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Toni Kazic

Toni Kazic

Associate Professor of Computer Science

Computer Science,



Toni Kazic is an associate professor and the C. W. LaPierre Professor in the Department of Computer Science. She received a B.S. in microbiology from the University of Illinois, Urbana, in 1975, and a Ph.D. in genetics from the University of Pennsylvania in 1984. Trained chiefly as a bacterial geneticist and molecular biologist with heavy biochemical emphases, she worked on purine biosynthesis, DNA repair, and deletion formation in Escherichia coli while her interests in computational biology subconsciously developed. In 1989 she switched her primary research technique from laboratory to computational experimentation. In 2006 she began genetic and computational experiments for a computational study of the networks involved in producing a set of complex phenotypes in maize.

Her research is focused on understanding and inferring biochemical networks, and the development of the necessary computational tools to do so. Currently, her group is developing The Agora, an electronic infrastructure for community deposit, review, and querying of biochemical information (; and studying how to infer the mechanisms responsible for forming lesions (spots) on the leaves of maize. The latter is a prime example of how a complex network (over 200 genes) produces a very wide variation in observable phenotypes, and serves as a model system for the development of algorithmic inference methods. She also studies methods to provide semantic interoperability among independent databases and to reason over such information. Prior work has included representational methods for biochemical compounds and reactions and building the databases needed to support complex computations.

Research focus

Analysis, inference, representation, and simulation of biochemical networks, Chemical Informatics, Computational Biology, Declarative databases, Deconvolution of complex phenotypes, Dementias, Federated databases, Formal languages for the representation of biological and computational semantics; graph algorithms and grammars, The semantic web, Pattern formation in complex phenotypes of Zea mays, Bioinformatics

Instruction focus

Honors, Awards, and Appointments

  • LaPierre Professor of Computer Science, 2007-present.
  • Fellow American College of Medical Informatics (elected 2004).
  • Invited Researcher Institute for New Generation Computer Technology (ICOT), Tokyo, Japan (1994).
  • NIH NRSA pre- and post-doctoral fellowships, 1976-1987.
  • James Scholar (1971-1973) and Dean’s List (1973-1975), University of Illinois, Urbana-Champaign; and State of Illinois County Scholarship,1971-1975.
  • Secretary, International Society for Computational Biology (2005-2006), member of its board of directors, (1998-2006), chair of its nominations committee(2002-2003), and member of its finance and governance committees (2003-2006).
  • Associate member, Joint Committee on Biochemical Nomenclature of the International Union of Biochemistry and Molecular Biology and the International Union of Pure and Applied Chemistry} (the Enzyme Commission; 2002-present).
  • Member, meeting program committees, Intelligent Systems in Molecular Biology (ISMB; 2007, 2002; 1999-1998; 1995-1996, 1993)
  • American Medical Informatics Association (AMIA; 2005)
  • Pacific Symposium on Biocomputing (PSB; 2006, 2005, 1997-1999); Scientific and Statistical Databases Meeting 2002.
  • Member, meeting organizing committees, Biopathways Consortium meeting (2001) and the Second Electronic Computational Chemistry Conference (1995)
  • Genome Informatics Workshop 2000
  • Atlantic Symposium on Computational Biology 2001
  • Genome Information Systems and Technology 2001
  • IEEE Workshop on Shape and Pattern Matching in Computational Biology (1994-1995).
  • Co-chair, Motifs in Biology: Analysis of Ambiguous Data, minitrack of the Hawaii International Conference on Systems Sciences (1994).
  • Moderator of sessions at the ISMB (1996) and Bioinformatics (1997) meetings.

Selected Publications

  1. Chi-Ren Shyu, Jason Green, D. P. K. Lun, Toni Kazic, M. Schaeffer, and Ed Coe. Image Analysis for Mapping Immeasurable Phenotypes in Maize, in IEEE Signal Processing Magazine, Vol. 24, No. 3 , May 2007; 116-119
  2. Chi-Ren Shyu, Jaturon Harnsomburana, Jason Green, Adrian Barb, Toni Kazic, M. Schaeffer, and Ed Coe. Searching and mining visually-observed phenotypes of maize mutants, in Journal of Bioinformatics and Computational Biology, Special Issue on Making Sense of Mutations Requires Knowledge Management, Vol. 5, No. 6 , December 2007; 1193-1213
  3. P. Shapshak, R. Duncan, J. Turchen, A. Nath, A. Minagar, P. Kangueane, W. Davis, F. Chiappelli, F. Elkomy, R. Seth, and Toni Kazic. Bioinformatics models in drug abuse and NeuroAIDS: Using and developing databases, in Bioinformation, Vol. 1 2006; 86-88
  4. A. Minagar, P. Shapshak, E. M. Duran, A. S. Kablinger, J. S. Alexander, R. E. Kelley, R. Seth, and Toni Kazic. Hiv-associated dementia, Alzheimer’s disease, multiple sclerosis, and schizophrenia, in gene expression review. J. Neurol. Sci., Vol. 224 2004; 3-17
  5. Toni Kazic, Ed Coe, Mary Polacco, and Chi-Ren Shyu. Whither biological database research, in OMICS: A Journal of Integrative Biology, Vol. 7, No. 1 2003; 61-65
  6. Toni Kazic, Semiotes: a semantics for sharing., in Bioinformatics, Vol. 16 2000; 1129-1144
  7. Toni Kazic, Elements of a more comprehensive theory of computing, in BioSystems, Vol. 52 1999; 111-122