Shuye Pu

Summary

Affiliation: The Hospital for Sick Children
Country: Canada

Publications

  1. doi request reprint Local coherence in genetic interaction patterns reveals prevalent functional versatility
    Shuye Pu
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto, ON, Canada
    Bioinformatics 24:2376-83. 2008
  2. pmc Up-to-date catalogues of yeast protein complexes
    Shuye Pu
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto ON, M5G 1X8
    Nucleic Acids Res 37:825-31. 2009
  3. pmc Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human
    Shuye Pu
    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Canada
    PLoS ONE 5:e14122. 2010
  4. pmc OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms
    Yanqi Hao
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto, ON, Canada
    Bioinformatics 27:883-4. 2011
  5. pmc DAnCER: disease-annotated chromatin epigenetics resource
    Andrei L Turinsky
    Hospital for Sick Children, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    Nucleic Acids Res 39:D889-94. 2011
  6. doi request reprint Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae
    Mohan Babu
    Banting and Best Department of Medical Research, Donnelly Centre, 160 College Street, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Nature 489:585-9. 2012
  7. ncbi request reprint Identifying functional modules in the physical interactome of Saccharomyces cerevisiae
    Shuye Pu
    Department of Structural Biology, Hospital for Sick Children, Toronto, ON, Canada
    Proteomics 7:944-60. 2007
  8. doi request reprint Challenges and rewards of interaction proteomics
    Shoshana J Wodak
    Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
    Mol Cell Proteomics 8:3-18. 2009
  9. ncbi request reprint GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks
    James Vlasblom
    Structural Biology and Biochemistry Program, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
    Bioinformatics 22:2178-9. 2006
  10. doi request reprint The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses
    Tuan On
    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
    Proteins 78:2075-89. 2010

Collaborators

Detail Information

Publications16

  1. doi request reprint Local coherence in genetic interaction patterns reveals prevalent functional versatility
    Shuye Pu
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto, ON, Canada
    Bioinformatics 24:2376-83. 2008
    ....
  2. pmc Up-to-date catalogues of yeast protein complexes
    Shuye Pu
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto ON, M5G 1X8
    Nucleic Acids Res 37:825-31. 2009
    ..Some of these partially supported and as yet unsupported complexes may be interesting candidates for experimental follow up. Both catalogues are freely available at: http://wodaklab.org/cyc2008/...
  3. pmc Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human
    Shuye Pu
    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Canada
    PLoS ONE 5:e14122. 2010
    ..Information on all the candidate CM domains and genes reported here is publicly available...
  4. pmc OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms
    Yanqi Hao
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto, ON, Canada
    Bioinformatics 27:883-4. 2011
    ..Any newly identified PPIs can be validated by checking whether their orthologs interact in another organism...
  5. pmc DAnCER: disease-annotated chromatin epigenetics resource
    Andrei L Turinsky
    Hospital for Sick Children, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    Nucleic Acids Res 39:D889-94. 2011
    ..DAnCER is freely available at http://wodaklab.org/dancer/...
  6. doi request reprint Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae
    Mohan Babu
    Banting and Best Department of Medical Research, Donnelly Centre, 160 College Street, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Nature 489:585-9. 2012
    ..Our analysis reveals unexpected physical associations underlying the membrane biology of eukaryotes and delineates the global topological landscape of the membrane interactome...
  7. ncbi request reprint Identifying functional modules in the physical interactome of Saccharomyces cerevisiae
    Shuye Pu
    Department of Structural Biology, Hospital for Sick Children, Toronto, ON, Canada
    Proteomics 7:944-60. 2007
    ..Lastly, it is shown that employing identical procedures to process the latest purification datasets significantly improves the convergence between the resulting interactome descriptions...
  8. doi request reprint Challenges and rewards of interaction proteomics
    Shoshana J Wodak
    Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
    Mol Cell Proteomics 8:3-18. 2009
    ..The challenges and rewards of interaction proteomics are reviewed here using as an example the latest comprehensive high throughput analyses of protein interactions in yeast...
  9. ncbi request reprint GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks
    James Vlasblom
    Structural Biology and Biochemistry Program, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada
    Bioinformatics 22:2178-9. 2006
    ..The public-domain open software environment Cytoscape has been developed with the goal of facilitating the design and development of such software tools by the scientific community...
  10. doi request reprint The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses
    Tuan On
    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
    Proteins 78:2075-89. 2010
    ..As such, in addition to informing on the evolution of CM as a system, this study provides a set of comparative genomic approaches that can be generally applied to any biological systems...
  11. doi request reprint High-throughput analyses and curation of protein interactions in yeast
    Shoshana J Wodak
    Molecular Structure and Function Program, Hospital for Sick Children, Toronto, ON, Canada
    Methods Mol Biol 759:381-406. 2011
    ....
  12. doi request reprint Protein-protein interaction networks: the puzzling riches
    Shoshana J Wodak
    Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5K 1X8, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada Electronic address
    Curr Opin Struct Biol 23:941-53. 2013
    ..Lastly, we present a brief overview of the literature-curated protein interaction data stored in public databases, which are often relied upon for independent validation of newly derived interaction networks. ..
  13. ncbi request reprint Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation
    Edyta Marcon
    Banting and Best Department of Medical Research, University of Toronto, CCBR, 160 College Street, Toronto, ON M5S 3E1, Canada
    Cell Rep 8:297-310. 2014
    ..We show that RCCD1 is a partner of histone H3K36 demethylase KDM8 and demonstrate that both are important for cell-cycle-regulated transcriptional repression in centromeric regions and accurate mitotic division. ..
  14. pmc Phenotypic switching induced by damaged matrix is associated with DNA methyltransferase 3A (DNMT3A) activity and nuclear localization in smooth muscle cells (SMC)
    Jia Xin Jiang
    Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada Division of Urology, Hospital for Sick Children, Toronto, Ontario, Canada Department of Physiology, University of Toronto, Toronto, Ontario, Canada
    PLoS ONE 8:e69089. 2013
    ..Matrix has a profound effect on the regulation of SMC phenotype, which is associated with altered expression, localization of DNMTs and discrete changes DNA methylation. ..
  15. doi request reprint Risk estimates for complex disorders: comparing personal genome testing and family history
    Lila Aiyar
    1 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada 2 Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada 3 Fetal Diagnostic Center, Kapiolani Medical Center for Women and Children, Honolulu, Hawaii, USA
    Genet Med 16:231-7. 2014
    ..g., family history analysis). We sought to analyze the concordance of risk estimates generated by family history analysis and by personal genome testing...
  16. ncbi request reprint Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    Nevan J Krogan
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, Ontario M5S 3E1, Canada
    Nature 440:637-43. 2006
    ..The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology...