Research Biographies

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PROFESSOR RICHARD BALDOCK

Biomedical Systems Analysis

Head of Biomedical Systems Analysis


Richard Baldock

Contact Details

E-mail address: richard.baldock@igmm.ed.ac.uk
Telephone: +44 (0)131 467 8434
Fax: +44 (0)131 467 8456
Address: MRC Human Genetics Unit MRC IGMM, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh EH4 2XU
Research Programme: EMAP: eMouse Atlas Project

 

 

Research Areas

My background is in theoretical physics and my research in the Human Genetics Unit is directed to understanding the genetic control of development. In collaboration with Dr Duncan Davidson I have developed the atlas-based concept for spatio-temporal databases in biomedicine and in particular the Edinburgh Mouse Atlas and associated databases (www.e-mouseatlas.org). In this context my research interests span image processing for 3D model reconstruction, spatio-temporal data-mapping, in situ gene-expression pattern analysis, bioinformatics, atlas-based biomedical databases, high throughput data capture and analysis, data/database interoperability and e-science.

 

The Mouse Atlas programme has a pivotal role in the delivery of embryo gene-expression resources internationally with direct involvement in special systems databases (www.gudmap.org, www.euregene.org), high throughput data capture (www.eurexpress.org), human embryo (www.ncl.ac.uk/ihg/EADHB, www.dgemap.org) and most recently a chick embryo atlas.

 

Recent Publications

  • Armit C, Venkataraman S, Richardson L, Stevenson P, Moss J, Graham L, Ross A, Yang Y, Burton N, Rao J, Hill B, Rannie D, Wicks M, Davidson D, Baldock R: eMouseAtlas, EMAGE, and the spatial dimension of the transcriptome
    Mamm Genome 23:514-524, 2012.
    PubMed Abstract
  • Husz ZL, Burton N, Hill B, Milyaev N, Baldock RA: Web tools for large-scale 3D biological images and atlases. BMC Bioinformatics 13:122, 2012.
    PubMed Abstract
  • Davies JA, Little MH, Aronow B, Armstrong J, Brennan J, Lloyd-Macgilp S, Armit C, Harding S, Piu X, Roochun Y, Haggarty B, Houghton D, Davidson D, Baldock R: Access and Use of the GUDMAP Database of Genitourinary Development
    Methods Mol Biol 886:185-201, 2012.
    PubMed Abstract
  • Milyaev N, Osumi-Sutherland D, Reeve S, Burton N, Baldock RA, Armstrong JD: The Virtual Fly Brain browser and query interface
    Bioinformatics 28:411-415, 2012.
    PubMed Abstract
  • Baldock RA, Burger A: Biomedical atlases: systematics, informatics and analysis
    Adv Exp Med Biol 736:655-677, 2012.
    PubMed Abstract
  • Stevenson P, Richardson L, Venkataraman S, Yang Y, Baldock R: The BioMart interface to the eMouseAtlas gene expression database EMAGE. Database (Oxford) 2011:bar029, 2011.
  • Guberman JM, Ai J, Arnaiz O, Baran J, Blake A, Baldock R, Chelala C, Croft D, Cros A, Cutts RJ, Di GA, Forbes S, Fujisawa T, Gadaleta E, Goodstein DM, Gundem G, Haggarty B, Haider S, Hall M, Harris T, Haw R, Hu S, Hubbard S, Hsu J, Iyer V, Jones P, Katayama T, Kinsella R, Kong L, Lawson D, Liang Y, Lopez-Bigas N, Luo J, Lush M, Mason J, Moreews F, Ndegwa N, Oakley D, Perez-Llamas C, Primig M, Rivkin E, Rosanoff S, Shepherd R, Simon R, Skarnes B, Smedley D, Sperling L, Spooner W, Stevenson P, Stone K, Teague J, Wang J, Wang J, Whitty B, Wong DT, Wong-Erasmus M, Yao L, Youens-Clark K, Yung C, Zhang J, Kasprzyk A: BioMart Central Portal: an open database network for the biological community. Database (Oxford) 2011:bar041, 2011.
    PubMed Abstract
  • Gaudet, P.; Bairoch, A.; Field, D.; Sansone, S.A.; Taylor, C.; Attwood, T.K.; Bateman, A.; Blake, J.A.; Bult, C.J.; Cherry, J.M.; Chisholm, R.L.; Cochrane, G.; Cook, C.E.; Eppig, J.T.; Galperin, M.Y.; Gentleman, R.; Goble, C.A.; Gojobori, T.; Hancock, J.M.; Howe, D.G.; Imanishi, T.; Kelso, J.; Landsman, D.; Lewis, S.E.; Mizrachi, I.K.; Orchard, S.; Ouellette, B.F.; Ranganathan, S.; Richardson, L.; Rocca-Serra, P.; Schofield, P.N.; Smedley, D.; Southan, C.; Tan, T.W.; Tatusova, T.; Whetzel, P.L.; White, O. and Yamasaki, C. Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res 39(Database issue):D7-10, 2011
    PubMed Abstract
  • Hawrylycz, M.; Baldock, R.A.; Burger, A.; Hashikawa, T.; Johnson, G.A.; Martone, M.; Ng, L.; Lau, C.; Larsen, S.D.; Nissanov, J.; Puelles, L.; Ruffins, S.; Verbeek, F.; Zaslavsky, I. and Boline, J. Digital atlasing and standardization in the mouse brain. PLoS Comput.Biol 7(2):e1001065, 2011 PubMed Abstract
  • Ringwald M, Iyer V, Mason JC, Stone KR, Tadepally HD, Kadin JA, Bult CJ, Eppig JT, Oakley DJ, Briois S, Stupka E, Maselli V, Smedley D, Liu S, Hansen J, Baldock R, Hicks GG, Skarnes WC: The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium. Nucleic Acids Res 39:D849-D855, 2011
    PubMed Abstract
  • Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, Magen A, Canidio E, Pagani M, Peluso I, Lin-Marq N, Koch M, Bilio M, Cantiello I, Verde R, De Masi C, Bianchi SA, Cicchini J, Perroud E, Mehmeti S, Dagand E, Schrinner S, Nurnberger A, Schmidt K, Metz K, Zwingmann C, Brieske N, Springer C, Hernandez AM, Herzog S, Grabbe F, Sieverding C, Fischer B, Schrader K, Brockmeyer M, Dettmer S, Helbig C, Alunni V, Battaini MA, Mura C, Henrichsen CN, Garcia-Lopez R, Echevarria D, Puelles E, Garcia-Calero E, Kruse S, Uhr M, Kauck C, Feng G, Milyaev N, Ong CK, Kumar L, Lam M, Semple CA, Gyenesei A, Mundlos S, Radelof U, Lehrach H, Sarmientos P, Reymond A, Davidson DR, Dolle P, Antonarakis SE, Yaspo ML, Martinez S, Baldock RA, Eichele G, Ballabio A: A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol 9:e1000582, 2011.
    PubMed Abstract
  • Harding SD, Armit C, Armstrong J, Brennan J, Cheng Y, Haggarty B, Houghton D, Lloyd-Macgilp S, Pi X, Roochun Y, Sharghi M, Tindal C, McMahon AP, Gottesman B, Little MH, Georgas K, Aronow BJ, Potter SS, Brunskill EW, Southard-Smith EM, Mendelsohn C, Baldock RA, Davies JA, Davidson D: The GUDMAP database - an online resource for genitourinary research. Development 138:2845-2853, 2011. 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.) 249-265, 2008

  • Baldock, R. A. and Burger, A. Anatomical Ontologies: Linking Names to Places in Biology. In: Anatomy Ontologies for Bioinformatics: Principles and Practice. Burger, A.; Davidson, D. and Baldock, R.A. (eds.) 197-211, 2008