Professor Tom Freeman

The Roslin Institute

Research Interests

Our work covers a number of disparate but related areas of systems biology, and utilises a combination of cutting edge bioinformatics approaches to data mining and visualisation, together with experimental studies to create and test models of biological pathways. Our main objectives of the work are:

1. to develop new approaches to the visualisation and analysis of large network graphs derived from biological data

2. to a develop a clear understanding of the activation states of macrophages and other leukocyte populations in various differentiation/activation states in vivo and in vitro, primarily through the exploration the transcriptomics networks

3. to create human and machine readable in silico models of known signalling pathways and transcriptional networks associated with infection and pro-inflammatory stimuli

4. the analysis and modelling of the human cell cycle

Selected Publications

  • Catriona Ford, Sofia Petrova, John Pound, JorineJ L P Voss, Lynsey Melville, Margaret Paterson, Sarah Farnworth, AwenM Gallimore, Simone Cuff, Helen Wheadon, Edwina Dobbin, CarolAnne Ogden, IngridE Dumitriu, Donald Dunbar, PaulG Murray, Dominik Ruckerl, Judith Allen, David Hume, Nico vanRooijen, John Goodlad, Tom Freeman, Christopher Gregory. 2015. Oncogenic Properties of Apoptotic Tumor Cells in Aggressive B Cell Lymphoma. Current Biology Vol: 25 Pages: 577-588. More»
  • Tom C Freeman, Richard Axton, J Kenneth Baillie, Malcolm E Fisher, Lesley Forrester, Thomas Ha, Andru Tomoiu, Kim M Summers, David A Hume and 42 others. 2015. Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science Vol: 347 Pages: 1010-4. More»
  • J. Kenneth Baillie, Colin A. Semple, Robert S. Young, Malcolm E. Fisher, Thomas J. Ha, Anagha Joshi, Alison Meynert, James G. D. Prendergast, Kim M. Summers, Tom C. Freeman, Martin S. Taylor, David A. Hume and 40 others. 2014. A promoter-level mammalian expression atlas. Nature Vol: 507 Pages: 462-+. More»
  • Sobia Raza, Mark W Barnett, Zohar Barnett-Itzhaki, Ido Amit, David A Hume, Tom C Freeman. 2014. Analysis of the transcriptional networks underpinning the activation of murine macrophages by inflammatory mediators. Journal of Leukocyte Biology Vol: 96 Pages: 265-274. More»
  • J. Xue, SusanneV. Schmidt, J. Sander, A. Draffehn, W. Krebs, I. Quester, D. De┬áNardo, TruptiD. Gohel, M. Emde, L. Schmidleithner, H. Ganesan, A. Nino-Castro, MichaelR. Mallmann, L. Labzin, H. Theis, M. Kraut, M. Beyer, E. Latz, Tom Freeman, T. Ulas, JoachimL. Schultze. 2014. Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation. Immunity Vol: 40 Pages: 274-288. More»
  • Neil A Mabbott, J Kenneth Baillie, Helen Brown, Tom C Freeman, David A Hume. 2013. An expression atlas of human primary cells: inference of gene function from coexpression networks. BMC Genomics Vol: 14. More»
  • Tamasin Doig, David A Hume, Thanos Theocharidis, John Goodlad, Christopher D Gregory, Tom C Freeman. 2013. Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment. BMC Genomics Vol: 14. More»
  • David A Hume, Neil Mabbott, Sobia Raza, Tom C Freeman. 2013. Can DCs be distinguished from macrophages by molecular signatures?. Nature Immunology Vol: 14 Pages: 187-9. More»
  • Tom C Freeman, Alasdair Ivens, J Kenneth Baillie, Dario Beraldi, Mark W Barnett, David Dorward, Alison Downing, Lynsey Fairbairn, Ronan Kapetanovic, Sobia Raza, Andru Tomoiu, Ramiro Alberio, Chunlei Wu, Andrew I Su, Kim M Summers, Christopher K Tuggle, Alan L Archibald, David A Hume. 2012. A gene expression atlas of the domestic pig. BMC Biology Vol: 10. More»
  • Thanos Theocharidis, Stjin van Dongen, Anton J. Enright, Tom C. Freeman. 2009. Network visualization and analysis of gene expression data using BioLayout Express(3D). Nature Protocols Vol: 4 Pages: 1535-1550. More»
  • Sobia Raza, Neil McDerment, Paul A Lacaze, Kevin Robertson, Steven Watterson, Ying Chen, Michael Chisholm, George Eleftheriadis, Stephanie Monk, Maire O'Sullivan, Arran Turnbull, Douglas Roy, Athanasios Theocharidis, Peter Ghazal, Tom C Freeman. 2010. Construction of a large scale integrated map of macrophage pathogen recognition and effector systems. BMC Systems Biology Vol: 4. More»