Gully Burns

Project Leader (Bioinformatics and computational biology not elsewhere classified)

Marina del Rey, CA 90292

I am primarily concerned with developing pragmatic biomedical knowledge engineering systems for scientists that (a) provide directly useful functionality in their everyday use and (b) is based on innovative, cutting edge computer science that transforms our ability to use knowledge. I was originally trained as a physicist at Imperial College in London before switching to do a Ph.D. in neuroscience at Oxford, and I think that the quantitative nature of physical theory has greatly influenced how I am trying to transform other subjects. I came to work at USC in 1997, developing the 'NeuroScholar' project in Larry Swanson's lab before joining the Information Sciences Institute in 2006. I run a group working on Biomedical Knowledge Engineering as a project leader in the ISI Intelligent Systems Division, affiliated to the Information Integration Group. I write a little: maintaining a blog called 'Building a Breakthrough Machine'.


  • Layout-aware text extraction from full-text PDF of scientific articles DOI: 10.1186/1751-0473-7-7
  • Text mining for the biocuration workflow DOI: 10.1093/database/bas020
  • Toward interoperable bioscience data DOI: 10.1038/ng.1054
  • Database of NIH grants using machine-learned categories and graphical clustering DOI: 10.1038/nmeth.1619
  • Enabling collaborative research using the Biomedical Informatics Research Network (BIRN) DOI: 10.1136/amiajnl-2010-000032
  • Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case DOI: 10.1186/1471-2105-12-351
  • Biomedical knowledge engineering tools based on experimental design: A case study based on neuroanatomical tract-tracing experiments DOI: 10.1145/1597735.1597768
  • The NIH visual browser: An interactive visualization of biomedical research DOI: 10.1109/IV.2009.105
  • An analysis of the abstracts presented at the annual meetings of the Society for Neuroscience from 2001 to 2006. DOI: 10.1371/journal.pone.0002052
  • Intelligent approaches to mining the primary research literature: Techniques, systems, and examples DOI: 10.1007/978-3-540-75767-2_2
  • Extracting data records from unstructured biomedical full text
  • Infrastructure for annotation-driven information extraction from the primary scientific literature: Principles and practice DOI: 10.1109/SERVICES.2007.34
  • NeuroScholar's Electronic Laboratory Notebook and its application to neuroendocrinology DOI: 10.1385/NI:4:2:139
  • The NeuARt II system: A viewing tool for neuroanatomical data based on published neuroanatomical atlases DOI: 10.1186/1471-2105-7-531
  • Tools for knowledge acquisition within the NeuroScholar system and their application to anatomical tract-tracing data DOI: 10.1186/1747-5333-1-10
  • Projections from the subfornical region of the lateral hypothalamic area DOI: 10.1002/cne.20764
  • Tools and approaches for the construction of knowledge models from the neuroscientific literature
  • Software engineering tools and approaches for neuroinformatics: The design and implementation of the View-Primitive Data Model framework (VPDMf) DOI: 10.1016/S0925-2312(02)00414-9
  • Advanced database methodology for the Collation of Connectivity data on the Macaque brain (CoCoMac) DOI: 10.1098/rstb.2001.0908
  • Knowledge management of the neuroscientific literature: The data model and underlying strategy of the NeuroScholar system DOI: 10.1098/rstb.2001.0909
  • Towards a federated neuroscientific knowledge management system using brain atlases DOI: 10.1016/S0925-2312(01)00520-3
  • Analysis of the connectional organization of neural systems associated with the hippocampus in rats
  • Anatomical connectivity defines the organization of clusters of cortical areas in the macaque monkey and the cat
  • Computational analysis of functional connectivity between areas of primate cerebral cortex
  • Neuroscholar 1.00, A neuroinformatics databasing website DOI: 10.1016/S0925-2312(99)00092-2
  • The connectional organization of the cortico-thalamic system of the cat DOI: 10.1093/cercor/9.3.277
  • Non-metric multidimensional scaling in the analysis of neuroanatomical connection data and the organization of the primate cortical visual system
  • Analysis of connectivity: Neural systems in the cerebral cortex
  • Scaling and brain connectivity [8]
  • Scaling and brain connectivity [9]

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