Search Results - "Yunping Zhu"

The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics by Deutsch, Eric W, Bandeira, Nuno, Sharma, Vagisha, Perez-Riverol, Yasset, Carver, Jeremy J, Kundu, Deepti J, García-Seisdedos, David, Jarnuczak, Andrew F, Hewapathirana, Suresh, Pullman, Benjamin S, Wertz, Julie, Sun, Zhi, Kawano, Shin, Okuda, Shujiro, Watanabe, Yu, Hermjakob, Henning, MacLean, Brendan, MacCoss, Michael J, Zhu, Yunping, Ishihama, Yasushi, Vizcaíno, Juan A

“…Abstract The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of…”
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The ProteomeXchange consortium at 10 years: 2023 update by Deutsch, Eric W, Bandeira, Nuno, Perez-Riverol, Yasset, Sharma, Vagisha, Carver, Jeremy J, Mendoza, Luis, Kundu, Deepti J, Wang, Shengbo, Bandla, Chakradhar, Kamatchinathan, Selvakumar, Hewapathirana, Suresh, Pullman, Benjamin S, Wertz, Julie, Sun, Zhi, Kawano, Shin, Okuda, Shujiro, Watanabe, Yu, MacLean, Brendan, MacCoss, Michael J, Zhu, Yunping, Ishihama, Yasushi, Vizcaíno, Juan Antonio

“…Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources…”
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Extraction, structural and functional properties of Haematococcus pluvialis protein after pigment removal by Zhu, Yunping, Zhao, Xiaoyan, Zhang, Xiaowei, Liu, Hongkai

“…Protein from Haematococcus pluvialis (H. pluvialis) residues after pigment removal was prepared by alkaline extraction and acid precipitation. And the…”
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AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility by Gao, Zhiqiang, Chang, Cheng, Yang, Jinghan, Zhu, Yunping, Fu, Yan

“…The selection of proteotypic peptides, that is, detectable unique representatives of proteins of interest, is a key step in targeted proteomics. To date, much…”
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MoGCN: A Multi-Omics Integration Method Based on Graph Convolutional Network for Cancer Subtype Analysis by Li, Xiao, Ma, Jie, Leng, Ling, Han, Mingfei, Li, Mansheng, He, Fuchu, Zhu, Yunping

“…In light of the rapid accumulation of large-scale omics datasets, numerous studies have attempted to characterize the molecular and clinical features of…”
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Amino acid, structure and antioxidant properties of Haematococcus pluvialis protein hydrolysates produced by different proteases by Zhu, Yunping, Zhao, Xiaoyan, Zhang, Xiaowei, Liu, Hongkai, Ao, Qiang

“…Summary The impact of different protease hydrolysis on the amino acid, structure and antioxidant properties of H. pluvialis protein (HP) was investigated…”
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Universal Spectrum Identifier for mass spectra by Deutsch, Eric W., Perez-Riverol, Yasset, Carver, Jeremy, Kawano, Shin, Mendoza, Luis, Van Den Bossche, Tim, Gabriels, Ralf, Binz, Pierre-Alain, Pullman, Benjamin, Sun, Zhi, Shofstahl, Jim, Bittremieux, Wout, Mak, Tytus D., Klein, Joshua, Zhu, Yunping, Lam, Henry, Vizcaíno, Juan Antonio, Bandeira, Nuno

“…Mass spectra provide the ultimate evidence to support the findings of mass spectrometry proteomics studies in publications, and it is therefore crucial to be…”
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Spatially resolved proteomic map shows that extracellular matrix regulates epidermal growth by Li, Jun, Ma, Jie, Zhang, Qiyu, Gong, Huizi, Gao, Dunqin, Wang, Yujie, Li, Biyou, Li, Xiao, Zheng, Heyi, Wu, Zhihong, Zhu, Yunping, Leng, Ling

“…Human skin comprises stratified squamous epithelium and dermis with various stromal cells and the extracellular matrix (ECM). The basement membrane (BM), a…”
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DeepRTAlign: toward accurate retention time alignment for large cohort mass spectrometry data analysis by Liu, Yi, Yang, Yun, Chen, Wendong, Shen, Feng, Xie, Linhai, Zhang, Yingying, Zhai, Yuanjun, He, Fuchu, Zhu, Yunping, Chang, Cheng

“…Retention time (RT) alignment is a crucial step in liquid chromatography-mass spectrometry (LC-MS)-based proteomic and metabolomic experiments, especially for…”
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Enzyme-assisted extraction of astaxanthin from Haematococcus pluvialis and its stability and antioxidant activity by Zhao, Xiaoyan, Zhang, Xiaowei, Liu, Hongkai, Zhu, Haitao, Zhu, Yunping

“…The release of bioactive pigments could be potentially improved by enzyme degradation of plant cell wall polysaccharides. In this study, the objective was to…”
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The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction by Li, Mansheng, He, Qiang, Yang, Chunyuan, Ma, Jie, He, Fuchu, Chen, Tao, Zhu, Yunping

“…With the rapid increase in the amount of Protein-Protein Interaction (PPI) data, the establishment of an event-centered PPI ontology that contains temporal and…”
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ACP-DRL: an anticancer peptides recognition method based on deep representation learning by Xu, Xiaofang, Li, Chaoran, Yuan, Xinpu, Zhang, Qiangjian, Liu, Yi, Zhu, Yunping, Chen, Tao

“…Cancer, a significant global public health issue, resulted in about 10 million deaths in 2022. Anticancer peptides (ACPs), as a category of bioactive peptides,…”
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Research Progress of α-Glucosidase Inhibitors Produced by Microorganisms and Their Applications by Ren, Fei, Ji, Nairu, Zhu, Yunping

“…Based on the easy cultivation of microorganisms and their short cycle time, research on α-glucosidase inhibitors (α-GIs) of microbial origin is receiving…”
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Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work by Deutsch, Eric W., Vizcaíno, Juan Antonio, Jones, Andrew R., Binz, Pierre-Alain, Lam, Henry, Klein, Joshua, Bittremieux, Wout, Perez-Riverol, Yasset, Tabb, David L., Walzer, Mathias, Ricard-Blum, Sylvie, Hermjakob, Henning, Neumann, Steffen, Mak, Tytus D., Kawano, Shin, Mendoza, Luis, Van Den Bossche, Tim, Gabriels, Ralf, Bandeira, Nuno, Carver, Jeremy, Pullman, Benjamin, Sun, Zhi, Hoffmann, Nils, Shofstahl, Jim, Zhu, Yunping, Licata, Luana, Quaglia, Federica, Tosatto, Silvio C. E., Orchard, Sandra E.

“…The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled…”
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LexA, an SOS response repressor, activates TGase synthesis in Streptomyces mobaraensis by Shi, Xinyu, Yan, Hao, Yuan, Fang, Li, Guoying, Liu, Jingfang, Li, Chunli, Yu, Xiaobin, Li, Zilong, Zhu, Yunping, Wang, Weishan

“…Transglutaminase (EC 2.3.2.13, TGase), an enzyme that catalyzes the formation of covalent cross-links between protein or peptide molecules, plays a critical…”
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In-depth method assessments of differentially expressed protein detection for shotgun proteomics data with missing values by Wang, Jinxia, Li, Liwei, Chen, Tao, Ma, Jie, Zhu, Yunping, Zhuang, Jujuan, Chang, Cheng

“…Considering as one of the major goals in quantitative proteomics, detection of the differentially expressed proteins (DEPs) plays an important role in…”
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In-depth serum proteomics reveals biomarkers of psoriasis severity and response to traditional Chinese medicine by Xu, Meng, Deng, Jingwen, Xu, Kaikun, Zhu, Tiansheng, Han, Ling, Yan, Yuhong, Yao, Danni, Deng, Hao, Wang, Dan, Sun, Yaoting, Chang, Cheng, Zhang, Xiaomei, Dai, Jiayu, Yue, Liang, Zhang, Qiushi, Cai, Xue, Zhu, Yi, Duan, Hu, Liu, Yuan, Li, Dong, Zhu, Yunping, Radstake, Timothy R D J, Balak, Deepak M W, Xu, Danke, Guo, Tiannan, Lu, Chuanjian, Yu, Xiaobo

“…Serum and plasma contain abundant biological information that reflect the body's physiological and pathological conditions and are therefore a valuable sample…”
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Dynamic atlas of immune cells reveals multiple functional features of macrophages associated with progression of pulmonary fibrosis by Lv, Jiaoyan, Gao, Haoxiang, Ma, Jie, Liu, Jiachen, Tian, Yujie, Yang, Chunyuan, Li, Mansheng, Zhao, Yue, Li, Zhimin, Zhang, Xuegong, Zhu, Yunping, Zhang, Jianhong, Wu, Li

“…Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial lung disease with a high mortality rate and unclarified aetiology. Immune response is elaborately…”
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Protocol for identifying and comparing molecular prognosis subtypes of IgAN using R by Wang, Juan, Liu, Yi, Chen, Xizhao, Li, Mansheng, Zhu, Yunping

“…By providing a comprehensive view of protein dynamics, quantitative proteomics has emerged as a powerful tool for a better understanding of disease mechanisms…”
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Identification of functional gene modules by integrating multi-omics data and known molecular interactions by Chen, Xiaoqing, Han, Mingfei, Li, Yingxing, Li, Xiao, Zhang, Jiaqi, Zhu, Yunping

“…Multi-omics data integration has emerged as a promising approach to identify patient subgroups. However, in terms of grouping genes (or gene products) into…”
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