Research Topics
Genomes and Genes | B AndrewsSummaryAffiliation: University of Toronto Country: Canada Publications
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Publications
A quantitative literature-curated gold standard for kinase-substrate pairsSara 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...- Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction networkLan 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... - Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiaeTeresa 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... - Bringing order to protein disorder through comparative genomics and genetic interactionsJeremy 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... - Yeast functional genomics and cell biology: no longer in the darkHelena 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... - Systematic genetic array analysis links the Saccharomyces cerevisiae SAGA/SLIK and NuA4 component Tra1 to multiple cellular processesStephen 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... - A genome-wide synthetic dosage lethality screen reveals multiple pathways that require the functioning of ubiquitin-binding proteins Rad23 and Dsk2Chang 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... 
The cyclin family of budding yeast: abundant use of a good ideaB 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...- Quantitative analysis of fitness and genetic interactions in yeast on a genome scaleAnastasia 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.... - Transcriptional coregulation by the cell integrity mitogen-activated protein kinase Slt2 and the cell cycle regulator Swi4K 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... - A family of cyclin-like proteins that interact with the Pho85 cyclin-dependent kinaseV 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... - A yeast taf17 mutant requires the Swi6 transcriptional activator for viability and shows defects in cell cycle-regulated transcriptionN 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... - Interactions between Pho85 cyclin-dependent kinase complexes and the Swi5 transcription factor in budding yeastV 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... - Regulation of cell cycle transcription factor Swi4 through auto-inhibition of DNA bindingK 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... - In vivo analysis of the domains of yeast Rvs167p suggests Rvs167p function is mediated through multiple protein interactionsK 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... - Systematic genetic analysis with ordered arrays of yeast deletion mutantsA 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... - Functions of Pho85 cyclin-dependent kinases in budding yeastJ 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... - 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 cerevisiaeY Ho
Department of Molecular and Medical Genetics, University of Toronto, ON, Canada
Proc Natl Acad Sci U S A 94:581-6. 1997.... - Mammalian Cdk5 is a functional homologue of the budding yeast Pho85 cyclin-dependent protein kinaseD 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... - The PCL2 (ORFD)-PHO85 cyclin-dependent kinase complex: a cell cycle regulator in yeastV 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... 
The genetic landscape of a cellMichael 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...- An essential component of a C-terminal domain phosphatase that interacts with transcription factor IIF in Saccharomyces cerevisiaeJ 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... - DRYGIN: a database of quantitative genetic interaction networks in yeastJudice 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... - The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distributionK 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... - Mapping pathways and phenotypes by systematic gene overexpressionRichelle 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... - Experimental approaches to identify genetic networksMichael 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... - High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutantsPaul 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... - Dissection of a complex phenotype by functional genomics reveals roles for the yeast cyclin-dependent protein kinase Pho85 in stress adaptation and cell integrityDongqing 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... - G1 transcription factors are differentially regulated in Saccharomyces cerevisiae by the Swi6-binding protein Stb1Michael 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... - Late-G1 cyclin-CDK activity is essential for control of cell morphogenesis in budding yeastJason 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... - CDK activity antagonizes Whi5, an inhibitor of G1/S transcription in yeastMichael 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... - Global mapping of the yeast genetic interaction networkAmy 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... - Regulation of cell polarity through phosphorylation of Bni4 by Pho85 G1 cyclin-dependent kinases in Saccharomyces cerevisiaeJian 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... - Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeastPinay 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... - Regulation of the yeast amphiphysin homologue Rvs167p by phosphorylationHelena 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... - Small open reading frames: not so small anymoreRichelle Sopko
Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8
Genome Res 16:314-5. 2006 - Old drugs, new tricks: using genetically sensitized yeast to reveal drug targetsTim Hughes
Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada M5G 1L6
Cell 116:5-7. 2004.... - Characterization of the yeast amphiphysins Rvs161p and Rvs167p reveals roles for the Rvs heterodimer in vivoHelena 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... - Interaction of the Saccharomyces cerevisiae cortical actin patch protein Rvs167p with proteins involved in ER to Golgi vesicle traffickingHelena 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... - Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeastAinslie 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... - Pho85, a multifunctional cyclin-dependent protein kinase in budding yeastDongqing 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... - Systematic mapping of genetic interaction networksScott 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... - Interaction of yeast Rvs167 and Pho85 cyclin-dependent kinase complexes may link the cell cycle to the actin cytoskeletonJ 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... - Cyclin partners determine Pho85 protein kinase substrate specificity in vitro and in vivo: control of glycogen biosynthesis by Pcl8 and Pcl10D 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... - The protein kinase Pho85 is required for asymmetric accumulation of the Ash1 protein in Saccharomyces cerevisiaeH 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... - SBF cell cycle regulator as a target of the yeast PKC-MAP kinase pathwayK 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... - Harvesting the genome's bounty: integrative genomicsP Jorgensen
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5
Cold Spring Harb Symp Quant Biol 68:431-43. 2003
Research Grants
- Mapping the reference genetic network of a eukaryotic cellChad 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. ..