Publications

Results 1-146 of 146 (Search time: 0.002 seconds).

Issue DateTitleAuthor(s)RelationscopusWOSFulltext/Archive link
12023SARS-CoV-2 N protein mediates intercellular nucleic acid dispersion, a feature reduced in OmicronWu, Jung-Lin; Kuan, I.-I.; Guo, Jing-You; Hsu, Wei-Chia; Tang, Wei-Chun; Chan, Hsin-Ju; Chen, Yu-Ju ; Chen, Bi-Chang ; Wu, Han-Chung ; Liao, James C.iScience 26(2), 105995
22022S-glutathionylation of Hsp90 enhances its degradation and correlates with favorable prognosis of breast cancerShih, Yu-Yin; Lin, Hsien-Ya; Jan, Hau-Ming; Chen, Yu-Ju ; Ong, Lih-Lih; Yu, Alice Lin-Tsing; Lin, Chun-Hung Redox Biology 57, 102501
32022Membrane proteomic profiling enhances drug target detectionChan, Hsin‐Ju; Chen, Li‐Yu; Chiu, Huan‐Chi; Chen, Yu‐Ju Journal of the Chinese Chemical Society 69(8), 1338-1345
42022Ligand-assisted imprinting-probe-labeling strategy reveals Siglec-7 - glycoprotein interactionsLi, Pei‐Jhen; Kawade, Sachin Kisan; Adak, Avijit K.; Shen, Yu‐Ju; Fan, Chen‐Yo; Hsieh, Yu‐Heng; Angata, Takashi ; Chen, Yu‐Ju ; Lin, Chun‐ChengJournal of the Chinese Chemical Society 69(8), 1326-1337
52022Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscapeKitata Reta Birhanu; Yang Jhih‐Ci; Chen Yu‐Ju Mass Spectrometry Reviews 42(6), 2324-2348
62022Phosphoproteomics reveals the role of constitutive KAP1 phosphorylation by B-cell receptor signaling in chronic lymphocytic leukemiaWu, Jung-Lin; Wu, Hsin-Yi; Wu, Shang-Ju; Tsai, Ho-Yang; Weng, Shao-Hsing; Lin, Kuen-Tyng; Lin, Liang-In; Yao, Chi-Yuan; Zamanova, Margarita; Lee, Yi-Yuan; Angata, Takashi ; Tien, Hwei-Fang; Chen, Yu-Ju ; Lin, Kuo-I Molecular Cancer Research 20(8), 1222-1232
72022Molecular basis and role of Siglec-7 ligand expression on chronic lymphocytic leukemia B cellsChang, L.-Y.; Liang, S.-Y.; Lu, S.-C.; Tseng, H.-C.; Tsai, H.-Y.; Tang, C.-J.; Sugata, M.; Chen, Y.-J.; Chen, Y. -J. ; Wu, S.-J.; Lin, K.-I ; Khoo, K.-H. ; Angata, T. Frontiers in Immunology 13, 840388
82022Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometryGebreyesus, Sofani Tafesse; Siyal, Asad Ali; Kitata, Reta Birhanu; Chen, Eric Sheng-Wen; Enkhbayar, Bayarmaa; Angata, Takashi ; Lin, Kuo-I ; Chen, Yu-Ju ; Tu, Hsiung-LinNature Communications 13, 37
92021Sample Size-Comparable Spectral Library Enhances Data-Independent Acquisition-Based Proteome Coverage of Low-Input CellsSiyal, Asad Ali; Chen, Eric Sheng-Wen; Chan, Hsin-Ju; Kitata, Reta Birhanu; Yang, Jhih-Ci; Tu, Hsiung-Lin; Chen, Yu-Ju Analytical Chemistry 93(51), 17003-17011
102021ZIC-cHILIC-Based StageTip for Simultaneous Glycopeptide Enrichment and Fractionation toward Large-Scale N-SialoglycoproteomicsYi-Ju Chen; Ta-Chi Yen; Yu-Hsien Lin; Yan-Lin Chen; Kay-Hooi Khoo ; Yu-Ju Chen Analytical Chemistry 93(48), 15931-15940
112021ZIC-cHILIC Functionalized Magnetic Nanoparticle for Rapid and Sensitive Glycopeptide Enrichment from <1 µL SerumTiara Pradita; Yi-Ju Chen; Elias Gizaw Mernie; Sharine Noelle Bendulo; Yu-Ju Chen Nanomaterials 11(9), 2159
122021Nanoprobe-Based Mass Spectrometry and Fourier Transform Infrared Spectroscopy for Rapid Phospholipid ProfilingElias Gizaw Mernie; Mei-Chun Tseng; Wen-Ti Wu; Tzu-Ming Liu; Yu-Ju Chen Journal of the Chinese Chemical Society 69(1), 94-106
132021A data-independent acquisition-based global phosphoproteomics system enables deep profilingKitata, Reta Birhanu; Choong, Wai-Kok; Tsai, Chia-Feng; Lin, Pei-Yi; Chen, Bo-Shiun; Chang, Yun-Chien; Nesvizhskii, Alexey I.; Sung, Ting-Yi; Chen, Yu-Ju Nature Communications 12, 2539
142021Integrating site-specific peptide reporters and targeted mass spectrometry enables rapid substrate-specific kinase assay at the nanogram cell levelReyes Aaron James F.; Kitata Reta Birhanu; dela Rosa Mira Anne C.; Wang Yi-Ting; Lin Pei-Yi; Yang Pan-Chyr; Friedler Assaf; Yitzchaik Shlomo; Chen Yu-Ju Analytica Chimica Acta 1155, 338341
152021An Enzyme-Mediated Aza-Michael Addition Is Involved in the Biosynthesis of an Imidazoyl Hybrid Product of Conidiogenone BHewage, Ranuka T.; Huang, Rou-Jie; Lai, Shu-Jung; Lien, Ya-Chu; Weng, Shao-Hsing; Li, Dehai; Chen, Yu-Ju ; Wu, Shih-Hsiung ; Chein, Rong-Jie ; Lin, Hsiao-Ching Organic Letters 23(5), 1904-1909
162020Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studiesXuan, Yue; Bateman, Nicholas W.; Gallien, Sebastien; Goetze, Sandra; Zhou, Yue; Navarro, Pedro; Hu, Mo; Parikh, Niyati; Hood, Brian L.; Conrads, Kelly A.; Loosse, Christina; Kitata, Reta Birhanu; Piersma, Sander R.; Chiasserini, Davide; Zhu, Hongwen; Hou, Guixue; Tahir, Muhammad; Macklin, Andrew; Khoo, Amanda; Sun, Xiuxuan; Crossett, Ben; Sickmann, Albert; Chen, Yu-Ju ; Jimenez, Connie R.; Zhou, Hu; Liu, Siqi; Larsen, Martin R.; Kislinger, Thomas; Chen, Zhinan; Parker, Benjamin L.; Cordwell, Stuart J.; Wollscheid, Bernd; Conrads, Thomas P.Nature Communications 11, 5248
172020Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and ProgressionYi-Ju Chen; Theodoros I Roumeliotis; Ya-Hsuan Chang; Ching-Tai Chen; Chia-Li Han; Miao-Hsia Lin; Huei-Wen Chen; Gee-Chen Chang; Yih-Leong Chang; Chen-Tu Wu; Mong-Wei Lin; Min-Shu Hsieh; Yu-Tai Wang; Yet-Ran Chen ; Inge Jonassen; Fatemeh Zamanzad Ghavidel; Ze-Shiang Lin; Kuen-Tyng Lin; Ching-Wen Chen; Pei-Yuan Sheu; Chen-Ting Hung; Ke-Chieh Huang; Hao-Chin Yang; Pei-Yi Lin; Ta-Chi Yen; Yi-Wei Lin; Jen-Hung Wang; Lovely Raghav; Chien-Yu Lin; Yan-Si Chen; Pei-Shan Wu; Chi-Ting Lai; Shao-Hsing Weng; Kang-Yi Su; Wei-Hung Chang; Pang-Yan Tsai; Ana I Robles; Henry Rodriguez; Yi-Jing Hsiao; Wen-Hsin Chang; Ting-Yi Sung ; Jin-Shing Chen; Sung-Liang Yu; Jyoti S Choudhary; Hsuan-Yu Chen ; Pan-Chyr Yang; Yu-Ju Chen Cell 182(1), 226-244.e17
182020Palmitoyl Acyltransferase Activity of ZDHHC13 Regulates Skin Barrier Development Partly by Controlling PADi3 and TGM1 Protein StabilityLi-Ying Chen; Kuo-Ray Lin; Yi-Ju Chen; Yun-Jung Chiang; Kun-Chin Ho; Li-Fen Shen; I-Wen Song; Kai-Ming Liu; Hsin-Fang Yang-Yen; Yu-Ju Chen ; Yuan-Tsong Chen; Fu-Tong Liu ; Jeffrey JY Yen Journal of Investigative Dermatology 140(5), 959-970.e3
192020Transcriptomic and Proteomic Profiling of Human Mesenchymal Stem Cell Derived from Umbilical Cord in the Study of Preterm BirthChien, Chih‐Wei; Lo, Yu‐Shu; Wu, Hsin‐Yi; Hsuan, Yogi; Lin, Chi‐Kang; Chen, Yu-Ju ; Lin, Willie; Han, Chia‐LiPROTEOMICS – Clinical Applications 14(1), 1900024
202020Identification of Conomarphin Variants in the Conus eburneus Venom and the Effect of Sequence and PTM Variations on Conomarphin ConformationsItang, Corazon Ericka Mae M.; Gaza, Jokent T.; Masacupan, Dan Jethro M.; Batoctoy, Dessa Camille R.; Chen, Yu-Ju ; Nellas, Ricky B.; Yu, Eizadora T.Marine Drugs 18(10), 503
212019Nanomatrix-Assisted Laser Desorption-Ionization Mass Spectrometry for Oligosaccharides ProfilingElias Gizaw Mernie; Leta Deressa Tolesa; Ming-Jer Lee; Mei-Chun Tseng ; Yu-Ju Chen 
222019Direct Oligosaccharide Profiling using Thin-Layer Chromatography Coupled with Ionic Liquid-Stabilized Nanomatri-Assisted Laser Desorption-Ionization Mass SpectrometryElias Gizaw Mernie; Leta Deressa Tolesa; Ming-Jer Lee; Mei-Chun Tseng ; Yu-Ju Chen 
232019Fluorescence “Turn-on” Lectin Sensors Fabricated by Ligand-Assisted Labeling Probes for Detecting Protein–Glycoprotein InteractionsLi, Pei-Jhen; Anwar, Mohammad Tarigue; Fan, Chen-Yo; Juang, Duane S.; Lin, Hsin-Yi; Chang, Tsung-Che; Kawade, Sachin Kisan; Chen, Hsiang-Jung; Chen, Yu-Ju ; Tan, Kui-Thong; Lin, Chun-ChengBiomacromolecules 21(2), 815-824
242018DNA Demethylation by DNMT3A and DNMT3B in vitro and of Methylated Episomal DNA in Transiently Transfected CellsChatterjee, Biswanath; Lin, Miao-Hsia; Chen, Chun-Chang; Peng, Kai-Lin; Wu, Mu-Sheng; Tseng, Mei-Chun ; Chen, Yu-Ju ; Shen, Che-Kun JamesBiochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1861(11), 1048-1061
252018Evaluating the Possibility of Detecting Variants in Shotgun Proteomics via LeTE-Fusion Analysis PipelineTung-Shing Mamie Lih; Wai-Kok Choong; Yu-Ju Chen ; Ting-Yi Sung Journal of Proteome Research 17(9), 2937-2952
262018Inducing hair follicle neogenesis with secreted proteins enriched in embryonic skinFan, Sabrina Mai-Yi; Tsai, Chia-Feng; Yen, Chien-Mei; Lin, Miao-Hsia; Wang, Wei-Hung; Chan, Chih-Chieh; Chen, Chih-Lung; Phua, Kyle K.L.; Pan, Szu-Hua; Plikus, Maksim V.; Yu, Sung-Liang; Chen, Yu-Ju ; Lin, Sung-JanBiomaterials 167, 121-131
272018Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane ProteinsWeldemariam, Mehari Muuz; Han, Chia-Li; Shekari, Faezeh; Kitata, Reta Birhanu; Chuang, Ching-Yu; Hsu, Wei-Ting; Kuo, Hung-Chih; Choong, Wai-Kok; Sung, Ting-Yi ; He, Fu-Chu; Chung, Maxey, Ching Ming; Salekdeh, Ghasem Hosseini; Chen, Yu-Ju Journal of Proteome Research 17(12), 4138-4151
282018Surface markers of human embryonic stem cells: a meta analysis of membrane proteomics reportsShekari, Faezeh; Han, Chia-Li; Lee, Jaesuk; Mirzaei, Mehdi; Gupta, Vivek; Haynes, Paul A.; Lee, Bonghee; Baharvand, Hossein; Chen, Yu-Ju ; Hosseini, Salekdeh GhasemExpert Review of Proteomics 15(11), 911-922
292018Alteration of mesenchymal stem cells polarity by laminar shear stimulation promoting β-catenin nuclear localizationChen, Wei-Ta; Hsu, Wei-Tse; Yen, Meng-Hua; Changou, Chun A.; Han, Chia-Li; Chen, Yu-Ju ; Cheng, Ji-Yen; Chang, Tzu-Hao; Lee, Oscar Kuang-Sheng; Ho, Jennifer Hui-ChunBiomaterials 190-191, 1-10
302018Glycoproteomic Alterations in Drug-Resistant Nonsmall Cell Lung Cancer Cells Revealed by Lectin Magnetic Nanoprobe-Based Mass SpectrometryWaniwan, Juanilita T.; Chen, Yi-Ju; Capangpangan, Rey; Weng, Shao-Hsing; Chen, Yu-Ju Journal of Proteome Research 17(11), 3761-3773
312018Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known FunctionPaik, Young-Ki; Lane, Lydie; Kawamura, Takeshi; Chen, Yu-Ju ; Cho, Je-Yoel; LaBaer, Joshua; Yoo, Jong Shin; Domont, Gilberto; Corrales, Fernando; Omenn, Gilbert S.; Archakov, Alexander; Encarnación-Guevara, Sergio; Lui, Siqi; Salekdeh, Ghasem Hosseini; Cho, Jin-Young; Kim, Chae-Yeon; Overall, Christopher M.Journal of Proteome Research 17(12), 4042-4050
322017iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND AlgorithmHui-Yin Chang; Ching-Tai Chen; Chu-Ling Ko; Yi-Ju Chen; Yu-Ju Chen ; Wen-Lian Hsu ; Chiun-Gung Juo; Ting-Yi Sung Analytical Chemistry 89(24), 13128-13136
332017Proteome analysis of human embryonic stem cells organellesFaezeh Shekari; Hossein Nezari; Mehran Rezaei Larijani; Chia-Li Han; Hossein Baharvand; Yu-Ju Chen ; Ghasem Hosseini SalekdehJournal of Proteomics 162, 108-118
342017Exploring the expression bar code of SAA variants for gastric cancer detectionDeng-Chyang Wu; Kai-Yi Wang; Sophie S.W. Wang; Ching-Min Huang; Yi-Wei Lee; Michael Isaac Chen; Szu-An Chuang; Shu-Hua Chen; Ying-Wei Lu; Chun-Cheng Lin; Ka-Wo Lee; Wen-Hung Hsu; Wu Kun-Pin; Yu-Ju Chen PROTEOMICS 17(11), 1600356
352017Role of S-Palmitoylation by ZDHHC13 in Mitochondrial function and Metabolism in LiverLi-Fen Shen; Yi-Ju Chen; Kai-Ming Liu; Amir N. Saleem Haddad; I-Wen Song; Hsiao-Yuh Roan; Li-Ying Chen; Jeffrey J. Y. Yen; Yu-Ju Chen ; Jer-Yuarn Wu; Yuan-Tsong ChenScientific Reports 7(1):2128
362017Identification of Potential Plasma Biomarkers for Nonalcoholic Fatty Liver Disease by Integrating Transcriptomics and Proteomics in Laying HensMeng-Tsz Tsai; Yu-Jen Chen; Ching-Yi Chen; Mong-Hsun Tsai; Chia-Li Han; Yu-Ju Chen ; Harry J Mersmann; Shih-Torng DingThe Journal of Nutrition 147(3), 293-303
372017Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategyNai-Wen Chang; Hong-Jie Dai; Yung-Yu Shih; Chi-Yang Wu; Mira Anne C Dela Rosa; Rofeamor P Obena; Chen, Yu-Ju ; Wen-Lian Hsu ; Yen-Jen OyangDatabase (Oxford) 2017, bax082
382016Untargeted, Spectral Library-Free Analysis of Data Independent Acquisition Proteomics Data Generated Using Orbitrap Mass SpectrometersChih-Chiang Tsou; Chia-Feng Tsai; Guoci Teo; Yu-Ju Chen ; Alexey I. NesvizhskiiPROTEOMICS 16(15-16), 2257-2271
392016Temporal Regulation of Lsp1 O-GlcNAcylation and Phosphorylation During Apoptosis of Activated B cellsJung-Lin Wu; Hsin-Yi Wu; Dong-Yan Tsai; Ming-Feng Chiang; Yi-Ju Chen; Shijay Gao; Chun-Cheng Lin; Chun-Hung Lin; Kay-Hooi Khoo ; Yu-Ju Chen ; Kuo-I Lin NATURE COMMUNICATIONS 7: 12526
402016Functionalized HgTe Nanoparticles Promote Laser-Induced Solid Phase Ionization/Dissociation for Comprehensive Glycan SequencingIndah Primadona; Yin-Hung Lai; Rey Y. Capangpangan; Rofeamor P. Obena; Mei-Chun Tseng; Ming-Feng Huang; Huan-Tsung Chang; Shiou-Ting Li; Chung-Yi Wu ; Wei-Ting Chien; Chun-Cheng Lin; Yi-Sheng Wang; Yu-Ju Chen ANALYST 141(21), 6093-6103
412016The Shp2-induced epithelial disorganization defect is reversed by HDAC6 inhibition independent of Cdc42Sui-Chih Tien; Hsiao-Hui Lee; Ya-Chi Yang; Miao-Hsia Lin; Yu-Ju Chen ; Zee-Fen ChangNature Communications 7:10420
422015Informatics View on the Challenges of Identifying Missing Proteins From Shotgun ProteomicsWai-Kok Choong; Hui-Yin Chang; Ching-Tai Chen; Chia-Feng Tsai; Wen-Lian Hsu ; Ting-Yi Sung ; Yu-Ju Chen Journal of Proteome Research 14(12), 5396-5407
432015Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic ProfilingBaby Rorielyn Dimayacyac-Esleta; Chia-Feng Tsai; Reta Birhanu Kitata; Pei-Yi Lin; Wai Kok Choong; Tai-Du Lin; Yi-Ting Wang; Shao-Hsing Weng; Pan-Chyr Yang; Susan Arco; Ting-Yi Sung ; Yu-Ju Chen Analytical Chemistry 87(24), 12016-12023
442015Monodispersity of Magnetic Immuno-Nanoprobes Enhances the Detection Sensitivity of Low Abundance Biomarkers in One Drop of SerumRey Y. Capangpangan; Mira Anne C. dela Rosa; Rofeamor P. Obena; Yu-Jen Chou; Der-Lii Tzou ; Shao-Ju Shih; Ming-Hsi Chiang ; Chun-Cheng Lin; Yu-Ju Chen ANALYST 140, 7678-7686
452015Mining Missing Membrane Proteins by High-pH Reverse Phase StageTip Fractionation and Multiple Reaction Monitoring Mass SpectrometryKitata, Reta Birhanu; Dimayacyac-Esleta, Baby Rorielyn; Choong, Wai-Kok; Chia-Feng Tsai; Tai-Du Lin; Chih-Chiang Tsou; Shao-Hsing Weng; Yi-Ju Chen; Pan-Chyr Yang; Arco, Susan; Nesvizhskii, Alexey; Ting-Yi Sung ; Yu-Ju Chen Journal of Proteome Research 14(9), 3658-3669
462015Qualification and Verification of Serological Biomarker Candidates for Lung Adenocarcinoma by Targeted Mass SpectrometryHsin-Yi Wu; Yih-Gang Goan; Ying-Hua Chang; Yi-Fang Yang; Hsiao-Jen Chang; Pin-Nan Cheng; Chih-Chieh Wu; Victor Zgoda; Yu-Ju Chen ; Pao-Chi LiaoJOURNAL OF PROTEOME RESEARCH 14(8), 3039-3050
472015Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome ProjectHorvatovich, Péter; Lundberg, Emma; Yu-Ju Chen ; Ting-Yi Sung ; Fuchu He; Edouard Nice; Robert Goode; Simon Yu; Shoba Ranganathan; Mark Baker; Gilberto Domont; Erika Velasquez; Dong Li; Siqi Liu; Quanhui Wang; Qing-Yu He; Rajasree Menon; Yuanfang Guan; Fernando Corrales; Victor Segura; José Ignacio Casal; Alberto Pascual-Montano; Juan Albar; Manuel Fuentes; Maria Gonzalez-Gonzalez; Paula Diez; Nieves Ibarrola; Rosa Degano; Yassene Mohammed; Christoph Borchers; Andrea Urbani; Alessio Soggiu; Tadashi Yamamoto; Alexander Archakov; Elena Ponomarenko; Andrey Lisitsa; Cheryl Lichti; Ekaterina Mostovenko; Roger Kroes; Melinda Rezeli; Akos Vegvari; Thomas Fehniger; Rainer Bischoff; Juan Antonio Vizcaíno; Eric Deutsch; Lydie Lane; Carol Nilsson; György Marko-Varga; Gilbert Omenn; Seul-Ki Jeong; Jin-Young Cho; Young-Ki Paik; William HancockJOURNAL OF PROTEOME RESEARCH 14(9), 3415-3431
482015Effect of Sialylation on EGFR Phosphorylation and Resistance to Tyrosine Kinase InhibitionHsin-Yung Yen; Ying-Chih Liu; Nai-Yu Chen; Chia-Feng Tsai; Yi-Ting Wang; Yu-Ju Chen ; Tsui-Ling Hsu ; Pan-Chyr Yang; Chi-Huey Wong Proceedings of the National Academy of Sciences of the United States of America(PNAS) 112(22), 6955-6960
492015Cyclic Alopecia and Abnormal Epidermal Cornification in Zdhhc13-Deficient Mice Reveal the Importance of Palmitoylation in Hair and Skin DifferentiationLiu, KM; Chen, YJ; Shen, LF; Saleem, Haddad AN; Song, IW; Chen, LY; Chen, YJ ; Wu, JY ; Yen, JJY ; Chen, YT JOURNAL OF INVESTIGATIVE DERMATOLOGY 135, 2603-2610
502015UV-activated multilayer nanomatrix provides one-step tunable carbohydrate structural characterization in MALDI-MSRofeamor P. Obena; Mei-Chun Tseng ; Indah Primadona; Jun Hsiao; I.-Che Li; Rey Y. Capangpangan; Hsiu-Fong Lu; Wan-Sheung Li; Ito Chao ; Chun-Cheng Lin; Yu-Ju Chen Chemical Science 6, 4790-4800
512015Integrating proteomics with electrochemistry for identifying kinase biomarkersEinav Amit; Rofeamor Palarca Obena; Yi-Ting Wang; Roman Zhuravel; Aaron Reyes; Shir Elbaz; Dvir Rotem; Danny Porath; Assaf Friedler; Yu-Ju Chen ; Shlomo YitzchaikChemical Science 6, 4756-4766
522015GSHSite: Exploiting An Iteratively Statistical Method to Identify S-Glutathionylation Sites with Substrate SpecificityYi-Ju Chen; Cheng-Tsung Lu; Kai-Yao Huang; Hsin-Yi Wu; Chen, Yu-Ju ; Tzong-Yi LeePLoS One 10(4):e0118752. doi: 10.1371/journal.pone.0118752
532015Large-Scale Determination of Absolute Phosphorylation Stoichiometries in Human Cells by Motif-Targeting Quantitative ProteomicsChia-Feng Tsai; Yi-Ting Wang; Hsin-Yung Yen; Chih-Chiang Tsou; Wei-Chi Ku; Pei-Yi Lin; Hsuan-Yu Chen ; Alexey Nesvizhskii; Yasushi Ishihama; Chen, Yu-Ju NATURE COMMUNICATIONS 6, 6622
542015MAGIC: An Automated N-Linked Glycoprotein Identification Tool Using a Y1-Ion Pattern Matching Algorithm and in Silico MS2 ApproachKe-Shiuan Lynn; Chen-Chun Chen; T. Mamie Lih; Cheng-Wei Cheng; Wan-Chih Su; Chun-Hao Chang; Chia-Ying Cheng; Wen-Lian Hsu ; Yu-Ju Chen ; Ting-Yi Sung Analytical Chemistry 87(4), 2466-2473
552015Glutathionylspermidine in the Modification of Protein SH Groups: The Enzymology and Its Application to Study Protein GlutathionylationJason Ching-Yao Lin; Bing-Yu Chiang; Chi-Chi Chou; Tzu-Chieh Chen; Yi-Ju Chen; Yu-Ju Chen ; Chun-Hung Lin Molecules 20(1), 1452-1474
562014Characterization and Identification of Protein O-GlcNAcylation Sites with Substrate SpecificityHsin-Yi Wu; Cheng-Tsung Lu; Hui-Ju Kao; Yi-Ju Chen; Yi-Ju Chen ; Tzong-Yi LeeBMC BIOINFORMATICS 15, S1
572014DbSNO 2.0: A Resource for Exploring Structural Environment, Functional and Disease Associations, and Regulatory Networks of Protein S-NitrosylationYi-Ju Chen; Cheng-Tsung Lu; Min-Gang Su; Kai-Yao Huang; Wei-Chieh Ching; Hsiao-Hsiang Yang; Yen-Chen Liao; Yu-Ju Chen ; Tzong-Yi LeeNUCLEIC ACIDS RESEARCH 43(D1), D503-D511
582014Distinct Subpopulations of Head and Neck Cancer Cells with Different Levels of Intracellular Reactive Oxygen Species Exhibit Diverse Stemness, Proliferation, and ChemosensitivityChing-Wen Chang; Yu-Syuan Chen; Shiu-Huey Chou; Chia-Li Han; Chen, Yu-Ju ; Cheng-Chieh Yang; Chih-Yang Huang; Jeng-Fan LoCANCER RESEARCH DOI: 10.1158/0008-5472.CAN-14-0626
592014Incorporating Amino Acids Composition and Functional Domains for Identifying Bacterial Toxin ProteinsMin-Gang Su; Chien-Hsun Huang; Tzong-Yi Lee; Yu-Ju Chen ; Hsin-Yi WuBioMed Research International 2014, 972692
602014An Intelligent System for Identifying Acetylated Lysine on Histones and Nonhistone ProteinsCheng-Tsung Lu; Tzong-Yi Lee; Yu-Ju Chen ; Yi-Ju ChenBioMed research International 528650
612014Sequential One-Pot Enzymatic Synthesis of Oligo-N-Acetyllactosamine and Its Multi-Sialylated ExtensionsWei-Ting Chien; Chien-Fu Liang; Ching-Ching Yu; Chien-Hung Lin; Si-Peng Li; Indah Primadona; Yu-Ju Chen ; Kwok Kong T. Mong; Chun-Cheng LinCHEMICAL COMMUNICATIONS 50, 5786-5789
622014Cancer-associated fibroblasts regulate the plasticity of lung cancer stemness via paracrine signallingChen, WJ; Ho, CC; Chang, YL; Chen, HY; Lin, CA; Ling, TY; Yu, SL; Yuan, SS ; Chen, YJ ; Lin, CY; Pan, SH; Chou, HY; Chen, YJ; Chang, GC; Chu, WC; Lee, YM; Lee, JY; Lee, PJ; Li, KC; Chen, HW; Yang, PCNature communications 5, 3472
632013Interaction Modes and Approaches to Glycopeptide and Glycoprotein EnrichmentChen-Chun Chen; Wan-Chih Su; Bao-Yu Huang; Yu-Ju Chen ; Hwan-Ching Tai; Rofeamor Palarca ObenaANALYST 139 (4), 688-704
642013Methods for Detection and Characterization of Protein S-nitrosylationChen, Yi-Ju; Ching, Wei-Chieh; Lin, Yu-Pei; Chen, Yu-Ju Methods 62(2), p.138-150
652013Thyroid Storm and Incidental Anterior Mediastinal Teratoma: Coincidence or Correlation?Cheng-An Wang; Wei-Ta Chen; Ho-Shun Cheng; Cheng-Chih Chung; Yu-Ju Chen ; Ming-Hsiung HsiehActa Cardiological Sinica 29: 467-470
662013Decoding the disease-associated proteins encoded in the human chromosome 4Chen, Lien-Chin; Liu, Mei-Ying; Hsiao, Yung-Chin; Chong, Wai-Kok; Wu, Hsin-Yi; Hsu, Wen-Lian; Liao, Pao-Chi; Sung, Ting-Yi; Tsai, Shih-Feng; Yu, Jau-Song; Chen, Yu-Ju Journal of Proteome Research 12, 33-44
672013DbPTM 3.0: An Informative Resource for Investigating Substrate Site Specificity and Functional Association of Protein Post-Translational ModificationsLu, Cheng-Tsung; Huang, Kai-Yao; Su, Min-Gang; Lee, Tzong-Yi; Bretana, Neil Arvin; Chang, Wen-Chi; Chen, Yi-Ju; Chen, Yu-Ju ; Huang, Hsien-DaNUCLEIC ACIDS RESEARCH  41(D1): D295-D305
682013An iTRAQ Proteomic Study Reveals an Association between Diet-induced Enhanced Fatty-acid Metabolism and the Development of Glucose Intolerance in Prediabetic MiceHo, Jennifer; Lee, Oscar; Fu, Yun-Ju; Shih, Hung-Ta; Tseng, Chien-Yu; Chung, Cheng-Chih; Han, Chia-Li; Chen, Yu-Ju JOURNAL OF PROTEOME RESEARCH 12 (3), pp1120-1133
692012dbSNO: a Database of Cysteine S-nitrosylationLee, Tzong-Yi; Chen, Yi-Ju; Lu, Cheng-Tsung; Ching, Wei-Chieh; Teng, Yu-Chuan; Huang, Hsien-Da; Chen, Yu-Ju BIOINFORMATICS 28(17), 2293-2295
702012Complementary Fe3+- and Ti4+-immobilized metal ion affinity chromatography for purification of acidic and basic phosphopeptidesLai, Alan Chuan-Ying; Tsai, Chia-Feng; Hsu, Chuan-Chih; Sun, Yu-Ni; Chen, Yu-Ju RAPID COMMUNICATIONS IN MASS SPECTROMETRY 26, 2186-2194
712012Tumor cells require thymidylate kinase to prevent dUTP incorporation during DNA repair.Hu, CM ; Yeh, MT; Tsao, N; Chen, CW; Gao, QZ; Chang, CY; Lee, MH; Fang, JM; Sheu, SY; Lin, CJ; Tseng, MC ; Chen, YJ ; Chang, ZFCANCER CELL 22(1),36-50
722011Rapid and specific influenza virus detection by functionalized magnetic nanoparticles and mass spectrometryChou, Tzu-Chi; Hsu, Wei; Wang, Ching-Ho; Chen, Yu-Ju ; Fang, Jim-MinJOURNAL OF NANOBIOTECHNOLOGY 9, 52
732011Iron Oxide Nanomatrix Facilitates Metal Ionization in Matrix-Assisted Laser Desorption/Ionization Mass SpectrometryObena, Rofeamor; Lin, Po-Chiao; Lu, Ying-Wei; Li, I-Che; del Mundo, Florian; Arco, Susan; Nuesca, Guillermo; Lin, Chun-Cheng; Chen, Yu-Ju ANALYTICAL CHEMISTRY 83(24), 9337-9343
742011In-depth identification of pathways related to cisplatin-induced hepatotoxicity through an integrative method based on an informatics-assisted label-free protein quantitation and microarray gene expression approachCho, Young-Eun; Singh, Thoudam S. K.; Lee, Hyun-Chul; Moon, Pyong-Gon; Lee, Jeong-Eun; Lee, Myung-Hoon; Choi, Eung-Chil; Chen, Yu-Ju ; Kim, Sang-Hyun; Baek, Moon-ChangMOLECULAR & CELLULAR PROTEOMICS 10, 1074
752011Surface marker epithelial cell adhesion molecule and E-cadherin facilitate the identification and selection of induced pluripotent stem cellsChen, HF; Chuang, CY; Lee, WC; Huang, HP; Wu, HC ; Ho, HN; Chen, YJ ; Kuo, HC STEM CELL REVIEWS 7(3), 722-735
762011SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificityLee, Tzong-Yi; Chen, Yi-Ju; Lu, Tsung-Cheng; Huang, Hsien-Da; Chen, Yu-Ju PLoS One 6(7),1-11
772011Nanoprobe-based Immobilized Metal Affinity Chromatography for Sensitive and Complementary Enrichment of Multiply Phosphorylated PeptidesWu, Huan-Ting; Hsu, Chuan-Chih; Tsai, Chia-Feng; Lin, Po-Chiao; Lin, Chun-Cheng; Chen, Yu-Ju PROTEOMICS 13,11, 2639-2653
782011Phosphoproteomics identifies oncogenic Ras signaling targets and their involvement in lung adenocarcinomas.Sudhir, P. -R.; Hsu, C. -L.; Wang, Y. -T.; Chen, Y. -J. ; Sung, T. -Y. ; Hsu, W. -L. ; Yang, U. -C.; Chen, J. -Y. PLoS One 6(5), e20199
792011Identification of SEC61 Beta and Its Autoantibody As Biomarkers for Colorectal CancerFan, Chung-Wei; Chan, Chung-Chuan; Chen, Kuei-Tien; Twu, Jen; Huang, Ya-Shu; Han, Chia-Li; Chen, Yu-Ju ; Yu, Jau-Song; Chang, Yu-Sun; Kuo, Yung-Bin; Chan, Err-ChengCLINICA CHIMICA ACTA 412 (11-12), 887–893
802011An Informatics-assisted Label-free Approach for Personalized Tissue Membrane Proteomics: Case Study on Colorectal CancerHan, Chia-Li; Chen, Jinn-Shiun; Chan, Err-Cheng; Wu, Chien-Peng; Yu, Kun-Hsing; Chen, Kuei-Tien; Tsou, Chih-Chiang; Tsai, Chia-Feng; Chien, Chih-Wei; Kuo, Yung-Bin; Lin, Pei-Yi; Yu, Jau-Song; Hsueh, Chuen; Chen, Min-Chi; Chan, Chung-Chuan; Chang, Yu-Sun; Chen, Yu-Ju MOLECULAR & CELLULAR PROTEOMICS 10,1-15
812011Nanoparticle-assisted MALDI-TOF MS combined with Seed-Layer Surface Preparation for Quantification of Small MoleculesHo, Yi-Chi; Tseng, Mei-Chun ; Lu, Ying-Wei; Lin, Chun-Cheng; Chen, Yu-Ju ; Fuh, Ming-RenANALYTICA CHIMICA ACTA 697, 1-7
822011Interplay between SIN3A and STAT3 mediates chromatin conformational changes and GFAP expression during cellular differentiation.Cheng, PY; Lin, YP; Chen, YL; Lee, YC; Tai, CC; Wang, YT; Chen, YJ ; Kao, CF ; Yu, J PloS one 6(7), e22018
832010S-alkylating labeling strategy for site-specific identification of the s-nitrosoproteomeChen, Yi-Ju; Ku, Wei-Chi; Lin, Pei-Yi; Chou, Hsiao-Chiao; Khoo, Kay-Hooi ; Chen, Yu-Ju JOURNAL OF PROTEOME RESEARCH 9(12), 6417–6439
842010Dihydrobenzoic Acid Modified Nanoparticle as a MALDI-TOF MS Matrix for Soft Ionization and Structure Determination of Small Molecules with Diverse StructuresTseng, Mei-Chun ; Obena, Rofeamor; Lu, Ying-Wei; Lin, Po-Chiao; Lin, Ping-Yu; Yen, Yung-Sheng; Lin, Jiann-Tsuen; Huang, Li-De; Lu, Kuang-Lieh ; Lai, Long-Li; Lin, Chun-Cheng; Chen, Yu-Ju JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 21, 1930-1939
852010The Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative. Preparation and characterisation of the carbonate-washed membrane standardPeng, Lifeng; Kapp, Eugene A.; Fenyö, David; Kwon, Min-Seok; Jiang, Pu; Wu, Songfeng; Jiang, Ying; Aguilar, Marie-Isabel; Ahmed, Nikhat; Baker, Mark S.; Cai, Zongwei; Chen, Yu-Ju ; Van Chi, Phan; Chung, Maxey C. M.; He, Fuchu; Len, Alice C. L.; Liao, Pao-Chi; Nakamura, Kazuyuki; Ngai, Sai Ming; Paik, Young-Ki; Pan, Tai-Long; Poon, Terence C. W.; Salekdeh, Ghasem Hosseini; Simpson, Richard J.; Sirdeshmukh, Ravi; Srisomsap, Chantragan; Svasti, Jisnuson; Tyan, Yu-Chang; Dreyer, Florian S.; McLauchlan, Danyl; Rawson, Pisana; Jordan, T. WilliamPROTEOMICS 10, 4142–4148
862010An Informatics-assisted Label-free Quantitation Strategy that Depicts Phosphoproteomic Profiles in Lung Cancer Cell InvasionWang, Yi-Ting; Tsai, Chia-Feng; Hong, Tzu-Chan; Tsou, Chih-Chiang; Lin, Pei-Yi; Pan, Szu-Hua; Hong, Tse-Ming; Yang, Pan-Chyr; Sung, Ting-Yi ; Hsu, Wen-Lian ; Chen, Yu-Ju JOURNAL OF PROTEOME RESEARCH 9(11), 5582-5597
872010Comparison of Membrane Fraction Proteomic Profiles of Normal and Cancerous Human Colorectal Tissues with Gel-assisted Digestion and iTRAQ Labeling Mass SpectrometryChen, Jinn-Shiun; Chen, Kuei-Tien; Fan, Chung-Wei; Han, Chia-Li; Chen, Yu-Ju ; Yu, Jau-Song; Chang, Yu-Sun; Chien, Chih-Wei; Wu, Chien-Peng; Hung, Ray-Ping; Chan, Err-ChengFEBS JOURNAL 277, 3028–3038
882010Identification of in vivo phosphorylation sites of lens proteins from porcine eye lenses by a gel-free phosphoproteomics approachChiou, SH ; Huang, CH; Lee, IL; Wang, YT; Liu, NY; Tsay, YG; Chen, YJ MOLECULAR VISION 16, 294-302
892010Temporal Proteomics Profiling of Lipid Rafts in CCR6-Activated T Cells Reveals the Integration of Actin Cytoskeleton DynamicsLin, Shu-Ling; Chien, Chih-Wei; Han, Chia-Li; Chen, Eric S. -W.; Kao, Shao-Hsuan; Chen, Yu-Ju ; Liao, FangJOURNAL OF PROTEOME RESEARCH 9 (1), 283–297
902010IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validationTsou, Chih-Chiang; Tsai, Chia-Feng; Tsui, Ying-Hao; Sudhir, Putty-Reddy; Wang, Yi-Ting; Chen, Yu-Ju ; Chen, Jeou-Yuan ; Sung, Ting-Yi ; Hsu, Wen-Lian Molecular and Cellular Proteomics 9(1), 131-144
912009Fabrication of Oriented Antibody-Conjugated Magnetic Nanoprobes and Their Immunoaffinity ApplicationLin, Po-Chiao; Chen, Shu-Hua; Wang, Kai-Yi; Chen, Mu-Lin; Adak, Avijit Kumar; Hwu, Jih-Ru R.; Chen, Yu-Ju ; Lin, Chun-ChengANALYTICAL CHEMISTRY 81 (21), 8774–8782
922009Role for L-Fucosidase in the Contro; of Helicobacter pylori-infected Gastric Cancer CellsLiu, Ta-Wei; Ho, Ching-Wen; Huang, Hsing-Hung; Chang, Sue-Ming; Popat, Shide S.; Wang, Yi-Ting; Wu, Ming-Shiang; Chen, Yu-Ju ; Lin, Chun-HungPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 106, 14581-14586
932009MaXIC-Q Web: A Fully Automated Web Service Using Statistical and Computational Methods for Protein Quantitation Based on Stable Isotope Labeling and LC-MSTsou, Chih-Chiang; Tsui, Yin-Hao; Yian, Yi-Hwa; Chen, Yi-Ju; Yang, Han-Yin; Yu, Chuan-Yih; Lynn, Ke-Shiuan; Chen, Yu-Ju ; Sung, Ting-Yi ; Hsu, Wen-Lian Nucleic Acids Research 37(suppl_2), W661-W669
942009Complementary quantitative proteomics reveals that transcription factor AP-4 mediates E-box-dependent complex formation for transcriptional repression of HDM2Ku, Wei-Chi; Chiu, Sung-Kay; Chen, Yi-Ju; Huang, Hsin-Hung; Wu, Wen-Guey; Chen, Yu-Ju MOLECULAR & CELLULAR PROTEOMICS 8, 2034-2050
952008A Multiplexed Quantitative Strategy for Membrane Proteomics: Opportunities for Mining Therapeutic Targets for Autosomal Dominant Polycystic Kidney DiseaseHan, Chia-Li; Chien, Chih-Wei; Chen, Wen-Cheng; Chen, Yet-Ran; Wu, Chien-Peng; Li, Hung ; Chen, Yu-Ju MOLECULAR & CELLULAR PROTEOMICS 7(10), 1983-1997
962008Nitric Oxide Physiological Responses and Delivery Mechanisms Probed by Water-soluble Roussin’s Red Ester and{Fe(NO)2}10 DNICChen, Yi-Ju; Ku, Wei-Chi; Feng, Li-Ting; Tsai, Ming-Li; Hsieh, Chung-Hung; Hsu, Wen-Hwei; Liaw, Wen-Feng; Hung, Chen-Hsiung ; Chen, Yu-Ju JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 130(33), 10929-10938
972008Multiplexed Immunoassay: Quantitation and Profiling of Serum Biomarkers Using Magnetic Nanoprobes and MALDI-TOF MSWang, Kai-Yi; Chuang, Szu-An; Lin, Po-Chiao; Huang, Li-Shing; Chen, Shu-Hua; Ouarda, Saib; Pan, Wen-Harn ; Lee, Ping-Ying; Lin, Chun-Cheng; Chen, Yu-Ju Analytical chemistry 80(16), 6159-6167
982008Immobilized Metal Affinity Chromatography Revisited: pH/acid Control toward High Selectivity in PhosphoproteomicsTsai, Chia-Feng; Wang, Yi-Ting; Chen, Yet-Ran; Lai, Chen-Yu; Lin, Pei-Yi; Pan, Kuan-Ting; Chen, Jeou-Yuan ; Khoo, Kay-Hooi ; Chen, Yu-Ju JOURNAL OF PROTEOME RESEARCH 7(9), 4058-4069
992008Globotriose-Functionalized Gold Nanoparticles as Multivalent Probes for Shiga-like ToxinChien, Yuh-Yih; Jan, Mi-Dan; Adak, Avijit Kumar; Tzeng, Hsiao-Chien; Lin, Yen-Ping; Chen, Yu-Ju ; Wang, Ken-Tseng; Chen, Chien-Tien; Chen, Chia-Chun; Lin, Chun-ChengCHEMBIOCHEM 9, 1100-1109
1002008Proteomic Profiles of Bronchoalveolar Lavage Fluid from Patients with Ventilator- associated Pneumonia by Gel-assisted Digestion and 2DLC/MS/MSLu, Yen-Ta; Han, Chia-Li; Wu, Chien-Liang; Yu, Tien-Min; Chien, Chih-Wei; Liu, Ching-Lung; Chen, Yu-Ju PROTEOMICS 2, 1208-1212
1012007Nanoprobe-Based Affinity Mass Spectrometry for Cancer Marker Protein ProfilingHuang, Li-Shing; Chien, Yuh-Yih; Chen, Shu-Hua; Lin, Po-Chiao; Wang, Kai-Yi; Chou, Po-Hung; Lin, Chun-Cheng; Chen, Yu-Ju Nanomaterials for Cancer Diagnosis. (U.S.A : Wiley-VCH)
1022007Targeted Protein Quantitation and Profiling Using PVDF Affinity Probe and MALDI-TOF MSChen, Shu-Hua; Liao, Hsin-Kai; Chang, Chih-Yang; Juo, Chiun-Gung; Chen, Jenn-Han; Chan, Sunney I.; Chen, Yu-Ju PROTEOMICS 7, 3038–3050
1032007Functionalized Magnetic Nanoparticles for Small-Molecule Isolation, Identification, and QuantificationLin, Po-Chiao; Tseng, Mei-Chun ; Su, An-Kai; Lin, Chun-Cheng; Chen, Yu-Ju Analytical Chemistry 79(9), 3401-3408
1042007Nanomaterial Based Affinity Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Biomolecules and Pathogenic BacteriaChiu, Tai-Chia; Huang, Li-Shing; Lin, Po-Chiao; Chen, Yu-Chie; Chen, Yu-Ju ; Lin, Chun-Cheng; Chang, Huan-TsungRecent Patents on Nanotechnology 1, 99-111
1052007Evaluation of Serum Amyloid A as a Biomarker for Gastric CancerChan, De-Chuan; Chen, Cheng-Jueng; Chu, Heng-Cheng; Chang, Wei-Kuo; Yu, Jyh-Cherng; Chen, Yu-Ju ; Wen, Li-Li; Huang, Su-Ching; Ku, Chih-Hung; Liu, Yao-Chi; Chen, Jenn-HanANNALS OF SURGICAL ONCOLOGY 14, 84-93
1062006Quantitative Proteomic and Genomic Profiling Reveals Metastasis-Related Protein Expression Patterns in Gastric Cancer CellsChen, Yet-Ran ; Juan, Hsueh-Fen; Huang, Hsuan-Cheng; Huang, Hsin-Hung; Lee, Ya-Jung; Liao, Mei-Yueh; Tseng, Chien-Wei; Lin, Li-Ling; Chen, Jeou-Yuan ; Wang, Mei-Jung; Chen, Jenn-Han; Chen, Yu-Ju JOURNAL OF PROTEOME RESEARCH 5(10), 2727-2742
1072006Multi-Q: a fully automated tool for multiplexed protein quantitationLin, WT; Hung, WN; Yian, YH; Wu, KP; Han, CL; Chen, YR ; Chen, YJ ; Sung, TY; Hsu, WLJournal of proteome research 5(9), 2328-2338
1082006Site-specific Protein Modification through Cu-I-catalyzed 1,2,3-Triazole Formation and Its Implementation in Protein Microarray FabricationLin, Po-Chiao; Ueng, Shau-Hua; Tseng, Mei-Chun ; Ko, Jia-Ling; Huang, Kuo-Ting; Yu, Sheng-Chieh; Adak, Avijit Kumar; Chen, Yu-Ju ; Lin, Chun-ChengAngewandte Chemie (International Edition in English) 45(26), 4286-4290
1092006Star-shaped Molecules Containing Polyalkynyl Groups with Metal Moieties on Benzene and Triphenylene CoresHuang, Chiung-Cheng; Lin, Ying-Chih; Lin, Ping-Yu; Chen, Yu-Ju EUROPEAN JOURNAL OF ORGANIC CHEMISTRY 19, 4510-4518
1102006Ethylene Glycol-Protected Magnetic Nanoparticles for Multiplexed Immunoassay in Human PlasmaLin, Po-Chiao; Chou, Po-Hung; Chen, Shu-Hua; Liao, Hsin Kai; Wang, Kai-Yi; Chen, Yu-Ju ; Lin, Chun-ChengSMALL 2(4), 485-489
1112006Improved Analysis of Membrane Protein by PVDF-Aided, Matrix-Assisted Laser Desorption/Ionization Mass SpectrometryChang, Chih-Yang; Liao, Hsin-Kai; Juo, Chiun-Gung; Chen, Shu-Hua; Chen, Yu-Ju ANALYTICA CHIMICA ACTA 556,237-246
1122006Determination of SMN1/SMN2 Gene Dosage by a Quantitative Genotyping Platform Combining Capillary Electrophoresis and MALDI-TOF Mass SpectrometryKao, Hung-Yi; Su, Yi-Ning; Liao, Hsin-Kai; Liu, Ming S.; Chen, Yu-Ju CLINICAL CHEMISTRY 52, 361-369
1132006Contribution of Guanine Exchange Factor H1 in Phorbol Ester-induced ApoptosisChang, Yuan-Chen; Lee, Hsiao-Hui; Chen, Yu-Ju ; Bokoch, Gary M.; Chang, Zee-FenCELL DEATH AND DIFFERENTIATION 13, 2023-2032
1142005Structural characterization of sialic acid synthase by electrospray mass spectrometry—A tetrameric enzyme composed of dimeric dimersHuang, Hsin-Hung; Liao, Hsin-Kai; Chen, Yu-Ju ; Hwang, Tzann-Shun; Lin, Yi-Han; Lin, Chun-Hung Journal of the American Society for Mass Spectrometry 16, 324-332
1152005Parallel Minisequencing Followed by Multiplex Matrix-assisted Laser Desorption/ Ionization Mass Spectrometry Assay for Beta-thalassemia MutationsLiao, Hsin-Kai; Su, Yi-Ning; Kao, Hung-Yi; Hung, Chia-Cheng; Wang, Hsueh-Ting; Chen, Yu-Ju JOURNAL OF HUMAN GENETICS 50, 139-150
1162005Molecular Identification of Canine Podocalyxin-like Protein 1 as a Renal Tubulogenic RegulatorCheng, Hsin-Yuan; Lin, Yu-Yu; Yu, Chun-Ying; Chen, Jen-Yau; Shen, Kuo-Fang; Lin, Wei-Ling; Liao, Hsin-Kai; Chen, Yu-Ju ; Liu, Chen-Hsuan; Pang, Victor Fei; Jou, Tzuu-ShuhJOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY 16, 1612-1622
1172005Application of Mass Spectrometry in Clinical ProteomicsChang, Yu-Wang; Chen, Shu-Hua; Chen, Yu-Ju Formosan Journal of Medicine 9, 637-649
1182005Carbohydrate-Encapsulated Gold Nanoparticles for Rapid Target Protein Identification and Binding Epitope MappingChen, Yu-Ju ; Chen, Shu-Hua; Chien, Yuh-Yih; Chang, Yu-Wan; Liao, Hsin-Kai; Chang, Chih-Yang; Jan, Mi-Dan; Wang, Ken-Tseng; Lin, Chun-ChengCHEMBIOCHEM 6, 1169-1173
1192005Nanoprobe-Based Affinity Mass Spectrometry for Selected Protein Profiling in Human PlasmaChou, Po-Hung; Chen, Shu-Hua; Liao, Hsin-Kai; Lin, Po-Chiao; Her, Gour-Rong; Lai, Alan Chuan-Ying; Chen, Jenn-Han; Lin, Chun-Cheng; Chen, Yu-Ju ANALYTICAL CHEMISTRY 77, 5990-5997
1202005Study of the Preferred Modification Sites of the Quinone Methide Intermediate Resulting from the Latent Trapping Device of the Activity Probes for HydrolasesLo, Lee-Chiang; Chiang, Ying-Ling; Kuo, Chi-Hsien; Liao, Hsin-Kai; Chen, Yu-Ju ; Lin, Jing-JerBIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 326, 30-35
1212005Os(CO)2(η2-SC5H4N(O))(η2-SCSH4N): Structural Evidence for the Transformation of Pyridine-2-thione N-Oxide to Pyridine-2-thiolate in Osmium ComplexesLee, Fang-Yuan; Huang, Jiann-Jyh; Chen, Yu-Ju ; Lin, Kuan-Jiuh; Lee, Gene-Hsiang; Peng, Shie-Ming; Hwu, Jih-Ru; Lu, Kuang-LiehJOURNAL OF ORGANOMETALLIC CHEMISTRY 690, 441-449
1222004Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath)Kao, WC; Chen, YR ; Yi, EC; Lee, H; Tian, Q; Wu, KM; Tsai, SF; Yu, SS; Chen, YJ ; Aebersold, R; Chan, SIJournal of biological chemistry 279(49), 51554-51560
1232004Purification, Tandem Mass Characterization, and Inhibition Studies of Oxidosqualene- lanosterol Cyclase Enzyme from Bovine LiverWu, Tung-Kung; Huang, Chiao-Yin; Ko, Cheng-Yu; Chang, Cheng-Hsiang; Chen, Yu-Ju ; Liao, Hsin-KaiARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS 421, 42-53
1242004Plasma proteome of Severe Acute Respiratory Syndrome (SARS) analyzed by two-dimensional gel electrophoresis and mass spectrometry.Chen, Jenn-Han; Chang, Yu-Wang; Yao, Chen-Wen; Chiueh, Tzong-Shi; Huang, Su-Chin; Chien, Ko-Yi; Chen, An; Chang, Feng-Yee; Wong, Chi-Huey; Chen, Yu-Ju PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101, 17039-17044
1252004Specific Recognition of DNA Bulge Structure by Matrix-assisted Laser Desorption/ Ionization Time-of-flight Mass SpectrometryChen, Po-Jui; Wang, Hsueh-Ting; Cheng, Chien-Chung; Chen, Yu-Ju RAPID COMMUNICATIONS IN MASS SPECTROMETRY 18, 609-616
1262004Synthesis and Crystal Structure of Core-Modified Benziporphyrin: Thia-ρ- BenziporphyrinHung, Chen-Hsiung; Lin, Cheng-Yu; Lin, Ping-Yu; Chen, Yu-Ju TETRAHEDRON LETTERS  45, 129-132
1272004Identification of Tumor-associated Plasma Biomarkers Using Proteomic Techniques: From Mouse to HumanJuan, Hsueh-Fen; Chen, Jenn-Han; Hsu, Wei-Tse; Huang, Su-Ching; Chen, Shui-Tein; Lin, John Yi-Chung; Chang, Yu-Wang; Chiang, Chih-Yin; Wen, Li-Li; Chan, De-Chuan; Liu, Yao-Chi; Chen, Yu-Ju PROTEOMICS 4, 2766-2775
1282004Nuclear Efflux of Heterogeneous Nuclear Ribonucleoprotein C1/C2 in Apoptotic Cells: A Novel Nuclear Export Dependent on Rho-Associated Kinase ActivationLee, Hsiao-Hui; Chien, Chung-Liang; Liao, Hsin-Kai; Chen, Yu-Ju ; Cheng, Zee-FenJOURNAL OF CELL SCIENCE 117, 5579-5589
1292003Synthesis of α-(2→5) Neu5Gc OligomersRen, Chien-Tai ; Chen, Chien-Sheng; Yu, Yi-Ping; Tsai, Yow-Fu; Lin, Ping-Yu; Chen, Yu-Ju ; Zou, Wei; Wu, Shih-Hsiung CHEMISTRY-A EUROPEAN JOURNAL 9(5), 1085-1095
1302003Mechanistic aspect of Co(HAPP)(TFA)2 in DNA bulge-specific recognition.Cheng, Chien-Chung; Huang-Fu, Wei-Chun; Hung, Kuo-Chan; Chen, Po-Jui; Wang, Wen-Jwu; Chen, Yu-Ju NUCLEIC ACIDS RESEARCH 31, 2227-2233
1312003Mass Spectrometry – Based ProteomicsChen, Yu-Ju ; Liao, Hsin-KaiCHEMISTRY 61,235-247
1322003Production of High-Quality Particulate Methane Monooxygenase in High Yields from methylococcus capsulatus (bath) with a Hollow-Fiber Membrane BioreactorYu, Steve S. -F; Chen, Kelvin H. -C.; Tseng, Mandy Y. -H.; Wang, Yane-Shih; Tseng, Chiu-Feng; Chen, Yu-Ju ; Huang, Ded-Shih; Chan, Sunney I.JOURNAL OF BACTERIOLOGY 185(5915-24)
1332002Structural characterization of Escherichia coli sialic acid synthaseHwang, TS; Hung, CH; Teo, CF; Chen, GT; Chang, LS; Chen, SF; Chen, YJ ; Lin, CH Biochem Biophys Res Commun 295, 167-173
1342002Study of the Dissociation of CH3SCH3+ by Collisional Activation: Evidence of Nonstatistical BehaviorChen, Yu-Ju ; Fenn, P. T.; Lau, Kai-Chung; Ng, C. Y.; Law, Chi-Kin; Li, Wai-KeeJOURNAL OF PHYSICAL CHEMISTRY A 106, 9729-9736
1352001Self-assembly of Tetrametallic Square [Re4(CO)12Br4(μ-pz)4] (pz = pyrazine) from [Re(CO)4Br(pz)]. A Mechanistic ApproachRajendran, T.; Manimaran, Bala; Lee, Fang-Yuan; Chen, Po-Jui; Lin, Su-Ching ; Lee, Gene-Hsiang; Peng, Shie-Ming; Chen, Yu-Ju ; Lu, Kuang-LiehJournal of the Chemical Society, Dalton Transactions 2001(22), 3346-3351
1362001Observation of CH4 (v(2)=1 or v(4)=1) in the Reaction Cl + CH4 by Time-resolved Fourier-transform Absorption SpectroscopyChen, Yu-Ju ; Lin, Shiaw-Ruey; Lee, Yuan-PernJOURNAL OF CHEMICAL PHYSICS 115, 6513-6521
1372001Detection of ClCO with Time-resolved Fourier-transform Infrared Absorption SpectroscopyChen, Shih-Hao; Chu, Li-Kung; Chen, Yu-Ju ; Chen, I-Chia; Lee, Yuan-PernCHEMICAL PHYSICS LETTERS 333, 365-370
1382001Direct Identification of Product CH2SH+/CH3S+ Structures in the Dissociation of  CH3CH2SH+ and CH3SCH3+ via Collisional ActivationChen, Yu-Ju ; Fenn, P. T.; Ng, C. Y.CHEMICAL PHYSICS LETTERS 336, 105-108
1391998A study of Dissociation of CH3CH2SH+ by Collisional Activation: Evidence of Non-Statistical BehaviorFenn, P. T.; Chen, Yu-Ju ; Stimson, S.; Ng, C. Y.; Li, Wai- Kee; Ma, N. L.JOURNAL OF CHEMICAL PHYSICS 108, 8020-8028
1401998Rotational-Resolved Pulsed Field Ionization Photoelectron Bands of H-2(+)(X-2 Sigma(+)(g), v(+) = 0, 2, 9, and 11) Using Multibunch Synchrotron RadiationStimson, S.; Chen, Yu. -Ju ; Evans, M.; Hsu, C. -W.; Heimann, P.; Liao, C. -L.; Ng, C. Y.CHEMICAL PHYSICS LETTERS 289, 507-515
1411997A Molecular Beam Photoionization Mass Spectrometric Studies of Cr(CO)6, Mo(CO)6, and W(CO)6Chen, Yu-Ju ; Liao, C. L.; Ng, C. Y.JOURNAL OF CHEMICAL PHYSICS 107, 4527-4536
1421997Dissociation of CH3SH+ by Collisional Activation: Evidence of Non-Statistical BehaviorFenn, P. T.; Chen, Yu-Ju ; Stimson, S.; Ng, C. Y.JOURNAL OF PHYSICAL CHEMISTRY A 101, 6513-6522
1431997Bond Selective Dissociation of CH3SH+ and C2H5SH+ via Collisional ActivationChen, Yu-Ju ; Fenn, P. T.; Ng, C. Y.JOURNAL OF CHEMICAL PHYSICS 106, 8274-8277
1441996A High Resolution Photoionization Study of Ne and Ar: Observation of Mass Analyzed Threshold Ions Using Synchrotron Radiation and Direct Current Electric FieldsHsu, C. -W.; Lu, K. T.; Evans, M.; Chen, Yu-Ju ; Ng, C. Y.; Heimann, P.JOURNAL OF CHEMICAL PHYSICS 105, 3950-3961
1451995Combining Theory with Experiment: Assessment of the Thermochemistry of SFn, SFn+, and SFn-Cheung, Y. -S.; Chen, Yu-Ju ; Ng, C. Y.; Chiu, See-Wing; Li, Wai- KeeJOURNAL OF THE AMERICAN CHEMICAL SOCIETY 117,9725-9733
146-A Chemically Functionalized Magnetic Nanoplatform for Rapid and Specific Biomolecular Recognition and SeparationLin, Po-Chiao; Yu, Ching-Ching; Wu, Huan-Ting; Lu, Ying-Wei; Han, Chia-Li; Su, An-Kai; Chen, Yu-Ju ; Lin, Chun-ChengBIOMACROMOLECULES 14 (1), pp 160–168