B Andrews

Summary

Affiliation: University of Toronto
Country: Canada

Publications

  1. pmc A quantitative literature-curated gold standard for kinase-substrate pairs
    Sara Sharifpoor
    Department of Molecular Genetics, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, M3S 3E1, Canada
    Genome Biol 12:R39. 2011
  2. pmc Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
    Lan V Zhang
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    J Biol 4:6. 2005
  3. pmc Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
    Teresa Reguly
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
    J Biol 5:11. 2006
  4. pmc Bringing order to protein disorder through comparative genomics and genetic interactions
    Jeremy Bellay
    Department of Computer Science and Engineering, University of Minnesota, 200 Union Street SE, Minneapolis, MN 55455, USA
    Genome Biol 12:R14. 2011
  5. pmc Yeast functional genomics and cell biology: no longer in the dark
    Helena Friesen
    Department of Medical Genetics and Microbiology, University of Toronto, 1 Kings College Circle, Toronto, M5S 1A8, Canada
    Genome Biol 4:352. 2003
  6. pmc Systematic genetic array analysis links the Saccharomyces cerevisiae SAGA/SLIK and NuA4 component Tra1 to multiple cellular processes
    Stephen M T Hoke
    Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, N6A 5C1, Canada
    BMC Genet 9:46. 2008
  7. pmc A genome-wide synthetic dosage lethality screen reveals multiple pathways that require the functioning of ubiquitin-binding proteins Rad23 and Dsk2
    Chang Liu
    Institute of Biotechnology, Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78245, USA
    BMC Biol 7:75. 2009
  8. ncbi request reprint The cyclin family of budding yeast: abundant use of a good idea
    B Andrews
    Department of Molecular and Medical Genetics, University of Toronto, Canada
    Trends Genet 14:66-72. 1998
  9. pmc Quantitative analysis of fitness and genetic interactions in yeast on a genome scale
    Anastasia Baryshnikova
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Nat Methods 7:1017-24. 2010
  10. pmc Transcriptional coregulation by the cell integrity mitogen-activated protein kinase Slt2 and the cell cycle regulator Swi4
    K Baetz
    Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
    Mol Cell Biol 21:6515-28. 2001

Research Grants

Collaborators

Detail Information

Publications47

  1. pmc A quantitative literature-curated gold standard for kinase-substrate pairs
    Sara Sharifpoor
    Department of Molecular Genetics, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, M3S 3E1, Canada
    Genome Biol 12:R39. 2011
    ..We show that this gold standard can be used to assess published high-throughput datasets, suggesting that it will enable similar rigorous assessments in the future...
  2. pmc Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
    Lan V Zhang
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
    J Biol 4:6. 2005
    ..Recurring patterns of interconnection, or 'network motifs', have revealed biological insights for networks containing either one or two types of interaction...
  3. pmc Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
    Teresa Reguly
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto ON M5G 1X5, Canada
    J Biol 5:11. 2006
    ..Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference...
  4. pmc Bringing order to protein disorder through comparative genomics and genetic interactions
    Jeremy Bellay
    Department of Computer Science and Engineering, University of Minnesota, 200 Union Street SE, Minneapolis, MN 55455, USA
    Genome Biol 12:R14. 2011
    ..Despite its apparent functional importance, the sheer range of different roles played by protein disorder often makes its exact contribution difficult to interpret...
  5. pmc Yeast functional genomics and cell biology: no longer in the dark
    Helena Friesen
    Department of Medical Genetics and Microbiology, University of Toronto, 1 Kings College Circle, Toronto, M5S 1A8, Canada
    Genome Biol 4:352. 2003
    ..A report on the Cold Spring Harbor Laboratory meeting 'Yeast Cell Biology', Cold Spring Harbor, USA, 12-17 August 2003...
  6. pmc Systematic genetic array analysis links the Saccharomyces cerevisiae SAGA/SLIK and NuA4 component Tra1 to multiple cellular processes
    Stephen M T Hoke
    Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, N6A 5C1, Canada
    BMC Genet 9:46. 2008
    ..To identify genetic interactions for TRA1 and provide insight into its function we have performed a systematic genetic array analysis (SGA) on tra1SRR3413, an allele that is defective in transcriptional regulation...
  7. pmc A genome-wide synthetic dosage lethality screen reveals multiple pathways that require the functioning of ubiquitin-binding proteins Rad23 and Dsk2
    Chang Liu
    Institute of Biotechnology, Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78245, USA
    BMC Biol 7:75. 2009
    ..Although many strategies have been developed for substrate isolation, the identification of physiological targets of proteolytic pathways has proven to be quite challenging...
  8. ncbi request reprint The cyclin family of budding yeast: abundant use of a good idea
    B Andrews
    Department of Molecular and Medical Genetics, University of Toronto, Canada
    Trends Genet 14:66-72. 1998
    ..The cyclin family of budding yeast is reviewed from a functional perspective with an emphasis on what genetic and biochemical experiments have revealed about cyclin-CDK substrates...
  9. pmc Quantitative analysis of fitness and genetic interactions in yeast on a genome scale
    Anastasia Baryshnikova
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Nat Methods 7:1017-24. 2010
    ....
  10. pmc Transcriptional coregulation by the cell integrity mitogen-activated protein kinase Slt2 and the cell cycle regulator Swi4
    K Baetz
    Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
    Mol Cell Biol 21:6515-28. 2001
    ..Our results establish a new Slt2-dependent mode of Swi4 regulation and suggest roles for Swi4 beyond its prominent role in controlling cell cycle transcription...
  11. pmc A family of cyclin-like proteins that interact with the Pho85 cyclin-dependent kinase
    V Measday
    Department of Molecular and Medical Genetics, University of Toronto, Canada
    Mol Cell Biol 17:1212-23. 1997
    ..Our studies suggest that Pho85 associates with multiple cyclins and that subsets of cyclins may direct Pho85 to perform distinct roles in cell growth and division...
  12. pmc A yeast taf17 mutant requires the Swi6 transcriptional activator for viability and shows defects in cell cycle-regulated transcription
    N Macpherson
    Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M55 1A8, Canada
    Genetics 154:1561-76. 2000
    ..The cell cycle and transcriptional defects caused by taf17(slm7-1) are consistent with the role of TAF(II)s as modulators of transcriptional activation and may reflect a role for TAF17 in regulating activation by SBF and MBF...
  13. ncbi request reprint Interactions between Pho85 cyclin-dependent kinase complexes and the Swi5 transcription factor in budding yeast
    V Measday
    Department of Molecular and Medical Genetics, University of Toronto, Rm 4285 Medical Sciences Building, 1 Kings College Circle, Toronto, Ontario, Canada M5S 1A8
    Mol Microbiol 35:825-34. 2000
    ..Our results are consistent with misregulation of Swi5 activity in vivo in the absence of Pho85 and implicate Swi5 as a potential substrate of Pho85 cyclin-dependent kinase complexes...
  14. pmc Regulation of cell cycle transcription factor Swi4 through auto-inhibition of DNA binding
    K Baetz
    Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
    Mol Cell Biol 19:6729-41. 1999
    ..The interaction of the carboxy-terminal region of Swi4 with Swi6 alleviates this inhibition, allowing Swi4 to bind DNA...
  15. pmc In vivo analysis of the domains of yeast Rvs167p suggests Rvs167p function is mediated through multiple protein interactions
    K Colwill
    Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
    Genetics 152:881-93. 1999
    ..Upon activation, Rvs167p enters a multiprotein complex, making critical contacts in its BAR domain and redundant or minor contacts with its SH3 domain...
  16. ncbi request reprint Systematic genetic analysis with ordered arrays of yeast deletion mutants
    A H Tong
    Banting and Best Department of Medical Research, University of Toronto, Toronto ON, Canada M5G 1L6
    Science 294:2364-8. 2001
    ..Systematic application of this approach should produce a global map of gene function...
  17. ncbi request reprint Functions of Pho85 cyclin-dependent kinases in budding yeast
    J Moffat
    Department of Molecular and Medical Genetics, University of Toronto, Canada
    Prog Cell Cycle Res 4:97-106. 2000
    ..In this chapter, we review the functions of the various Pcl-Pho85 complexes in budding yeast. We focus on the known biological roles of Pho85 with an emphasis on Pho85 substrates and cyclin-Cdk specificity...
  18. pmc Role of the casein kinase I isoform, Hrr25, and the cell cycle-regulatory transcription factor, SBF, in the transcriptional response to DNA damage in Saccharomyces cerevisiae
    Y Ho
    Department of Molecular and Medical Genetics, University of Toronto, ON, Canada
    Proc Natl Acad Sci U S A 94:581-6. 1997
    ....
  19. pmc Mammalian Cdk5 is a functional homologue of the budding yeast Pho85 cyclin-dependent protein kinase
    D Huang
    Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, Canada M5S 1A8
    Proc Natl Acad Sci U S A 96:14445-50. 1999
    ..Our results suggest the existence of a functionally conserved pathway involving Cdks and actin-regulatory proteins that promotes reorganization of the actin cytoskeleton in response to regulatory signals...
  20. ncbi request reprint The PCL2 (ORFD)-PHO85 cyclin-dependent kinase complex: a cell cycle regulator in yeast
    V Measday
    Department of Molecular and Medical Genetics, University of Toronto, Ontario, Canada
    Science 266:1391-5. 1994
    ..Because PHO85 and another cyclin-like molecule, PHO80, also take part in inorganic phosphate metabolism, this cdk enzyme may integrate responses to nutritional conditions with the cell cycle...
  21. doi request reprint The genetic landscape of a cell
    Michael Costanzo
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Science 327:425-31. 2010
    ..We also demonstrate that extensive and unbiased mapping of the genetic landscape provides a key for interpretation of chemical-genetic interactions and drug target identification...
  22. pmc An essential component of a C-terminal domain phosphatase that interacts with transcription factor IIF in Saccharomyces cerevisiae
    J Archambault
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6
    Proc Natl Acad Sci U S A 94:14300-5. 1997
    ..Sequence comparison reveals that residues 173-357 of Fcp1 correspond to an amino acid motif present in proteins of unknown function predicted in many organisms...
  23. pmc DRYGIN: a database of quantitative genetic interaction networks in yeast
    Judice L Y Koh
    Banting and Best Department of Medical Research, The Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, Canada
    Nucleic Acids Res 38:D502-7. 2010
    ..DRYGIN version 1.0 currently holds more than 5.4 million measurements of genetic interacting pairs involving approximately 4500 genes, and is available at http://drygin.ccbr.utoronto.ca...
  24. pmc The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution
    K Colwill
    Programme in Molecular Biology adn Cancer, Mount Sinai Hospital, Toronto, Canada
    EMBO J 15:265-75. 1996
    ..Overexpression of the active Clk/Sty kinase caused a redistribution of SR proteins within the nucleus. These results suggest that Clk/Sty kinase directly regulates the activity and compartmentalization of SR splicing factors...
  25. ncbi request reprint Mapping pathways and phenotypes by systematic gene overexpression
    Richelle Sopko
    Department of Medical Genetics and Microbiology, University of Toronto, 1 King s College Circle, Toronto, Ontario M5S 1A8, Canada
    Mol Cell 21:319-30. 2006
    ..Large-scale application of this approach should provide a strategy for identifying target molecules regulated by specific signaling pathways...
  26. ncbi request reprint Experimental approaches to identify genetic networks
    Michael Costanzo
    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
    Curr Opin Biotechnol 17:472-80. 2006
    ..Many of these experimental approaches have been adopted and adapted to study other systems, including worm, fly, fish and mammalian cultured cells, using an ingenious set of molecular tools...
  27. pmc High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants
    Paul Jorgensen
    Department of Medical Genetics and Microbiology, University of Toronto, Ontario M5S 1A8, Canada
    Genetics 162:1091-9. 2002
    ..In principle, SGAM should be applicable to the analysis of multigenic traits. Large-scale construction of ordered mutations in other model organisms would broaden the application of this approach...
  28. pmc Dissection of a complex phenotype by functional genomics reveals roles for the yeast cyclin-dependent protein kinase Pho85 in stress adaptation and cell integrity
    Dongqing Huang
    Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8
    Mol Cell Biol 22:5076-88. 2002
    ..The integration of multiple genomics approaches is likely to be a generally useful strategy for extracting functional information from pleiotropic mutant phenotypes...
  29. pmc G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1
    Michael Costanzo
    Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8
    Mol Cell Biol 23:5064-77. 2003
    ..Chromatin immunoprecipitation experiments confirm that Stb1 localizes to promoters of MBF-regulated genes. Our data indicate that, contrary to previous models, MBF and SBF have unique components and might be distinctly regulated...
  30. ncbi request reprint Late-G1 cyclin-CDK activity is essential for control of cell morphogenesis in budding yeast
    Jason Moffat
    Department of Medical Genetics and Microbiology, University of Toronto, 1 Kings College Circle, Rm 4287, Medical Sciences Building, Toronto, Ontario, M5S 1A8, Canada
    Nat Cell Biol 6:59-66. 2004
    ..We conclude that a burst of late G1 cyclin-CDK activity is essential for establishing cell polarity and development of the cleavage apparatus...
  31. ncbi request reprint CDK activity antagonizes Whi5, an inhibitor of G1/S transcription in yeast
    Michael Costanzo
    Department of Medical Genetics and Microbiology, University of Toronto, 1 King s College Circle, Toronto, M5S 1A8, Canada
    Cell 117:899-913. 2004
    ..Elimination of CDK activity at the end of mitosis allows Whi5 to reenter the nucleus to again repress G1/S transcription. These findings harmonize G1/S control in eukaryotes...
  32. ncbi request reprint Global mapping of the yeast genetic interaction network
    Amy Hin Yan Tong
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5G 1L6
    Science 303:808-13. 2004
    ..Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms...
  33. pmc Regulation of cell polarity through phosphorylation of Bni4 by Pho85 G1 cyclin-dependent kinases in Saccharomyces cerevisiae
    Jian Zou
    Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Mol Biol Cell 20:3239-50. 2009
    ..Our data suggest that misregulated Bni4 may bind in an uncontrolled manner to an essential component that resides at the bud neck, causing catastrophic morphogenesis defects...
  34. doi request reprint Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeast
    Pinay Kainth
    Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ont M5S3E1E1, Canada
    Methods 48:258-64. 2009
    ..The method is extensible to any transcription factor or signalling pathway for which an appropriate reporter gene can be devised...
  35. pmc Regulation of the yeast amphiphysin homologue Rvs167p by phosphorylation
    Helena Friesen
    Department of Molecular and Medical Genetics, University of Toronto, Toronto, Canada, M5S 1A8
    Mol Biol Cell 14:3027-40. 2003
    ..Our results suggest that phosphorylation of Rvs167p by a cyclin-dependent kinase and by a MAP kinase is an important mechanism for regulating protein complexes involved in actin cytoskeleton function...
  36. ncbi request reprint Small open reading frames: not so small anymore
    Richelle Sopko
    Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8
    Genome Res 16:314-5. 2006
  37. ncbi request reprint Old drugs, new tricks: using genetically sensitized yeast to reveal drug targets
    Tim Hughes
    Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada M5G 1L6
    Cell 116:5-7. 2004
    ....
  38. pmc Characterization of the yeast amphiphysins Rvs161p and Rvs167p reveals roles for the Rvs heterodimer in vivo
    Helena Friesen
    Department of Medical Genetics and Microbiology, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 1A8
    Mol Biol Cell 17:1306-21. 2006
    ..Our studies implicate heterodimerization of amphiphysin family proteins in various functions related to cell polarity, cell integrity, and vesicle trafficking during vegetative growth and the mating response...
  39. pmc Interaction of the Saccharomyces cerevisiae cortical actin patch protein Rvs167p with proteins involved in ER to Golgi vesicle trafficking
    Helena Friesen
    Department of Molecular and Medical Genetics, University of Toronto, Ontario, Canada
    Genetics 170:555-68. 2005
    ..Since Rvs167p has a previously characterized role in endocytosis and we have shown here that it interacts with proteins involved in Golgi vesicle trafficking, we suggest that Rvs167p may have a general role in vesicle trafficking...
  40. ncbi request reprint Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast
    Ainslie B Parsons
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
    Cell 126:611-25. 2006
    ..This compendium should serve as a valuable key for interpreting cellular effects of novel compounds with similar activities...
  41. ncbi request reprint Pho85, a multifunctional cyclin-dependent protein kinase in budding yeast
    Dongqing Huang
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Mol Microbiol 66:303-14. 2007
    ..Recently, genetic screens for synthetic lethality and synthetic dosage lethality, and proteomic screens for in vitro Pho85 substrates, have revealed more details about how Pho85 functions to regulate a variety of cellular processes...
  42. doi request reprint Systematic mapping of genetic interaction networks
    Scott J Dixon
    Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 1A7, Canada
    Annu Rev Genet 43:601-25. 2009
    ..Together, our emerging knowledge of the genetic wiring diagrams of eukaryotic and prokaryotic cells is providing a new understanding of the relationship between genotype and phenotype...
  43. ncbi request reprint Interaction of yeast Rvs167 and Pho85 cyclin-dependent kinase complexes may link the cell cycle to the actin cytoskeleton
    J Lee
    Department of Molecular and Medical Genetics University of Toronto Toronto Canada
    Curr Biol 8:1310-21. 1998
    ..Loss of Pcl1, Pcl2 and related Pho85 cyclins results in budding defects, suggesting that Pcl-Pho85 complexes function in cell morphogenesis early in the cell cycle; their precise role is not clear, however...
  44. pmc Cyclin partners determine Pho85 protein kinase substrate specificity in vitro and in vivo: control of glycogen biosynthesis by Pcl8 and Pcl10
    D Huang
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202 5122, USA
    Mol Cell Biol 18:3289-99. 1998
    ..This genetic result suggests an additional role for Pho85 in the negative regulation of glycogen accumulation that is independent of Pcl8 and Pcl10...
  45. ncbi request reprint The protein kinase Pho85 is required for asymmetric accumulation of the Ash1 protein in Saccharomyces cerevisiae
    H J McBride
    Department of Pathology, University of Utah, Salt Lake City, UT 84132, USA
    Mol Microbiol 42:345-53. 2001
    ..We observe that Ash1 protein is phosphorylated by Pho85 in vitro and that Ash1 stability increases in a pho85 mutant. These data suggest that phosphorylation of Ash1 by Pho85 governs stability of Ash1 protein...
  46. ncbi request reprint SBF cell cycle regulator as a target of the yeast PKC-MAP kinase pathway
    K Madden
    Department of Biology, Yale University, Post Office Box 208103, New Haven, CT 06520 8103, USA
    Science 275:1781-4. 1997
    ..These studies provide evidence for a direct role of the PKC1 pathway in the regulation of the yeast cell cycle and cell growth and indicate that conserved signaling pathways can act to control key regulators of cell division...
  47. ncbi request reprint Harvesting the genome's bounty: integrative genomics
    P Jorgensen
    Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
    Cold Spring Harb Symp Quant Biol 68:431-43. 2003

Research Grants1

  1. Mapping the reference genetic network of a eukaryotic cell
    Chad L Myers; Fiscal Year: 2010
    ..Genetic interaction reference maps produced by the project will provide valuable insights into gene function, drug target analysis and the link between genotype and phenotype, including the genetic basis of human disease. ..