Youhe Gao

Summary

Affiliation: Chinese Academy of Medical Sciences
Country: China

Publications

  1. pmc Using an isolated rat kidney model to identify kidney origin proteins in urine
    Lulu Jia
    Department of Physiology and Pathophysiology, National Key Laboratory of Medical Molecular Biology Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing, China
    PLoS ONE 8:e66911. 2013
  2. pmc Novel nonphosphorylated peptides with conserved sequences selectively bind to Grb7 SH2 domain with affinity comparable to its phosphorylated ligand
    Dan Zhang
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine, Peking Union Medical College, Beijing, China
    PLoS ONE 7:e29902. 2012
  3. pmc An attempt to understand kidney's protein handling function by comparing plasma and urine proteomes
    Lulu Jia
    Department of Physiology and Pathophysiology, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
    PLoS ONE 4:e5146. 2009
  4. pmc Characterization of diverse internal binding specificities of PDZ domains by yeast two-hybrid screening of a special peptide library
    Yi Mu
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, P R China
    PLoS ONE 9:e88286. 2014
  5. pmc Unrestrictive identification of post-translational modifications in the urine proteome without enrichment
    Liu Liu
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine, 5 Dong Dan San Tiao, Beijing, China
    Proteome Sci 11:1. 2013
  6. pmc A comparison of E15.5 fetus and newborn rat serum proteomes
    Lilong Wei
    Department of Physiology and Pathophysiology, National Key Laboratory of Medical Molecular Biology Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
    Proteome Sci 10:64. 2012
  7. doi request reprint Proteomics strategy to identify substrates of LNX, a PDZ domain-containing E3 ubiquitin ligase
    Zhengguang Guo
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
    J Proteome Res 11:4847-62. 2012
  8. doi request reprint Systematic analysis of a simple adaptor protein PDZK1: ligand identification, interaction and functional prediction of complex
    Siqi Hu
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine, Peking Union Medical College, Beijing, China
    Cell Physiol Biochem 24:231-42. 2009
  9. ncbi request reprint A high efficiency strategy for binding property characterization of peptide-binding domains
    Eli Song
    Proteomics Research Center, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences Peking Union Medical College, 100005 Beijing, China
    Mol Cell Proteomics 5:1368-81. 2006
  10. doi request reprint Differential ConA-enriched urinary proteome in rat experimental glomerular diseases
    Yan Wang
    Department of Physiology and Pathophysiology, School of Basic Medicine Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, 5 Dongdan Santiao, Beijing 100005, China
    Biochem Biophys Res Commun 371:385-90. 2008

Collaborators

Detail Information

Publications37

  1. pmc Using an isolated rat kidney model to identify kidney origin proteins in urine
    Lulu Jia
    Department of Physiology and Pathophysiology, National Key Laboratory of Medical Molecular Biology Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing, China
    PLoS ONE 8:e66911. 2013
    ..When compared with existing candidate biomarkers, over ninety percent of the kidney origin proteins in urine identified in this study have not been examined as candidate biomarkers of kidney diseases. ..
  2. pmc Novel nonphosphorylated peptides with conserved sequences selectively bind to Grb7 SH2 domain with affinity comparable to its phosphorylated ligand
    Dan Zhang
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine, Peking Union Medical College, Beijing, China
    PLoS ONE 7:e29902. 2012
    ..Such nonphosphorylated peptides may be useful for rational design of drugs targeted against cancers that express high levels of Grb7 protein...
  3. pmc An attempt to understand kidney's protein handling function by comparing plasma and urine proteomes
    Lulu Jia
    Department of Physiology and Pathophysiology, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
    PLoS ONE 4:e5146. 2009
    ..Comparing these two proteomes may help us understand the protein handling aspect of kidney function in a way, however, which has been unavailable until the recent advances in proteomics technology...
  4. pmc Characterization of diverse internal binding specificities of PDZ domains by yeast two-hybrid screening of a special peptide library
    Yi Mu
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, P R China
    PLoS ONE 9:e88286. 2014
    ..These results suggest that the internal PBMs binding ability of PDZ domains may have been underestimated. The data provided diverse internal binding properties for several PDZ domains that may help identify their novel binding partners. ..
  5. pmc Unrestrictive identification of post-translational modifications in the urine proteome without enrichment
    Liu Liu
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine, 5 Dong Dan San Tiao, Beijing, China
    Proteome Sci 11:1. 2013
    ..Unspecified PTMs were searched by MODa and PEAKS 6 automated software, followed by a manual search to screen out in vivo PTMs by removing all in vitro PTMs and amino acid substitutions...
  6. pmc A comparison of E15.5 fetus and newborn rat serum proteomes
    Lilong Wei
    Department of Physiology and Pathophysiology, National Key Laboratory of Medical Molecular Biology Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
    Proteome Sci 10:64. 2012
    ..abstract:..
  7. doi request reprint Proteomics strategy to identify substrates of LNX, a PDZ domain-containing E3 ubiquitin ligase
    Zhengguang Guo
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
    J Proteome Res 11:4847-62. 2012
    ..This strategy can potentially be extended to a variety of E3s that contain protein interaction domain(s), thereby serving as a powerful tool for the comprehensive identification of their substrates on a proteomic scale...
  8. doi request reprint Systematic analysis of a simple adaptor protein PDZK1: ligand identification, interaction and functional prediction of complex
    Siqi Hu
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine, Peking Union Medical College, Beijing, China
    Cell Physiol Biochem 24:231-42. 2009
    ..This strategy can be extended to the study of other adaptor proteins that contain peptide-binding domains...
  9. ncbi request reprint A high efficiency strategy for binding property characterization of peptide-binding domains
    Eli Song
    Proteomics Research Center, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences Peking Union Medical College, 100005 Beijing, China
    Mol Cell Proteomics 5:1368-81. 2006
    ..This strategy can be easily extended to a variety of peptide-binding domains as a powerful tool for comprehensive analysis of domain binding property in proteomic scale...
  10. doi request reprint Differential ConA-enriched urinary proteome in rat experimental glomerular diseases
    Yan Wang
    Department of Physiology and Pathophysiology, School of Basic Medicine Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, 5 Dongdan Santiao, Beijing 100005, China
    Biochem Biophys Res Commun 371:385-90. 2008
    ..1 glomerulonephritis, respectively...
  11. doi request reprint Comparative proteome analysis of splenic lymphocytes in senescence-accelerated mice
    Yuanming Luo
    National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
    Gerontology 55:559-69. 2009
    ....
  12. doi request reprint Oscore: a combined score to reduce false negative rates for peptide identification in tandem mass spectrometry analysis
    Chen Shao
    Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
    J Mass Spectrom 44:25-31. 2009
    ..By a three-way comparison among Oscore, PeptideProphet and another logistic regression model which made use of PeptideProphet's variables, the main contributor for the improvement made by Oscore is discussed...
  13. doi request reprint Improving peptide identification using an empirical peptide retention time database
    Wei Sun
    Proteomics Research Center, Department of Physiology and Pathophysiology, School of Basic Medicine Peking Union Medical College, Beijing, PR China
    Rapid Commun Mass Spectrom 23:109-18. 2009
    ..This approach is suitable for large-scale clinical proteomics research, in which tens of LC/MS/MS analyses are run for different samples with similar components...
  14. doi request reprint Strategy for studying the liver secretome on the organ level
    Yang Zhang
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine, Peking Union Medical College, Beijing, China
    J Proteome Res 9:1894-901. 2010
    ..The strategy can be used in physiology research and biomarker discovery for diseases in the liver as well as other organs...
  15. ncbi request reprint Human urine proteome analysis by three separation approaches
    Wei Sun
    Proteomics Research Center, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P R China
    Proteomics 5:4994-5001. 2005
    ..The effects of sample preparation, separation and identification methods on the overlapping rate of different experiments are discussed...
  16. doi request reprint Using enrichment index for quality control of secretory protein sample and identification of secretory proteins
    Yong Chen
    Department of Physiology and Pathophysiology, Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences Peking Union Medical College, Tsinghua University, Beijing, China
    J Mass Spectrom 44:397-403. 2009
    ..We suggest that this assessment method is helpful for systemic research of secretory proteins and biomarker discovery for diseases such as cancer...
  17. pmc A tool for biomarker discovery in the urinary proteome: a manually curated human and animal urine protein biomarker database
    Chen Shao
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, China
    Mol Cell Proteomics 10:M111.010975. 2011
    ..Therefore, it is not clear how well the animal models mimic human diseases...
  18. pmc Molecular characterization and ligand binding specificity of the PDZ domain-containing protein GIPC3 from Schistosoma japonicum
    Yi Mu
    National Key Laboratory of Medical Molecular Biology, Dept, of Physiology and Pathophysiology, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, P, R, China
    Parasit Vectors 5:227. 2012
    ..PSD-95/Dlg/ZO-1 (PDZ) domain-containing proteins are recognized as potential targets for the next generation of drug development. However, the PDZ domain-containing protein family in parasites has largely been unexplored...
  19. ncbi request reprint Microwave-assisted protein preparation and enzymatic digestion in proteomics
    Wei Sun
    Proteomics Research Center and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Peking Union Medical College Chinese Academy of Medical Sciences, Beijing 100005, China
    Mol Cell Proteomics 5:769-76. 2006
    ..This new application of microwave technology to protein mixture preparation and enzymatic digestion will hasten the application of proteomic techniques to biological and clinical research...
  20. ncbi request reprint An integrated machine learning system to computationally screen protein databases for protein binding peptide ligands
    Ling Zhang
    Proteomics Research Center, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences Peking Union Medical College, 5 Dong Dan San Tiao, 100005 Beijing, China
    Mol Cell Proteomics 5:1224-32. 2006
    ..A large fraction of predictions has already been experimentally confirmed by other independent research groups, indicating a satisfying generalization capability for future applications in identifying protein interactions...
  21. ncbi request reprint Concanavalin A-captured glycoproteins in healthy human urine
    Linjie Wang
    Proteomics Research Center, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100080, China
    Mol Cell Proteomics 5:560-2. 2006
    ..Knowledge of the urine glycoproteome is important in understanding kidney and body function...
  22. doi request reprint Identification and characterization of cow's milk proteins from the rat intestinal lymph using a proteomic strategy
    Xundou Li
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
    Proteomics 13:2649-56. 2013
    ..Understanding the common features of these proteins might help to develop protein drugs taken orally, so that therapeutic proteins might embody fusion domains for cross-barrier transport or translocation. ..
  23. doi request reprint Applications of urinary proteomics in biomarker discovery
    Chen Shao
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Peking Union Medical College, Beijing, 100005, China
    Sci China Life Sci 54:409-17. 2011
    ..Finally, we propose that establishing a data-sharing platform for data collection and integrating results from all urinary biomarker studies will help promote the development of urinary proteomics...
  24. pmc Screening E3 substrates using a live phage display library
    Zhengguang Guo
    Department of Physiology and Pathophysiology, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine, Peking Union Medical College, Beijing, China Department of Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences School of Basic Medicine, Peking Union Medical College, Beijing, China
    PLoS ONE 8:e76622. 2013
    ..The whole strategy is rather simple and efficient. Non-degradation substrates can be discovered. This strategy can be extended to any E3s as long as the E3 does not ubiquitinate the empty phage. ..
  25. ncbi request reprint Rapid characterization of the binding property of HtrA2/Omi PDZ domain by validation screening of PDZ ligand library
    Sucan Ma
    Proteomics Research Center, National Key Laboratory of Medical Molecular Biology, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing, 100005, China
    Sci China C Life Sci 50:412-22. 2007
    ..Moreover, this study proves the high efficiency and practicability of the newly developed validation screening of candidate ligand library method for binding property characterization of peptide-binding domains...
  26. ncbi request reprint A systematical analysis of tryptic peptide identification with reverse phase liquid chromatography and electrospray ion trap mass spectrometry
    Wei Sun
    Proteomics Research Center National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100005, China
    Genomics Proteomics Bioinformatics 2:174-83. 2004
    ..Moreover, in this study the identified peptides present three types of redundancy, namely identification, charge, and sequence redundancy, which may repress low abundance protein identification...
  27. doi request reprint Nucleic acids in protein samples interfere with phosphopeptide identification by immobilized-metal-ion affinity chromatography and mass spectrometry
    Yaojun Li
    National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
    Mol Biotechnol 43:59-66. 2009
    ..We showed that ACN precipitation approximately doubled the phosphopeptide number identified by IMAC and mass spectrometry, indicating that nucleic acid removal significantly improves the identification of phosphopeptides...
  28. ncbi request reprint [Application of peptide retention time in proteome research]
    Chen Shao
    Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
    Se Pu 28:128-34. 2010
    ..Additionally, post-translational modifications (PTM) could be identified by combining retention time shifts and mass deviation information...
  29. doi request reprint Urimem, a membrane that can store urinary proteins simply and economically, makes the large-scale storage of clinical samples possible
    Lulu Jia
    Department of Physiology and Pathophysiology, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing, 100005, China
    Sci China Life Sci 57:336-9. 2014
    ..Even more objective large-scale prospective studies will be possible. This method has the potential to change the landscape of medical research and medical practice. ..
  30. pmc Discovery and Confirmation of Ligand Binding Specificities of the Schistosoma japonicum Polarity Protein Scribble
    Pengfei Cai
    MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, The Peoples Republic of China Department of Microbiology and Parasitology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, The Peoples Republic of China
    PLoS Negl Trop Dis 8:e2837. 2014
    ..However, the parasite-derived PDZ domains and their associated functions are still largely unknown...
  31. ncbi request reprint Comparative proteome analysis of breast cancer and normal breast
    Yuanming Luo
    National Laboratory of Medical Molecular Biology, Institute of Basic Med Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
    Mol Biotechnol 29:233-44. 2005
    ..The differentially expressed proteins may be used as potential candidate markers for diagnostic purposes or for determination of tumor sensitivity to therapy. The functional implications of the identified proteins are discussed...
  32. ncbi request reprint Effects of Three Commonly-used Diuretics on the Urinary Proteome
    Xundou Li
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
    Genomics Proteomics Bioinformatics 12:120-6. 2014
    ..Moreover, the distinct effects of diuretics on the urinary proteome may provide clues to the mechanisms of diuretics. ..
  33. ncbi request reprint Comparison at the peptide level with post-translational modification consideration reveals more differences between two unenriched samples
    JianRui Yin
    Department of Pathophysiology, National Key Laboratory of Medical Molecular Biology Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100005, China
    Rapid Commun Mass Spectrom 28:1364-70. 2014
    ....
  34. ncbi request reprint AMASS: software for automatically validating the quality of MS/MS spectrum from SEQUEST results
    Wei Sun
    Proteomics Research Center, National Key Laboratory of Medical Molecular, Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical, Sciences, Beijing, People s Republic of China
    Mol Cell Proteomics 3:1194-9. 2004
    ..We believe the use of AMASS and Rscore can result in a more accurate identification of peptide MS/MS spectra and reduce the time and energy for manual validation...
  35. ncbi request reprint A method for generation of arbitrary peptide libraries using genomic DNA
    Haiming Huang
    Department of Pathophysiology, National Key Laboratory of Medical Molecular Biology, Proteomics Research Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, PR China
    Mol Biotechnol 30:135-42. 2005
    ..Our results showed that in addition to various native carboxy-terminal tails, synectin could also bind to many artificial ones, some of which contained a consensus sequence--(S/T)XC-COOH...
  36. ncbi request reprint Construction of a non-redundant human SH2 domain database
    Haiming Huang
    Department of Pathophysiology National Key Laboratory of Medical Molecular Biology Proteomics Research Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences Peking Union Medical College, Beijing 100005, China
    Genomics Proteomics Bioinformatics 2:119-22. 2004
    ..Some proteins in the same group have been reported to have similar binding motifs experimentally. The tree might provide clues about possible functions of hypothetical proteins for further experimental verification...
  37. ncbi request reprint Changes of proteins induced by anticoagulants can be more sensitively detected in urine than in plasma
    Menglin Li
    National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
    Sci China Life Sci 57:649-56. 2014
    ..Our data indicates that urine may serve as a source for more sensitive detection of protein biomarkers than plasma. ..