Affiliation: Johns Hopkins University
- Genetic Interaction Motif Finding by expectation maximization--a novel statistical model for inferring gene modules from synthetic lethalityYan 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...
- The thymus during HIV disease: role in pathogenesis and in immune recoveryPing 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...
- Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeastPing Ye
The Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
BMC Bioinformatics 6:270. 2005....
- Gene function prediction from congruent synthetic lethal interactions in yeastPing 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...
- Global synthetic-lethality analysis and yeast functional profilingSiew 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....
- A DNA integrity network in the yeast Saccharomyces cerevisiaeXuewen 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...
- Reconstitution of thymic function in HIV-1 patients treated with highly active antiretroviral therapyPing 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...
- Measuring emigration of human thymocytes by T-cell receptor excision circlesPing 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...
- Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural modelPeter A Meyer
Department of Molecular Biology and Genetics, Cornell University, 221 Biotechnology Building, Ithaca, New York 14853, USA
Structure 14:973-82. 2006....
- Fcp1 directly recognizes the C-terminal domain (CTD) and interacts with a site on RNA polymerase II distinct from the CTDMan 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...
- Reevaluation of T cell receptor excision circles as a measure of human recent thymic emigrantsPing 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...
- An agarose-acrylamide composite native gel system suitable for separating ultra-large protein complexesMan 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...
- Lack of good correlation of serum CC-chemokine levels with human immunodeficiency virus-1 disease stage and response to treatmentPing 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....
- The effects of different HIV type 1 strains on human thymic functionPing 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...
- G-protein-coupled receptors in aldosterone-producing adenomas: a potential cause of hyperaldosteronismPing 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...