D S Yuan

Summary

Affiliation: Johns Hopkins University
Country: USA

Publications

  1. pmc Zinc-regulated genes in Saccharomyces cerevisiae revealed by transposon tagging
    D S Yuan
    Division of Pediatric Gastroenterology and Nutrition, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287 2631, USA
    Genetics 156:45-58. 2000
  2. ncbi 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
  3. pmc High-resolution spatial normalization for microarrays containing embedded technical replicates
    Daniel S Yuan
    Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
    Bioinformatics 22:3054-60. 2006
  4. pmc Improved microarray methods for profiling the Yeast Knockout strain collection
    Daniel S Yuan
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Nucleic Acids Res 33:e103. 2005
  5. pmc Dithizone staining of intracellular zinc: an unexpected and versatile counterscreen for auxotrophic marker genes in Saccharomyces cerevisiae
    Daniel S Yuan
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 6:e25830. 2011
  6. doi Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray
    Pamela B Meluh
    Department of Molecular Biology and Genetics, The High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
    Methods Mol Biol 416:221-47. 2008
  7. pmc Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools
    Brian D Peyser
    McKusick Nathans Institute of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
    Nucleic Acids Res 33:e140. 2005
  8. ncbi A robust toolkit for functional profiling of the yeast genome
    Xuewen Pan
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Mol Cell 16:487-96. 2004
  9. pmc dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae
    Xuewen Pan
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
    Methods 41:206-21. 2007
  10. ncbi 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

Collaborators

  • Joel S Bader
  • Xiaoling Wang
  • Rafael A Irizarry
  • Yan Qi
  • Xuewen Pan
  • Jef D Boeke
  • Brian D Peyser
  • Pamela B Meluh
  • Forrest A Spencer
  • Hajime Kobayashi
  • Junbiao Dai
  • Yu yi Lin
  • Ou Chen
  • Siew Loon Ooi
  • Hailiang Huang
  • Edel M Hyland
  • Graham C Walker
  • Jin Ying Lu
  • Carol Tiffany
  • Sharon Sookhai-Mahadeo
  • William J Broughton
  • Yingming Zhao
  • Lyle A Simmons
  • Ping Ye
  • Carol W Tiffany

Detail Information

Publications13

  1. pmc Zinc-regulated genes in Saccharomyces cerevisiae revealed by transposon tagging
    D S Yuan
    Division of Pediatric Gastroenterology and Nutrition, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287 2631, USA
    Genetics 156:45-58. 2000
    ..These findings illustrate the utility of transposon tagging as an approach for studying regulated gene expression in yeast...
  2. ncbi 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
    ....
  3. pmc High-resolution spatial normalization for microarrays containing embedded technical replicates
    Daniel S Yuan
    Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
    Bioinformatics 22:3054-60. 2006
    ..These artifacts introduce biases that are spatially correlated. The ability of current methodologies to detect and correct such biases is limited...
  4. pmc Improved microarray methods for profiling the Yeast Knockout strain collection
    Daniel S Yuan
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Nucleic Acids Res 33:e103. 2005
    ..The materials, protocols, data and associated software described here comprise a suite of experimental resources that should facilitate the use of TAG microarrays for a wide variety of genetic screens...
  5. pmc Dithizone staining of intracellular zinc: an unexpected and versatile counterscreen for auxotrophic marker genes in Saccharomyces cerevisiae
    Daniel S Yuan
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 6:e25830. 2011
    ..Many potential applications exist for dithizone staining, both as a versatile counterscreen for auxotrophic marker genes and as a powerful new tool for the genetic analysis of a biomedically important vesicular organelle...
  6. doi Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray
    Pamela B Meluh
    Department of Molecular Biology and Genetics, The High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
    Methods Mol Biol 416:221-47. 2008
    ..Analysis of double-mutant strains is of growing importance in defining the spectrum of essential cellular functionalities and in understanding how these functionalities interrelate...
  7. pmc Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools
    Brian D Peyser
    McKusick Nathans Institute of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
    Nucleic Acids Res 33:e140. 2005
    ....
  8. ncbi A robust toolkit for functional profiling of the yeast genome
    Xuewen Pan
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Mol Cell 16:487-96. 2004
    ..Direct comparison revealed that these techniques are more robust than existing methods in functional profiling of the yeast genome. Widespread application of these tools will elucidate a comprehensive yeast genetic network...
  9. pmc dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae
    Xuewen Pan
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
    Methods 41:206-21. 2007
    ..This technology has been effectively adapted to study other types of genome-wide genetic interactions including gene-compound synthetic lethality, secondary mutation suppression, dosage-dependent synthetic lethality and suppression...
  10. ncbi 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...
  11. pmc A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation
    Yu yi Lin
    High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Genes Dev 22:2062-74. 2008
    ..These new characterizations of the HDA and NuA4 complexes demonstrate how systematic analyses of genetic interactions may help illuminate the mechanisms of intricate cellular processes...
  12. pmc Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants
    Junbiao Dai
    High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Cell 134:1066-78. 2008
    ....
  13. pmc Multiple Ku orthologues mediate DNA non-homologous end-joining in the free-living form and during chronic infection of Sinorhizobium meliloti
    Hajime Kobayashi
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Microbiol 67:350-63. 2008
    ..Moreover, SKu2-YFP foci formed in response to IR in non-dividing bacteroids, indicating that NHEJ system is functional even during the chronic infection phase of symbiosis...