisition approach to study the proteome change from early to later phases of tomato pathogenesis responses. International Journal of Molecular Sciences, 20(4). E863
Y. L. Chen, W. H. Chang, C. Y. Lee, Y. R. Chen* (2019) An Improved Scoring Method for the Identification of Endogenous Peptides based on Mascot MS/MS Ion Search. Analyst, 144(9), 3045-3055
Y. L. Chen, K. T. Fan, S. C. Hung and Y. R. Chen* (2019) The role of peptides cleaved from protein precursors in eliciting plant stress reactions. New Phytologist, doi: 10.1111/nph.16241
K. S. Hung, C. C. Hsiao, T. W. Pai*, C. H. Hu, W. S. Tzou, W. D. Wang and Y. R. Chen (2018) Functional enrichment analysis based on long noncoding RNA associations. BMC SYSTEMS BIOLOGY, 12(Suppl 4), 45
Y. R Shen, H. Y. Wang, Y. C. Kuo, S. C. Shih, C. H. Hsu, Y. R. Chen, S. R. Wu, C. Y. Wang , P. L. Kuo* (2017) SEPT12 phosphorylation results in loss of the septin ring/sperm annulus, defective sperm motility and poor male fertility. PLOS Genetics, 13(3), e1006631
W. C. Yang, T. F. Kuo, T. Y. Chen, S. T. Jiang, K. W. Chen, Y. M. Chiang, Y. J. Hsu, Y. J. Liu, H. M. Chen, K. Yokoyama, K. C. Tsai, H. H. Yeh, Y. R. Chen, M. T. Yang, and C. Y. Yang (2017) Protein disulfide isomerase a4 acts as a novel regulator of cancer growth through the procaspase pathway. ONCOGENE, 36(39), 5484-5496
I. W. Chou, Y. H. Cheng, Y. R. Chen, P. C. H. Hsieh*, K. King (2017) Fenugreek Compound (N55) Lowers Plasma Glucose through the Enhancement of Response of Physiological Glucagon-like peptide-1. Scientific reports, 7(1), 12265
J. Y. Mao, H. W. LI, S. C. Wei, S. G. Harroun, M. Y. Lee, H. Y. Lin, C. Y. Chung, C. H. Hsu, Y. R. Chen, H. J. Lin*, C. C. Huang (2017) DNA Modulates the Interaction of Genetically Engineered DNA-Binding Proteins and Gold Nanoparticles: Diagnosis of High-Risk HPV Infection. ACS applied materials & interfaces, 9(51), 44307-44315
M. D. Pham, T. C. Wen, H. C. Li, P. H. Hsieh, Y. R. Chen, H. C. Chang* and C. C. Han* (2016) Streamlined Membrane Proteome Preparation for Shotgun Proteomics Analysis with Triton X-100 Cloud Point Extraction and Nanodiamond Solid Phase Extraction. Materials, 9(5), 385-401
M. Tsednee, Y. C. Huang, Y. R. Chen and K. C. Yeh* (2016) Identification of Metal Species by ESI-MS/MS Through Release of Free Metals from The Corresponding Metal-Ligand Complexes. Scientific Reports, 6, 26785
H. M. Jan, Y. C. Chen, Y. Y. Shih, Y. C. Huang, Z. Tu, A. B. Ingel, S. W. Liu, M. S. Wu, J. Gervay-Huage, K. T. Mong, Y. R. Chen, C. H. Lin* (2016) Metabolic labelling of cholesteryl glucosides in Helicobacter pylori reveals how the uptake of human lipids enhances bacterial virulence. CHEMICAL SCIENCE, 7(9), 6208-6216
Shu-Yi Yin, Thomas Efferth, Feng-Yin Jian, Yung-Hsiang Chen, Chia-I Liu, Andrew H.J. Wang, Yet-Ran Chen, Pei-Wen Hsiao, Ning-Sun Yang (2016) Immunogenicity of Mammary Tumor Cells Can be Induced by Shikonin Via Direct Binding-Interference with Hnrnpa1. Oncotarget, 7(28), 43629-43653
J. Y. Hsu, J. F. Hsu, Y. R. Chen, C. L. Shih, Y. S. Hsu, Y. J. Chen, S. H. Tsai, P. C. Liao* (2016) Urinary exposure marker discovery for toxicants using ultra-high pressure liquid chromatography coupled with Orbitrap high resolution mass spectrometry and three untargeted metabolomics approaches. ANALYTICA CHIMICA ACTA, 939, 73-83
W. C. Wei, S. Y. Lin, C. W. Lan, Y. C. Hang, C. Y. Lin, P. W. Hsaio, Y. R. Chen, W. C. Yang, N. S. Yang* (2016) Inhibiting MDSC differentiation from bone marrow with phytochemical polyacetylenes drastically impairs tumor metastasis. SCIENTIFIC REPORTS, 6, 36663
K. S. Lynn, M. L. Cheng, T. Y. Sung, Y. R. Chen, C. Hsu, A. Chen, T. M. Lih, H. Y. Chang, C. J. Huang, M. S. Shiao, W. H. Pan*, and W. L. Hsu (2015) Metabolite identification for mass spectrometry-based metabolomics using multiple types of correlated ion information. ANALYTICAL CHEMISTRY, 87(4), 2143-2151
Y. C. Kuo, Y. R. Shen, H. I. Chen, Y. H. Lin, Y. Y. Wang, Y. R. Chen, C. Y. Wang, and P. L. Kuo* (2015) SEPT12 orchestrates the formation of mammalian sperm annulus by organizing core octameric complexes with other SEPT proteins. JOURNAL OF CELL SCIENCE, 128(5), 923-34
C. H. Tsai, S. F. Tzeng, S. C. Hsieh, C. Y Lin, C .J. Tsai, Y. R. Chen, Y. C. Yang, Y. W. Chou, M. T. Lee, P. W. Hsiao* (2015) Development of a standardized and effect-optimized herbal extract of Wedelia chinensis for prostate cancer. Phytomedicine, 22(3), 406-14
P. C. Lin, W. C. Hu, S. C. Lee, Y. L. Chen, C. Y. Lee, Y. R. Chen, L. Y. Liu, P. Y. Chen, S. S. Lin* and Y. C. Chang (2015) Application of an Integrated Omics Approach for Identifying Host Proteins That Interact With Odontoglossum ringspot virus Capsid Protein. MOLECULAR PLANT-MICROBE INTERACTIONS, 28(6), 711-726
P. S. Chien, H. G. Nam and Y. R. Chen* (2015) A salt-regulated peptide derived from the CAP superfamily protein negatively regulates salt-stress tolerance in Arabidopsis. Journal of Experimental Botany, 66(17), 5301-5313
J. Koubek, Y. R. Chen, R. P. Cheng and J. J. T. Huang* (2015) Nonorthogonal tRNA(Amber)(cys) for protein and nascent chain labeling. RNA, 21(9), 1672-82
H. J. Chen, Y. C. Shen, Y. J Shiao, K. T. Liou, W. H. Hsu, P. H. Hsieh, C. Y. Lee, Y. R. Chen* and Y. L. Lin (2015) Multiplex Brain Proteomic Analysis Revealed the Molecular Therapeutic Effects of Buyang Huanwu Decoction on Cerebral Ischemic Stroke Mice. PLoS One, 10(10), e0140823
C. H. Chen, T. H. Hu, T. C. Huang, Y. L. Chen, Y. R. Chen, C. C. Cheng*, and C. T. Chen (2015) Delineation of G-Quadruplex Alkylation Sites Mediated by 3,6-Bis(1-methyl-4-vinylpyridinium iodide)carbazole-Aniline Mustard Conjugates. CHEMISTRY-A EUROPEAN JOURNAL, 21(48), 17379-17390
J. Catinot, J. B. Huang, P. Y. Huang, M. Y. Tseng, Y. L. Chen, S. Y. Gu, W. S. Lo, L. C. Wang, Y. R. Chen, L. Zimmerli* (2015) ETHYLENE RESPONSE FACTOR 96 positively regulates Arabidopsis resistance to necrotrophic pathogens by direct binding to GCC elements of jasmonate - and ethylene-responsive defence genes. Plant Cell & Environment, 38(12), 2721-2734
L. T. Huang*, C. C. Wu, L. F. Lai, M. M. Gromiha, C. S.Wang, Y. R. Chen (2014) Data mining application in biomedical informatics for probing into protein stability upon double mutation. Applied Mathematics & Information Sciences, 8(1L), 125-132
S. L. Lee, C. W. Li, K. W. Koh, H. Y. Chuang. Y. R. Chen, C. S. Lin and M. T. Chan* (2014) MSRB7 Reverses Oxidation of GSTF2/3 to Confer Tolerance of Arabidopsis Thaliana to Oxidative Stress. Journal of Experimental Botany, 65(17), 5049-5062
H. M. Hsu, Y. Lee, P. H. Hsu, H. W. Liu, C. H. Chu, Y. W. Chou, Y. R. Chen, S. H. Chen and J. H. Tai* (2014) Signal transduction triggered by iron to induce the nuclear importation of a Myb3 transcription factor in the parasitic protozoan Trichomonas vaginalis. Journal of Biological Chemistry, 289(42), 29334-29349
Y. L. Chen, C. Y. Lee, K. T. Cheng, W. H. Chang, R. N. Huang, H. G. Nam and Y. R. Chen* (2014) Quantitative Peptidomics Study Reveals a Wound-Induced Peptide from PR-1 Regulates Immune Signaling in Tomato. Plant Cell, 26(10), 4135-4148
W. H. Chang, C. Y. Lee, C. Y. Lin; M. C. Chen, W. S. Tzou and Y. R. Chen* (2013) UniQua: a universal signal processor for MS-based qualitative and quantitative proteomics applications. Analytical chemistry, 85(2), 890-897
B. Wiench, Y. R. Chen, M. Paulsen, R. Hamm, S. Schroder, N.S. Yang, and T. Efferth* (2013) Integration of Different "-omics" Technologies Identifies Inhibition of the IGF1R-Akt-mTOR Signaling Cascade Involved in the Cytotoxic Effect of Shikonin against Leukemia Cells. Evidence-Based Complementary and Alternative Medicine, 2013, 818709
Lin HY, Shih CY, Liu HC, Chang J, Chen YL, Chen YR, Lin HT, Chang YY, Hsu CH, Lin HJ* (2013) Identification and characterization of an extracellular alkaline phosphatase in the marine diatom Phaeodactylum tricornutum. Marine biotechnology, 15(4), 425-436
Y. C. Chang, Y. H. Yu, J. Y. Shew, W. J. Lee, J. J. Hwang, Y. H. Chen, Y. R. Chen, P. C. Wei, L. M. Chuang, W. H. Lee* (2013) Deficiency of NPGPx, an oxidative stress sensor, leads to obesity in mice and human. EMBO Molecular Medicine, 5(8), 1165-1179
J. Koubek, K. F. Lin, Y. R. Chen, R. P. Cheng*, J. J. Huang (2013) Strong anion-exchange fast performance liquid chromatography as a versatile tool for preparation and purification of RNA produced by in vitro transcription. RNA-A PUBLICATION OF THE RNA SOCIETY, 19(10), 1449-1459
J. H. Weng, M. R. Liang, C. H. Chen, S. K. Tong, T. C. Huang, S. P. Lee, Y. R. Chen, C. T. Chen*, and B. Chung (2013) Pregnenolone activates CLIP-170 to promote microtubule growth and cell migration. NATURE CHEMICAL BIOLOGY, 9(10), 636-642
T. K. Huang, C. L. Han, S. I. Lin, Y. J. Chen, Y. C. Tsai, Y. R. Chen, J. W. Chen, W. Y. Lin, P. M. Chen, T. Y. Liu, Y. S. Chen, C. M. Sun, and T. J. Chiou* (2013) Identification of Downstream Components of Ubiquitin-Conjugating Enzyme PHOSPHATE2 by Quantitative Membrane Proteomics in Arabidopsis Roots. Plant Cell, 25(10), 4044-4060
C. J. Chen, W. Y. Chen, M. C. Tseng and Y. R. Chen* (2012) Tunnel Frit: A Nonmetallic In-Capillary Frit for Nanoflow Ultra High-Performance Liquid Chromatography-Mass Spectrometry Applications. ANALYTICAL CHEMISTRY, 84(1), 297-303
M. Tsednee, Y. W. Mak, Y. R. Chen and K. C. Yeh* (2012) A sensitive LC-ESI-Q-TOF-MS method reveals novel phytosiderophores and phytosiderophore–iron complexes in barley. New Phytologist, 195(4), 951-961
H. C. Tseng, H. W. Kao, M. R. Ho, Y. R. Chen, T. W. Lin, P. C. Lyu and W. C. Lin* (2011) Cytoskeleton network and cellular migration modulated by nuclear-localized receptor tyrosine kinase ROR1. Anticancer research, 31(12), 4239-4249
C. J. Chen, M. C. Tseng, H. J. Lin, T. W. Lin and Y. R. Chen* (2010) Visual Indicator for Surfactant Abundance in MS-Based Membrane and General Proteomics Applications. ANALYTICAL CHEMISTRY, 82(19), 8283-8290
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