Tom C Freeman

Summary

Affiliation: University of Edinburgh
Country: UK

Publications

  1. pmc Structural and functional annotation of the porcine immunome
    Harry D Dawson
    USDA ARS, Beltsville Human Nutrition Research Center, Diet, Genomics, Immunology Laboratory, Beltsville, MD 20705, USA
    BMC Genomics 14:332. 2013
  2. pmc A gene expression atlas of the domestic pig
    Tom C Freeman
    The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9PS, UK
    BMC Biol 10:90. 2012
  3. pmc The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways
    Tom C Freeman
    Division of Pathway Medicine, University of Edinburgh Medical School, The Chancellor s Building, College of Medicine, 49 Little France Crescent, Edinburgh, UK
    BMC Syst Biol 4:65. 2010
  4. pmc The impact of breed and tissue compartment on the response of pig macrophages to lipopolysaccharide
    Ronan Kapetanovic
    The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Edinburgh EH25 9RG, United Kingdom
    BMC Genomics 14:581. 2013
  5. doi request reprint Network visualization and analysis of gene expression data using BioLayout Express(3D)
    Athanasios Theocharidis
    The Roslin Institute, R D SVS, University of Edinburgh, Roslin Biocentre, Midlothian, Scotland, UK
    Nat Protoc 4:1535-50. 2009
  6. pmc Construction of a large scale integrated map of macrophage pathogen recognition and effector systems
    Sobia Raza
    Division of Pathway Medicine, University of Edinburgh, The Chancellor s Building, College of Medicine, 49 Little France Crescent, Edinburgh EH16 4SB, UK
    BMC Syst Biol 4:63. 2010
  7. pmc A logic-based diagram of signalling pathways central to macrophage activation
    Sobia Raza
    Division of Pathway Medicine, University of Edinburgh, The Chancellor s Building, College of Medicine, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
    BMC Syst Biol 2:36. 2008
  8. doi request reprint Macrophages.com: an on-line community resource for innate immunity research
    Christelle Robert
    The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
    Immunobiology 216:1203-11. 2011
  9. pmc Identification of novel genes selectively expressed in the follicle-associated epithelium from the meta-analysis of transcriptomics data from multiple mouse cell and tissue populations
    Atsushi Kobayashi
    The Roslin Institute and Royal Dick School of Veterinary Sciences, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
    DNA Res 19:407-22. 2012
  10. pmc Construction, visualisation, and clustering of transcription networks from microarray expression data
    Tom C Freeman
    Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, United Kingdom
    PLoS Comput Biol 3:2032-42. 2007

Collaborators

Detail Information

Publications17

  1. pmc Structural and functional annotation of the porcine immunome
    Harry D Dawson
    USDA ARS, Beltsville Human Nutrition Research Center, Diet, Genomics, Immunology Laboratory, Beltsville, MD 20705, USA
    BMC Genomics 14:332. 2013
    ..The completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems...
  2. pmc A gene expression atlas of the domestic pig
    Tom C Freeman
    The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9PS, UK
    BMC Biol 10:90. 2012
    ..The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue/cell types. These data were subjected to network correlation analysis and clustering...
  3. pmc The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways
    Tom C Freeman
    Division of Pathway Medicine, University of Edinburgh Medical School, The Chancellor s Building, College of Medicine, 49 Little France Crescent, Edinburgh, UK
    BMC Syst Biol 4:65. 2010
    ..However, implementing and agreeing how best to do this is currently the subject of some debate...
  4. pmc The impact of breed and tissue compartment on the response of pig macrophages to lipopolysaccharide
    Ronan Kapetanovic
    The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Edinburgh EH25 9RG, United Kingdom
    BMC Genomics 14:581. 2013
    ..Pig breeds have been reported to differ in their resistance to infectious disease. In this study we examine whether there are corresponding differences in gene expression in innate immune cells..
  5. doi request reprint Network visualization and analysis of gene expression data using BioLayout Express(3D)
    Athanasios Theocharidis
    The Roslin Institute, R D SVS, University of Edinburgh, Roslin Biocentre, Midlothian, Scotland, UK
    Nat Protoc 4:1535-50. 2009
    ....
  6. pmc Construction of a large scale integrated map of macrophage pathogen recognition and effector systems
    Sobia Raza
    Division of Pathway Medicine, University of Edinburgh, The Chancellor s Building, College of Medicine, 49 Little France Crescent, Edinburgh EH16 4SB, UK
    BMC Syst Biol 4:63. 2010
    ..This information has been assembled into a large integrated directional network and represented graphically using the modified Edinburgh Pathway Notation (mEPN) scheme...
  7. pmc A logic-based diagram of signalling pathways central to macrophage activation
    Sobia Raza
    Division of Pathway Medicine, University of Edinburgh, The Chancellor s Building, College of Medicine, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
    BMC Syst Biol 2:36. 2008
    ..However, these pathways are commonly viewed as separate entities rather than an integrated network of molecular interactions...
  8. doi request reprint Macrophages.com: an on-line community resource for innate immunity research
    Christelle Robert
    The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
    Immunobiology 216:1203-11. 2011
    ..com resource using publicly available data, as well as in-house generated knowledge. In so doing we aim to provide a user-friendly community website and a community portal for access to comprehensive sets of macrophage-related data...
  9. pmc Identification of novel genes selectively expressed in the follicle-associated epithelium from the meta-analysis of transcriptomics data from multiple mouse cell and tissue populations
    Atsushi Kobayashi
    The Roslin Institute and Royal Dick School of Veterinary Sciences, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
    DNA Res 19:407-22. 2012
    ..This study provides new insight into the FAE transcriptome. Further characterization of the candidate genes identified here will aid the identification of novel regulators of cell function in the FAE...
  10. pmc Construction, visualisation, and clustering of transcription networks from microarray expression data
    Tom C Freeman
    Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, United Kingdom
    PLoS Comput Biol 3:2032-42. 2007
    ..This work has been implemented in a freely available open-source application named BioLayout Express(3D)...
  11. pmc Combined genome-wide expression profiling and targeted RNA interference in primary mouse macrophages reveals perturbation of transcriptional networks associated with interferon signalling
    Paul Lacaze
    Division of Pathway Medicine, The University of Edinburgh, The Chancellor s Building, College of Medicine, Edinburgh, UK
    BMC Genomics 10:372. 2009
    ..Genome-wide changes in transcript abundance caused by siRNA activity were measured using exon-level microarrays in the presence or absence of IFNgamma...
  12. doi request reprint Reprogramming pig fetal fibroblasts reveals a functional LIF signaling pathway
    Alison J Thomson
    The Roslin Institute and Royal Dick School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, United Kingdom
    Cell Reprogram 14:112-22. 2012
    ..This demonstration of LIF-dependence in reprogrammed pig cells supports the notion that the connection between LIF/STAT3 signaling and the core regulatory network of pluripotent stem cells is a conserved pathway in mammals...
  13. pmc Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment
    Tamasin N Doig
    Centre for Inflammation Research, University of Edinburgh, The Queen s Medical Research Institute, Edinburgh, UK
    BMC Genomics 14:469. 2013
    ....
  14. pmc An expression atlas of human primary cells: inference of gene function from coexpression networks
    Neil A Mabbott
    The Roslin Institute and Royal Dick School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Edinburgh EH25 9RG, UK
    BMC Genomics 14:632. 2013
    ..Here we have combined a large number of publically available microarray datasets derived from human primary cells and analysed large correlation graphs of these data...
  15. pmc Expression of mesenchyme-specific gene signatures by follicular dendritic cells: insights from the meta-analysis of microarray data from multiple mouse cell populations
    Neil A Mabbott
    The Roslin Institute and Royal Dick School of Veterinary Sciences, University of Edinburgh, Easter Bush, Midlothian, UK
    Immunology 133:482-98. 2011
    ..Together, these data suggest FDC are a specialized mesenchymal cell population within the germinal centres of lymphoid tissues...
  16. pmc The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions
    Michal Letek
    Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh, United Kingdom
    PLoS Genet 6:e1001145. 2010
    ..The regulatory integration of chromosomal metabolic genes under the control of the HGT-acquired plasmid PAI is thus an important element in the cooptive virulence of R. equi...
  17. doi request reprint Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations
    Neil A Mabbott
    The Roslin Institute and Royal Dick School of Veterinary Studies, The University of Edinburgh, Roslin Biocentre, Roslin, Midlothian, UK
    Immunobiology 215:724-36. 2010
    ....