Research Biographies

DR DUNCAN DAVIDSON

Biomedical Systems Analysis

Visiting Worker

Contact Details

Research Areas
I am interested in how best to represent information about embryonic development in a computer-readable form in order to make it accessible to bioinformatics. A typical problem is how to represent patterns of gene expression that reflect signals and responses between cells in the embryo because these do not simply correspond with named anatomical structures so cannot readily be described in words. This problem led Richard Baldock and I to develop the eMAP Mouse Atlas and, with Jeff Christiansen, the EMAGE database of gene expression in which patterns of expression are mapped into the space of the embryo and can be interrogated by purely spatial searches (genex.hgu.mrc.ac.uk). This has also led me to develop other gene expression databases associated with large-scale gene expression projects (www.GUDMAP.org; www.EuReGene.org ; www.Eurexpress.org ). I am currently working on how best to represent the temporal aspects of development, particularly at different scales. This includes representation of the dynamics of gene expression, cell lineage, morphogenesis and differentiation.

Recent Publications

• Richardson, L.; Venkataraman, S.; Stevenson, P.; Yang, Y.; Burton, N.; Rao, J.; Fisher, M.; Baldock, R.A.; Davidson, D.R. and Christiansen, J.H. EMAGE mouse embryo spatial gene expression database: 2010 update. Nucleic Acids Res 38(Database issue): D703-D709, 2010 PubMed Abstract
• Lemos, M.C.; Harding, B.; Reed, A.; Jeyabalan, J.; Walls, G.; Bowl, M.; Sharpe, J.; Wedden, S.; Moss, J.; Ross, A.; Davidson, D. and Thakker, R. Genetic background influences embryonic lethality and the occurrence of neural tube defects in Men1 null mice: relevance to genetic modifiers. J Endocrinol 203:133-142, 2009 PubMed Abstract
• Vendrell, V.; Summerhurst, K.; Sharpe, J.; Davidson, D. and Murphy, P. Gene expression analysis of canonical Wnt pathway transcriptional regulators during early morphogenesis of the facial region in the mouse embryo. Gene Expr.Patterns. 9(5):296-305, 2009 PubMed Abstract
• Delaurier, A.; Burton, N.; Bennett, M.; Baldock, R.; Davidson, D.; Mohun, T.J. and Logan, M.P. The Mouse Limb Anatomy Atlas: an interactive 3D tool for studying embryonic limb patterning.
  BMC Dev Biol 8:83, 2008 PubMed Abstract
• Deutsch, E.W.; Ball, C.A.; Berman, J.J.; Bova, G.S.; Brazma, A.; Bumgarner, R.E.; Campbell, D.; Causton, H.C.; Christiansen, J.H.; Daian, F.; Dauga, D.; Davidson, D.R.; Gimenez, G.; Goo, Y.A.; Grimmond, S.; Henrich, T.; Herrmann, B.G.; Johnson, M.H.; Korb, M.; Mills, J.C.; Oudes, A.J.; Parkinson, H.E.; Pascal, L.E.; Pollet, N.; Quackenbush, J.; Ramialison, M.; Ringwald, M.; Salgado, D.; Sansone, S.A.; Sherlock, G.; Stoeckert, C.J., Jr.; Swedlow, J.; Taylor, R.C.; Walashek, L.; Warford, A.; Wilkinson, D.G.; Zhou, Y.; Zon, L.I.; Liu, A.Y. and True, L.D. Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).
  Nat Biotechnol 26(3):305-312, 2008 PubMed Abstract
• Fisher, M.E.; Clelland, A.K.; Bain, A.; Baldock, R.A.; Murphy, P.; Downie, H.; Tickle, C.; Davidson, D.R. and Buckland, R.A. Integrating technologies for comparing 3D gene expression domains in the developing chick limb. Dev Biol 317(1):13-23, 2008 PubMed Abstract
• McMahon, A.P.; Aronow, B.J.; Davidson, D.R.; Davies, J.A.; Gaido, K.W.; Grimmond, S.; Lessard, J.L.; Little, M.H.; Potter, S.S.; Wilder, E.L. and Zhang, P. GUDMAP: the genitourinary developmental molecular anatomy project. J Am Soc Nephrol 19(4):667-671, 2008
  PubMed Abstract
• Raciti, D.; Reggiani, L.; Geffers, L.; Jiang, Q.; Bacchion, F.; Subrizi, A.E.; Clements, D.; Tindal, C.; Davidson, D.R.; Kaissling, B. and Brandli, A.W. Organization of the pronephric kidney revealed by large-scale gene expression mapping. Genome Biol 9(5):R84, 2008 PubMed Abstract
• Summerhurst, K.; Stark, M.; Sharpe, J.; Davidson, D. and Murphy, P. 3D representation of Wnt and Frizzled gene expression patterns in the mouse embryo at embryonic day 11.5 (Ts 19).
  Gene Expression Patterns 8:331-348, 2008 PubMed Abstract
• Venkataraman, S.; Stevenson, P.; Yang, Y.; Richardson, L.; Burton, N.; Perry, T.P.; Smith, P.; Baldock, R.A.; Davidson, D.R. and Christiansen, J.H. EMAGE--Edinburgh Mouse Atlas of Gene Expression: 2008 update. Nucleic Acids Res 36(Database issue): D860-D865, 2008
  PubMed Abstract

Book

• Burger, A., Davidson, D., and Baldock, R.A. (eds.) Anatomy Ontologies for Bioinformatics: Principles and Practice. Springer, 2008

Book Chapters

• Christiansen, J.H.; Davidson, D. and Baldock, R.A. Management of Spatially Organized Biological Data using EMAGE. In: Bioinformatics for Systems Biology. Krawetz, S. (Ed.) Humana Press, New York, 2nd edition, 461-476, 2009
• Baldock, R. A. and Davidson, D. The Edinburgh Mouse Atlas. In: Anatomy Ontologies for Bioinformatics: Principles and Practice. Burger, A.; Davidson, D. and Baldock, R. (eds.) Springer, 249-265, 2008
• Davidson, D. Time in Anatomy. In: Anatomy Ontologies for Bioinformatics:Principles and Practice. Burger, A.; Davidson, D. and Baldock, R. (eds.) Springer, 213-247, 2008