Charles Boone

Summary

Affiliation: University of Toronto
Country: Canada

Publications

  1. pmc SH3 interactome conserves general function over specific form
    Xiaofeng Xin
    The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Mol Syst Biol 9:652. 2013
  2. pmc Regulatory circuitry governing morphogenesis in Saccharomyces cerevisiae and Candida albicans
    Rebecca S Shapiro
    Department of Molecular Genetics University of Toronto Toronto, ON Canada
    Cell Cycle 11:4294-5. 2012
  3. pmc Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pH(c) in Saccharomyces cerevisiae
    Rick Orij
    Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
    Genome Biol 13:R80. 2012
  4. 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
  5. 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
  6. 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
  7. pmc An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae
    Guillaume Lesage
    Department of Biology, McGill University, Montréal PQ H3A 1B1, Canada
    BMC Genet 6:8. 2005
  8. ncbi Exploring genetic interactions and networks with yeast
    Charles Boone
    Banting and Best Department of Medical Research and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada
    Nat Rev Genet 8:437-49. 2007
  9. pmc Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins
    Raffi Tonikian
    Terrence Donnelly Center for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    PLoS Biol 7:e1000218. 2009
  10. pmc RMI1/NCE4, a suppressor of genome instability, encodes a member of the RecQ helicase/Topo III complex
    Michael Chang
    Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
    EMBO J 24:2024-33. 2005

Detail Information

Publications105 found, 100 shown here

  1. pmc SH3 interactome conserves general function over specific form
    Xiaofeng Xin
    The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Mol Syst Biol 9:652. 2013
    ..Nevertheless, orthologous SH3 domain-mediated interactions are highly rewired. Our results suggest a model of network evolution where general function of the SH3 domain network is conserved over its specific form...
  2. pmc Regulatory circuitry governing morphogenesis in Saccharomyces cerevisiae and Candida albicans
    Rebecca S Shapiro
    Department of Molecular Genetics University of Toronto Toronto, ON Canada
    Cell Cycle 11:4294-5. 2012
    ..Comment on: Ryan O, et al. Science 2012; 337:1353-6...
  3. pmc Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pH(c) in Saccharomyces cerevisiae
    Rick Orij
    Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
    Genome Biol 13:R80. 2012
    ..Since small changes in pH(c) can lead to major changes in metabolism, signal transduction, and phenotype, we decided to analyze pH(c) control...
  4. 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...
  5. 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...
  6. 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...
  7. pmc An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae
    Guillaume Lesage
    Department of Biology, McGill University, Montréal PQ H3A 1B1, Canada
    BMC Genet 6:8. 2005
    ....
  8. ncbi Exploring genetic interactions and networks with yeast
    Charles Boone
    Banting and Best Department of Medical Research and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada
    Nat Rev Genet 8:437-49. 2007
    ..A comparative understanding of genetic-interaction networks promises insights into some long-standing genetic problems, such as the nature of quantitative traits and the basis of complex inherited disease...
  9. pmc Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins
    Raffi Tonikian
    Terrence Donnelly Center for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    PLoS Biol 7:e1000218. 2009
    ....
  10. pmc RMI1/NCE4, a suppressor of genome instability, encodes a member of the RecQ helicase/Topo III complex
    Michael Chang
    Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
    EMBO J 24:2024-33. 2005
    ..In addition, rmi1Delta strains fail to fully activate Rad53 upon exposure to DNA-damaging agents, suggesting that Rmi1 is also an important part of the Rad53-dependent DNA damage response...
  11. 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...
  12. pmc Identifying transcription factor functions and targets by phenotypic activation
    Gordon Chua
    Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 1A8
    Proc Natl Acad Sci U S A 103:12045-50. 2006
    ..The general strategy outlined here presents a straightforward approach to discovery of TF activities and mapping targets that could be adapted to any organism with transgenic technology...
  13. ncbi Formins direct Arp2/3-independent actin filament assembly to polarize cell growth in yeast
    Marie Evangelista
    Department of Biology, Queen s University, Kingston, Ontario, Canada
    Nat Cell Biol 4:260-9. 2002
    ..Unlike the assembly of cortical actin patches, cable assembly requires profilin but not the Arp2/3 complex. Thus formins control a distinct pathway for assembling actin filaments that organize the overall polarity of the cell...
  14. pmc Elg1 forms an alternative RFC complex important for DNA replication and genome integrity
    Mohammed Bellaoui
    Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
    EMBO J 22:4304-13. 2003
    ..We propose that Elg1-RFC functions both in normal DNA replication and in the DNA damage response...
  15. doi Global map of SUMO function revealed by protein-protein interaction and genetic networks
    Taras Makhnevych
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
    Mol Cell 33:124-35. 2009
    ....
  16. ncbi Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone
    Rongmin Zhao
    Department of Biochemistry, Medical Sciences Building, 1 King s College Circle, University of Toronto, Toronto, ON, M5S 1A8, Canada
    Cell 120:715-27. 2005
    ..These cofactors interact physically and functionally with the conserved AAA(+)-type DNA helicases Rvb1/Rvb2, which are key components of several chromatin remodeling factors, thereby linking Hsp90 to epigenetic gene regulation...
  17. pmc Genetic dissection of parallel sister-chromatid cohesion pathways
    Hong Xu
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 1A8, Canada
    Genetics 176:1417-29. 2007
    ....
  18. ncbi 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...
  19. 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
    ....
  20. ncbi The synthetic genetic interaction spectrum of essential genes
    Armaity P Davierwala
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario, M5G 1L6, Canada
    Nat Genet 37:1147-52. 2005
    ....
  21. doi Dosage suppression genetic interaction networks enhance functional wiring diagrams of the cell
    Leslie Magtanong
    Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
    Nat Biotechnol 29:505-11. 2011
    ..This work suggests that integrating the results of dosage suppression studies with other interaction networks could generate insights into the functional wiring diagram of a cell...
  22. pmc Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs
    Sara Sharifpoor
    Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, Ontario M5S3E1, Canada
    Genome Res 22:791-801. 2012
    ..Our study provides a valuable resource to unravel novel functional relationships and pathways regulated by kinases and outlines a general strategy for deciphering mutant phenotypes from large-scale GI networks...
  23. doi Charting the genetic interaction map of a cell
    Michael Costanzo
    Banting and Best Department of Medical Research and Department of Molecular Genetics, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
    Curr Opin Biotechnol 22:66-74. 2011
    ....
  24. ncbi 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...
  25. pmc Molecular chaperone Hsp90 stabilizes Pih1/Nop17 to maintain R2TP complex activity that regulates snoRNA accumulation
    Rongmin Zhao
    Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
    J Cell Biol 180:563-78. 2008
    ..As a consequence, the chaperone is shown to affect box C/D accumulation and maintenance, especially under stress conditions. Hsp90 and R2TP proteins are also involved in the proper accumulation of box H/ACA small nucleolar RNAs...
  26. pmc Functional analysis with a barcoder yeast gene overexpression system
    Alison C Douglas
    Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
    G3 (Bethesda) 2:1279-89. 2012
    ..As a proof-of-principle, we describe the properties of the barFLEX overexpression collection and its application in synthetic dosage lethality studies under different environmental conditions...
  27. pmc The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast
    Gabriel Musso
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Genome Res 18:1092-9. 2008
    ....
  28. ncbi 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...
  29. pmc Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress
    Johnny M Tkach
    Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
    Nat Cell Biol 14:966-76. 2012
    ..This method identifies response pathways that were not detected in genetic and protein interaction screens, and can be readily applied to any form of chemical or genetic stress to reveal cellular response pathways...
  30. doi Yeast Barcoders: a chemogenomic application of a universal donor-strain collection carrying bar-code identifiers
    Zhun Yan
    Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
    Nat Methods 5:719-25. 2008
    ..1% of all essential yeast genes. These experiments validate both the Barcoders and the DAmP strain collection as useful tools for genome-wide chemical-genetic assays...
  31. doi SGAM: an array-based approach for high-resolution genetic mapping in Saccharomyces cerevisiae
    Michael Costanzo
    Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, M5S 3E1, Toronto, ON, Canada
    Methods Mol Biol 548:37-53. 2009
    ....
  32. ncbi Chemical-genetic approaches for exploring the mode of action of natural products
    Andres Lopez
    Banting and Best Department of Medical Research and Department of Medical Genetics and Microbiology, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Canada
    Prog Drug Res 66:237, 239-71. 2008
    ..Extensive application of chemical genetics in yeast has the potential to develop a small molecule inhibitor for the majority of all approximately 6000 yeast genes...
  33. pmc Global linkage map connects meiotic centromere function to chromosome size in budding yeast
    Anastasia Baryshnikova
    Banting and Best Department of Medical Research, The Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    G3 (Bethesda) 3:1741-51. 2013
    ....
  34. pmc Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis
    Franco J Vizeacoumar
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    J Cell Biol 188:69-81. 2010
    ..Although we focused on spindle disassembly in a proof-of-principle study, our integrated HCS-SGA method can be applied to virtually any pathway, making it a powerful means for identifying specific cellular functions...
  35. ncbi Exploration of essential gene functions via titratable promoter alleles
    Sanie Mnaimneh
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, ON M5G 1L6, Canada
    Cell 118:31-44. 2004
    ..We furthermore show that these strains are compatible with automated genetic analysis. This study underscores the importance of analyzing mutant phenotypes and provides a resource to complement the yeast knockout collection...
  36. pmc PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae
    Ke Jin
    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
    Nucleic Acids Res 40:D687-94. 2012
    ..0 contains 78,194 morphological images and 1,909,914 cells covering six subcellular compartments or structures for 775 ts alleles spanning 491 essential genes. PhenoM is freely available at http://phenom.ccbr.utoronto.ca/...
  37. pmc Protein complexes are central in the yeast genetic landscape
    Magali Michaut
    The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    PLoS Comput Biol 7:e1001092. 2011
    ..Furthermore the analysis methods we develop are applicable to other species for which genetic interactions will progressively become more available...
  38. pmc Mms1 and Mms22 stabilize the replisome during replication stress
    Jessica A Vaisica
    Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
    Mol Biol Cell 22:2396-408. 2011
    ..Taken together, these data indicate that Mms1 and Mms22 are important for maintaining the integrity of the replisome when DNA replication forks are slowed by hydroxyurea and thereby promote efficient recovery from replication stress...
  39. pmc Chemical-genetic profiling of imidazo[1,2-a]pyridines and -pyrimidines reveals target pathways conserved between yeast and human cells
    Lisa Yu
    Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
    PLoS Genet 4:e1000284. 2008
    ....
  40. pmc Global analysis of SUMO chain function reveals multiple roles in chromatin regulation
    Tharan Srikumar
    Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
    J Cell Biol 201:145-63. 2013
    ....
  41. pmc ITSN-1 controls vesicle recycling at the neuromuscular junction and functions in parallel with DAB-1
    Wei Wang
    Program in Developmental and Stem Cell Biology, The Hospital for Sick Children 101 College Street, TMDT East Tower, Toronto, Ontario M5G 1L7, Canada
    Traffic 9:742-54. 2008
    ..These results show for the first time that intersectin and Eps15 proteins function in the same genetic pathway, and appear to function synergistically with the clathrin-coat-associated sorting protein, Disabled, for viability...
  42. 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...
  43. doi Global gene deletion analysis exploring yeast filamentous growth
    Owen Ryan
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
    Science 337:1353-6. 2012
    ..cerevisiae and C. albicans...
  44. ncbi 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...
  45. doi Synthetic genetic array (SGA) analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe
    Anastasia Baryshnikova
    Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
    Methods Enzymol 470:145-79. 2010
    ....
  46. pmc Systematic exploration of essential yeast gene function with temperature-sensitive mutants
    Zhijian Li
    Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Nat Biotechnol 29:361-7. 2011
    ..This mutant collection should facilitate a wide range of systematic studies aimed at understanding the functions of essential genes...
  47. pmc Shifted Transversal Design smart-pooling for high coverage interactome mapping
    Xiaofeng Xin
    Banting and Best Department of Medical Research and Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Genome Res 19:1262-9. 2009
    ..Screening-sequencing remains an appropriate method for quickly producing low-coverage interactomes, while STD pooling appears as the method of choice for obtaining maps with higher coverage...
  48. ncbi Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways
    Ainslie B Parsons
    Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5G 1L6, Canada
    Nat Biotechnol 22:62-9. 2004
    ..This method thus provides a powerful means for inferring mechanism of action...
  49. doi 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...
  50. ncbi Genomic approaches for identifying DNA damage response pathways in S. cerevisiae
    Michael Chang
    Biochemistry, University of Toronto, Toronto, Ontario, Canada
    Methods Enzymol 409:213-35. 2006
    ..These techniques take advantage of the S. cerevisiae gene deletion mutant collection, either as an ordered array or as a pool, and can be automated for high throughput...
  51. pmc Mrc1 is required for sister chromatid cohesion to aid in recombination repair of spontaneous damage
    Hong Xu
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 1A8, Canada
    Mol Cell Biol 24:7082-90. 2004
    ....
  52. pmc Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II
    Nevan J Krogan
    Banting and Best Department of Medical Research, Toronto Yeast Proteomics Organization, University of Toronto, Toronto, Ontario, Canada M5G 1L6
    Mol Cell Biol 23:4207-18. 2003
    ..SET2 also interacts genetically with components of the Set1 and Set3 complexes, suggesting that Set1, Set2, and Set3 similarly affect transcription by RNAPII...
  53. pmc A specificity map for the PDZ domain family
    Raffi Tonikian
    Terrence Donnelly Center for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    PLoS Biol 6:e239. 2008
    ..These findings indicate that many viruses produce PDZ ligands that disrupt host protein complexes for their own benefit, and that highly pathogenic strains target PDZ domains involved in cell polarity and growth...
  54. ncbi A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules
    Amy Hin Yan Tong
    Banting and Best Department of Medical Research and Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5G 1L6
    Science 295:321-4. 2002
    ..Las17 (Bee1), a member of the Wiskott-Aldrich Syndrome protein (WASP) family of actin-assembly proteins, showed multiple SH3 interactions, many of which were confirmed in vivo by coimmunoprecipitation...
  55. doi Combining functional genomics and chemical biology to identify targets of bioactive compounds
    Cheuk Hei Ho
    Banting and Best Department of Medical Research and Department of Molecular Genetics, The Donnelly Centre, University of Toronto, 160 College St, Toronto, ON, Canada M5S 3E1
    Curr Opin Chem Biol 15:66-78. 2011
    ..Here we review yeast chemical genomic assays strategies for drug target identification...
  56. pmc A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds
    Cheuk Hei Ho
    Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
    Nat Biotechnol 27:369-77. 2009
    ..We used the MoBY-ORF library to identify the genetic basis of several drug-resistant mutants and in this analysis discovered a new class of sterol-binding compounds...
  57. pmc Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes
    Scott J Dixon
    Banting and Best Department of Medical Research and Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Room 1330, Toronto, ON, Canada M5S 3E1
    Proc Natl Acad Sci U S A 105:16653-8. 2008
    ..We define a conserved yeast network (CYN) composed of 106 genes and 144 interactions and suggest that this network may help understand the shared biology of diverse eukaryotic species...
  58. ncbi 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
    ....
  59. doi Chemical-genomic profiling: systematic analysis of the cellular targets of bioactive molecules
    Kerry Andrusiak
    Banting and Best Department of Medical Research and Department of Molecular Genetics, Donnelly Centre, University of Toronto, 160 College St, Toronto, ON, Canada M5S 3E1
    Bioorg Med Chem 20:1952-60. 2012
    ..Herein, we briefly review CG profiling, focusing on emerging cross-species technologies and novel drug-synergy applications, as well as outlining needs within the field...
  60. pmc A comparative genomic approach for identifying synthetic lethal interactions in human cancer
    Raamesh Deshpande
    Authors Affiliations Department of Computer Science and Engineering Program in Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis Department of Surgery, Mayo Clinic, Rochester, Minnesota Department of Laboratory Medicine and Pathology, Molecular Genetics Lab, Mayo Clinic, Rochester, Minnesota Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada Chemical Genomics Research Group, RIKEN Advance Science Institute, Saitama, Japan and Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
    Cancer Res 73:6128-36. 2013
    ..These results suggest therapeutic targets for cancers harboring mutations in SMARCB1 or ASPSCR1 and highlight the potential of a targeted, cross-species strategy for identifying synthetic lethal interactions relevant to human cancer...
  61. pmc Network evolution: rewiring and signatures of conservation in signaling
    Mark G F Sun
    Department of Computer Science, University of Toronto, Toronto, Canada
    PLoS Comput Biol 8:e1002411. 2012
    ..In summary, we uncover several network evolution mechanisms likely to generalize across peptide recognition modules...
  62. ncbi Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries
    Raffi Tonikian
    Department of Molecular and Medical Genetics, University of Toronto, 4398 Medical Sciences Building, 1 King s College Circle, University of Toronto, Toronto, Ontario, Canada M5S 1A8
    Nat Protoc 2:1368-86. 2007
    ..The affinity selection process described thereafter enables a single researcher to efficiently probe the recognition profiles of numerous PRMs in a 1 week time period...
  63. doi A picture is worth a thousand words: genomics to phenomics in the yeast Saccharomyces cerevisiae
    Franco J Vizeacoumar
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
    FEBS Lett 583:1656-61. 2009
    ....
  64. pmc Mode of selection and experimental evolution of antifungal drug resistance in Saccharomyces cerevisiae
    James B Anderson
    Department of Botany, University of Toronto, Mississauga, Ontario L5L 1C6, Canada
    Genetics 163:1287-98. 2003
    ..In a variation of experiment 2, haploids showed a higher frequency of resistance than diploids, suggesting that degree of dominance and ploidy are important factors in the evolution of antifungal drug resistance...
  65. ncbi Yeast genomics and proteomics in drug discovery and target validation
    Ainslie B Parsons
    Banting and Best Department of Medical Research, Department of Molecular and Medical Genetics, University of Toronto, Toronto, M3G 1L6 Canada
    Prog Cell Cycle Res 5:159-66. 2003
    ..This review will focus on current genetic, genomic, and proteomic methodologies in S. cerevisiae that have the potential to be useful in drug discovery and target validation...
  66. pmc Mapping the functional yeast ABC transporter interactome
    Jamie Snider
    Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Nat Chem Biol 9:565-72. 2013
    ..The interaction network presented here will be a powerful resource for increasing our fundamental understanding of the cellular role and regulation of ABC transporters. ..
  67. doi Mapping interactomes with high coverage and efficiency using the shifted transversal design
    Xiaofeng Xin
    Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
    Methods Mol Biol 812:147-59. 2012
    ..This chapter focuses on the construction and usage of STD arrays for large-scale yeast two-hybrid interactome mapping...
  68. pmc A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities
    Franco J Vizeacoumar
    1 Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada 2 Saskatchewan Cancer Agency, Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
    Mol Syst Biol 9:696. 2013
    ..Our reference network suggests that many cancer vulnerabilities remain to be discovered through systematic derivation of a network of differentially essential genes in an isogenic cancer cell model. ..
  69. doi eSGA: E. coli synthetic genetic array analysis
    Gareth Butland
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada
    Nat Methods 5:789-95. 2008
    ....
  70. pmc Genome-wide lethality screen identifies new PI4,5P2 effectors that regulate the actin cytoskeleton
    Anjon Audhya
    Department of Cellular and Molecular Medicine, The Howard Hughes Medical Institute, University of California, San Diego School of Medicine, La Jolla, CA, USA
    EMBO J 23:3747-57. 2004
    ..Together, these data suggest that Slm1 and Slm2 function downstream of PI4,5P(2) and the TORC2 kinase pathway to control actin cytoskeleton organization...
  71. pmc Systematic yeast synthetic lethal and synthetic dosage lethal screens identify genes required for chromosome segregation
    Vivien Measday
    Wine Research Centre and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
    Proc Natl Acad Sci U S A 102:13956-61. 2005
    ..Our study shows that systematic genetic screens are a powerful means to discover roles for uncharacterized genes and genes with alternative functions in chromosome maintenance that may not be discovered by using proteomics approaches...
  72. ncbi Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile
    Maya Schuldiner
    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94143, USA
    Cell 123:507-19. 2005
    ..Extension of this strategy to other logically connected gene subsets in yeast and higher eukaryotes should provide critical insights into the functional/organizational principles of biological systems...
  73. ncbi Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex
    Michael Christopher Keogh
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Cell 123:593-605. 2005
    ..This pathway apparently acts to negatively regulate transcription because deleting the genes for Set2 or Rpd3C(S) bypasses the requirement for the positive elongation factor Bur1/Bur2...
  74. ncbi Functional genomics and proteomics: charting a multidimensional map of the yeast cell
    Gary D Bader
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 460, 10021, New York, NY, USA
    Trends Cell Biol 13:344-56. 2003
    ..Here we review several different genomics and proteomics technologies and describe bioinformatics methods for exploring these data to make new discoveries...
  75. ncbi Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery
    Terry Roemer
    Elitra Canada, Montreal, Quebec, Canada, H2X 3Y8
    Mol Microbiol 50:167-81. 2003
    ..albicans essential gene set, and their respective conditional mutant strains may be directly used as sensitive whole-cell assays for drug screening...
  76. ncbi From worm genetic networks to complex human diseases
    Howard Bussey
    Nat Genet 38:862-3. 2006
  77. pmc The GTPase Arf1p and the ER to Golgi cargo receptor Erv14p cooperate to recruit the golgin Rud3p to the cis-Golgi
    Alison K Gillingham
    Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 2QH, England, UK
    J Cell Biol 167:281-92. 2004
    ..Tassin, C. Fedriani, and M. Bornens. 2004. Cell. 118:323-335). In contrast, we find that this region binds to the Golgi in a GRAB domain-dependent manner, suggesting that GMAP-210 may not link the Golgi to gamma-tubulin and centrosomes...
  78. ncbi Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map
    Sean R Collins
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA
    Nature 446:806-10. 2007
    ..This modification, in turn, enables a ubiquitin ligase complex containing the cullin Rtt101 to ensure genomic integrity during DNA replication...
  79. ncbi The Shwachman-Bodian-Diamond syndrome protein mediates translational activation of ribosomes in yeast
    Tobias F Menne
    Medical Research Council MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nat Genet 39:486-95. 2007
    ..Thus, our data link defective late 60S ribosomal subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition...
  80. ncbi Playing tag with the yeast proteome
    Brenda J Andrews
    Nat Biotechnol 21:1297-9. 2003
  81. pmc A network of multi-tasking proteins at the DNA replication fork preserves genome stability
    Martin E Budd
    Braun Laboratories, California Institute of Technology, Pasadena, California, USA
    PLoS Genet 1:e61. 2005
    ..These include not only Okazaki fragment processing and DNA repair but also chromatin dynamics...
  82. pmc Identification of protein complexes required for efficient sister chromatid cohesion
    Melanie L Mayer
    Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada V5Z 4H4
    Mol Biol Cell 15:1736-45. 2004
    ..Furthermore, we find that genes involved in mitotic spindle integrity and positioning have a previously unrecognized role in sister chromatid cohesion...
  83. ncbi Identification of a novel lysophospholipid acyltransferase in Saccharomyces cerevisiae
    Shilpa Jain
    Department of Bioscience and Biotechnology, Drexel University, Philadelphia, Pennsylvania 19104, USA
    J Biol Chem 282:30562-9. 2007
    ..Therefore, Lpt1p, a member of the membrane-bound o-acyltransferase gene family, seems to work in conjunction with Slc1 to mediate the incorporation of unsaturated acyl chains into the sn-2 position of phospholipids...
  84. pmc The Saccharomyces cerevisiae homolog of p24 is essential for maintaining the association of p150Glued with the dynactin complex
    I Alexandra Amaro
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Genetics 178:703-9. 2008
    ..The genetic interaction of ldb18Delta with stu1-5 also supports the notion that dynein/dynactin helps to generate a spindle pole separating force...
  85. pmc The interaction network of the chaperonin CCT
    Carien Dekker
    Cancer Research UK Centre for Cell and Molecular Biology, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
    EMBO J 27:1827-39. 2008
    ..Our results therefore provide a rich framework for understanding the function of CCT in several essential cellular processes, including epigenetics and cell division...
  86. ncbi Synthetic genetic array analysis in Saccharomyces cerevisiae
    Amy Hin Yan Tong
    Methods Mol Biol 313:171-92. 2006
    ..This array-based approach automates yeast genetic analysis in general and can be easily adapted for a number of different screens, including genetic suppression, plasmid shuffling, dosage lethality, or suppression...
  87. pmc Fus1p interacts with components of the Hog1p mitogen-activated protein kinase and Cdc42p morphogenesis signaling pathways to control cell fusion during yeast mating
    Bryce Nelson
    Department of Biology, Queen s University, Kingston, Ontario K7L 3N6, Canada
    Genetics 166:67-77. 2004
    ..Taken together, our results suggest that Fus1p acts as a scaffold for the assembly of a cell surface complex involved in polarized secretion of septum-degrading enzymes and inhibition of HOG pathway signaling to promote cell fusion...
  88. pmc Synthetic lethal analysis implicates Ste20p, a p21-activated potein kinase, in polarisome activation
    April S Goehring
    Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403 1229, USA
    Mol Biol Cell 14:1501-16. 2003
    ..Together, these results suggest that one function of Ste20p may be to activate the polarisome complex by phosphorylation of Bni1p...
  89. ncbi Functional genomics of intracellular peptide recognition domains with combinatorial biology methods
    Sachdev S Sidhu
    Department of Protein Engineering, Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
    Curr Opin Chem Biol 7:97-102. 2003
    ..In addition, libraries of phage-displayed PDZ and SH3 domains have been used to identify the residues responsible for ligand recognition, and also to engineer domains with altered specificities...
  90. ncbi A conserved RING finger protein required for histone H2B monoubiquitination and cell size control
    William W Hwang
    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
    Mol Cell 11:261-6. 2003
    ..Notably, analysis of mutants demonstrates a function for Bre1/Lge1-dependent H2B monoubiquitination in the control of cell size...
  91. pmc A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage
    Michael Chang
    Departments of Biochemistry and Medical Genetics and Microbiology, University of Toronto, Toronto, ON, Canada M5S 1A8
    Proc Natl Acad Sci U S A 99:16934-9. 2002
    ..These genes may promote replication fork stability or processivity during encounters between replication forks and DNA damage...
  92. ncbi Role of formins in actin assembly: nucleation and barbed-end association
    David Pruyne
    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Science 297:612-5. 2002
    ..This combination of properties suggests a direct role for formins in regulating nucleation and polarization of unbranched filamentous actin structures...
  93. pmc Sequential and distinct roles of the cadherin domain-containing protein Axl2p in cell polarization in yeast cell cycle
    Xiang Dong Gao
    Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 6058, USA
    Mol Biol Cell 18:2542-60. 2007
    ..Together, these results suggest that Axl2p plays sequential and distinct roles in the regulation of cellular morphogenesis in yeast cell cycle...
  94. ncbi Golgi targeting of ARF-like GTPase Arl3p requires its Nalpha-acetylation and the integral membrane protein Sys1p
    Subba Rao Gangi Setty
    Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, 421 Curie Blvd BRB 2 3 room 1010, Philadelphia, PA 19104 6058, USA
    Nat Cell Biol 6:414-9. 2004
    ..Chemical crosslinking and fluorescence microscopy experiments demonstrate that localization of Arl3p also requires Sys1p, a Golgi-localized integral membrane protein, which may serve as a receptor for acetylated Arl3p...
  95. pmc Interaction between a Ras and a Rho GTPase couples selection of a growth site to the development of cell polarity in yeast
    Keith G Kozminski
    Departments of Biology and Cell Biology, University of Virginia, Charlottesville, Virginia 22904, USA
    Mol Biol Cell 14:4958-70. 2003
    ....
  96. pmc Genetic interactions of MAF1 identify a role for Med20 in transcriptional repression of ribosomal protein genes
    Ian M Willis
    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
    PLoS Genet 4:e1000112. 2008
    ..The data suggest that Mediator and Maf1 function in parallel pathways to negatively regulate RP mRNA and tRNA synthesis...
  97. ncbi Pol32 is required for Pol zeta-dependent translesion synthesis and prevents double-strand breaks at the replication fork
    Michelle Hanna
    Department of Microbiology and Immunology, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Sask, Canada
    Mutat Res 625:164-76. 2007
    ..Lack of any of the above activities will cause double strand breaks at or near the replication fork that require recombination as well as Rad9 for cell survival...
  98. pmc Inorganic phosphate deprivation causes tRNA nuclear accumulation via retrograde transport in Saccharomyces cerevisiae
    Rebecca L Hurto
    Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210, USA
    Genetics 176:841-52. 2007
    ....
  99. ncbi Genetic and molecular interactions of the Erv41p-Erv46p complex involved in transport between the endoplasmic reticulum and Golgi complex
    Leah M Welsh
    Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
    J Cell Sci 119:4730-40. 2006
    ..We report a strong interaction between the Erv41p-Erv46p complex and endoplasmic reticulum glucosidase II. Strains lacking a cycling Erv41p-Erv46p complex display a mild glycoprotein processing defect...
  100. pmc The phosphatidylinositol 4,5-biphosphate and TORC2 binding proteins Slm1 and Slm2 function in sphingolipid regulation
    Mitsuaki Tabuchi
    Department of Cellular and Molecular Medicine and Howard Hughes Medical Institute, University of California, San Diego, School of Medicine, La Jolla, CA 92093 0668, USA
    Mol Cell Biol 26:5861-75. 2006
    ..Together, our data suggest that Slm1 and Slm2 define a molecular link between phosphoinositide and sphingolipid signaling and thereby regulate actin cytoskeleton organization...
  101. ncbi Identification of a bacterial type III effector family with G protein mimicry functions
    Neal M Alto
    Department of Pharmacology, Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
    Cell 124:133-45. 2006
    ..The activities of IpgB2, IpgB1, and Map are dependent on an invariant WxxxE motif found in numerous effectors leading to the speculation that they all function by a similar molecular mechanism...