Edinburgh Research Explorer

Tom Freeman

(Former employee or visitor)

Profile photo

Willingness to take PhD students: Yes

Education/Academic qualification

1987Doctor of Philosophy (PhD), Royal Postgraduate Medical School, Hammersmith Hospital, London
1983Bachelor of Science, Sheffield Polytechnic, S. Yorks

Current Research Interests

Network modelling and experimental manipulation of clinically relevant immune pathways.


Tom obtained his degree in Biochemistry from Sheffield and then a PhD in Physiology at Hammersmith Hospital London.

For much of his post-doctoral career he has worked on various aspects of functional genomics and systems biology. Whilst at the Hinxton Genome Campus he led the gene Expression Group at Sanger Institute, before moving on to lead the UK National Microarray Programme at the MRC HGMP-RC.

Since his move to Edinburgh in 2006 his work combines wet lab and computational methods to examine biological systems with particular interests in macrophage biology, the cell cycle, and data visualisation.

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


Student supervision

Currently registered PhD Students:
First Supervisor: Sz-Hau Chen, UofE, registered Oct. 2011, Bruno Giotti, UofE and Fahmi Nazarie, UofE registered Oct. 2012.

Second Supervisor: Yvonne Beck, registered Oct. 2012; Elisa Anastasi registered Oct. 2011; James Vincenti, UofE, registered Oct. 2010; Catherine Dalziel, U. of Glasgow, registered Oct. 2009.

Previously, first supervisor to Dr Sobia Raza, UofE, Oct. 2007–August 2011; Dr Kenneth Baillie, UofE, Oct. 2009-2012; Dr Ella Palmer, U. of Cambridge, Oct. 2002-Sept. 2005.

Second supervisor to Dr Alistair Dixon, Dr Amilie Gubitz, Dr Charles Shaw-Smith, Dr Lawrence Petalidis, Dr Chris Thorn, U. of Cambridge between 1997-2005.

Course Instructor/Organiser
Elective Course leader for '
Making sense of disease pathways', a 12 week module delivered to Biomedical Sciences BSc students, University of Edinburgh.

Research supervisor and guest lecturer on the 
Division of Pathway Medicine's MSc in Genomics and Pathway Biology.

Instructor on the Wellcome Trust Advanced Course in Functional Genomics and Systems Biology 1998-to date.

Training school on rabbit and pig genome analysis, The Genome Analysis Centre (TGAC), Norwich, UK, 22nd-26th October, 2012.

Workshop on Gene Network Analysis: Visualization and Interpretation of Genomic Data, EADGENE_S Network, Ljubljana, Slovenia. June 5th – 7th, 2012.

Instructor, Transcriptomics, Santiago, Chile, January 2011.

Instructor, IB2010 Gene networks for bench scientists, Churchill College, Cambridge March 2010.

Course Organiser, Network Visualisation and Analysis of Biological Systems, National eScience Centre, Edinburgh April 2009.

Instructor, Seminários Avançados em Tecnologia de Microarrays, Instituto Israelita de Ensino e Pesquisa Albert Einstein, Säo Paulo, Brazil. March 2009.

Instructor on 3S Biology Summer School, Trento, Italy, 2008


Research Grants - University of Edinburgh
Development of a Rapid Processing Pipeline and Graph-based Visualization for the Analysis of Next Generation Sequencing Data Applicants: T.C. Freeman (PI) and A.J. Enright. 
BBSRC grant (ref BB/I001107/1). Nov. 2012-Oct. 2014.

Integrating systems biology and transgenic technologies to unlock the secrets of Sertoli cell development and function. Applicants: L. Smith (PI), T.C. Freeman, P. O’Shaughnessy.
BBSRC grant (ref BB/J015105/1). 

The impact of systematic viral infections on the innate immune response in the brain in chronic neurodegeneration. Applicants: J. Manson (PI), J. Fazakerley, T.C. Freeman, V.H. Perry. 
MRC grant, Jan. 2012-Dec. 2014.

BioLayout Express3D: A Community Resource for the Network Visualisation and Analysis of Biological Data and Pathways. Applicants: T.C. Freeman (PI) and A.J. Enright BBSRC grant (ref BB/I001107/1). July 2010-June 2013.

Combating swine influenza initiative. Roslin applicants: A. Archibald and T.C. Freeman 
BBSRC grant (ref BB/H014292/1). Oct. 2009-Sept. 2010.

GenISIS: Genetics of Influenza Susceptibility in Scotland: a parallel study to the mechanisms of severe influenza consortium (MOSAIC). Applicants: J.K. Baillie, D.A. Hume, T.C. Freeman, G. Faulkner, T. Walsh, K. Rowan, C. Bailey, C Hayley. 
Chief Scientist Office, Scotland. Nov. 2009-Nov. 2010.

Development of a Web-Based Resource for the Macrophage Research Community
Applicants: D.A. Hume and T.C. Freeman
BBSRC grant (ref BB/G02260711/1). July 2009-June 2012.

Development of network analysis tool Biolayout Express3D
BBSRC Grant (ref: BB/F003722/1) Oct. 2007 – Feb. 2009

Applicant: T.C. Freeman
BBSRC Case Studentship with ImuThes Ltd. ‘Targeting of Macrophage Signalling Activity by DNA Therapeutics’ Oct. 2007 – Dec. 2010.
Applicant: T.C. Freeman

Previous Funding

MRC HGMP-RC, Hinxton
Establishment of a Leukaemia Research Fund Microarray Facility
LRF Project Grant Nov. 2002 - Nov. 2005
Applicant: T.C. Freeman

MRC Programme Grant Supplement, Synthesis of Oligonucleotide Probes for Use in the Fabrication of Human and Mouse Specific Microarrays
MRC Supplement Grant April 2003 
Applicant: T.C. Freeman

A UK Distributed Network for Expression Profiling using DNA Microarrays (UKNEM) MRC Programme Grant July 2001 – June 2003
Principle Investigators T.C. Freeman, HGMP-RC, Cambridge, A.J. Greenfield, MGU, Harwell.

Additional to above UKNEM
BBSRC July 2001 – June 2003 
Applicant: T.C. Freeman
Extension to UKNEM
MRC/BBSRC July 2003 - Sept. 2004.
Applicant: T.C. Freeman

Sanger Institute, Hinxton
Novel Therapeutics from Functional Genomics.
Applicant: T.C. Freeman, The Sanger Centre, Cambs. 
Co-applicant: P. Richardson, Dept. of Pharmacology, University of Cambridge.
Parke-Davis Pharmaceuticals
Nov. 1997-Oct. 2000

Discovering Novel Therapeutic Targets using Multiple Gene Expression Analysis of Single Neurons. 
Grant holder: Peter Richardson, Dept. of Pharmacology, University of Cambridge.
Co-applicant: T.C. Freeman, The Sanger Centre, Cambs.
Parke-Davis Pharmaceuticals
Nov. 1997-Oct. 2000

A C. elegans Whole Genome DNA Microarray for Monitoring Global Patterns in Gene Expression. 
Grant holder: P. Kuwabara, The Sanger Centre, Cambs.
Co-applicants: A. Coulson and T.C. Freeman, The Sanger Centre, Cambs.
Biotechnology and Biological Research Sciences Council
April 1999-March 2002

Patent Applications:
1. Design for Automated (Lucidea) Slide Processor
Applicant: Medical Research Council 
Inventor: T.C. Freeman
Filing date: 27/03/96
Issued Patent No. (US): 5,958,760 
Licensed to and produced by GE Healthcare

2. Method for Analysing Gene Expression in Single Cells 
Applicant: Medical Research Council 
Inventors: Freeman T.C., Richardson P.J. and Dixon A.K.
Filing date: 05/08/98
Application No.: 9817055.8

3. Identification and characterization of 10 apoptosis-inducing genes for use in gene therapy 
Applicant: Imperial College Inovations 
Inventors: Freeman T.C., Palmer E., and Miller A.
Filing date: 22-12-05
Application No.: 0526212.6

Founder & Director
Fios Genomics Limited
Registered address: 
Fios Genomics Limited
10 Melville Crescent
Company Number: SC313809
Spin out from the Division of Pathway Medicine, University of Edinburgh specialising in genomics data analysis services.

Highlighted research outputs

  1. A gene expression atlas of the domestic pig

    Research output: Contribution to journalArticle

  2. Can DCs be distinguished from macrophages by molecular signatures?

    Research output: Contribution to journalLetter

  3. Oncogenic Properties of Apoptotic Tumor Cells in Aggressive B Cell Lymphoma

    Research output: Contribution to journalArticle

  4. A promoter-level mammalian expression atlas

    Research output: Contribution to journalArticle

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Research activities & awards

  1. Makers Faire

    Activity: Participating in or organising an event typesPublic Engagement – Festival/Exhibition

View all (1) »

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