Yu‐Ju Chen

发表

MAGIC: an automated N-linked glycoprotein identification tool using a Y1-ion pattern matching algorithm and in silico MS² approach.

Chen-Chun Chen, Wan-Chih Su, W. Hsu, 2015, Analytical chemistry.

IDEAL-Q, an Automated Tool for Label-free Quantitation Analysis Using an Efficient Peptide Alignment Approach and Spectral Data Validation*

Chih-Chiang Tsou, W. Hsu, Ting-Yi Sung, 2009, Molecular & Cellular Proteomics.

Phosphoproteomics Identifies Oncogenic Ras Signaling Targets and Their Involvement in Lung Adenocarcinomas

W. Hsu, Ting-Yi Sung, Yu‐Ju Chen, 2011, PloS one.

Launching the C-HPP neXt-CP50 Pilot Project for Functional Characterization of Identified Proteins with No Known Function.

G. Omenn, Yu‐Ju Chen, J. LaBaer, 2018, Journal of proteome research.

Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics.

W. Hsu, Ting-Yi Sung, Wai-Kok Choong, 2015, Journal of proteome research.

Characterization and identification of protein O-GlcNAcylation sites with substrate specificity

Yu-Ju Chen, Yi-Ju Chen, Tzong-Yi Lee, 2014, BMC Bioinformatics.

SNOSite: Exploiting Maximal Dependence Decomposition to Identify Cysteine S-Nitrosylation with Substrate Site Specificity

Hsien-Da Huang, Tzong-Yi Lee, Yu-Ju Chen, 2011, PloS one.

Proteome analysis of human embryonic stem cells organelles.

Yu‐Ju Chen, H. Baharvand, G. Salekdeh, 2017, Journal of proteomics.

In-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 Approach*

Yu-Ju Chen, Sang-Hyun Kim, Yu‐Ju Chen, 2011, Molecular & Cellular Proteomics.

A Quest for Missing Proteins: update 2015 on Chromosome-Centric Human

Cheryl F. Lichti, Robert J A Goode, S. Ranganathan, 2015 .

Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.

Juan Antonio Vizcaíno, Yassene Mohammed, Ekaterina Mostovenko, 2015, Journal of proteome research.

Chromosome-centric Human Proteome Project (C-HPP): Chromosome 12.

Henry H. N. Lam, A. Pandey, R. Sirdeshmukh, 2014, Journal of proteome research.

Decoding the disease-associated proteins encoded in the human chromosome 4.

W. Hsu, Ting-Yi Sung, Wai-Kok Choong, 2013, Journal of proteome research.

Evaluating the Possibility of Detecting Variants in Shotgun Proteomics via LeTE-Fusion Analysis Pipeline.

Ting-Yi Sung, Wai-Kok Choong, Yu-Ju Chen, 2018, Journal of proteome research.

The Impact of dUTPase on Ribonucleotide Reductase-Induced Genome Instability in Cancer Cells.

Y. Yen, Yu‐Ju Chen, Xiyong Liu, 2016, Cell reports.

Analysis of Protein Stability by the Cycloheximide Chase Assay.

A. Nesvizhskii, Yih-Leong Chang, Yu‐Ju Chen, 2015, Bio-protocol.

Direct Oligosaccharide Profiling using Thin-Layer Chromatography Coupled with Ionic Liquid-Stabilized Nanomatrix-Assisted Laser Desorption-Ionization Mass Spectrometry.

Yu‐Ju Chen, Ming-Jer Lee, M. Tseng, 2019, Analytical chemistry.

iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm.

W. Hsu, Ting-Yi Sung, Ching-Tai Chen, 2017, Analytical chemistry.

Production of High-Quality Particulate Methane Monooxygenase in High Yields from Methylococcus capsulatus (Bath) with a Hollow-Fiber Membrane Bioreactor

Yu‐Ju Chen, Yane-Shih Wang, Sunney I. Chan, 2003, Journal of bacteriology.

Effect of sialylation on EGFR phosphorylation and resistance to tyrosine kinase inhibition

Chi‐Huey Wong, Yu‐Ju Chen, Pan‐Chyr Yang, 2015, Proceedings of the National Academy of Sciences.

Absolute Phosphorylation Stoichiometry Analysis by Motif-Targeting Quantitative Mass Spectrometry.

Yu‐Ju Chen, Y. Ishihama, Chia-Feng Tsai, 2017, Methods in molecular biology.

A Cloud-Based Metabolite and Chemical Prioritization System for the Biology/Disease-Driven Human Proteome Project.

I. Kohane, Kun‐Hsing Yu, Christopher Ré, 2018, Journal of proteome research.

&bgr;-Amyloid Induces Pathology-Related Patterns of Tau Hyperphosphorylation at Synaptic Terminals

B. Hyman, Hwan‐Ching Tai, Yu‐Ju Chen, 2018, Journal of neuropathology and experimental neurology.

Reduced symmetric dimethylation stabilizes vimentin and promotes metastasis in MTAP‐deficient lung cancer

Yu‐Ju Chen, Hsuan-Yu Chen, Sung-Liang Yu, 2022, EMBO reports.

Regulation of miRNA Biogenesis and Histone Modification by K63-Polyubiquitinated DDX17 Controls Cancer Stem-like Features.

Wei-Chung Cheng, Yu‐Ju Chen, Kou-Juey Wu, 2019, Cancer research.

The Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative. Preparation and characterisation of the carbonate‐washed membrane standard

Florian S. Dreyer, Eugene A. Kapp, R. Sirdeshmukh, 2010, Proteomics.

Molecular Basis and Role of Siglec-7 Ligand Expression on Chronic Lymphocytic Leukemia B Cells

Yu‐Ju Chen, K. Khoo, S. Liang, 2022, Frontiers in Immunology.

Glutathionylspermidine in the Modification of Protein SH Groups: The Enzymology and Its Application to Study Protein Glutathionylation

Yu‐Ju Chen, Chun-Hung Lin, Yi‐Ju Chen, 2015, Molecules.

Thymidylate kinase is critical for DNA repair via ATM‐dependent Tip60 complex formation

Yu‐Ju Chen, Yi-Ting Wang, Z. Chang, 2018, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Tumor cells require thymidylate kinase to prevent dUTP incorporation during DNA repair.

Yu‐Ju Chen, Jim-Min Fang, S. Sheu, 2012, Cancer cell.

Immobilized metal affinity chromatography revisited: pH/acid control toward high selectivity in phosphoproteomics.

Yu‐Ju Chen, K. Khoo, K. Pan, 2008, Journal of proteome research.

Global Analysis of Cdc14 Dephosphorylation Sites Reveals Essential Regulatory Role in Mitosis and Cytokinesis.

Yu‐Ju Chen, Yi-Ting Wang, Yu-Chen Chen, 2014, Molecular & cellular proteomics : MCP.

Role of S-Palmitoylation by ZDHHC13 in Mitochondrial function and Metabolism in Liver

Yu‐Ju Chen, J. Yen, Yuan-Tsong Chen, 2017, Scientific Reports.

Cyclic Alopecia and Abnormal Epidermal Cornification in Zdhhc13-Deficient Mice Reveal the Importance of Palmitoylation in Hair and Skin Differentiation.

Yu‐Ju Chen, J. Yen, Yuan-Tsong Chen, 2015, The Journal of investigative dermatology.

Incorporating Amino Acids Composition and Functional Domains for Identifying Bacterial Toxin Proteins

Tzong-Yi Lee, Yu‐Ju Chen, Hsin‐Yi Wu, 2014, BioMed research international.

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project.

R. Aebersold, C. Lindskog, R. Moritz, 2022, Journal of proteome research.

A photo-cleavable biotin affinity tag for the facile release of a photo-crosslinked carbohydrate-binding protein.

Yu‐Ju Chen, Tsung-Che Chang, Chun‐Cheng Lin, 2016, Bioorganic & medicinal chemistry.

Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies

Hongwen Zhu, Bernd Wollscheid, Albert Sickmann, 2020, Nature Communications.

Phosphoproteomics Reveals HMGA1, a CK2 Substrate, as a Drug-Resistant Target in Non-Small Cell Lung Cancer

Ting-Yi Sung, Wai-Kok Choong, Yu‐Ju Chen, 2017, Scientific Reports.

Decoding the Effect of Isobaric Substitutions on Identifying Missing Proteins and Variant Peptides in Human Proteome.

Ting-Yi Sung, Wai-Kok Choong, Yu-Ju Chen, 2017, Journal of proteome research.

Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project.

R. Aebersold, C. Lindskog, R. Moritz, 2021, Journal of proteome research.

Sequential phosphoproteomic enrichment through complementary metal-directed immobilized metal ion affinity chromatography.

Ting-Yi Sung, Wai-Kok Choong, Yu-Ju Chen, 2014, Analytical chemistry.

An Alternative of Phosphopeptide Identification using Inclusion List-Driven Targeted Liquid-Tandem Mass Spectrometry for Label-Free Quantitative Tyrosine Phosphoproteomics: Application of Src Inhibitor-Related Signaling Pathway Analyses in Lung Cancer

Yu‐Ju Chen, Wei-Sheng Wu, Hsin‐Yi Wu, 2014 .

Nanoprobe‐based immobilized metal affinity chromatography for sensitive and complementary enrichment of multiply phosphorylated peptides

Yu-Ju Chen, Chia-Feng Tsai, Yu‐Ju Chen, 2011, Proteomics.

Inducing hair follicle neogenesis with secreted proteins enriched in embryonic skin.

Sung-Jan Lin, Yu‐Ju Chen, Sung-Liang Yu, 2018, Biomaterials.

Systematic Protein Prioritization for Targeted Proteomics Studies through Literature Mining.

Jung-Hsien Chiang, Chi-Shiang Wang, Tsung-Lu Michael Lee, 2018, Journal of proteome research.

Atomic force microscopy characterization of kinase-mediated phosphorylation of a peptide monolayer

Yu‐Ju Chen, D. Porath, A. Friedler, 2016, Scientific Reports.

Integrating proteomics with electrochemistry for identifying kinase biomarkers† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5sc00560d Click here for additional data file. Click here for additional data file.

Rofeamor P. Obena, Yu‐Ju Chen, D. Porath, 2015, Chemical science.

Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane Proteins.

Reta Birhanu Kitata, Ting-Yi Sung, Wai-Kok Choong, 2018, Journal of proteome research.

Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics

Chih-Chiang Tsou, A. Nesvizhskii, Yu‐Ju Chen, 2015, Nature Communications.

An informatics-assisted label-free quantitation strategy that depicts phosphoproteomic profiles in lung cancer cell invasion.

Wen-Lian Hsu, Ting-Yi Sung, Yu-Ju Chen, 2010, Journal of proteome research.

Quantitative proteomics reveals diverse roles of miR-148a from gastric cancer progression to neurological development.

H. Juan, Hsuan-Cheng Huang, Yu‐Ju Chen, 2013, Journal of proteome research.

Complementary Fe(3+)- and Ti(4+)-immobilized metal ion affinity chromatography for purification of acidic and basic phosphopeptides.

Yu‐Ju Chen, Chia-Feng Tsai, Alan Chuan-Ying Lai, 2012, Rapid communications in mass spectrometry : RCM.

GPER‐induced signaling is essential for the survival of breast cancer stem cells

Yu‐Ju Chen, Jyh‐cherng Yu, Hsin‐Yi Wu, 2019, International journal of cancer.

Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling.

Reta Birhanu Kitata, Ting-Yi Sung, Wai-Kok Choong, 2015, Analytical chemistry.

DNA Demethylation by DNMT3A and DNMT3B in vitro and of Methylated Episomal DNA in Transiently Transfected Cells.

Yu‐Ju Chen, Miao-Hsia Lin, M. Tseng, 2018, Biochimica et biophysica acta. Gene regulatory mechanisms.

Phosphoproteomics characterization of novel phosphorylated sites of lens proteins from normal and cataractous human eye lenses

Yu‐Ju Chen, Chia-Feng Tsai, Yi-Ting Wang, 2011, Molecular vision.

Identification of in vivo phosphorylation sites of lens proteins from porcine eye lenses by a gel-free phosphoproteomics approach

Yu‐Ju Chen, Yi-Ting Wang, Y. Tsay, 2010, Molecular vision.

dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications

Hsien-Da Huang, Yu-Ju Chen, Yi-Ju Chen, 2012, Nucleic Acids Res..

RegPhos 2.0: an updated resource to explore protein kinase–substrate phosphorylation networks in mammals

Hsien-Da Huang, Yu-Ju Chen, Yi-Ju Chen, 2014, Database J. Biol. Databases Curation.

Untargeted, spectral library‐free analysis of data‐independent acquisition proteomics data generated using Orbitrap mass spectrometers

Alexey I Nesvizhskii, Guo Ci Teo, Yu-Ju Chen, 2016, Proteomics.

Phosphoproteomic analysis of human mesenchymal stromal cells during osteogenic differentiation.

O. Lee, W. Hsu, Ting-Yi Sung, 2012, Journal of Proteome Research.

Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry.

Alexey I Nesvizhskii, Ting-Yi Sung, Wai-Kok Choong, 2015, Journal of proteome research.

Phosphoproteomics by Highly Selective IMAC Protocol

Yu‐Ju Chen, Chia-Feng Tsai, Yi-Ting Wang, 2011 .

S-alkylating labeling strategy for site-specific identification of the s-nitrosoproteome.

Wei-Chi Ku, Kay-Hooi Khoo, Yu-Ju Chen, 2010, Journal of proteome research.

Standardization and Harmonization of Distributed Multi-National Proteotype Analysis supporting Precision Medicine Studies

Connie R. Jimenez, Sander R. Piersma, Hongwen Zhu, 2020, bioRxiv.

Phosphoproteomic analysis of Rhodopseudomonas palustris reveals the role of pyruvate phosphate dikinase phosphorylation in lipid production.

H. Juan, Hsuan-Cheng Huang, Yu‐Ju Chen, 2012, Journal of proteome research.

A data-independent acquisition-based global phosphoproteomics system enables deep profiling

Reta Birhanu Kitata, A. Nesvizhskii, Ting-Yi Sung, 2021, Nature Communications.

Nanoprobe‐based mass spectrometry and Fourier transform infrared spectroscopy for rapid phospholipid profiling

Yu‐Ju Chen, M. Tseng, Elias Gizaw Mernie, 2021, Journal of the Chinese Chemical Society.

Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications.

Wen-Lian Hsu, Ting-Yi Sung, Yu-Ju Chen, 2013, Journal of proteome research.

Endothelial Yin Yang 1 Phosphorylation at S118 Induces Atherosclerosis Under Flow

Yu‐Ju Chen, S. Chien, Hsin‐Yi Wu, 2021, Circulation research.

Quantitative proteomic and genomic profiling reveals metastasis-related protein expression patterns in gastric cancer cells.

Hsuan-Cheng Huang, Hsueh-Fen Juan, Yu-Ju Chen, 2006, Journal of proteome research.

Nitric oxide physiological responses and delivery mechanisms probed by water-soluble Roussin's red ester and {Fe(NO)2}10 DNIC.

Yu‐Ju Chen, W. Hsu, M. Tsai, 2008, Journal of the American Chemical Society.

Phosphoproteomic analyses reveal that galectin-1 augments the dynamics of B-cell receptor signaling.

Yu‐Ju Chen, Chu-Wei Kuo, K. Khoo, 2014, Journal of proteomics.

Integrating site-specific peptide reporters and targeted mass spectrometry enables rapid substrate-specific kinase assay at the nanogram cell level.

Reta Birhanu Kitata, Yu‐Ju Chen, Pan‐Chyr Yang, 2021, Analytica chimica acta.

Qualification and Verification of Serological Biomarker Candidates for Lung Adenocarcinoma by Targeted Mass Spectrometry.

Yu‐Ju Chen, Hsin‐Yi Wu, P. Liao, 2015, Journal of proteome research.

Electrochemical biosensors based on peptide-kinase interactions at the kinase docking site

Yu‐Ju Chen, A. Friedler, S. Yitzchaik, 2021, bioRxiv.

An Enzyme-Mediated Aza-Michael Addition Is Involved in the Biosynthesis of an Imidazoyl Hybrid Product of Conidiogenone B.

Yu‐Ju Chen, Shih-Hsiung Wu, Hsiao‐Ching Lin, 2021, Organic letters.

Identification of Conomarphin Variants in the Conus eburneus Venom and the Effect of Sequence and PTM Variations on Conomarphin Conformations

Ricky B. Nellas, Yu‐Ju Chen, E. Yu, 2020, Marine drugs.

Ultra-streamlined single cell proteomics by all-in-one chip and data-independent-acquisition mass spectrometry

Reta Birhanu Kitata, Yu-Ju Chen, Asad Ali Siyal, 2021 .