2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1997

Our Publications


Ramakrishnan, C., W. A. Baumgartner Jr., et al. (2010) Building the Scientific Knowledge Mine (SciKnowMine): a community-driven framework for text mining tools in direct service to biocuration. in Language Resources and Evaluation (LREC). Malta. [Paper]


Herr, B.W., E. M. Talley, et al. (2009) The NIH Visual Browser: An Interactive Visualization of Biomedical Research. in 13th International Conference on Information Visualization (IV09). Barcelona, Spain. [Paper]

Burns, G. and T. Russ (2009). Biomedical Knowledge Engineering tools based on Experimental Design: a case study based on neuroanatomical tract-tracing experiments. KCAP 2009, Long Beach CA. [Paper]

Burns, G., T. Russ, et al. (2009). BioScholar: A knowledge engineering system for biology and it's application to neural connectivity data. 2nd Congress of the International Neuroinformatics Coordinating Facility (INCF2009), Pilsen, Czech Republic. [Poster]

Burns, G. A. P. C., M. Krallinger, et al. (2009). Biocuration Workflow Catalogue - Text Mining for the Biocuration Workflow. 3rd International Biocurators Meeting, Berlin.[Slides|White Paper]

Burns, G. A. P. C., T. Russ, et al. (2009). Using Knowledge Engineering Approaches to Reason About Neuroanatomical Experiments. Society for Neuroscience Annual Meeting, Chicago, IL.[Poster]


Burns, G.A., D. Newman, B. Herr, A. Holloway, P. Smyth, and K. Borner (2008), "Analyses over multiple scientific text corpora: combining MEDLINE, CRISP and the proceedings of the annual meetings of the Society for Neuroscience"Annual Meeting for the Society for Neuroscience. [Poster (66MB!)]

Burns G, Hovy E and Ingulfsen T (2008). Biomedical knowledge engineering approaches driven by processing the primary experimental literature. Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.011 [Poster][Handout]

Feng, D., G.A.P.C. Burns, and E.H. Hovy. 2008. Towards Automated Semantic Analysis on Large Scale Biomedical Text. Poster. Proceedings of the International Joint Conference on NLP (IJCNLP). Hyderabad, India.

Burns, G.A.P.C., D. Feng, and E.H. Hovy (2008), "Intelligent Approaches to Mining the Primary Research Literature: Techniques, Systems, and Examples", in "Computational Intelligence in Medical Informatics", A. Kelemen, et al., Editors Springer.


Burns, G., D. Feng, T. Ingulfsen, and E. Hovy (2007), "Infrastructure for Annotation-Driven Information Extraction from the Primary Scientific Literature: Principles and Practice". in 1st IEEE International Workshop on Service Oriented Technologies for Biological Databases and Tools (SOBDAT 2007). Salt-Lake City.

Feng, D., G. Burns, and E. Hovy (2007), "Extracting Data Records from Unstructured Biomedical Full Text". in The Joint Meeting of Conference on Empirical Methods in Natural Language Processing and Conference on Computational Natural Language Learning (EMNLP-CoNLL 2007). Prague, Czech Republic.


GAPC Burns, W-C Cheng, RH Thompson, LW Swanson, 2006, 'The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases ' BMC Bioinformatics, 7, 731.

GAPC Burns, W-C Cheng, 2006, 'Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data' Journal of Biomedical Discovery and Collaboration 2006, 1:8 (3 July 2006)

A. Khan, J. Hahn, W.-C. Cheng, A. Watts and G. A. P. C. Burns, 2005, 'NeuroScholar's Electronic Laboratory Notebook and its Application to Neuroendocrinology', Neuroinformatics, 4:139-160


M. Saxena, S. Kim, G. Burns, A. Khan, J. Su, Y. Hamadi, S. Ghandeharizadeh, 2005, 'An overview of Sangam: A system for integrating data to investigate stress-circuitry-gene coupling', IVNET

M. Goto, N.S. Canteras, G. Burns, L.W. Swanson, 2005, 'Projections from the Subfornical Region of the Lateral Hypothalamic Area", J.Comp. Neurol. 493(3):412-38


Chen, Burns, Shahabi, 2004, 'Two-Phase Decision Fusion based on User Preference.' The Hawaii International Conference on Computer Sciences, Hawaii

E. Alwagait and S. Ghandeharizadeh, 2004, 'A Comparison of Alternative Web Service Allocation and Scheduling Policies', IEEE International Conference on Services Computing (SCC), Shanghai, China


Burns, Cheng, Zhang & Ghandeharizadeh, 2003, 'Web services as tools within a scientific knowledge engineering environment', Proceedings of Sci '03, Miami FL.

Burns, Khan, Ghandeharizadeh, O'Neill and Chen, 2003, 'Tools and Approaches for the Construction of Knowledge Models from the Neuroscientific Literature.' Neuroinformatics 1:81-109

S. Song, K. Chan, A. Golypayegani, S. Ghandeharizadeh, C. Shahabi and G. Burns, 2003, 'Tools for knowledge management of the neuroscientific literature, plugins for the NeuroScholar system', Computational Neuroscience, Chicago, IL


Burns, Bian, Cheng, Kapadia, Shahabi and Ghandeharizadeh, 2002, Software engineering tools and approaches for neuroinformatics: the design and implementation of the View-Primitive Data Model framework, VPDMf, Neurocomputing, 44-46:1049-1056

Burns, Stephan, Ludäscher, Gupta and Kötter, 2002, 'Towards a federated neuroscientific knowledge management system using brain atlases', Neurocomputing, 38-40: 1633-1641


Burns, (2001a), 'Knowledge management of the neuroscientific literature: the data model of the NeuroScholar system. ', Phil Trans R Soc, B, 356: 1187-1208

Burns, (2001b), 'Knowledge Mechanics and the Neuroscholar Project: A New Approach to Neuroscientific Theory', In 'Computing the Brain, A Guide to Neuroinformatics' ed. Arbib & Grethe, Academic Press, New York, pp. 319-338.


Burns and Young (2000), 'Analysis of the connectional organization of neural systems associated with the hippocampus in rats', Phil Trans R Soc, B, 355: 55-70


Burns (1999). Neuroscholar 1.00, A neuroinformatics databasing website. Neurocomputing 26:963-970

Shahabi, Dashti, Burns, Ghandeharizadeh, Jian, Swanson, 1999, ' Visualization of spatial neuroanatomical data' Visual'99, Amsterdam, Netherlands


Burns (1999). 'Neural Connectivity in the Rat:Theory, Methods and Applications'. Oxford University D.Phil Thesis (~500 pages)

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