Ping Ye

Summary

Affiliation: Johns Hopkins University
Country: USA

Publications

  1. pmc Genetic Interaction Motif Finding by expectation maximization--a novel statistical model for inferring gene modules from synthetic lethality
    Yan Qi
    Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA
    BMC Bioinformatics 6:288. 2005
  2. ncbi request reprint The thymus during HIV disease: role in pathogenesis and in immune recovery
    Ping Ye
    Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
    Curr HIV Res 2:177-83. 2004
  3. pmc Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast
    Ping Ye
    The Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
    BMC Bioinformatics 6:270. 2005
  4. pmc Gene function prediction from congruent synthetic lethal interactions in yeast
    Ping Ye
    Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, USA
    Mol Syst Biol 1:2005.0026. 2005
  5. ncbi request reprint Global synthetic-lethality analysis and yeast functional profiling
    Siew Loon Ooi
    High Throughput Biology Center, Institute of Genetic Medicine, Department of Biostatistics, Johns Hopkins University School of Medicine, 339 Broadway Research Building, 733 North Broadway, Baltimore, MD 21205, USA
    Trends Genet 22:56-63. 2006
  6. ncbi request reprint A DNA integrity network in the yeast Saccharomyces cerevisiae
    Xuewen Pan
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
    Cell 124:1069-81. 2006
  7. ncbi request reprint Reconstitution of thymic function in HIV-1 patients treated with highly active antiretroviral therapy
    Ping Ye
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Clin Immunol 106:95-105. 2003
  8. ncbi request reprint Measuring emigration of human thymocytes by T-cell receptor excision circles
    Ping Ye
    Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI, USA
    Crit Rev Immunol 22:483-97. 2002
  9. ncbi request reprint Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model
    Peter A Meyer
    Department of Molecular Biology and Genetics, Cornell University, 221 Biotechnology Building, Ithaca, New York 14853, USA
    Structure 14:973-82. 2006
  10. pmc Fcp1 directly recognizes the C-terminal domain (CTD) and interacts with a site on RNA polymerase II distinct from the CTD
    Man Hee Suh
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Proc Natl Acad Sci U S A 102:17314-9. 2005

Collaborators

Detail Information

Publications15

  1. pmc Genetic Interaction Motif Finding by expectation maximization--a novel statistical model for inferring gene modules from synthetic lethality
    Yan Qi
    Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA
    BMC Bioinformatics 6:288. 2005
    ..Probabilistic algorithms that identify gene modules based on motif discovery are highly appropriate for the analysis of synthetic lethal genetic interaction data and have great potential in integrative analysis of heterogeneous datasets...
  2. ncbi request reprint The thymus during HIV disease: role in pathogenesis and in immune recovery
    Ping Ye
    Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
    Curr HIV Res 2:177-83. 2004
    ..Immunologic interventions aiming at restoring thymic function in AIDS patients are also reviewed...
  3. pmc Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast
    Ping Ye
    The Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
    BMC Bioinformatics 6:270. 2005
    ....
  4. pmc Gene function prediction from congruent synthetic lethal interactions in yeast
    Ping Ye
    Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, USA
    Mol Syst Biol 1:2005.0026. 2005
    ..These in silico methods can predict phenotypes and gene functions and are applicable to genomic synthetic lethality screens in yeast and analogous RNA interference screens in metazoans...
  5. ncbi request reprint Global synthetic-lethality analysis and yeast functional profiling
    Siew Loon Ooi
    High Throughput Biology Center, Institute of Genetic Medicine, Department of Biostatistics, Johns Hopkins University School of Medicine, 339 Broadway Research Building, 733 North Broadway, Baltimore, MD 21205, USA
    Trends Genet 22:56-63. 2006
    ....
  6. ncbi request reprint A DNA integrity network in the yeast Saccharomyces cerevisiae
    Xuewen Pan
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
    Cell 124:1069-81. 2006
    ..This network will guide more detailed characterization of mechanisms governing DNA integrity in yeast and other organisms...
  7. ncbi request reprint Reconstitution of thymic function in HIV-1 patients treated with highly active antiretroviral therapy
    Ping Ye
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
    Clin Immunol 106:95-105. 2003
    ..We further predict that protease inhibitors have high levels of efficacy directly suppressing viral replication within the thymus, while reverse transcriptase inhibitors have low efficacy...
  8. ncbi request reprint Measuring emigration of human thymocytes by T-cell receptor excision circles
    Ping Ye
    Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, MI, USA
    Crit Rev Immunol 22:483-97. 2002
    ..Our findings suggest that T-cell dynamics are key to the accuracy of TREC concentrations as a useful measurement of human RTEs...
  9. ncbi request reprint Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model
    Peter A Meyer
    Department of Molecular Biology and Genetics, Cornell University, 221 Biotechnology Building, Ithaca, New York 14853, USA
    Structure 14:973-82. 2006
    ....
  10. pmc Fcp1 directly recognizes the C-terminal domain (CTD) and interacts with a site on RNA polymerase II distinct from the CTD
    Man Hee Suh
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Proc Natl Acad Sci U S A 102:17314-9. 2005
    ..We speculate that Fcp1 interaction with the non-CTD site may mediate its stimulatory effect on transcription elongation reported previously...
  11. ncbi request reprint Reevaluation of T cell receptor excision circles as a measure of human recent thymic emigrants
    Ping Ye
    Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 0620, USA
    J Immunol 168:4968-79. 2002
    ..Therefore, we suggest that T cell turnover should be examined together with TREC concentration as a measure of RTE. If peripheral T cell division remains relatively unchanged, then TREC concentration indeed reflects thymic output...
  12. ncbi request reprint An agarose-acrylamide composite native gel system suitable for separating ultra-large protein complexes
    Man Hee Suh
    Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
    Anal Biochem 343:166-75. 2005
    ..The CNG technique is particularly suitable for capturing dynamic protein-protein interactions as exemplified here by the formation and demonstration of RNA polymerase II-Fcp1 complex...
  13. ncbi request reprint Lack of good correlation of serum CC-chemokine levels with human immunodeficiency virus-1 disease stage and response to treatment
    Ping Ye
    Departments of Microbiology and Immunology, Internal Medicine, and Pathology, University of Michigan Medical School, Ann Arbor, MI USA
    J Lab Clin Med 143:310-9. 2004
    ....
  14. ncbi request reprint The effects of different HIV type 1 strains on human thymic function
    Ping Ye
    Department of Microbiology and Immunology, The University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
    AIDS Res Hum Retroviruses 18:1239-51. 2002
    ..We predict that both viral and host factors play key roles in controlling thymic infection, including strain virulence and health status of the thymus...
  15. ncbi request reprint G-protein-coupled receptors in aldosterone-producing adenomas: a potential cause of hyperaldosteronism
    Ping Ye
    Department of Physiology, Medical College of Georgia, 1120 15th Street, Augusta, Georgia 30912, USA
    J Endocrinol 195:39-48. 2007
    ..There are also sporadic increased expressions of these genes in the CPAs. Together, these findings suggest a potential role of altered GPCR expression in many cases of PA and provide candidate GPCR for further study...