John S Reece-Hoyes

Summary

Affiliation: University of Massachusetts Medical School
Country: USA

Publications

  1. pmc Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping
    John S Reece-Hoyes
    Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Nat Methods 8:1059-64. 2011
  2. pmc Yeast one-hybrid assays: a historical and technical perspective
    John S Reece-Hoyes
    Program in Systems Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
    Methods 57:441-7. 2012
  3. pmc Yeast one-hybrid assays for gene-centered human gene regulatory network mapping
    John S Reece-Hoyes
    Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Nat Methods 8:1050-2. 2011
  4. pmc Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns
    John S Reece-Hoyes
    Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Clarendon Way, Leeds, LS2 9JT, West Yorkshire, UK
    BMC Genomics 8:27. 2007
  5. pmc A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks
    John S Reece-Hoyes
    Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, School of Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
    Genome Biol 6:R110. 2005
  6. ncbi request reprint Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping
    Vanessa Vermeirssen
    Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Nat Methods 4:659-64. 2007
  7. pmc The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors
    John S Reece-Hoyes
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Nucleic Acids Res 37:3689-98. 2009
  8. pmc Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network
    John S Reece-Hoyes
    University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Cell 51:116-27. 2013
  9. pmc A regulatory cascade of three transcription factors in a single specific neuron, DVC, in Caenorhabditis elegans
    Huiyun Feng
    Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
    Gene 494:73-84. 2012
  10. pmc Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
    Natalia J Martinez
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 18:2005-15. 2008

Collaborators

Detail Information

Publications17

  1. pmc Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping
    John S Reece-Hoyes
    Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Nat Methods 8:1059-64. 2011
    ..eY1H assays will be an important tool for mapping gene regulatory networks in Caenorhabditis elegans and other model organisms as well as in humans...
  2. pmc Yeast one-hybrid assays: a historical and technical perspective
    John S Reece-Hoyes
    Program in Systems Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
    Methods 57:441-7. 2012
    ..We will discuss several of these technical variations in detail, and also provide some ideas for how Y1H assays can be further improved...
  3. pmc Yeast one-hybrid assays for gene-centered human gene regulatory network mapping
    John S Reece-Hoyes
    Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Nat Methods 8:1050-2. 2011
    ..We present Y1H resources, including clones for 988 of 1,434 (69%) predicted human transcription factors, that can be used to detect both known and new interactions between human DNA regions and transcription factors...
  4. pmc Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns
    John S Reece-Hoyes
    Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Clarendon Way, Leeds, LS2 9JT, West Yorkshire, UK
    BMC Genomics 8:27. 2007
    ..elegans transcription factor genes was examined, in vivo, with a reporter gene approach...
  5. pmc A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks
    John S Reece-Hoyes
    Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, School of Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
    Genome Biol 6:R110. 2005
    ....
  6. ncbi request reprint Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping
    Vanessa Vermeirssen
    Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Nat Methods 4:659-64. 2007
    ..Both strategies outperform library screens in terms of coverage, confidence and throughput. These versatile strategies can be adapted both to TFs in other systems and, likely, to other biomolecules and assays as well...
  7. pmc The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors
    John S Reece-Hoyes
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Nucleic Acids Res 37:3689-98. 2009
    ..Together, our data indicate that there are at least two types of CES-1 target genes and, therefore, that the molecular function of Snail-type TFs is more plastic than previously appreciated...
  8. pmc Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network
    John S Reece-Hoyes
    University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Cell 51:116-27. 2013
    ..Our multiparameter analyses provide unique insights into the evolutionary dynamics that shaped TF networks. ..
  9. pmc A regulatory cascade of three transcription factors in a single specific neuron, DVC, in Caenorhabditis elegans
    Huiyun Feng
    Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, The University of Leeds, Leeds, UK
    Gene 494:73-84. 2012
    ..Both CEH-14 and CEH-63 individually bound the mbr-1 promoter in a yeast one-hybrid assay. A model is proposed suggesting that CEH-14 activates ceh-63 and then along with CEH-63 co-ordinately activates mbr-1...
  10. pmc Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity
    Natalia J Martinez
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 18:2005-15. 2008
    ..Finally, our data suggest that post-transcriptional mechanisms contribute to differential miRNA expression. The data and strains described here will provide a valuable guide and resource for the functional analysis of C. elegans miRNAs...
  11. pmc Gene-centered yeast one-hybrid assays
    John S Reece-Hoyes
    University of Massachusetts Medical School, Worcester, MA, USA
    Methods Mol Biol 812:189-208. 2012
    ..We have shown Y1H to be a robust method for detecting interactions between a variety of DNA elements and multiple families of TFs...
  12. ncbi request reprint A gene-centered C. elegans protein-DNA interaction network
    Bart Deplancke
    Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, 01605, USA
    Cell 125:1193-205. 2006
    ..We provide additional in vivo evidence for multiple PDIs and illustrate how the PDI network provides insights into metazoan differential gene expression at a systems level...
  13. pmc Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters
    Juan I Fuxman Bass
    Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA, Center for Autoimmune Genomics and Etiology CAGE, Cincinnati Children s Hospital Medical Center, Cincinnati, OH 45229, USA and Divisions of Rheumatology and Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, OH 45229, USA
    Nucleic Acids Res 42:153-62. 2014
    ..Altogether, our data suggest that C. elegans gene regulation may be additive through the combined effects of multiple regulatory regions. ..
  14. ncbi request reprint Components of both major axial patterning systems of the Bilateria are differentially expressed along the primary axis of a 'radiate' animal, the anthozoan cnidarian Acropora millepora
    Danielle M De Jong
    Comparative Genomics Centre, Molecular Sciences Building 21, James Cook University, Townsville, Qld 4811, Australia
    Dev Biol 298:632-43. 2006
    ..Thus, although some specific gene functions appear to be conserved between cnidarians and higher animals, no simple relationship exists between axial patterning systems in the two groups...
  15. ncbi request reprint A consensus Oct1 binding site is required for the activity of the Xenopus Cdx4 promoter
    John S Reece-Hoyes
    Area 11, Department of Biology, University of York, York YO10 5YW, UK
    Dev Biol 282:509-23. 2005
    ..These data suggest a conserved function for octamer-binding proteins in the regulation of Cdx family members...
  16. ncbi request reprint Coral development: from classical embryology to molecular control
    Eldon E Ball
    Research School of Biological Sciences, Australian National University, Canberra, Australian Capital Territory
    Int J Dev Biol 46:671-8. 2002
    ..We also describe a recent preliminary whole genome initiative, a coral EST database...
  17. ncbi request reprint Cloning and expression of the Cdx family from the frog Xenopus tropicalis
    John S Reece-Hoyes
    Department of Biology, University of York, York, United Kingdom
    Dev Dyn 223:134-40. 2002
    ..In common with the Cdx genes of other vertebrates, the Xenopus tropicalis Cdx genes show overlapping and dynamic patterns of expression in posterior regions of the embryo through the early stages of development...