Publications

Reverse-chronological list of publications from the MouseAtlas and collaborative projects.

  1. Solomon Adebayo, Kenneth McLeod, Ilinca Tudose, David Osumi-Sutherland, Tony Burdett, Richard Baldock, Albert Burger and Helen Parkinson (2016) PhenoImageShare: an image annotation and query infrastructure, Journal of Biomedical Semantics. 7(1):1-10. doi: 10.1186/s13326-016-0072-2

  2. Armit C & Richardson L. (2016) Digital Graphical Resources and Developmental Anatomy in the Mouse. Kaufman's Atlas of Mouse Development Supplement Elsevier. 295-206.

  3. Price D, Graham E, Moss J, Armit C, Baldock R (2016) Coronal Sections. Kaufman's Atlas of Mouse Development Supplement Elsevier. :3-49.

  4. Richard Baldock, Jonathan Bard, Duncan R. Davidson and Gillian Morriss-Kay (2016) Kaufman's Atlas of Mouse Development Supplement Elsevier.

  5. Lorna Richardson, Liz Graham, Julie Moss, Nick Burton, Yogmatee Roochun, Chris Armit and Richard Baldock (2015) Developing the eHistology Atlas. Database,. bav105:1-6. doi: 10.1093/database/bav105

  6. Armit C (2015) Into the blue: the importance of murine lacZ gene expression profiling in understanding and treating human disease. Dis Model Mech.. 8(11):1341-3. doi: 10.1242/dmm.023606

  7. Armit C, Richardson L, Hill B, Yang Y, Baldock RA (2015) eMouseAtlas Informatics: Embryo Atlas and Gene Expression Database. Mamm Genome. 26:431-40. doi: 10.1007/s00335-015-9596-5

  8. Terry F. Hayamizu, Richard A. Baldock and Martin Ringwald (2015) Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data Mamm Genome. 26:422–430. doi: 10.1007/s00335-015-9584-9

  9. Rachel L Berry, Derya Ozdemir, Bruce Aronow, Nils O Lindstrom, TatianaDudnakova, Anna Thornburn, Paul Perry, Richard Baldock, Chris Armit, Anagha Joshi, Cecile Jeanpierre, Jingdong Shan, Seppo Vainio, James Baily, David Brownstein, Jamie, A Davies, Nick D Hastie, and Peter Hohenstein, (2015) Deducing the stage of origin of Wilms tumours from a developmental series of Wt1 mutants, Disease Models & Mechanisms May 14, 2015, doi: 10.1242/dmm.018523

  10. Elizabeth Graham, Julie Moss, Nick Burton, Chris Armit, Lorna Richardson and Richard Baldock (2015) The atlas of mouse development eHistology resource Development. 142:1909-1911. doi: 10.1242/dev.124917

  11. Kylie M Georgas, Jane Armstrong, Janet R Keast, Christine E Larkins, Kirk M McHugh, E Michelle Southard-Smith, Martin J Cohn, Ekatherina Batourina, Hanbin Dan, Kerry Schneider, Dennis P Buehler, Carrie B Wiese, Jane Brennan, Jamie A Davies, Simon D Harding, Richard A Baldock, Melissa H Little, Chad M Vezina, and Cathy Mendelsohn, (2015) An illustrated anatomical ontology of the developing mouse lower urogenital tract, Development May 15;142(10):1893-908. doi: 10.1242/dev.117903.

  12. Smedley D, … Baldock R, et al, (2015) The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res. doi: 10.1093/nar/gkv350

  13. Bill Hill and Richard A. Baldock, (2015) Constrained distance transforms for spatial atlas registration, BMC Bioinformatics 2015, 16:90,  doi:10.1186/s12859-015-0504-5

  14. Bernard de Bono, Soroush Safaei, Pierre Grenon, David P. Nikerson, Samuel Alexander, Michiel Helvensteijn, Joost N. Kok, Natallia Kokash, Alan Wu, Tommy Yu, Peter Hunter and Richard A. Baldock, (2015) The Open Physiology workflow: modelling processes over physiological circuitboards of interoperable tissue units, Front. Physiology, 6:24, doi: 10.3389/fphys.2015.00024

  15. Zaslavsky I, Baldock RA and Boline J (2014) Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases. Front. Neuroinform. 8:74. doi: 10.3389/fninf.2014.00074

  16. Richardson L, Moss J, Graham E, Burton N, Armit C, Baldock R (2015) Developing the eHistology Atlas. Database (Oxford) 2015. . bav105 doi: 10.1093/database/bav105

  17. Lorna Richardson, Peter Stevenson, Shanmugasundaram Venkataraman, Yiya Yang, Nick Burton, Jianguo Rao, Jeffrey H. Christiansen, Richard A. Baldock and Duncan R. Davidson, EMAGE: Electronic Mouse Atlas of Gene Expression, in Mouse Molecular Embryology Chapter 5, Ed Mark Lewandoski, Methods in Molecular Biology 1092 (2014) p61, doi: 10.1007/978-1-60327-292-6_5

  18. Sofia Pavlou, Katy Astell, Ioannis Kasioulis, Milica Gakovic, Richard Baldock, Veronica van Heyningen, Pedro Couthino, (2014) Pleiotropic Effects of Sox2 during the Development of the Zebrafish Epithalamus. PLoS ONE 9(1): e87546. doi:10.1371/journal.pone.0087546.

  19. Richardson L, Venkataraman S, Stevenson P, Yang Y, Moss J, Graham L, Burton N, Hill B, Rao J, Baldock RA, Armit C (2014)., EMAGE mouse embryo spatial gene expression database: (2014 update) Nucleic Acids Res. 42(1):D835-44. doi: 10.1093/nar/gkt1155

  20. Bernard de Bono, Pierre Grenon, Richard Baldock and Peter Hunter, Functional Tissue Units and their Primary Motifs in Multi-Scale Physiology, Journal of Biomedical Semantics (2013) 4:22 doi:10.1186/2041-1480-4-22

  21. Terry F Hayamizu,Michael N Wicks, Duncan R Davidson, Albert Burger, Martin Ringwald and Richard A Baldock, EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update, Journal of Biomedical Semantics.2013, 4:15. doi:10.1186/2041-1480-4-15

  22. Liangxiu Han, Zheng Xie, Richard Baldock, "Automatic Data Reuse for Accelerating Data Intensive Applications in the Cloud", IEEE the Proceedings of the 8th Internet Technology and Secured Transactions (ICITST-2013). pp.600-605. ISBN 978-1-908320-16-2, London, UK, 9-12, December, 2013. doi:10.1109/ICIST.2013.6747621

  23. Xie, Z., Han, L., Baldock, R., "Augmented Petri Net Cost Model for Optimisation of Large Bioinformatics Workflows Using Cloud,” the Proceedings of IEEE 7th European Modelling Symposium on Mathematical Modelling and Computer Simulation, pp. 191-195, Manchester, UK, 20-23 Nov 2013. ISBN 978-1-4799-2577-3.

  24. Zheng Xie, Liangxiu Han and Richard A Baldock, Enhancing Parallelism of Data-Intensive Bioinformatics Applications, 8th EUROSIM Congress on Modelling and Simulation (EUROSIM 2013), 2013. (preprint pdf)

  25. Frances Wong, Monique C M Welten, Claire Anderson, Andrew A Bain, Jiahui Liu, Michael N Wicks, Gordana Pavlovska, Megan G Davey, Paula Murphy, Duncan Davidson, Cheryll A Tickle, Claudio D Stern, Richard A Baldock, and David W Burt, eChickAtlas: an introduction to the database, Genesis 51 (2013) 365-371 doi:10.1002/dvg.22374

  26. Timothy Mohun, David J Adams, Richard Baldock, Shoumo Bhattacharya, Andrew J Copp, Myriam Hemberger, Corinne Houart, Matt E Hurles, Elizabeth Robertson, James C Smith, Tom Weaver, and Wolfgang Weninger, Deciphering the Mechanisms of Developmental Disorders (DMDD): a new programme for phenotyping embryonic lethal mice, Disease Models and Mechanisms 6 (2013) 562-566. doi:10.1242/dmm.011957

  27. David Adams, Richard Baldock, Shoumo Bhattacharya, Andrew J Copp, Mary Dickinson, Nicholas D E Greene, Mark Henkelman, Monica Justice, Timothy Mohun, Stephen A Murray, Erwin Pauws, Michael Raess, Janet Rossant, Tom Weaver and David West, Bloomsbury report on mouse embryo phenotyping: recommendations from the IMPC workshop on embryonic lethal screening, Disease Models and Mechanisms 6 (2013) 571-579 doi:10.1242/dmm.011833

  28. Liangxiu Han, Jano van Hemert, Ian Overton, Paolo Besana and Richard Baldock, Analysing Gene Expression Imaging Data in Developmental Biology, in “THE DATA BONANZA: Improving Knowledge Discovery for Science, Engineering and Business”, Eds M Atkinson et al, (John Wiley and Sons Ltd., 2013) p327-351.

  29. Chris Armit, Shanmugasundaram Venkataraman, Lorna Richardson, Peter Stevenson, Julie Moss, Liz Graham, Allyson Ross, Yiya Yang,Nicholas Burton, Jianguo Rao, Bill Hill, Dominic Rannie, Mike Wicks, Duncan Davidson and Richard Baldock, eMouseAtlas, EMAGE, and the spatial dimension of the transcriptome, Mammalian Genome 23 (2012) 514-524 doi:10.1007/s00335-012-9407-1

  30. Jamie A Davies, Melissa H Little, Kylie Georgas, Bruce Aronow, Jane Armstrong, Jane Brennan, Sue Lloyd-MacGilp, Chris Armit, Simon Harding, Xinjun Piu, Yogmatee Roochun, Bernard Haggarty, Derek Houghton, Duncan Davidson, and Richard Baldock, Access and Use of the GUDMAP Database of Genitourinary Development, Methods in Molecular Biology, 886 (2012) 185-201. doi:10.1007/978-1-61779-851-1_17

  31. Zsolt L Husz, Nicolas Burton, Bill Hill, Nestor Milaev and Richard A Baldock, Web tools for large-scale 3D biological images and atlases, BMC Bioinformatics 13:122 (2012), doi:10.1186/1471-2105-13-122

  32. Milyaev N, Osumi-Sutherland D, Reeve S, Burton N, Baldock RA and Armstrong JD, The Virtual Fly Brain browser and query interface, Bioinformatics 28 (2012) 411-5, Epub 2011 Dec 16 DOI: 10.1093/bioinformatics/btr677.

  33. Baldock R A. and Burger A, , Biomedical Atlases: systematics, informatics and analysis., Advances and Experimental and Medical Biology 736 (2012) 655-677 DOI: 10.1007/978-1-4419-7210-1_39

  34. Peter Stevenson, Lorna Richardson, Shanmugasundaram Venkataraman, Yiya Yang, and Richard Baldock , The BioMart interface to the eMouseAtlas gene expression database EMAGE., Database (2011) Vol. 2011 doi:10.1093/database/bar029.

  35. Jonathan M. Guberman, J. Ai, O. Arnaiz, Joachim Baran, Andrew Blake, Richard Baldock, Claude Chelala, David Croft, Anthony Cros, Rosalind J. Cutts, A. Di Génova, Simon Forbes, T. Fujisawa, E. Gadaleta, D. M. Goodstein, Gunes Gundem, Bernard Haggarty, Syed Haider, Matthew Hall, Todd Harris, Robin Haw, S. Hu, Simon Hubbard, Jack Hsu, Vivek Iyer, Philip Jones, Toshiaki Katayama, R. Kinsella, Lei Kong, Daniel Lawson, Yong Liang, Nuria Lopez-Bigas, J. Luo, Michael Lush, Jeremy Mason, Francois Moreews, Nelson Ndegwa, Darren Oakley, Christian Perez-Llamas, Michael Primig, Elena Rivkin, S. Rosanoff, Rebecca Shepherd, Reinhard Simon, B. Skarnes, Damian Smedley, Linda Sperling, William Spooner, Peter Stevenson, Kevin Stone, J. Teague, Jun Wang, Jianxin Wang, Brett Whitty, D. T. Wong, Marie Wong-Erasmus, L. Yao, Ken Youens-Clark, Christina Yung, Junjun Zhang and Arek Kasprzy , BioMart Central Portal: an open database network for the biological communit., Database (2011) Vol. 2011 doi: 10.1093/database/bar041.

  36. Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch Mizrachi, Sandra Orchard, B.F. Francis Ouellette, Shoba Ranganathan, Lorna Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin W. Tan, Tatiana Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki, and on behalf of the BioDBCore working group, Towards BioDBcore: a community-defined information specification for biological databases, Database (2011) Vol. 2011 doi:10.1093/database/baq027.

  37. Pereira, P.N.G., Dobreva, M.P., Graham,L., Huylebroeck, D., Lawson, K.A. and Zwijsen, A.N., Amnion formation in the mouse embryo: the single amniochorionic fold model, BMC Developmental Biology (2011) 11:48, pp1-13, doi:10.1186/1471-213X-11-48.

  38. Simon D. Harding, Chris Armit, Jane Armstrong, Jane Brennan, Ying Cheng, Bernard Haggarty, Derek Houghton, Sue Lloyd-MacGilp, Xingjun Pi, Yogmatee Roochun, Mehran Sharghi, Christopher Tindal, Andrew P. McMahon, Brian Gottesman, Melissa H. Little, Kylie Georgas, Bruce J. Aronow, S. Steven Potter, Eric W. Brunskill, Richard A. Baldock, Jamie A. Davies, and Duncan Davidson, The GUDMAP Database – An Online Resource for Genitourinary Research, Development (2011) Jul; 138(13):2845-53. doi:10.1242/dev.063594

  39. Liangxiu Han; Jano van Hemert; Richard Baldock, Automatically Identifying and Annotating Mouse Embryo Gene Expression Patterns, Bioinformatics 2011, doi:10.1093/bioinformatics/btr105

  40. Andrea Splendianai, Albert Burger, Adrian Paschke, Paolo Romano and M. Scott Marshall, Biomedical semantics in the Semantic Web., Journal of Biomedical Semantics 2011, 2(Suppl 1):S1.

  41. 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

  42. 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

  43. 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

  44. 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

  45. Kenneth McLeod, Gus Ferguson and Albert Burger, Argudas: arguing with gene expression information., In proceedings of the 3rd international workshop on semantic web applications and tools for the life sciences. 10th December 2010, Berlin, Germany.

  46. Xunxian Wang, Susan Lindsay and Richard Baldock, From spatial-data to 3D models of the developing human brain, Methods (San Diego, Calif.), 2010 Feb, 50, no. 2, pp. 96–104. doi:10.1016/j.ymeth.2009.09.006

  47. 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

  48. 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 (Pubmed)

  49. Kenneth McLeod, Gus Ferguson, and Albert Burger, Using Argumentation to resolve conflict in Biological Databases. in Proceedings of the IJCAI-09 workshop on Computational Models of Natural Argument, 13 July 2009, Pasadena, CA.

  50. Burger, A.; Romano, P.; Paschke, A. and Splendiani, A. Semantic Web Applications and Tools for Life Sciences, 2008--preface. BMC Bioinformatics 10 Suppl 10:S1, 2009 (Biomed)

  51. 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)

  52. Sutherland, K.; McLeod, K.; Ferguson, G. and Burger, A. Knowledge-driven enhancements for task composition in bioinformatics. BMC Bioinformatics 10 Suppl 10:S12, 2009 (Pubmed)

  53. 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)

  54. 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) (Pubmed)

  55. 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 (Springerlink)
  56. 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. (Springerlink)

  57. 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. (IEEE Computer Society)

  58. 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).

  59. McLeod, K. and Burger, A. Towards the use of argumentation in bioinformatics: a gene expression case study. Bioinformatics 24(13):i304-i312, 2008 (Pubmed)

  60. 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)

  61. Karen Sutherland, Kenneth McLeod and Albert Burger Semantically Linking Web Pages to Web Services in Bioinformatics, 3rd International Applications of Semantic Technologies Workshop, Munich, Germany, 9 September 2008.

  62. 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)

  63. 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 (BMC).

  64. 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)

  65. 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. (PDF)

  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. (PDF)

  67. 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. (PDF)

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

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

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

  71. 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.

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

  73. Hancock, J. M., Adams, N. C., Aidinis, V., Blake, A., Bogue, M., Brown, S. D., Chesler, E. J., Davidson, D., Duran, C., Eppig, J. T. et al. Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources., Mamm Genome 18 (2007) 157-63.

  74. 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. (PDF)

  75. 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 .

  76. 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)

  77. 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)

  78. 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.

  79. Kenneth McLeod and Albert Burger Using argumentation to tackle inconsistency and incompleteness in online distributed life science resources. In Proceedings of IADIS International Conference Applied Computing 2007, Salamanca, Spain, February, 2007.

  80. 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)

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

  82. 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. (PDF)

  83. 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)

  84. Robert Stevens, Yeliz Yesilada, Michael Schroeder, Albert Burger, Patty Kostkova, Bianca Habermann, Rose Dieng-KuntzA Semantic Browser for a Web of Biomedicine. In Proceedings of Health Care and Life Sciences Workshop; Athens, Georgia, USA, Nov, 2006.

  85. Schroeder, M., Burger, A., Kostkova, P., Stevens, R., Haberman, B. and Dieng-Kuntz, R.From a Service-based eScience Infrastructure to a Semantic Web for the Life Sciences: The Sealife ProjectIn the Proceedings of the Workshop on Network Tools and Applications in Biology, NETTAB 2006, Sardinia, Italy, 10-13 July 2006.

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

  87. Aba-Sah Dadzie and Albert Burger, Providing visualisation support for the analysis of anatomy ontology data BMC Bioinformatics 6:74, 2005

  88. TE Willnow, C Antignac, AW Brändli, EI Christensen, RD Cox, D Davidson, JA Davies, O Devuyst, G Eichele, ND Hastie, PJ Verroust, A Schedl, and IC Meij, The European Renal Genome Project. An Integrated Approach Towards Understanding the Genetics of Kidney Development and Disease Organogenesis. 2005 Apr-Jun; 2(2): 42–47.
  89. Andreas Doms, Tim Furche, Albert Burger and Michael Schroeder, How to Query the GeneOntology In Proceedings of KRBIO'05: Symposium on Knowledge Representation in Bioinformatics, Espoo, Finland, 15-17 June 2005.
  90. 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. (PDF)

  91. 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).

  92. Gkoutos, G. V., Green, E. C., Mallon, A. M., Hancock, J. M. and Davidson, D., Using ontologies to describe mouse phenotypes., Genome Biol 6 (2005) R8.

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

  94. Konstantinos Karasavvas, Richard Baldock and Albert Burger, Criticality-Based Framework for Task Composition in Multi-Agent Bioinformatics Integration Systems, Bioinformatics Journal, Volume 21, No 14 (2004), pp 3155-3163 .
  95. 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).

  96. 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)

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

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

  99. 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.(PDF)

  100. 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).

  101. 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).

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

  103. 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. (PDF)

  104. Gkoutos, G. V., Green, E. C., Mallon, A. M., Blake, A., Greenaway, S., Hancock, J. M. and Davidson, D., Ontologies for the description of mouse phenotypes.. Comparative and Functional Genomics 5(6-7): (2004) pp545-51
  105. Albert Burger, Duncan Davidson and Richard Baldock, Formalization of Mouse Embryo Anatomy, Bioinformatics 20 (2004) pp259-267. (PDF)

  106. 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. (PDF)

  107. 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).

  108. 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).
  109. 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).

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

  111. 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

  112. 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. (PDF)

  113. 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.

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

  115. 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 .

  116. 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. (PDF)

  117. 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. (PDF)

  118. 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. (PDF)

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

  120. 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.

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

  122. 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.

  123. 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. (PDF)

  124. 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. (PDF)

  125. 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. (PDF)

  126. 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.

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

  128. 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.

  129. 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. (PDF)

  130. 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. (PDF)

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

  132. 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. (PDF)

  133. 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. (PDF)

  134. 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. (PDF)

  135. 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.

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

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

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

  139. 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. (PubMed)

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

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