Professor Albert Burger         

For many of the more recent papers listed below online links and/or pdf copies, as well as bibtex entries, can be found on my research group's web site (BISEL Publications).

2014

• Growing the INCF Digital Atlasing Infrastructure. Jyl Boline, Richard Baldock, Rembrandt Bakker, Albert Burger, James Gee, Christian Haselgrove, Mike Hawrylycz, Andreas Hess, G. Allan Johnson, Piotr Majka, Lydia L. Ng, Yuko Okamura-Oho, Seth W. Rufffins and Ilya Zaslavsky, INCF Congress: Neuro Informatics 2014, Leiden, the Netherlands, August 2014.  [Poster/Abstract]
• Visualisation of gene expression information within the context of the mouse anatomy. Andy J Taylor, Kenneth C McLeod, Chris J Armit, Richard Baldock and Albert G Burger. To appear in Proceedings of the 4th Symposium on Biological Data Visualization , 11-12 July 2014, Boston, USA.  [Conference/Workshop]

2013

• EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update. Hayamizu T.F., Wicks, M.N., Davidson, D.R., Burger, A., Ringwald, M. and Baldock, R. In Journal of Biomedical Semantics, 2013, 4:15  [Journal] 
• Towards the semantic representation of biological images: from pixels to regions, Kenneth McLeod and Albert Burger. To appear in: International Journal of Intelligent Information Technologies.  [Journal] 
• A conceptual approach to gene expression analysis enhanced by visual analytics. Cassio Melo, Constantinos Orphanides, Kenneth McLeod, Marie-Aude Aufaure, Simon Andrews and Albert Burger. Proceedings of the 28th ACM Symposium on Applied Computing, March 2013, Coimbra, Portugal.  [Conference/Workshop]

2012

• Biomedical Atlases: systematics, informatics and analysis. Richard Baldock, Albert Burger. Advances in experimental medicine and biology, 736 (2012) 655--677. [Journal] 
• Semantic Web Applications and Tools for the Life Sciences: SWAT4LS 2010. Albert Burger, Adrian Paschke, Paolo Romano, M Scott Marshall, Andrea Splendiani. BMC Bioinformatics, 13(Suppl 1):S1, 2012 [Journal] 
• Argudas:  lessons for argumentation in biology based on a gene expression use case. Kenneth McLeod, Gus Ferguson and Albert Burger. BMC Bioinformatics, 13(Suppl 1):S8, 2012 [Journal] 
• Semantic Web spatial representation of biomedical images, D. N. F. Awang Iskandar, Kenneth McLeod and Albert Burger, In Proceedings of the 2nd CUBIST Workshop, 2011 [Conference/Workshop]
• Registration workflows for the creation of INCF digital atlas hubs. yl Boline, Brian Avants, Richard Baldock, Rembrandt Bakker, Albert Burger, James Gee, Christian Haselgrove, Andreas Hess, Luis Ibanez, Stephen Larson, Piotr Majka, Yuko Okamura-Oho, Seth Ruffins and Ilya Zaslavsky, Neuro Informatics 2012.  [Poster/Abstract]
  

2011

• Biomedical semantics in the Semantic Web. Andrea Splendianai, Albert Burger, Adrian Paschke, Paolo Romano and M. Scott Marshall. Journal of Biomedical Semantics 2011, 2(Suppl 1):S1  [Journal] 
• Digital atlasing and standardisation in the mouse brain. Michael Hawrylycz, Richard A. Baldock, Albert Burger, Tsutomu Hashikawa, G. Allen Johnson, Maryann Martone, Lydi Ng, Chris Lau, Stephen Larsen, Jonathon Nissanov, Luis Puelles, Seth Ruffins, Fons Verbeek, Ilya Zaslavsky and Jyl Boline. PLOS Computational biology, 7(2): e1001065. 2011 [Journal] 
• Integrating Volumetric Biomedical Data in the Virtual Physiological Human. Albert Burger, Bernard de Bono, Peter Hunter, Jesús Bisbal- Riera, Alejandro F. Frangi, Corné Hoogendoorn, Duncan Davidson, Xu Gu and Richard Baldock. In Proceedings of First International Workshop on Managing Interoperability and compleXity in Health Systems, MIXHS'11, 28 October 2011, Glasgow, UK. [Conference/Workshop]
• Towards spatial description of biomedical atlases, Nurzi Juana Mohd Zaizi and Albert Burger, In Proceedings of eHealth 2011 [Conference/Workshop]
• Development of Standard Services for Integrating Rodent Brain Atlases Based on Spatial Location. Ilya Zaslavsky, Asif Memon, David Little, David Valentine, Stephen Larson, Raphael Ritz, Stephan Lamont, Richard Baldock, Rembrandt Bakker, Albert Burger, Christian Haselgrove, Mike Hawrylycz, Andreas Hess, Lydia Ng, Daren Lee, Seth Ruffins, Fons Verbeek, Janis Breeze and Jyl Boline. INCF Congress: Neuro Informatics 2011, Boston, USA, August 2014.  [Poster/Abstract]
  

2010

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

2009

• Knowledge-driven Enhancements for Task Composition in Bioinformatics. Karen Sutherland, Kenneth McLeod, Gus Ferguson and Albert Burger. BMC Bioinformatics, 10(Suppl 10):S12, 2009. [Journal] 
• Using Argumentation to resolve conflict in Biological Databases. Kenneth McLeod, Gus Ferguson and Albert Burger. In N. Green, F. Grasso, R. Kibble, and C. Reed (Editors) Proceedings of Computation Models of Natural Argument (CMNA) 9, pages 15--23, Pasadena, USA, July 2009. [Conference/Workshop]
• Sealife evaluation.  Gus Ferguson, Kenneth McLeod, Karen Sutherland and Albert Burger. Technical Report 0063, Dept of Computer Science, Heriot-Watt University 2009. [Technical Report]
• INCF Digital Atlasing Infrastructure: Managing Interoperable Atlas Spaces. Jyl Boline, Albert Burger, Tsutomu Hashikawa, G. Allan Johnson, Maryann Martone, Lydia Ng, Johathan Nissanov, Luis Puelles, Seth Ruffins, Fons Verbeek, Ilya Zaslavsky and Mike Hawrylycz. 2nd INCF Congress of Neuroinformatics Pilsen, Czech Republic - September 6-8, 2009. [Poster/Abstract]
• Digital Atlasing and Standardization in the Rodent Brain. Jyl Boline, Albert Burger, Tsutomu Hashikawa, G. Allan Johnson, Maryann Martone, Lydia Ng, Johathan Nissanov, Luis Puelles, Seth Ruffins, Fons Verbeek, Ilya Zaslavsky, Mike Hawrylycz. 2nd INCF Congress of Neuroinformatics Pilsen, Czech Republic - September 6-8, 2009. [Poster/Abstract]

2008

• Proceedings of International Workshop on Semantic Web Applications and Tools for the Life Sciences. Albert Burger, Adrian Paschke, Paolo Romano, Andrea Splendiani (Editors). (SWAT4LS) 2008, Edinburgh, November 2008. Published on CEUR-WS: 05-Feb-2009. [Edited Proceedings]
• The INCF Digital Brain Atlas Program: Building Community Consensus and Community Tools. J. Boline, A. Burger, et. al. INCF Workshop on Computational Developmental Neuroscience, Edinburgh, November 2008. [Poster/Abstract]
• Goal-Oriented Task Composition for Bioinformatics. Karen Sutherland and Albert Burger. International Workshop on Semantic Web Applications and Tools for the Life Sciences (SWAT4LS) 2008, Edinburgh, November 2008. Semantically Linking Web Pages to Web Services in Bioinformatics. [Poster/Abstract]
• Karen Sutherland, Kenneth McLeod and Albert Burger. 3rd International Applications of Semantic Technologies Workshop, Munich, Germany, 9 September 2008. [Conference/Workshop]
• Towards the use of Argumentation in Bioinformatics: A Gene Expression Case Study. Kenneth McLeod and Albert Burger. Bioinformatics 2008 24(13):i304-i312; doi:10.1093/bioinformatics/btn157. [Journal]
• Anatomy Ontologies for Bioinformatics: Principles and Practice. Albert Burger, Duncan Davidson and Richard Baldock (Editors). Springer, 2008, ISBN 978-1-84628-884-5. 2008. [Edited Book]
• XSPAN: A Cross-Species Anatomy Network. Albert Burger and Jonathan Bard. Chapter in Albert Burger, Duncan Davidson, Richard Baldock (Editors), Anatomy Ontologies for Bioinformatics: Principles and Practice, Springer, 2008. [Book Chapter]
• Anatomical Ontologies: Linking Names to Places in Biology. Richard Baldock and Albert Burger. Chapter in Albert Burger, Duncan Davidson, Richard Baldock (Editors), Anatomy Ontologies for Bioinformatics: Principles and Practice, Springer, 2008. [Book Chapter]

2007

• Task Composition for a Semantic Web Browser. Karen Sutherland, Kenneth McLeod and Albert Burger. 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). [Poster/Abstract]
• Data Integration in eHealth: A Domain/Disease Specific Roadmap. 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 and Joanna Wardlaw. Studies Health Technol Inform 126 (2007) 144-53. [Journal]
• Using argumentation to tackle inconsistency and incompleteness in online distributed life science resources. Kenneth McLeod and Albert Burger. In Proceedings of IADIS International Conference Applied Computing 2007, Salamanca, Spain, February, 2007. IADIS Press. [Conference/Workshop]
• Agent Technologies in the Life Sciences, Albert Burger, Chapter in Semantic Web: Revolutionizing Knowledge and Discovery in the Life Sciences. , Christopher Bake, and Kei-Hoi Cheung (Editors). Springer, 2007, pages 341-352. [Book Chapter]

2006

• From a Service-based eScience Infrastructure to a Semantic Web for the Life Sciences: The Sealife Project. Schroeder, M., Burger, A., Kostkova, P., Stevens, R., Haberman, B. and Dieng-Kuntz, R. In the Proceedings of the Workshop on Network Tools and Applications in Biology, NETTAB 2006, Sardinia, Italy, 10-13 July 2006.[Conference/Workshop]
• A Semantic Browser for a Web of Biomedicine. Robert Stevens, Yeliz Yesilada, Michael Schroeder, Albert Burger, Patty Kostkova, Bianca Habermann and Rose Dieng-Kuntz. In Proceedings of Health Care and Life Sciences Workshop; Athens, Georgia, USA, Nov, 2006. [Conference/Workshop]

2005

• A Criticality-Based Framework for Task Composition in Multi-Agent Bioinformatics Integration Systems. Konstantinos Karasavvas, Richard Baldock and Albert Burger. Bioinformatics Journal, Volume 21, No 14, pp 3155-3163, 2005. PubMed ID: 15890745. [Journal]
• Anatomical Ontologies: Names and Places in Biology. Richard Baldock and Albert Burger. Genome Biology, 6:108, 2005. [Journal]
• Providing visualisation support for the analysis of anatomy ontology data. Aba-Sah Dadzie and Albert Burger, BMC Bioinformatics, 6:74, 2005. Online: http://www.biomedcentral.com/1471-2105/6/74. [Journal]
• Towards Multiagent Planning and Distributed Query Processing Integration. Rosely Kumoi and Albert Burger, In Proceedings of the Eight Pacific Rim International Workshop on Multi-Agents - PRIMA2005, Kuala Lumpur, Malaysia, pp 163-178, September 2005. [Conference/Workshop]
• How to Query the GeneOntology. Andreas Doms, Tim Furche, Albert Burger and Michael Schroeder. In Proceedings of KRBIO'05: Symposium on Knowledge Representation in Bioinformatics, Espoo, Finland, 15-17 June 2005. [Conference/Workshop]
• A Tool For Supporting The Teaching Of Parallel Database Systems. E. Dempster, M. H. Williams, A. Burger and H. Taylor, IEEE Transactions on Education, Volume 48, No 2, pp 238-247, 2005. [Journal]
• The Edinburgh Mouse-Atlas Gene Expression Database. Albert Burger and Richard Baldock. Conference on Genome Informatics, Cold Spring Harbour, USA, October 2005. [Poster/Abstract]
• Towards a Semantic Mouse Atlas. Albert Burger. Workshop on Knowledge-Based Bioinformatics, Montreal, Canada, September 2005. [Poster/Abstract]
• Extending the Use of Anatomy Ontologies for Cross-Species Data Integration. Albert Burger, Stuart Aitken, Gus Ferguson, Sarah Luger, Kenneth McLeod, Werner Nutt, Bonnie Webber and Jonathan Bard. Workshop on Biomedical Ontology Engineering (in association with the 10th Conference on Artificial Intelligence in Medicine - AIME 05), Aberdeen, 24 July 2005. [Poster/Abstract]

2004

• Formalization of mouse embryo anatomy, Albert Burger, Duncan Davidson and Richard Baldock. Bioinformatics Journal , Volume 20, No 2, pp 259-267, January 2004. [Journal]
• Integrating partonomic hierarchies in anatomy ontologies, Albert Burger, Duncan Davidson, Yiya Yang and Richard Baldock, BMC Bioinformatics, 5:184, 2004. [Journal]
• The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data, Helen Parkison, 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 and Duncan Davidson, Comparative and Functional Genomics, 2004; 5:521-527. [Journal]
• Bioinformatics Integration and Agent Technology, Konstantinos Karasavvas, Richard Baldock and Albert Burger, Journal of Biomedical Informatics, Vol 37/3, pp 205-219, 2004. [Journal]
• A Scalable Mediator Approach to Process Large Biomedical 3-D Images, Konstantinos Liakos, Albert Burger and Richard Baldock, IEEE Transactions on Information Technology in Biomedicine, Volume 8, Issue 3, pp 354-359, Sept. 2004, ISSN 1089-7771. [Journal]
• Criticality-Based Task Composition in Distributed Bioinformatics Systems, Konstantinos Karasavvas, Richard Baldock and Albert Burger, 12th International Conference on Intelligent Systems for Molecular Biology , Glasgow, July, 2004, (short paper), published on-line: www.iscb.org/ismbeccb2004/accepted_papers.html). [Conference/Workshop]
• Distributed Processing of Large BioMedical 3D Images, Konstantinos Liakos, Richard Baldock and Albert Burger, in Proceedings of 6th International Meeting for High Performance Computing for Computational Science , Valencia, Spain, June 2004; (also published in Springer, Lecture Notes in Computer Science, Vol. 3402). [Conference/Workshop]
• The merits of the third dimension for visual analysis of multiple anatomy ontologies, Aba-Sah Dadzie and Albert Burger, Proceedings of International Conference on Bioinformatics and its Applications (ICBA'04), Fort Lauderdale, USA, December 2004. [Conference/Workshop]
• Proceedings of 21st British National Conference on Databases (BNCOD21), 2004. Lachlan MacKinnon, Albert Burger and Phil Trinder (Editors). [Edited Proceedings]
• Analytical response time estimation in parallel relational database systems, N. Tomov , E. Dempster , M. H. Williams , A. Burger , H. Taylor , P. J. B. King and P. Broughton, Parallel Computing, Volume 30, Issue 2, February 2004, Pages 249-283. [Journal]
• XSPAN: Linking Anatomy Ontologies Across Multiple Species, Albert Burger, 3rd E-BioSci/ORIEL Annual Workshop, Hinxton, England, October 2004. [Poster/Abstract]

2003

• EMAP and EMAGE: A Framework for Understanding Spatially Organised Data, Richard Baldock, Jonathan Bard, Albert Burger, Nicolas Burton, Jeff Christiansen, Guanjie Feng, Bill Hill, Derek Houghton, Matthew Kaufman, Jianguo Rao, James Sharpe, Allyson Ross, Peter Stevenson, Shanmugasundaram Venkataraman, Andrew Waterhouse, Yiya Yang, Duncan Davidson, Neuroinformatics Journal , Humana Press Inc., 2003. [Journal]
• Modelling Parallel Oracle For Performance Prediction, E. W Dempster, N T Tomov, M H Williams, H Taylor, D Marwick, A Burger and P Trinder, Distributed and Parallel Databases, Volume 13 Number 3, 2003. [Journal]

2002

• A Business in Transition: An Internet Based Information Management Project in a Small Engineering Company, Quintin Blane, Lachlan McKinnon, Albert Burger, International Journal of e-Business Strategy Management , Nov./Dec. issue, 2002. [Journal]
• A multi-agent bioinformatics integration system with adjustable autonomy: an overview, Konstantinos Karasavvas, Richard A. Baldock, Albert Burger, Proceedings of International Conference of Autonomous Agents and Multiagent Systems, pages 302-303, 2002. [Conference/Workshop]
• A Multi-agent Bioinformatics Integration System with Adjustable Autonomy, Konstantinos Karasavvas, Albert Burger, Richard A. Baldock, Proceedings of the 7th Pacific Rim International Conference on Artificial Intelligence, pages 492-501, 2002. [Conference/Workshop]
• The Edinburgh Mouse Atlas and Gene-Expression Database: A Spatio-Temporal Database for Biological Research, Albert Burger, Richard A. Baldock, Yiya Yang, Andrew Waterhouse, Derek Houghton, Nick Burton, Duncan Davidson, Proceedings of 14th International Conference on Scientific and Statistical Database Management, page 239, 2002. [Conference/Workshop]
• Developing Scientific Database Applications in a Grid Environment, Albert Burger, Proceedings of 14th International Conference on Scientific and Statistical Database Management, page 187, 2002. [Conference/Workshop]
• XSPAN: A Cross-Species Anatomy Network, Burger A, Webber B. Nutt W, Wagner S, Aitken S, Ferguson G, Holt PO’B, Bard J., Workshop on Standards and Ontologies for Functional Genomics (SOFG), November 2002, Hinxton, Cambridge. [Poster/Abstract]

2001

• Abstract Modelling to Explore Data Collection Options, Pauline Wilcox and Albert Burger, European Simulation Interoperability Workshop , pp629-637, 25-27 June 2001. [Conference/Workshop]

2000

• STEADY - A Tool for Predicting Performance of Parallel DBMSs, Euan W. Dempster, M. Howard Williams, Neven Tomov, Chai Seng Pua, Albert Burger, Peter J. B. King. 11th International Conference, TOOLS 2000 , Schaumburg, IL, USA, March 2000, Proceedings. Lecture Notes in Computer Science 1786 Springer 2000, ISBN 3-540-67260-5, pp. 362-365. [Journal]
• Advanced Distributed Simulation: A review of developments and their implication for data collection and analysis, Pauline Wilcox, Albert Burger and Peter Hoare, Simulation Practise and Theory (SIMPRA), pp201-231, No(3/4), Volume 8, 2000. [Conference/Workshop]
• Towards Verification and Validation of an Advanced Distributed Simulation Abstract Model (ADSAM), Pauline Wilcox, Albert Burger and Peter Hoare, Spring Simulation Interoperability Workshop, pp206-216. Vol 1, 26-31 March 2000, Orlando Florida. [Conference/Workshop]

Publications prior 2000