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This page contains selected publications for which I have electronic versions. These papers may be copyrighted by the publishers and are placed here to facilitate scientific dissemination of the work. The publications are arranged by topic:

All of the database and software papers are oriented toward biology applications or use examples from bioinformatics for illustration. This page also includes some unpublished papers that were written when I was at the Computational Molecular Biology Group at Baylor College of Medicine. There are some good (novel and/or practically useful) ideas in them, and since there are many more people interested in bioinformatics these days than have experience in it, I'm putting the papers here for people who would like to learn more about these topics.


  • Designing XML Databases Prentice-Hall, 2002. (web site)
    How to design XML databases, database management systems, and database systems. The book has several examples from bioinformatics.


  • Graph Data Models for Genomics Unpublished (pdf)
    Describes graph data models for biology data. This was the last paper I wrote on graph data models.
  • Data Note System for Capturing Laboratory Data Genomics, 43, pages 232-236, 1997. (pdf)
    A graph database used to capture information about experimental results. The investigator can use a graphical user interface to design a schema, and the system automatically generates data entry and query forms.
  • Graph Database Systems for Genomics (with ER Bergeman, CB Lawrence) IEEE Engineering in Medicine and Biology 11(6). Special issue on Managing Data for the Human Genome Project. November 1995. (pdf)
    Describes the design and application of graph database systems used for the Human Genome Project.
  • Querying a Genome Database Using Graphs (with ER Bergeman, CB Lawrence) Third International Conference on Bioinformatics and Genome Research, World Scientific Publishing 1996. (pdf)
    Introductory paper on representing genome data using graphs, querying a genome database using simple graph queries, and presenting the results via a web interface.
  • A Graph-Theoretic Data Model for Genome Mapping Databases (with ER Bergeman, CB Lawrence) In Proceedings of the Twenty-Sixth Annual Hawaii International Conference on System Sciences. January 1995. (This conference track became PSB) (pdf)
    Overview of using graph databases to represent genome data.
  • Querying on a Persistent Graph Logic Programming Language Unpublished (pdf)
    Theoretical description of an algorithm representing and querying data using graphs.


  • Graph Communication between Database System Components Fourth International Conference on Bioinformatics and Genome Research June 1995. (oral) (presentation pdf)
  • Conceptual Integration of Genome Databases via Reduced Autonomy and Domain-Specific Data Models Meeting on Interconnection of Molecular Biology Databases, Cambridge, England. July 1995.(html, presentation pdf)
  • Conceptual Models: Not Just for Design Anymore Meeting on Interconnection of Molecular Biology Databases, Stanford, CA. Aug 1994. (oral) (presentation pdf)
  • Integrating Genome and Biology Data (with CB Lawrence) Unpublished (pdf)
    This describes how to integrate biological data from using graphs and motivates the integration using biology. The approach is still useful and is being used today. It is particularly relevant in light of the work done by W3C on RDF and the semantic web.
  • Integrating Genome Data (ER Bergeman, CB Lawrence) Unpublished (pdf)
    Not only was this paper never published, it was not completed either. I'm putting this out here because it presents some of the issues involved in database integration for biology databases. Unfortunately, it is not dated as none of the issues described have been reasonably addressed.


  • A Graph Conceptual Model for Developing Human Genome Center Databases (with ER Bergeman, CB Lawrence) Computers in Biology and Medicine 26 (3). Special issue on Information Retrieval and Genomics. 1996. (included in 1997 IMIA Yearbook of Medical Informatics, Schattauer Publishing, Stuttgart, FRG) (pdf)
    Overview of graph conceptual modeling and an example of its application to object-oriented design.
  • How to Design a Genome Database (with ER Bergeman, CB Lawrence) First World Congress on Computational Medicine and Public Health, World Scientific Publishing. 1996. (pdf)
    Phased database design process from the perspective of the user, database, and interaction.
  • Modeling Domains with a Complex Structure (with ER Bergeman, CB Lawrence) Unpublished (pdf)
    How constructs from domain modeling, conceptual modeling, and semantic networks can be used to model the complex relationships in biology processes.
  • Application of Knowledge Base Design Techniques to Genetic Markers Fourth International Conference on Information and Knowledge Management (CIKM-95). ACM Press. November 1995. (pdf, presentation pdf, external abstract)
  • Theories and Tools for Designing Application-Specific Knowledge Base Data Models University of Michigan Ph.D. dissertation, University Microfilms. April 1993. (pdf, ps)


  • Viewing Genome Data as Objects for Application Development (ER Bergeman, M Graves, CB Lawrence.) Third International Conference on Intelligent Systems for Molecular Biology (ISMB-95). July 1995. (pdf)
    Method for accessing graph data through an object-oriented system.
  • Software Analysis for Laboratory Data (ER Bergeman, M Graves, CB Lawrence.) Unpublished (pdf)
    Pulls together ideas from several software engineering methodologies which are useful for biology and shows how to use them to develop a LIMS. Although this work predates UML, most of the techniques were incorporated into UML, so this paper now provides a rationale and techniques for using UML to develop a LIMS.
  • Using Tcl/Tk in Biology Research Application Development (ER Bergeman, M Graves) Fifth Annual Tcl/Tk Workshop 1997 (external abstract)

  • Brief description of an approach to rapid prototyping in biology research.


  • A generalization of location useful for modeling maps Unpublished (pdf)
    Describes a useful mechanism for integrating models of maps. Interesting for scientists trying to model genome maps in organisms not yet sequenced. Although I didn't realize it at the time, the same approach will also work to integrate sequence annotations.
  • Integrating Order and Distance Relationships from Heterogeneous Maps First International Conference on Intelligent Systems for Molecular Biology (ISMB-93) (pdf)
    Describes how to integrate relationships between different kinds of genome maps. A knowledge base was automatically generated from a formal specification that allowed relationships from genetic, physical, and radiation hybrid maps to be shared and integrated.
  • A Conceptual Model for Genome Mapping Data (with CB Lawrence) Department of Energy Human Genome Program Contractor-Grantee Workshop IV 1994 (external abstract)
    Brief overview of using graph models for genome mapping.


  • Coarse-grained scheduling for astronomy satellites (M Graves, B McCollum) SPIE Conference on Knowledge-Based Artificial Intelligence Systems in Aerospace and Industry, Orlando, FL, April 1994. (pdf)
  • A Constraint-Logic Based Implementation of the `Coarse-Grained' Approach to Data Acquisition Scheduling of the International Ultraviolet Explorer Orbiting Observatory (B McCollum, M Graves) Third International Symposium on Artificial Intelligence, Robotics, and Automation for Space (i-SAIRAS `94). Jet Propulsion Laboratory Pub. 94-23, Pasadena, CA, October 1994. (pdf)
  • Scheduling the IUE Satellite with Constraint Logic (B McCollum, M Graves) Robotic Telescopes: Current Capabilities, Present Developments, and Future Prospects for Automated Astronomy, GW Henry and JA Eaton, eds. Provo: Astronomical Society of the Pacific. 1995. (pdf)

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