University of Southern California

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2013

Modelling Functional Magnetic Resonance Imaging (fMRI) Experimental Variables in the Ontology of Experimental Variables and Values (OoEVV)Gully A. P. C. Burns, Jessica A. Turner
In Neuroimage
2013, - pages
http://www.sciencedirect.com/science/article/pii/S1053811913005181BibTex

Practical approach and infrastructure for the accelerated construction of biocuration systemsKevin B. Cohen, Marcelo Tallis, Blake, Judith, Eppig, Janan, Rocky Honda, Gully A. P. C. Burns
In Biocuration 2013
2013
https://docs.google.com/file/d/0B0EtY8vGMKNZRDFRUUNmcGZxbm8/edit?usp=drive_webBibTex

2012

Toward interoperable bioscience dataSansone, Susanna-Assunta, Rocca-Serra, Philippe, Field, Dawn, Maguire, Eamonn, Taylor, Chris, Hofmann, Oliver, Fang, Hong, Neumann, Steffen, Tong, Weida, Amaral-Zettler, Linda, Begley, Kimberly, Booth, Tim, Bougueleret, Lydie, Gully Burns, Chapman, Brad, Clark, Tim, Coleman, Lee-Ann, Copeland, Jay, Das, Sudeshna, de Daruvar, Antoine, de Matos, Paula, Dix, Ian, Edmunds, Scott, Evelo, Chris T, Forster, Mark J, Gaudet, Pascale, Gilbert, Jack, Goble, Carole, Griffin, Julian L, Jacob, Daniel, Kleinjans, Jos, Harland, Lee, Haug, Kenneth, Hermjakob, Henning, Sui, Shannan J Ho, Laederach, Alain, Liang, Shaoguang, Marshall, Stephen, McGrath, Annette, Merrill, Emily, Reilly, Dorothy, Roux, Magali, Shamu, Caroline E, Shang, Catherine a, Steinbeck, Christoph, Trefethen, Anne, Williams-Jones, Bryn, Wolstencroft, Katherine, Xenarios, Ioannis, Hide, Winston
In Nature Genetics
2012, 121–126 pages
http://www.nature.com/doifinder/10.1038/ng.1054BibTex

Text mining for the biocuration workflowHirschman, L., Burns, G. a. P. C., Krallinger, M., Arighi, C., Cohen, K. B., Valencia, a., Wu, C. H., Chatr-Aryamontri, a., Dowell, K. G., Huala, E., Lourenco, a., Nash, R., a.-L. Veuthey, Wiegers, T., Winter, a. G.
In Database
2012, bas020–bas020 pages
http://database.oxfordjournals.org/cgi/doi/10.1093/database/bas020BibTex

Layout-Aware Text Extraction from Full-text PDF of Scientific ArticlesRamakrishnan, Cartic, Patnia, Abhishek, Hovy, Eduard, Gully Burns
In Source Code for Biology and Medicine
2012, 7 pages
http://www.scfbm.org/content/7/1/7BibTex

A lightweight Ontology Design Pattern to curate and represent experimental variables from vaccine protection studies.Gully A. P. C. Burns, Dave, Drashti
In Vaccine and Drug Ontology in the Study of Mechanism and Effect, ICBO 2012
2012
http://www.isi.edu/sites/default/files/users/burns/bmkeg/icbo2012-06-28-12-1349-drashti.pdfBibTex

Bottom-up curation of terminology for experimental variables: the Ontology of Experimental Variables and Values (OoEVV)Gully A. P. C. Burns, Jessica A. Turner
In Bio-Ontologies SIG, ISMB
2012
http://www.isi.edu/sites/default/files/users/burns/bmkeg/ooevvFlash-final.pdfBibTex

Preliminary meta-analyses of experimental design with examples from HIV vaccine protection studiesMarcelo Tallis, Dave, Drashti, Gully Burns
In Discovery Informatics
2012
http://discoveryinformaticsinitiative.org/dis2012BibTex

2011

Database of NIH grants using machine-learned categories and graphical clusteringEdmund M. Talley, David Newman, Mimno, David, Herr, Bruce W, Wallach, Hanna M, Gully A. P. C. Burns, Leenders, A G Miriam, McCallum, Andrew
In Nature Methods
2011, 8(6):443-444 pages
http://dx.doi.org/10.1038/nmeth.1619BibTex

Knowledge Engineering Tools for Reasoning with Scientific Observations and Interpretations: a Neural Connectivity Use CaseRuss, T., Ramakrishnan, C., Hovy, E. H., Bota, M., Burns, GAPC
In BMC Bioinformatics
2011, 12: 351 pages
http://www.biomedcentral.com/1471-2105/12/351BibTex

Knowledge synthesis with maps of neural connectivityTallis, M., Thompson, R., Russ, T., Burns, GAPC
In Frontiers in Neuroinformatics
2011, 5:24 pages
http://dx.doi.org/10.3389/fninf.2011.00024BibTex

2010

Building the Scientific Knowledge Mine (SciKnowMine1): a community-driven framework for text mining tools in direct service to biocurationRamakrishnan, Cartic, Jr., William A. Baumgartner, Blake, Judith, Gully A. P. C. Burns, Cohen, K. Bretonnel, Drabkin, Harold, Eppig, Janan, Hovy, Eduard, Hsu, Chun-Nan, Hunter, Lawrence E., Tommy Ingulfsen, Livingston, Kevin, Onda, Hiroaki 'Rocky', Pokkunuri, Sandeep, Riloff, Ellen, Roeder, Christophe, Verspoor, Karin
In Language Resources and Evaluation (LREC)
2010BibTex

2009

Biomedical knowledge engineering tools based on experimental design: a case study based on neuroanatomical tract-tracing experimentsGully A. P. C. Burns, Thomas A. Russ
In K-CAP
2009, 173-174 pagesBibTex

Biomedical Knowledge Engineering tools based on Experimental Design: a case study based on neuroanatomical tract-tracing experimentsBurns, GAPC, Russ, T.
In KCAP 2009
2009BibTex

BioScholar: A knowledge engineering system for biology and it's application to neural connectivity data.Burns, GAPC, Russ, T., Ingulfsen, T., Hovy, E.
In 2nd Congress of the International Neuroinformatics Coordinating Facility (INCF2009)
2009BibTex

Biocuration Workflow Catalogue - Text Mining for the Biocuration WorkflowBurns, GAPC, Krallinger, M., Cohen, K. B., Wu, C. H., Hirschman, L.
In 3rd International Biocurators Meeting
2009BibTex

Using Knowledge Engineering Approaches to Reason About Neuroanatomical ExperimentsBurns, GAPC, Russ, T., Ingulfsen, T., Khan, A. M., Hovy, E.
In Society for Neuroscience Annual Meeting
2009BibTex

The NIH Visual Browser: An Interactive Visualization of Biomedical ResearchHerr, B. W., Talley, E. M., Burns, GAPC, Newman, D., LaRowe, G.
In 13th International Conference on Information Visualization (IV09)
2009BibTex

2008

Intelligent Approaches to Mining the Primary Research Literature: Techniques, Systems, and ExamplesGully Burns, Donghui Feng, Eduard H. Hovy
In Computational Intelligence in Medical Informatics
2008, 17-50 pagesBibTex

Biomedical knowledge engineering approaches driven by processing the primary experimental literature.Burns, GAPC, Hovy, E., Ingulfsen, T.
In Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008
2008
http://bmkeg.isi.edu/files/INCF-2008-burns-poster.pdfBibTex

Analyses over multiple scientific text corpora: combining MEDLINE, CRISP and the proceedings of the annual meetings of the Society for NeuroscienceBurns, G. A., Newman, D., Herr, B, Holloway, A., Smyth, P., Borner, K.
2008BibTex

Intelligent Approaches to Mining the Primary Research Literature: Techniques, Systems, and ExamplesGully A. P. C. Burns, Donghui Feng, Eduard H. Hovy
In Computational Intelligence in Medical Informatics
2008BibTex

Towards Automated Semantic Analysis on Large Scale Biomedical TextFeng, D., Burns, GAPC, Hovy, E. H.
In Proceedings of the International Joint Conference on NLP (IJCNLP).
2008BibTex

2007

Infrastructure for Annotation-Driven Information Extraction from the Primary Scientific Literature: Principles and PracticeGully Burns, Donghui Feng, Tommy Ingulfsen, Eduard H. Hovy
In 2007 IEEE International Conference on Services Computing - Workshops (SCW 2007), 9-13 July 2007, Salt Lake City, Utah, USA
2007, 122-129 pagesBibTex

2007 IEEE International Conference on Services Computing - Workshops (SCW 2007), 9-13 July 2007, Salt Lake City, Utah, USA
In IEEE SCW
2007BibTex

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

A snapshot of neuroscience: unsupervised natural language processing of abstracts from the Society for Neuroscience 2006 annual meetingBurns, GAPC, Herr, B, Newman, D., Ingulfsen, T., Pantel, P, Smyth, P.
In Annual Meeting of the Society for Neuroscience
2007, 100.6 / XX26 pages
http://f1000.com/posters/browse/summary/1092223BibTex

Using large-scale semi-automated information extraction for the biocuration of experimental observations: the million-paper challenge.Burns, GAPC, Ingulfsen, T., Feng, D., Hovy, E. H.
In 2nd International Biocurators meeting
2007
http://www.biocurator.org/talks/2007/Session5-Burns.pptBibTex

Extracting Data Records from Unstructured Biomedical Full TextFeng, D., Burns, G., Hovy, E.
In The Joint Meeting of Conference on Empirical Methods in Natural Language Processing and Conference on Computational Natural Language Learning (EMNLP-CoNLL 2007)
2007BibTex

2006

The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlasesGully A. P. C. Burns, Wei-Cheng Cheng, Richard H. Thompson, Larry W. Swanson
In BMC Bioinformatics
2006, 531 pagesBibTex

The NeuARt II system: a viewing tool for neuroanatomical data based on published neuroanatomical atlases.Burns, G., Cheng, W-C, Thompson, R. F., Swanson, L.
In BMC Bioinformatics
2006, 531 pages
http://www.biomedcentral.com/1471-2105/7/531/abstractBibTex

The NeuroScholar system as a Natural Language Processing platform for the neuroscience literatureBurns, G., Hovy, E.
In Annual Meeting of the Society for Neuroscience
2006BibTex

Tools for Knowledge Acquisition within the NeuroScholar system and their application to anatomical tract-tracing dataBurns, G. A., Cheng, W. C.
In J Biomed Discov Collab
2006, 10 pages
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16895608BibTex

NeuARt II Developers ManualCheng, W-C, Burns, GAPC
2006BibTex

NeuroScholar WebService Developer's ManualCheng, W-C, Burns, GAPC
2006BibTex

NeuroScholar's Electronic Laboratory Notebook and its Application to NeuroendocrinologyKhan, A. M., Hahn, JD, Cheng, W-C, Watts, A. G., Burns, GAPC
In Neuroinformatics
2006, 139-160 pagesBibTex

2005

Extracting and managing model parameters from the literature.Burns, G.
In World Assocation of Modellers, Biologically Accurate Modeling
2005BibTex

A 'Stress Management' System: Computational knowledge representation of experiments that delineate neural circuits and histochemical expression patterns based on the primary literature and raw dataBurns, GAPC, Khan, A. M., Cheng, W. C., Watts, A. G.
In 2005 Workshop on the Neuroendocrinology of Stress
2005BibTex

A computational knowledge representation for physiological experiments with direct links to the primary literature and raw dataBurns, GAPC, Khan, A. M., Cheng, W-C, Watts, A. G.
In Annual Meeting of the Society for Neuroscience
2005BibTex

Tools for knowledge representation, acquisition and retrieval of neuroanatomical data mapped onto a standard atlas.Cheng, W-C, Burns, GAPC, Thompson, R. H., Swanson, L. W.
In Annual Meeting of the Society for Neuroscience
2005, 571.4 pagesBibTex

Projections from the Subfornical Region of the Lateral Hypothalamic AreaGoto, M, Canteras, NS, Burns, GAPC, Swanson, L. W.
In J Comp Neurol
2005, 412-38 pagesBibTex

An Overview of Sangam: A System for Integrating Data to Investigate Stress-Circuitry-Gene CouplingSaxena, M, Kim, S, Burns, GAPC, Khan, AM., Su, J, Hamadi, Y, Ghandeharizadeh, S.
In IVNET, submitted
2005BibTex

2004

Two-phase Decision Fusion Based on User PreferenceChen, Y-S, Shahabi, C, Burns, GAPC
In Hawaii International Conference on Computer Sciences
2004BibTex

Histochemical studies of stress-activated paraventricular hypothalamic neuroendocrine neurons: a neuroinformatics-based digital lab notebook to relate the primary literature to raw, unpublished dataKhan, A. M., Cheng, W. C., Watts, A. G., Burns, GAPC
In Society for Neuroscience Annual Meeting
2004BibTex

2003

Web services as tools within a scientific knowledge engineering environmentBurns, GAPC, Cheng, W-C, Zhang, N, Ghandeharizadeh, S.
In SCI
2003BibTex

An example of a neuroinformatics knowledge model derived from the primary literature: Catecholaminergic regulation of hypothalamic paraventricular neuroendocrine neuronsBurns, G., Khan, A. M.
In Annual Meeting for the Society for Neuroscience
2003, 758.2 pagesBibTex

Tools and approaches for the construction of knowledge models from the neuroscientific literatureBurns, G. A., Khan, A. M., Ghandeharizadeh, S., O'Neill, M. A., Chen, Y. S.
In Neuroinformatics
2003, 81-109 pages
http://journals.humanapress.com/index.php?option=com_opbookdetails&article_code=NI:1:1:81BibTex

Tools for knowledge management of the neuroscientific literature, plugins for the NeuroScholar systemSong, S, Chan, K, Golypayegani, A, Ghandeharizadeh, S., Shahabi, C, Burns, GAPC
In Computational Neuroscience
2003BibTex

Guided Incremental Construction of Belief NetworksSutton, C., Burns, B., Morrison, C. T., Cohen, P. R.
In The Fifth International Symposium on Intelligent Data Analysis (IDA 2003).
2003BibTex

2002

Software engineering tools and approaches for neuroinformatics: the design and implementation of the View-Primitive Data Model framework (VPDMf)Gully A. P. C. Burns, Fang Bian, Wei-Cheng Cheng, Shyam Kapadia, Cyrus Shahabi, Shahram Ghandeharizadeh
In Neurocomputing
2002, 1049-1056 pagesBibTex

Software engineering tools and approaches for neuroinformatics: the design and implementation of the View-Primitive Data Model framework (VPDMf)Burns, GAPC, Bian, F, Cheng, W-C, Kapadia, S, Shahabi, C, Ghandeharizadeh, S.
In Neurocomputing
2002, 1049-1056 pagesBibTex

2001

Towards a federated neuroscientific knowledge management system using brain atlasesGully Burns, Klaas E. Stephan, Bertram Ludäscher, Amarnath Gupta, Rolf Kötter
In Neurocomputing
2001, 1633-1641 pagesBibTex

Towards a federated neuroscientific knowledge management system using brain atlasesBurns, GAPC, Stephan, KE, Ludäscher, B, Gupta, A, Kötter, R
In Neurocomputing
2001, 1633-1641 pagesBibTex

Knowledge management of the neuroscientific literature: the data model and underlying strategy of the NeuroScholar systemBurns, G. A.
In Philos Trans R Soc Lond B Biol Sci
2001, 1187-208 pages
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11545698BibTex

Analysis of the connectional organization of neural systems associated with the hippocampus in ratsBurns, G. A., Young, M. P.
In Philos Trans R Soc Lond B Biol Sci
2001, 55-70 pages
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10703044BibTex

Knowledge Mechanics and the NeuroScholar Project: A New Approach to Neuroscientific TheoryBurns, GAPC
In Computing the Brain, A guide to Neuroinformatics
2001, 319-335 pagesBibTex

The Neuroanatomical Rat Brain Viewer (NeuARt)Dashti, A. E., Burns, GAPC, Simmons, D. M., Swanson, L., Ghandeharizadeh, S., Shahabi, C, Stone, J., Jia, S.
In Computing the Brain: A Guide to Neuroinformatics
2001, 189-202 pagesBibTex

Advanced database methodology for the Collation of Connectivity data on the Macaque brain (CoCoMac)Stephan, KE, Kamper, L., Bozkurt, A., Burns, G. A., Young, M. P., Kotter, R.
In Philos Trans R Soc Lond B Biol Sci
2001, 1159-86 pages
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11545697BibTex

2000

Anatomical connectivity defines the organization of clusters of cortical areas in the macaque monkey and the catHilgetag, C. C., Burns, G. A., O'Neill, M. A., Scannell, J. W., Young, M. P.
In Philos Trans R Soc Lond B Biol Sci
2000, 91-110 pages
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10703046BibTex

Computational analysis of functional connectivity between areas of primate cerebral cortexStephan, KE, Hilgetag, C. C., Burns, G. A., O'Neill, M. A., Young, M. P., Kotter, R.
In Philos Trans R Soc Lond B Biol Sci
2000, 111-26 pages
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10703047BibTex

1999

Neuroscholar 1.00, a neuroinformatics databasing websiteGully Burns
In Neurocomputing
1999, 963-970 pagesBibTex

Visual Information and Information Systems, Third International Conference, VISUAL '99, Amsterdam, The Netherlands, June 2-4, 1999, Proceedings
In VISUAL
1999BibTex

Neuroscholar 1.00, a neuroinformatics databasing websiteBurns, GAPC
In Neurocomputing
1999, 963-970 pagesBibTex

The connectional organization of the cortico-thalamic system of the catScannell, J. W., Burns, G. A., Hilgetag, C. C., O'Neil, M. A., Young, M. P.
In Cereb Cortex
1999, 277-99 pages
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10355908BibTex

1997

Neural connectivity in the rat: theory, methods and applicationsBurns, GAPC
1997
http://www.neuroscholar.org/Download_files/Burns-DPhil-Thesis-1997.pdfBibTex

1994

Analysis of connectivity: neural systems in the cerebral cortexYoung, M. P., Scannell, J. W., Burns, G. A., Blakemore, C.
In Rev Neurosci
1994, 227-50 pages
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7889215BibTex

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