publications
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Here is a chronological list of publications from the MouseAtlas and collaborative projects. We do have reprints of some of these papers, please contact one of the authors or genexweb to obtain a reprint (if there are any left).

  1. Baldock, R.A., Bard J. , Kaufman M.H. and Davidson D, A real mouse for your computer, BioEssays 14 (1992) pp501-502. (MEDLINE)

  2. Baldock, R.A., Poole I, Video Camera Calibration for Optical Densitometry, Journal of Microscopy, 172 (1993) pp49-54.

  3. Ringwald, M, Baldock, R.A, Bard J, Kaufman M.H, Eppig J.T, Richardson J.E, Nadeau, J.H. and Davidson D, A database for mouse development, Science 265 (1994) pp2033-2034. (MEDLINE)

  4. Guest E, Automatic reconstruction from serial sections, (1994) PhD Thesis, Department of Artificial Intelligence, University of Edinburgh.

  5. Guest E. and Baldock, R.A, Automatic reconstruction of serial sections using the finite element method, BioImaging 3 (1995) pp154-167.

  6. Bard J B, Davies J A, Development, databases and the Internet, Bioessays 17(11) (1995) pp999-1001. (MEDLINE)

  7. Bard J B L, Baldock R A, Kaufman M and Davidson D, Graphical gene-expression database for mouse development, European Journal of Morphology 35(1) (1997) pp32-34.

  8. Kaufman M H,, Kaufman D B, Brune R M, Stark M, Armstrong J F and Clarke A R, Analysis of fused maxillary incisor dentition in p53-deficient exencephalic mice, Journal of Anatomy 191 (1997) pp57-64. (MEDLINE)

  9. Kaufman M.H, Brune R.T, Baldock, R.A, Bard J. and Davidson D, Computer-aided 3D reconstruction of serially sectioned mouse embryos: its use in integrating anatomical organization, Int.J. Dev. Bio. 41 (1997) pp223-233. (MEDLINE)

  10. Strachan T, Abitbol M, Davidson D and Becjmann J S, A New Dimension for the Human Genome Project: Towards Comprehansive Expression Maps, Nature Genetics 16(2) (1997) pp126-132. (MEDLINE)

  11. Bard J B L, Introduction: Making and filling gene-expression developmental databases, Seminars in Cell and Developmental Biology 8(5) (1997) pp455-458. (MEDLINE)

  12. Baldock R A, F J Verbeek and J-L Vonesch, 3-D Reconstructions for graphical databases of gene expression, Seminars in Cell and Developmental Biology 8(5) (1997) pp499-507. (MEDLINE)

  13. Davidson D, Bard J, Brune R, Burger A, Dubreuil C, Hill W, Kaufman M, Quinn J, Stark M, Baldock R, The mouse atlas and graphical gene-expression database, Seminars in Cell and Developmental Biology 8(5) (1997) pp509-517. (MEDLINE)

  14. Davidson D, Baldock R, A 3-D atlas and gene-expression database of mouse development: implications for a database of human development, Molecular Genetics of Early Human Development, Ed. T Strachan, S Lindsay and D J Wilson (BIOS Scientific Publishers Ltd, Oxford, 1997) pp239-260.

  15. Davidson D, Ringwald M, Dubreuil C, Gene expression databases, Guide to Human Genome Computing, Ed. M Bishop (Academic Press, London, 1998) pp??

  16. Davidson D, Baldock R, Bard J, Kaufman M, Richardson J E, Eppig J and Ringwald, M., Gene expression databases, In situ Hybridization, a practical approach, 2nd edition, Ed. D Wilkinson (IRL Press, Oxford, 1998) pp190-214.

  17. Jonathan B L Bard, Matthew H Kaufman, Christophe Dubreuil, Renske M Brune, Albert Burger, Richard A Baldock and Duncan R Davidson, An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature, Mechanisms of Development 74 (1998) pp111-20. (MEDLINE)

  18. M H Kaufman, R M Brune, D R Davidson and R A Baldock, Computer-generated three-dimensional reconstructions of serially sectioned mouse embryos, Journal of Anatomy, 193 (1998) pp323-36.

  19. Jonathan B L Bard, Richard A Baldock and Duncan R Davidson, Elucidating the genetic networks of development: a bioinformatics approach, Genome Research 8(9) (1998) pp859-63. (MEDLINE)

  20. Richard A Baldock, Chrisophe Dubreuil, Bill Hill and Duncan Davidson, The Edinburgh Mouse Atlas: Basic Structure and Informatics, Bioinformatics Databases and Systems, Ed. S Levotsky (Kluwer Academic Press, 1999), pp102-115.

  21. Richard A Baldock and Jim Graham, Image Processing and Analysis: A Practical Approach, (Oxford University Press, 1999).

  22. Richard Baldock and Bill Hill, Image Warping and Spatial Data Mapping, Image Processing and Analysis: A Practical Approach, Ed. R A Baldock and J. Graham, (Oxford University Press, 1999) pp261-288.

  23. Richard Baldock and Duncan Davidson, Gene Expression Databases, Genetics Databases, Ed. M. Bishop, (Academic Press, 1999), pp247-268.

  24. R M Brune, J B L Bard, C Dubreuil, E Guest, W Hill, M Kaufman, M Stark, D Davidson, and R A Baldock, A Three-Dimensional Model of the Mouse at Embryonic Day 9, Developmental Biology 216(2) (1999) pp457-68.

  25. Everett, C. A., Stark, M. H., West, J. D., Davidson, D. and Baldock, R. A., Three-dimensional reconstruction of tetraploid<->diploid chimaeric mouse blastocysts, Journal of Anatomy 196 (2000) pp341-346.

  26. Davidson, D., Bard, J., Kaufman, M. and Baldock, R. A., The Mouse Atlas Database: a community resource for mouse development, Trends in Genetics 17 (2001) pp49-51.

  27. Guest, E., Berry, e., Baldock, R.A., Fidrich, M. and Smith, M.A., Robust Point Corespondence Applied to Two- and Three-Dimensional Image Registration , IEEE Trans. on Pattern Analysis and Machine Intelligence 23 (2001) pp1-15 (pdf).

  28. Duncan Davidson and Richard Baldock., Bioinformatics Beyond Sequence: Mapping Gene Function in the Embryo , Nature Reviews Genetics 2 (2001) pp409-418.

  29. Mahy, N.L, Perry P.E., Gilchrist, S., Baldock, R.A. and Bickmore WA, Spatial localisation of active and inactive genes, and non-coding DNA, within chromosome territories., J. Cell Biol. 157 (2002) pp579-589.

  30. James Sharpe, Ulf Ahlgren, Paul Perry, Bill Hill, Allyson Ross, Jacob Hecksher-Serensen, Richard Baldock, Duncan Davidson, Optical Projection Tomography as a Tool for 3D Microscopy and Gene Expression Studies., Science. 296 (2002) pp541-545.

  31. Konstantinos Karasavvas, Albert Burger and Richard Baldock, A Multi-Agent Bioinformatics Integration System with Adjustable Autonomy, Lecture Notes in Computer Science, 2417 (2002) pp492-501

  32. Bill Hill, Richard Baldock, Andrew Wallace, Image Warping through Geometric Model Decomposition, Proceedings of SPIE 4794 (2002).

  33. Rob Baxter, Neil Chue Hong, Richard Baldock, Bill Hill andJames Sharpe, Bringing the Grid to the Biomedical Workbench, Proceedings of the 11 th IEEE International Symposium on High Performance Distributed Computing HPDC-11 2002 (HPDC’02)
    (2002) 417 (pdf).

  34. Albert Burger, Richard Baldock, YiyaYang, Andrew Waterhouse, Derek Houghton, Nick Burton, Duncan Davidson, The Edinburgh Mouse Atlas and Gene-Expression Database:
    A Spatio-Temporal Database for Biological Research    , Proceedings of the 14th International Conference on Scientific and Statistical Database Management (SSDBM’02) (2002) 239 (pdf).

  35. Richard Baldock, Jonathan Bard, ALbert Burger, Nicolas Burton, Jeff Christiansen, Guangjie Feng, Bill Hill, Derek Houghton, Mathew Kaufman, Jianguo Rao, James Sharpe, Allyson Ross, Peter Stevenson, Shanmugasundaram Venkataraman, Andrew Waterhouse, Yiya Yang, Duncan Davidson, EMAP and EMAGE: A Framework for Understanding Spatially Organised Data, Neuroinformatics 1 (2003) pp309-325 (pdf).

  36. Amy Hunter, Matthew H. Kaufman, Angus McKay, Richard Baldock, Martin W. Simmen and Jonathan B. L. Bard, An ontology of human developmental anatomy, J. Anat. 203 (2003) pp347­355.

  37. Albert Burger, Duncan Davidson and Richard Baldock, Formalization of Mouse Embryo Anatomy, Bioinformatics 20 (2004) pp259-267.

  38. Gkoutos G.V., Green E.C.J., Mallon A.M., Hancock J.M., Davidson D, Building mouse phenotype ontologies. Pac. Symp. Biocomput., (2004) pp178-89.

  39. Konstantinos A Karasavvas, Richard A Baldock and Albert Burger, Criticality-Based Task Composition in Distributed Bioinformatics Systems, ISMB (2004) (pdf).

  40. Janet Kerwin, Mark Scott, James Sharpe, Luis Puelles, Stephen C Robson, Margaret Martinez-de-la-Torre, Jose Luis Ferran, Guangjie Feng, Richard Baldock, Tom Strachan, Duncan Davidson, Susan Lindsay, 3 dimensional modelling of early human brain development using optical projection tomography, BMC Neuroscience 5 (2004) pp27 (pdf).

  41. Konstantinos Liakos, Albert Burger and Richard Baldock, A Scalable Mediator Approach to Process Large Biomedical 3-D Images, IEEE Transactions on Information Technology in Biomedicine 8 (2004) pp354-359 (pdf).

  42. The European Mouse Mutagenesis Consortium: Johan Auwerx, Phil Avner, Richard Baldock, Andrea Ballabio, Rudi Balling, Mariano Barbacid, Anton Berns, Allan Bradley, Steve Brown, Peter Carmeliet, Pierre Chambon, Roger Cox, Duncan Davidson, Kay Davies, Denis Duboule, Jiri Forejt, Francesca Granucci, Nick Hastie, Martin Hrabé de Angelis, Ian Jackson, Dimitris Kioussis, George Kollias, Mark Lathrop, Urban Lendahl, Marcos Malumbres, Harald von Melchner, Werner Müller, Juha Partanen, Paola Ricciardi-Castagnoli, Peter Rigby, Barry Rosen, Nadia Rosenthal, Bill Skarnes, A Francis Stewart, Janet Thornton, Glauco Tocchini-Valentini, Erwin Wagner, Walter Wahli & Wolfgang Wurst., The European dimension for the mouse genome mutagenesis program, Nature Genetics 36 (2004) pp927-927.

  43. K A Karasavvas, R Baldock and A Burger, Bioinformatics integration and agent technology, Journal of Biomedical Informatics 37 (2004) pp205-219 (pdf)

  44. Albert Burger, Duncan Davidson, Yiya Yang and Richard Baldock, Integrating Multiple Partonomic Hierarchies in Anatomy Ontologies, BMC Bioinformatics 5 (2004) 184 (pdf)

  45. Helen Parkinson, Stuart Aitken, Richard A. Baldock, Jonathan B.L. Bard, Albert Burger, Terry F. Hayamizu, Alan Rector, Martin Ringwald, Jeremy Rogers, Cornelius Rosse, Christian J. Stoeckert Jr. and Duncan Davidson,, The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data, Comparative and Functional Genomics 5 (2004) 521-527 (pdf)

  46. Konstantinos Liakos, Albert Burger and Richard Baldock, Distributed Processing of Large BioMedical 3D Images, VECPAR 2004, Ed. M. Dayde et al, Lecture Notes in Computer Science 3402 (2005) pp142-155 (pdf).

  47. Richard Baldock and Albert Burger, Anatomical ontologies: names and places in biology, Genome Biology, 6 (2005) 108.

  48. Guangjie Feng, Nick Burton, Bill Hill, Duncan Davidson, Janet Kerwin, Mark Scott, Susan Lindsay and Richard Baldock, JAtlasView: A Java Atlas-Viewer for Browsing Biomedical 3D Images and Atlases, BMC Bioinformatics 6:47 (2005) (pdf).

  49. Subrot Sarma, Janet Kerwin, Luis Puelles, Mark Scott, Tom Strachan, Guangjie Feng, James Sharpe, Duncan davidson, Richard Baldock Susan Lindsay, 3D modelling, gene expression mapping and post-mapping image analysis in the developing human brain, Brain Research Bulletin 66(2005)449-453.

  50. McLaren, A. and Lawson, K.A., How is the mouse germ-cell lineage established? Differentiation 73(2005)435-437.

  51. Jeffrey H. Christiansen, Yiya Yang, Shanmugasundaram Venkataraman, Lorna Richardson, Peter Stevenson, Nicholas Burton, Richard A. Baldock and Duncan R. Davidson. EMAGE: a spatial database of gene expression patterns during mouse embryo development. Nucl. Acids Res. 34 (2006): D637 (pdf)

  52. Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, Mills JC, Oudes A, Parkinson HE, Pascal LE, Quackenbush J, Ramialison M, Ringwald M, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Zhou Y, Liu AY, True LD. Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). OMICS. (2006) Summer;10(2):205-8.

  53. Christiansen JH. One ISH, two ISH, red ISH, blue ISH: choosing the right in situ hybridisation protocol. Development (2006) 133(24):4802-3. .

  54. Bill Hill, Richard A. Baldock The Constrained Distance Transform: Interactive Atlas Registration With Large Deformations Through Constrained Distances. DEFORM'06 - Workshop on Image Registration in Deformable Environments (2006)(pdf)

  55. Burger A. Agent Technologies in the Life Sciences. Chapter in Baker, Christopher and Cheung, Kei-Hoi, Editors, Semantic Web: Revolutionizing Knowledge and Discovery in the Life Sciences, Springer (2007), pp341-352.

  56. Jano van Hemert and Richard Baldock. Mining Spatial Gene Expression Data for Association Rules, Lecture Notes in Computer Science, Volume 4414 (2007)66-76. (pdf)

  57. Jenny Ure, Rob Proctor, Maryann Martone, David Porteous, Sharon Lloyd, Stephen Lawrie, Dominic Job, Richard Baldock, Alistair Philp, Dave Liewald, Frank Rakebrand, Alan Blaikie, Clare McKay, Stuart Anderson, John Ainsworth, Jano van Hemert, Ignacio Blanquer, Richard Sinnott, Christian Barillot, Frank Bernard Gibaud, Alan Williams, Mark Hartswood, Paul Watson, Leslie Smith, Albert Burger, Jessie Kennedy, Horacio Gonzalez-Velez, Robert Stevens, Oscar Coecho, Robin Morton, Pamela Linksted, Mylene Deschenne, Mark McGilchrist, Paul Johnson, Alex Vossi, Renate Gertz, Joanna Wardlaw Data Integration in eHealth: A Domain/Disease Specific Roadmap, Studies Health Technol Inform 126 (2007) 144-53. (pdf)

  58. Karen Sutherland, Kenneth McLeod and Albert Burger Task Composition for a Semantic Web Browser, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria, 21-25 July, 2007; Poster (extended abstract (pdf)).

  59. Little MH, Brennan J, Georgas K, Davies JA, Davidson DR, Baldock RA, Beverdam A, Bertram JF, Capel B, Chiu HS, Clements D, Cullen-McEwen L, Fleming J, Gilbert T, Herzlinger D, Houghton D, Kaufman MH, Kleymenova E, Koopman PA, Lewis AG, McMahon AP, Mendelsohn CL, Mitchell EK, Rumballe BA, Sweeney DE, Valerius MT, Yamada G, Yang Y andYu J A high-resolution anatomical ontology of the developing murine genitourinary tract, Gene Expr Patterns. 7(6) (2007) 680-99.

  60. Albert Burger, Duncan Davidson and Richard Baldock Anatomy Ontologies for Bioinformatics: Principles and Practice, (Springer, 2008).

  61. Richard Baldock and Albert Burger Anatomy Ontologies: Linking Names to Places in Biology, in "Anatomy Ontologies for Bioinformatics: Principles and Practice" (Springer, 2008) 197-212.

  62. Albert Burger and Jonathan Bard XSPAN - A Cross-Species Anatomy Network, in "Anatomy Ontologies for Bioinformatics: Principles and Practice" (Springer, 2008) 163-176.

  63. Duncan Davidson Time in Anatomy, in "Anatomy Ontologies for Bioinformatics: Principles and Practice" (Springer, 2008) 213-248.

  64. Richard Baldock and Duncan Davidson The Edinburgh Mouse Atlas, in "Anatomy Ontologies for Bioinformatics: Principles and Practice" (Springer, 2008) 249-266.

  65. Venkataraman S, Stevenson P, Yang Y, Richardson L, Burton N, Perry TP, Smith P, Baldock RA, Davidson DR, Christiansen JH. EMAGE: Edinburgh Mouse Atlas of Gene Expression: 2008 update. Nucleic Acids Res. 2008 36:D860-5.

  66. 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., 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., True, L.D. Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE), Nature Biotechnology. 2008 26:305-312.

  67. Malcolm E. Fisher, Allyson K. Clelland, Andrew Bain, Richard A. Baldock, Paula Murphy, Helen Downie, Cheryll Tickle, Duncan R. Davidson, Richard A. Buckland, Integrating technologies for comparing 3D gene expression domains in the developing chick limb, Developmental Biology 317 (2008) 13-23.

  68. J. I. van Hemert and R. A. Baldock, Matching Spatial Regions with Combinations of Interacting Gene Expression Patterns, Communications in Computer and Information Science (2008) 347-361.(pdf)

  69. April DeLaurier, Nicholas Burton, Michael Bennett, Richard Baldock, Duncan Davidson, Timothy J. Mohun and Malcolm P.O. Logan, The Mouse Limb Anatomy Atlas: an interactive 3D tool for studying embryonic limb patterning, BMC Developmental Biology 8 (2008) 83 (doi:10.1186/1471-213X-8-83).

  70. Han, L., van Hemert, J., Baldock, R. and Atkinson, M.P. Automating Gene Expression Annotation for Mouse Embryo , Lecture Notes in Computer Science (Advanced Data Mining and Applications, 5th International Conference), Springer, LNAI 5678 (2009) pp469-478 (preprint pdf).

  71. A. Barker and van Hemert, J.I. and R.A. Baldock and M.P. Atkinson An E-infrastructure to Support Collaborative Embryo Research, Cluster Computing and the Grid (2009) pp520-525.

  72. Christiansen JH, Davidson D and Baldock RA. Management of Spatially Organized Biological Data using EMAGE. In: Bioinformatics for Systems Biology, 2nd edition, Ed. S Krawetz (Humana Press, New York, 2009) pp461-476.

  73. Zsolt L. Husz, Thomas P. Perry, Bill Hill and Richard A. Baldock, Woolz IIP: A Tiled On-the-fly Sectioning Server for 3D Volumetric Atlases. 5th International Symposium on Visual Computing, 2009, Lecture Notes in Computer Science 5875 (2009) 924-933 (pdf, bibtex)

  74. Richardson L, Venkataraman S, Stevenson P, Yang Y, Burton N, Rao J, Fisher M. Baldock RA, Davidson DR, Christiansen JH. EMAGE mouse embryo spatial gene expression database: 2010 update. Nucleic Acids Research (2009) doi:10.1093/nar/gkp76

  75. Walter T, Shattuck D.W, Baldock R, Bastin M.E, Carpenter A.E, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan M.A, Schneider J.E, Tomancak P and Heriche J-K, Visualization of image data from cells to organisms, Nature Methods 7 no. 3s (2010)S26-S41 doi:10.1038/nmeth.1431

  76. Kerwin, J.; Yang, Y.; Merchan, P.; Sarma, S.; Thompson, J.; Wang, X.; Sandoval, J.; Puelles, L.; Baldock, R. and Lindsay, S., The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain, J Anat. 217 no.4 (2010) 289-299, doi:10.111/j.1469-7580.2010.01290.x

  77. 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. 2011 Jan;39(Database issue):D849-55. Epub 2010 Oct 6., doi:10.1093/nar/gkq879

  78. Bangs F, Welten M, Davey MG, Fisher M, Yin Y, Downie H, Paton B, Baldock R, Burt DW, Tickle C., Identification of genes downstream of the Shh signalling in the developing chick wing and syn-expressed with Hoxd13 using microarray and 3D computational analysis, Mech Dev. 2010 Sep-Dec;127(9-12):428-41. Epub 2010 Aug 12., doi:10.1016/j.mod.2010.08.001

  79. 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 Masi1 C, Bianchi SA, CicchiniJ, Perroud E, Mehmeti S, Dagand E, Schrinner S, Nürnberger A, Schmidt K, Metz K, Zwingmann C, Brieske N, Springer C, Martinez Hernandez A, Herzog S, Grabbe F, Sieverding C, Fischer B, Schrader K, Brockmeyer M, Dettmer S, Helbig C, Alunni V, Battaini M-A, Mura C, Henrichsen CN, Garcia-Lopez R, Echevarria D, Puelles E, Garcia-Calero E, Kruse S, Uhr M, Kauck C, Feng G, MilyaevN, Kee Ong C, Kumar L, Sze Lam M, Semple CA, Gyenesei A, Mundlos S, Radelof U, Lehrach H, Sarmientos P, Reymond A, Davidson DR, Dollé1 P, Antonarakis SE, Yaspo M-L, Martinez S, Baldock RA, Eichele G, Ballabio A., A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo, PLoS Biol 9(1) 2011: e1000582., doi:10.1371/journal.pbio.1000582

  80. Hawrylycz M, Baldock RA, Burger A, Hashikawa T, Johnson GA, et al., Digital Atlasing and Standardization in the Mouse Brain., PLoS Comput Biol 7(2) 2011: e1001065, doi:10.1371/journal.pcbi.1001065
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