T R Hughes

Summary

Affiliation: University of Toronto
Country: Canada

Publications

  1. pmc The draft genome and transcriptome of Cannabis sativa
    Harm van Bakel
    Banting and Best Department of Medical Research and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
    Genome Biol 12:R102. 2011
  2. pmc Conservation of core gene expression in vertebrate tissues
    Esther T Chan
    Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario, Canada
    J Biol 8:33. 2009
  3. pmc The functional landscape of mouse gene expression
    Wen Zhang
    Banting and Best Department of Medical Research, University of Toronto, 1 King s College Circle, Toronto, ON M5S 1A8, Canada
    J Biol 3:21. 2004
  4. pmc A race through the maze of genomic evidence
    Timothy R Hughes
    Genome Biol 9:S1. 2008
  5. pmc Signals and systems
    Nevan J Krogan
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA
    Genome Biol 7:313. 2006
  6. pmc A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
    Lourdes Pena-Castillo
    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S3E1, Canada
    Genome Biol 9:S2. 2008
  7. pmc TFCat: the curated catalog of mouse and human transcription factors
    Debra L Fulton
    Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
    Genome Biol 10:R29. 2009
  8. pmc Functional coordination of alternative splicing in the mammalian central nervous system
    Matthew Fagnani
    Banting and Best Department of Medical Research, Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada, M5S 3E1
    Genome Biol 8:R108. 2007
  9. pmc Information propagation within the Genetic Network of Saccharomyces cerevisiae
    Sharif Chowdhury
    Laboratory of Biosystem Dynamics, Computational Systems Biology Research Group, Tampere University of Technology, Tampere, Finland
    BMC Syst Biol 4:143. 2010
  10. pmc A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription
    Tomas Babak
    Banting and Best Department of Medical Research, 112 College St, Toronto, ON M5G 1L6, Canada
    BMC Genomics 6:104. 2005

Detail Information

Publications89

  1. pmc The draft genome and transcriptome of Cannabis sativa
    Harm van Bakel
    Banting and Best Department of Medical Research and Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
    Genome Biol 12:R102. 2011
    ..The molecular biology underlying cannabinoid biosynthesis and other traits of interest is largely unexplored...
  2. pmc Conservation of core gene expression in vertebrate tissues
    Esther T Chan
    Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario, Canada
    J Biol 8:33. 2009
    ..Alteration of gene regulation is thought to be a major mechanism in phenotypic variation and evolution, but relatively little is known about the broad patterns of conservation in gene expression in non-mammalian vertebrates...
  3. pmc The functional landscape of mouse gene expression
    Wen Zhang
    Banting and Best Department of Medical Research, University of Toronto, 1 King s College Circle, Toronto, ON M5S 1A8, Canada
    J Biol 3:21. 2004
    ....
  4. pmc A race through the maze of genomic evidence
    Timothy R Hughes
    Genome Biol 9:S1. 2008
  5. pmc Signals and systems
    Nevan J Krogan
    Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA
    Genome Biol 7:313. 2006
  6. pmc A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
    Lourdes Pena-Castillo
    Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S3E1, Canada
    Genome Biol 9:S2. 2008
    ..Several algorithms using diverse genomic data have been applied to this task in model organisms; however, the performance of such approaches in mammals has not yet been evaluated...
  7. pmc TFCat: the curated catalog of mouse and human transcription factors
    Debra L Fulton
    Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
    Genome Biol 10:R29. 2009
    ..All data and user-feedback mechanisms are available at the TFCat portal (http://www.tfcat.ca)...
  8. pmc Functional coordination of alternative splicing in the mammalian central nervous system
    Matthew Fagnani
    Banting and Best Department of Medical Research, Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada, M5S 3E1
    Genome Biol 8:R108. 2007
    ..However, the extent to which AS coordinates functions in a cell and tissue type specific manner is not known. Moreover, the sequence code that underlies cell and tissue type specific regulation of AS is poorly understood...
  9. pmc Information propagation within the Genetic Network of Saccharomyces cerevisiae
    Sharif Chowdhury
    Laboratory of Biosystem Dynamics, Computational Systems Biology Research Group, Tampere University of Technology, Tampere, Finland
    BMC Syst Biol 4:143. 2010
    ..Inferred connections are verified by gene enrichment...
  10. pmc A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription
    Tomas Babak
    Banting and Best Department of Medical Research, 112 College St, Toronto, ON M5G 1L6, Canada
    BMC Genomics 6:104. 2005
    ..However, these non-genic transcripts often appear to be low in abundance, and their functional significance is not known...
  11. pmc Simultaneous host and parasite expression profiling identifies tissue-specific transcriptional programs associated with susceptibility or resistance to experimental cerebral malaria
    Fiona E Lovegrove
    Institute of Medical Science, Department of Medicine, University of Toronto, Toronto, ON, Canada
    BMC Genomics 7:295. 2006
    ....
  12. pmc FunSpec: a web-based cluster interpreter for yeast
    Mark D Robinson
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
    BMC Bioinformatics 3:35. 2002
    ....
  13. pmc Considerations in the identification of functional RNA structural elements in genomic alignments
    Tomas Babak
    Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, 160 College St, Toronto, ON M5S 3E1 Canada
    BMC Bioinformatics 8:33. 2007
    ....
  14. pmc G+C content dominates intrinsic nucleosome occupancy
    Desiree Tillo
    Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
    BMC Bioinformatics 10:442. 2009
    ..However, the model is complicated, and it is not clear which specific DNA sequence properties are most important for intrinsic nucleosome-forming preferences...
  15. doi request reprint Introduction to "a handbook of transcription factors"
    T R Hughes
    Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
    Subcell Biochem 52:1-6. 2011
    ..This chapter briefly summarizes the topics in this volume...
  16. ncbi request reprint Yeast and drug discovery
    Timothy R Hughes
    Banting and Best Department of Medical Research, University of Toronto, 112 College St, Toronto, ON M5G 1L6, Canada
    Funct Integr Genomics 2:199-211. 2002
    ..It is likely that most of the benefits of yeast in discovery and development of therapeutic compounds have yet to be realized...
  17. pmc 'Validation' in genome-scale research
    Timothy R Hughes
    Banting and Best Department of Medical Research, and Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
    J Biol 8:3. 2009
    ..The individual 'validation' experiments typically included in papers reporting genome-scale studies often do not reflect the overall merits of the work...
  18. ncbi request reprint The promise of functional genomics: completing the encyclopedia of a cell
    Timothy R Hughes
    Banting and Best Department of Medical Research, University of Toronto, 112 College St, Room 307, Toronto, ON, M5G 1L6, Canada
    Curr Opin Microbiol 7:546-54. 2004
    ..This task seems increasingly feasible; however, progress to date suggests that increased interaction between systematic efforts and individual investigators will be critical to completing the encyclopedia of the yeast cell...
  19. pmc Most "dark matter" transcripts are associated with known genes
    Harm van Bakel
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    PLoS Biol 8:e1000371. 2010
    ..We conclude that, while there are bona fide new intergenic transcripts, their number and abundance is generally low in comparison to known exons, and the genome is not as pervasively transcribed as previously reported...
  20. ncbi request reprint 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...
  21. ncbi request reprint Transcriptional networks: reverse-engineering gene regulation on a global scale
    Gordon Chua
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Room 307, Toronto, Ontario M5G 1L6, Canada
    Curr Opin Microbiol 7:638-46. 2004
    ..The results indicate that a complete and comprehensive yeast transcriptional network will ultimately be achieved...
  22. pmc Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors
    Jorg Grigull
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
    Mol Cell Biol 24:5534-47. 2004
    ..Our results indicate that the abundance of ribosome biogenesis factors is controlled at the level of mRNA stability...
  23. 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...
  24. ncbi request reprint Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling
    Thomas Kislinger
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada
    Cell 125:173-86. 2006
    ..This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tissue and organelle proteomes of a leading model mammal...
  25. doi request reprint A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution
    Matthew T Weirauch
    Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
    Subcell Biochem 52:25-73. 2011
    ..We also examine the species distributions and inferred evolutionary histories of the various families, and the potential roles played by TF family expansion and dimerization...
  26. 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...
  27. ncbi request reprint Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs
    Brendan J Frey
    Electrical and Computer Engineering, University of Toronto, 10 King s College Rd, Toronto, Ontario M5S 3G4, Canada
    Nat Genet 37:991-6. 2005
    ..GenRate also detected tens of thousands of potential new exons and reconciled discrepancies in current cDNA databases by 'stitching' new transcribed regions into previously annotated genes...
  28. 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...
  29. ncbi request reprint A panoramic view of yeast noncoding RNA processing
    Wen Tao Peng
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, M5G 1L6, Toronto, Ontario, Canada
    Cell 113:919-33. 2003
    ..These data present a global view of yeast noncoding RNA processing and confirm that many currently uncharacterized yeast proteins are involved in biogenesis of noncoding RNA...
  30. pmc Global analysis of yeast RNA processing identifies new targets of RNase III and uncovers a link between tRNA 5' end processing and tRNA splicing
    Shawna L Hiley
    Banting and Best Department of Medical Research, University of Toronto 112 College Street, Toronto, ON M5G 1L6, Canada
    Nucleic Acids Res 33:3048-56. 2005
    ..This analysis demonstrates the applicability of microarray technology to the study of global analysis of ncRNA synthesis and provides an extensive directory of processing events mediated by yeast ncRNA processing enzymes...
  31. pmc Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model
    Fiona E Lovegrove
    Institute of Medical Science, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
    PLoS Pathog 4:e1000068. 2008
    ..Furthermore, differential susceptibility of mouse strains to malaria-induced ALI and CM suggests that distinct genetic determinants may regulate susceptibility to these two important causes of malaria-associated morbidity and mortality...
  32. ncbi request reprint High-definition macromolecular composition of yeast RNA-processing complexes
    Nevan J Krogan
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
    Mol Cell 13:225-39. 2004
    ..This study provides a high-resolution overview of the modular topology of noncoding RNA-processing machinery...
  33. doi request reprint Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression
    Jeffrey Fillingham
    Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Canada
    Mol Cell 35:340-51. 2009
    ..Our data suggest that this pathway may represent a chromatin regulatory mechanism that is broadly used across the genome...
  34. ncbi request reprint 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...
  35. ncbi request reprint A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1
    Nevan J Krogan
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6
    Mol Cell 12:1565-76. 2003
    ..We show that recruitment of Htz1 to chromatin requires the SWR-C. Moreover, like Htz1 and Bdf1, the SWR-C promotes gene expression near silent heterochromatin...
  36. ncbi request reprint GenRate: a generative model that reveals novel transcripts in genome-tiling microarray data
    Brendan J Frey
    Department of Electrical and Computer Engineering, University of Toronto, Ontario, Canada
    J Comput Biol 13:200-14. 2006
    ..As new problems arise, additional hidden variables can be incorporated into the model in a principled fashion, so we believe that GenRate will prove to be a useful tool in the new era of genome-wide tiling microarray analysis...
  37. ncbi request reprint 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
    ....
  38. pmc A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300
    May Khanna
    Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    RNA 15:2174-85. 2009
    ..Together, the results suggest multiple functions for Cwc21/SRm300 in the splicing process, including an important role in the activation of splicing in association with Isy1...
  39. 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...
  40. pmc A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters
    Gwenael Badis
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
    Mol Cell 32:878-87. 2008
    ....
  41. pmc Why are there still over 1000 uncharacterized yeast genes?
    Lourdes Pena-Castillo
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Genetics 176:7-14. 2007
    ..Notably, the uncharacterized gene set is highly enriched for genes whose only homologs are in other fungi. Achieving a full catalog of yeast gene functions may require a greater focus on the life of yeast outside the laboratory...
  42. ncbi request reprint 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...
  43. ncbi request reprint Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform
    Qun Pan
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
    Mol Cell 16:929-41. 2004
    ..These results demonstrate the utility of our quantitative microarray platform and data for revealing important global regulatory features of AS...
  44. pmc ESF1 is required for 18S rRNA synthesis in Saccharomyces cerevisiae
    Wen Tao Peng
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
    Nucleic Acids Res 32:1993-9. 2004
    ..These data indicate that Esf1p plays a direct role in early pre-rRNA processing...
  45. ncbi request reprint Microarray analysis of RNA processing and modification
    Timothy R Hughes
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    Methods Enzymol 410:300-16. 2006
    ..This chapter also describes practical aspects of microarray design, sample preparation, hybridization, and data analysis...
  46. ncbi request reprint Using expression profiling data to identify human microRNA targets
    Jim C Huang
    Department of Electrical and Computer Engineering, University of Toronto, 10 King s College Road, Toronto, Ontario M5S 3G4, Canada
    Nat Methods 4:1045-9. 2007
    ..Compared to sequence-based predictions, our high-scoring GenMiR++ predictions had much more consistent Gene Ontology annotations and were more accurate predictors of which mRNA levels respond to changes in let-7b levels...
  47. pmc Probing microRNAs with microarrays: tissue specificity and functional inference
    Tomas Babak
    Banting and Best Department of Medical Research, 112 College St, University of Toronto, Toronto, Ontario M5G 1L6, Canada
    RNA 10:1813-9. 2004
    ....
  48. pmc Detection and discovery of RNA modifications using microarrays
    Shawna L Hiley
    Banting and Best Department of Medical Research, University of Toronto 112 College Street, Toronto, ON M5G 1L6, Canada
    Nucleic Acids Res 33:e2. 2005
    ..Using this approach, we identified a previously undetected m1A modification in GlnCTG tRNA, the formation of which is catalyzed by the Gcd10/Gcd14 complex. complex...
  49. 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...
  50. pmc A survey of essential gene function in the yeast cell division cycle
    Lisa Yu
    Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
    Mol Biol Cell 17:4736-47. 2006
    ....
  51. doi request reprint Establishing legitimacy and function in the new transcriptome
    Harm van Bakel
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
    Brief Funct Genomic Proteomic 8:424-36. 2009
    ..Here, we discuss the challenges associated with discovery and characterization of non-traditional categories of non-coding RNA...
  52. doi request reprint Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
    Debashish Ray
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    Nat Biotechnol 27:667-70. 2009
    ..We anticipate that RNAcompete will be a valuable tool for the study of RNA-protein interactions...
  53. pmc High nucleosome occupancy is encoded at human regulatory sequences
    Desiree Tillo
    Department of Molecular Genetics, University of Toronto, Toronto, Canada
    PLoS ONE 5:e9129. 2010
    ..We propose that high nucleosome preference is directly encoded at regulatory sequences in the human genome to restrict access to regulatory information that will ultimately be utilized in only a subset of differentiated cells...
  54. ncbi request reprint Genetic selection of peptide inhibitors of biological pathways
    T C Norman
    Department of Physiology, University of California, San Francisco, CA 94143 0444, USA
    Science 285:591-5. 1999
    ....
  55. pmc Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4
    Nevan J Krogan
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6
    Proc Natl Acad Sci U S A 101:13513-8. 2004
    ..Because SWR-C-dependent recruitment of Htz1 occurs in both transcribed and centromeric regions, a NuA4/SWR-C/Htz1 pathway may regulate both transcription and centromere function in S. cerevisiae...
  56. pmc RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins
    Hilal Kazan
    Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
    PLoS Comput Biol 6:e1000832. 2010
    ..RNAcontext is an accurate and efficient motif finding method ideally suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RBPs for a wide range of RNA sequences and structures...
  57. 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...
  58. ncbi request reprint Alternative splicing of conserved exons is frequently species-specific in human and mouse
    Qun Pan
    CH Best Institute, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6
    Trends Genet 21:73-7. 2005
    ..The results thus provide evidence that species-specific AS of conserved exons constitutes an additional potential source of complexity and species-specific differences between mammals...
  59. ncbi request reprint SMAUG is a major regulator of maternal mRNA destabilization in Drosophila and its translation is activated by the PAN GU kinase
    Wael Tadros
    Graduate Department of Molecular and Medical Genetics, University of Toronto, 1 King s College Circle, Toronto, Ontario M5S 1A8, Canada
    Dev Cell 12:143-55. 2007
    ..SMG-dependent mRNAs are enriched for gene ontology annotations for function in the cell cycle, suggesting a possible causal relationship between failure to eliminate these transcripts and the cell cycle defects in smg mutants...
  60. ncbi request reprint Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment
    Emily Walker
    Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
    Cell Stem Cell 1:71-86. 2007
    ..By using this integrative approach, we have formulated novel networks describing gene repression of key developmental regulators in undifferentiated ESCs and successfully predicted the outcomes of genetic manipulation of these networks...
  61. ncbi request reprint Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function
    Eric Lecuyer
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
    Cell 131:174-87. 2007
    ..A searchable web resource documenting mRNA expression and localization dynamics has been established and will serve as an invaluable tool for dissecting localization mechanisms and for predicting gene functions and interactions...
  62. pmc Predicting the binding preference of transcription factors to individual DNA k-mers
    Trevis M Alleyne
    Department of Molecular Genetics, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
    Bioinformatics 25:1012-8. 2009
    ....
  63. doi request reprint Evaluation of data-dependent versus targeted shotgun proteomic approaches for monitoring transcription factor expression in breast cancer
    Charanjit Sandhu
    Program in Proteomics and Bioinformatics, Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research CCBR, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
    J Proteome Res 7:1529-41. 2008
    ....
  64. pmc Diversity and complexity in DNA recognition by transcription factors
    Gwenael Badis
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
    Science 324:1720-3. 2009
    ..This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks...
  65. pmc Zfp206 regulates ES cell gene expression and differentiation
    Wen Zhang
    Department of Molecular and Medical Genetics, University of Toronto, 4388 Medical Sciences Building, 1 King s College Circle, Toronto, ON M5S 1A8, Canada
    Nucleic Acids Res 34:4780-90. 2006
    ..Together, these data indicate that Zfp206 is a regulator of ES cell differentiation that controls a set of genes expressed very early in development, most of which themselves appear to be regulators...
  66. ncbi request reprint RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors
    Xiaoyu Chen
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
    Bioinformatics 23:i72-9. 2007
    ..Because RankMotif++ makes few assumptions about the relationship between binding affinity and the semi-quantitative readout, it is applicable to a wide variety of experimental assays of DNA-binding preference...
  67. ncbi request reprint Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters
    Lani F Wu
    Rosetta Inpharmatics, Kirkland, Washington, USA
    Nat Genet 31:255-65. 2002
    ..We present experimental validation confirming the involvement of several of these proteins in ribosomal RNA processing. Our methodology can be applied to a variety of genomics data types and organisms...
  68. pmc RAM: a conserved signaling network that regulates Ace2p transcriptional activity and polarized morphogenesis
    Bryce Nelson
    Department of Biology Queen s University, Kingston, Ontario K7L 3N6, Canada
    Mol Biol Cell 14:3782-803. 2003
    ..Our data suggest that the functional architecture of RAM signaling is similar to the S. cerevisiae mitotic exit network and Schizosaccharomyces pombe septation initiation network and is likely conserved among eukaryotes...
  69. ncbi request reprint How many new genes are there?
    Leo J Lee
    Science 311:1709-11; author reply 1709-11. 2006
  70. ncbi request reprint Rapid tRNA decay can result from lack of nonessential modifications
    Andrei Alexandrov
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
    Mol Cell 21:87-96. 2006
    ..The degradation of an endogenous tRNA species at a rate typical of mRNA decay demonstrates a critical role of nonessential modifications for tRNA stability and cell survival...
  71. ncbi request reprint The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs
    Feng Xing
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, New York 14642, USA
    J Biol Chem 279:17850-60. 2004
    ..We show that each of the four Dus proteins has a distinct position specificity: Dus1p for U(16) and U(17), Dus2p for U(20), Dus3p for U(47), and Dus4p for U(20a) and U(20b)...
  72. ncbi request reprint 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...
  73. ncbi request reprint A high-resolution atlas of nucleosome occupancy in yeast
    William Lee
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 5120, USA
    Nat Genet 39:1235-44. 2007
    ..A quantitative model of nucleosome occupancy indicates that DNA structural features may account for much of the global nucleosome occupancy...
  74. ncbi request reprint 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...
  75. pmc RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits
    Célia Jeronimo
    Laboratory of Gene Transcription, Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada H2W 1R7
    Mol Cell Biol 24:7043-58. 2004
    ....
  76. 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...
  77. pmc Esf2p, a U3-associated factor required for small-subunit processome assembly and compaction
    Tran Hoang
    Fonds National de la Recherche Scientifique, Universite Libre de Bruxelles, Institut de Biologie et de Médecine Moléculaires, Charleroi Gosselies, Belgium
    Mol Cell Biol 25:5523-34. 2005
    ..The identification of ABT1 in a large-scale analysis of the human nucleolar proteome indicates that its role may also be conserved in mammals...
  78. doi request reprint Plasmodium falciparum shows transcriptional versatility within the human host
    Fiona E Lovegrove
    McLaughlin Rotman Centre for Global Health, McLaughlin Centre for Molecular Medicine, MaRS Centre, Toronto ON, Canada
    Trends Parasitol 24:288-91. 2008
    ..These findings suggest that parasites exist in different physiological states in vivo, providing an important foundation for future studies investigating how these states might contribute to malaria pathogenesis and outcome...
  79. ncbi request reprint GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data
    Jim C Huang
    Probabilistic and Statistical Inference Group, Department of Electrical and Computer Engineering, University of Toronto Toronto, ON, Canada M5S 3G4
    Bioinformatics 21:i222-31. 2005
    ....
  80. ncbi request reprint H2B ubiquitylation acts as a barrier to Ctk1 nucleosomal recruitment prior to removal by Ubp8 within a SAGA-related complex
    Anastasia Wyce
    Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
    Mol Cell 27:275-88. 2007
    ..These findings reveal a mechanism by which H2B ubiquitylation acts as a barrier to Ctk1 association with active genes, while subsequent deubiquitylation by Ubp8 triggers Ctk1 recruitment at the appropriate point in activation...
  81. pmc H2B ubiquitin protease Ubp8 and Sgf11 constitute a discrete functional module within the Saccharomyces cerevisiae SAGA complex
    Kristin Ingvarsdottir
    The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
    Mol Cell Biol 25:1162-72. 2005
    ..These data indicate that Ubp8 and Sgf11 likely represent a new functional module within SAGA that is involved in gene regulation through H2B deubiquitylation...
  82. ncbi request reprint A novel role of Sp1 and Sp3 in the interferon-gamma -mediated suppression of macrophage lipoprotein lipase gene transcription
    Timothy R Hughes
    Cardiff School of Biosciences, Cardiff University, Museum Avenue, P O Box 911, Cardiff CF10 3US, United Kingdom
    J Biol Chem 277:11097-106. 2002
    ..In contrast, the cytokine decreased the DNA binding activity of Sp1 without affecting the protein levels. These studies therefore reveal a novel mechanism for IFN-gamma-mediated regulation of macrophage gene transcription...
  83. ncbi request reprint Interferon-gamma stimulates the expression of the inducible cAMP early repressor in macrophages through the activation of casein kinase 2. A potentially novel pathway for interferon-gamma-mediated inhibition of gene transcription
    James R Mead
    Cardiff School of Biosciences, Cardiff University, Museum Avenue, P O Box 911, Cardiff CF10 3US, United Kingdom
    J Biol Chem 278:17741-51. 2003
    ....
  84. ncbi request reprint p53 regulates cellular resistance to complement lysis through enhanced expression of CD59
    Rossen M Donev
    Department of Medical Biochemistry and Immunology, School of Medicine, Cardiff University, Cardiff, United Kingdom
    Cancer Res 66:2451-8. 2006
    ..Our data suggest that p53 and in vivo positive/negative regulators of p53 could be used to modulate susceptibility of tumor cells to complement lysis in chemotherapy...
  85. ncbi request reprint BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex
    R Nicholas Laribee
    Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
    Curr Biol 15:1487-93. 2005
    ..Our data reveal a novel function for the BUR kinase in transcriptional regulation through the selective control of histone modifications...
  86. ncbi request reprint Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme
    Célia Jeronimo
    Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de Recherches Cliniques de Montreal, Montreal, QC, Canada
    Mol Cell 27:262-74. 2007
    ..Our results define a high-density protein interaction network for the mammalian transcription machinery and uncover multiple regulatory factors that target the transcription machinery...
  87. ncbi request reprint Universal epistasis analysis
    Timothy R Hughes
    Nat Genet 37:457-8. 2005
  88. pmc The splicing factor Prp43p, a DEAH box ATPase, functions in ribosome biogenesis
    Nina B Leeds
    Department of Molecular Genetics and Cell Biology, University of Chicago, 920 E 58th St, Chicago, Illinois 60637, USA
    Mol Cell Biol 26:513-22. 2006
    ..The dual function for Prp43p in the cell raises the possibility that ribosome biogenesis and pre-mRNA splicing may be coordinately regulated...
  89. pmc Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
    Michael F Berger
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Cell 133:1266-76. 2008
    ..Our results provide an unprecedented level of resolution in the analysis of this simple domain structure and suggest that variation in sequence recognition may be a factor in its functional diversity and evolutionary success...