Department of Computer Science
27 Graves Place
Holland, Michigan 49423
(616) 395-7429
http://www.cs.hope.edu/~dejongh
Ph.D. in Computer Science (Artificial Intelligence), The Ohio State University, 1991.
M.S. in Computer Science, The Ohio State University, 1986.
B.S. in Computer Science and Mathematics, The Ohio State University, 1985.
M.A. in Theological Studies, Winebrenner Theological Seminary, 1998.
Assistant Professor of Computer Science, Hope College, Holland, Michigan, (since June, 2002)
Senior Software Engineer, NetGenics, Inc./LION bioscience Inc. (1998 – 2002)
Campus Minister, Great Commission Ministries (1991 – 1998)
Graduate Research Assistant, The Ohio State University (1987 – 1991)
Graduate Teaching Assistant, The Ohio State University (1986 – 1987)
International Society for Computational Biology
American Association for Artificial Intelligence
Association for Computing Machinery, Special Interest Group on Computer Science Education
(* designates Student co-author)
Tintle, N., Best, A., DeJongh, M., *VanBruggen, D., Heffron, F., Porwollik, S., Taylor, R., “Gene set analyses for interpreting microarray experiments on prokaryotic organisms,” BMC Bioinformatics, Vol. 9, No. 469, November, 2008.
Ramy K Aziz, Daniela Bartels, Aaron A Best, Matthew DeJongh, Terrence Disz, Robert A Edwards, *Kevin Formsma, Svetlana Gerdes, Elizabeth M Glass, Michael Kubal, Folker Meyer, Gary J Olsen, Robert Olson, Andrei L Osterman, Ross A Overbeek, Leslie K McNeil, Daniel Paarmann, Tobias Paczian, Bruce Parrello, Gordon D Pusch, Claudia Reich, Rick Stevens, Olga Vassieva, Veronika Vonstein, Andreas Wilke, Olga Zagnitko, “The RAST Server: Rapid Annotations using Subsystems Technology ,” BMC Genomics, Vol. 9, No. 75, February, 2008.
DeJongh, M., *Formsma, K., *Boillot, P., *Gould, J., *Rycenga, M., Best, A., “Toward the automated generation of genome-scale metabolic networks in the SEED,” BMC Bioinformatics, Vol. 8, No. 139, April, 2007.
DeJongh, M., *Van Dort, P., *Ramsay, B., “Linking Molecular Function and Biological Process Terms in the Gene Ontology for Gene Expression Data Analysis,” Conference Proceedings of the IEEE Engineering in Medicine and Biology Society, Vol. 4, pp. 2984-6, September, 2004.
McEntire, R., Karp, P., Abernethy, N., Olken, F., Kent, R., DeJongh, M., Tarczy-Hornoch, P., Benton, D., Pathak, D., Helt, G., Lewis, S., Kosky, A., Neumann, E., Hodnett, D., Tolda, L., and Topaloglou, T., “An Evaluation of Ontology Exchange Languages for Bioinformatics,” in Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, pp. 239-250, AAAI Press, Menlo Park, CA, 2000.
Johnson, T., Smith, J., Johnson, K., Amra, N., and DeJongh, M. “Diagrammatic Reasoning of Tabular Data,” in Narayanan, N. H., (ed.), Reasoning with Diagrammatic Representations: Papers from the 1992 AAAI Spring Symposium, pp. 161-164, AAAI Press, Menlo Park, CA, 1992.
Johnson, K., Johnson, T., Smith, J., DeJongh, M., Fischer, O., Amra, N., and Bayazitoglu, A., “RedSoar-A System for Red Blood Cell Antibody Identification,” in Proceedings of the Fifteenth Annual Symposium on Computer Applications in Medical Care, pp. 664-668, McGraw Hill, Washington, D.C., 1991.
DeJongh, M. and Smith, J., “Integrating Models of a Domain for Problem Solving,” in Proceedings of the Eleventh International Conference on Expert Systems and Their Applications, pp. 125-135, Avignon, France, 1991.
Best, A., DeJongh, M., Barton, A., Brown, J., Barney, C., “Models of Interdisciplinary Research and Service Learning at Hope College,” Council on Undergraduate Research Quarterly, December, 2007.
DeJongh, M., Burnatowska-Hledin, M., “Development and Implementation of an Introductory Bioinformatics Course at Hope College,” Special Issue on Bioinformatics of Transformations: Liberal Arts in the Digital Age, Vol. 2, No. 1, April, 2004.
Best, A., DeJongh, M., *Boillot, P., *Bowerman, N., *Formsma, K., *Frybarger, P., *Wilkening, J., “Toward the Automated Generation of Genome-scale Metabolic Networks in the SEED,” Poster presentation at the American Society for Microbiology 107th General Meeting, Toronto, Ontario, May, 2007.
Best, A., DeJongh, M., Tintle, N. “Interdisciplinary Research across Biology, Mathematics and Computer Science: Genome-scale Metabolic Reconstruction and Modeling of Microbial Life,” Invited Presentation at Midstates Consortium for Mathematics and Science: Interdisciplinary Science Education, St. Olaf College, Northfield, Minnesota, February 23-24, 2007.
DeJongh, M., Best, A., “Toward the Automatic Generation of Genome-Scale Metabolic Models in the SEED,” Poster Presentation at Department of Energy Genomics:GTL Awardee Workshop V, Bethesda, Maryland, February 11-14, 2007.
DeJongh, M., Burnatowska-Hledin, M., “Two Complementary Approaches to Teaching Bioinformatics at Hope College,” Invited Presentation at NITLE Bioinformatics Practicum, Bates College, Lewiston, Maine, June 19-21, 2006.
Best, A. and DeJongh, M. “A Research-based Approach to Teaching Bioinformatics: Microbial Genome Annotation and Metabolic Modeling using the SEED,” 13th American Society for Microbiology Conference for Undergraduate Educators, University of Central Florida, Orlando, Florida, May 19-21, 2006.
DeJongh, M. and Best, A. “Bioinformatics at Hope College,” Invited Presentation at Albion College Math and Biology Colloquium Series, Albion, Michigan, March 31, 2005.
DeJongh, M., “Beginning Programming in Perl for Bioinformatics,” Invited Presentation at the Education Workshop of the American Society for Cell Biology 44th Annual Meeting, Washington, D.C., December 4-8, 2004.
DeJongh, M. and Burnatowska-Hledin, M., “Report On the MITC Hands-on Teaching of Bioinformatics Workshop,” Invited Presentation at Voyage to Ithaka: Technology, Collaboration, and the Future of Liberal Arts Colleges, National Institute for Technology and Liberal Education, Chicago, Illinois, November 7-9, 2004.
DeJongh, M., “Beginning Programming in Perl for Bioinformatics,” at the Midwest Instructional Technology Center's Hands-on Teaching of Bioinformatics Workshop, Hope College, Holland, Michigan, May 13-15, 2004.
DeJongh, M., Burnatowska-Hledin, M., “An Introductory Course in Bioinformatics,” at the Midwest Instructional Technology Center's Hands-on Teaching of Bioinformatics Workshop, Hope College, Holland, Michigan, May 13-15, 2004.
DeJongh, M., Burhans, D., Doom, T., LeBlanc, M., “Bioinformatics in the Undergraduate Curriculum: Opportunities for Computer Science Educators,” at SIGCSE 2004, Norfolk, Virginia, March 3-7, 2004.
DeJongh, M., LeBlanc, M., “SIGCSE Special Projects Showcase: Bioinformatics in the Computer Science Curriculum,” at SIGCSE 2004, Norfolk, Virginia, March 3-7, 2004.
DeJongh, M., *Van Dort, P., *Ramsay, B., “Linking Molecular Function and Biological Process Terms in the Gene Ontology for Gene Expression Data Analysis,” Poster Presentation at Pacific Symposium in Biocomputing 2004, Kona, Hawaii, January 6-10, 2004.
DeJongh, M., “Introducing Bioinformatics into the Undergraduate Curriculum,” at Bio2010: Computational Solutions to Biological Problems, Washington University School of Medicine, June 24-26, 2003.
DeJongh, M. and Burnatowska-Hledin, M., “Introducing Bioinformatics into the Undergraduate Curriculum,” at Innovative Science Teaching: Enhancing Learning with Technology, DePauw University, May 31-June 1, 2003.
DeJongh, M. and Burnatowska-Hledin, M., “Introductory Bioinformatics Exercises using Internet Resources,” at Bioinformatics in the Undergraduate Curriculum, Dickinson College, March 21-22, 2003.
DeJongh, M. and Smith J., “The Use of Functional and Causal Knowledge in RED,” presented at the Eighth SOAR Workshop, University of Southern California, October, 1990.
DeJongh, M. and Smith J., “Integrating Multiple Models of Expertise,” presented at the AAAI Spring Symposium on Artificial Intelligence in Medicine, Stanford University, March, 1990.
DeJongh, M. and Smith J., “Bridging the Knowledge and Symbol Levels: Towards An Integrated Knowledge Engineering Environment,” presented at the AAAI Spring Symposium on Knowledge System Development Tools and Languages, Stanford University, March, 1989.
Frybarger, P., and DeJongh, M., “Generation and Refinement of Metabolic Reaction Networks in the SEED ,” at ISMB 2008, Toronto, Ontario, July 19-23, 2008.
Frybarger, P., “Expanding the Scope of Genome-Scale Metabolic Models,” at the Seventh Annual Celebration of Undergraduate Research and Creative Performance, Hope College, Holland, Michigan, March 28, 2008.
Formsma, K., and Boillot, P., “Comparative Metabolic Modeling of Prokaryotic Genomes,” at the Council for Undergraduate Research 2007 Posters on the Hill, Washington, DC, April 25, 2007.
Formsma, K., “Automatic Generation of Genome-Scale Metabolic Models,” at the SIGCSE 2007 Student Research Competition, Covington, Kentucky, March 7-10, 2007.
Boillot, P., Formsma S., “Automatic Generation of Genome-Scale Metabolic Models,” at the Sixth Annual Celebration of Undergraduate Research and Creative Performance, Hope College, Holland, Michigan, January 29, 2007.
Ambrose, J., Formsma S., Gould, J., “Integration of KEGG pathways into the SEED,” at the Argonne National Laboratory Symposium for Undergraduates in Science, Engineering and Mathematics, Argonne National Laboratory, Argonne, Illinois, November 4-5, 2005.
Blumenberg, K., Wilkening, M., “Mining Implicit Links in the Gene Ontology,” at the Eleventh Annual Consortium for Computing Sciences in Colleges: Midwest Conference, Kalamazoo College, Kalamzoo, Michigan, October 1-2, 2004.
Sumner, W. N., Evans, T., DeJongh, M., “Simulating the Effects of Speciation and Extinction Rates on Branch Lengths in Phylogenetic Trees,” at the International Conference for Mathematics in Biology and Medicine, University of Michigan, Ann Arbor, Michigan, July 25-28, 2004.
Ramsay, B., Van Dort, P., “Functional Modeling of Genes and Cellular Processes for Gene Expression Analysis,” at the SIGCSE 2004 Student Research Competition, Norfolk, Virginia, March 3-7, 2004.
Ramsay, B., Van Dort, P., “Functional Modeling of Genes and Cellular Processes,” at the Pew Midstates Science and Mathematics Consortium's Undergraduate Research Symposium, St. Louis, Missouri, November 14-16, 2003.
National Science Foundation, RUI: Automated Metabolic Reconstruction for All Sequenced Microbial Genomes with Dr. Aaron Best (Biology), Award Number MCB-0745100, August 2008 through July 2011.
Fulbright Research Scholar at the Laboratoire Bordelais de Recherche en Informatique, Bordeaux, France, Fulbright-Aquitaine Regional Council Award, January to June 2009.
Argonne National Laboratory, Guest Faculty Program, 2006 to present.
Hope College, Howard Hughes Medical Institute Faculty Development Grant for Interdisciplinary Research with Dr. Aaron Best (Biology) and Dr. Nathan Tintle (Mathematics), Summer, 2006.
Hope College, Howard Hughes Medical Institute Faculty Development Grant for Interdisciplinary Research with Dr. Aaron Best (Biology), Summer, 2005.
Hope College, Towsley Research Scholar Award, January, 2005.
National Computational Science Institute, Development of Virtual Applets to Increase the Understanding of Concepts in the Undergraduate Biology Curriculum at Hope College, with Debbie Swarthout, September, 2004.
Hope College Faculty Development Fund, Functional Modeling of Genes and Cellular Processes for Gene Expression Data Analysis, June, 2004.
Midwest Instructional Technology Center, Hands-on Teaching of Bioinformatics Workshop, with Maria Burnatowska-Hledin, May, 2004.
The Association for Computing Machinery, Special Interest Group in Computer Science Education: Bioinformatics in the Computer Science Curriculum, with Maria Burnatowska-Hledin at Hope College, and Mark LeBlanc and Betsey Dyer at Wheaton College, MA, July 2003.