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HOCK 331
Phone: 765-494-6933

Biological systems are controlled by extremely complex networks of interactions between genes, RNAs, proteins, and small molecules.  The Computational Systems Biology group investigates these complex interactions using computational analysis of genomics and systems biology data.  Our current projects include network analysis and meta-analysis of human-disease interactions, identification of novel regulatory structures in RNA, development of methods for predicting protein-RNA binding, genomic analysis of important protein families such as protein kinases, and next-generation RNA-Seq analysis of gene expression.

More broadly, we develop computational methods for finding patterns in sequences and structures that allow us to make inferences about the relationships between sequence, structure and function. These methods include elements of datamining, machine learning, modeling, and simulation in the context of biological data. One of our central emphases is using information from homologous molecules in different species to find the conserved structural elements that are associated with biological function.  More recently we have extended these approaches to the analysis of biological networks using genome wide expression, protein interaction, genetic interaction and metabolite data.  In addition to our major biological interests, we have ongoing interests the integration and management of biological data and methods for facilitating interaction between biological information resources.


B.S. Oregon State University, 1979

Ph.D. University of Wisconsin-Madison, 1985

Other Activities

Editorial Boards

  • Bioinformatics
  • Journal of Computational Biology and Chemistry
  • Journal of Molecular Microbiology & Biotechnology

Societies and Advisory Boards

  • President, International Society for Computational Biology
  • Chair, Protein Information Resource Scientific Oversight and Advisory Board
  • Member, Allele Frequency Database (ALFRED) Advisory Board
  • Member, Idaho INBRE External Advisoty Committee


Study Section

  • 2005 - Biodata Management and Analysis
  • 2005 - National Centers for Biomedical Computing
  • 2004 - National Centers for Biomedical Computing
  • 2002 - NIH Genome Study Section
  • 2002 - NCI Basic and Preclinical



  • 2005 - Purdue University Computational genomics of plant protein families.
  • 2005 - Biometrics ENAR Conference Investigation of plant phosphorylation using intergenomic comparison.
  • 2005 - DOE, Populus Annotation meeting Global annotation of the plant protein kinase family.
  • 2004 - Mid-Central bioinformatics Society The future of Biopinformatics.
  • 2004 - Purdue University Computational exploration of the kinome.
  • 2004 - University of Idaho Finding functionally important sequences using expectation-maximization.
  • 2004 - University of Indiana-Bloomington Computational exploration of the kinome.
  • 2003 - University of Maryland Exploring the plant kinome.
  • 2003 - University of California, Riverside Genomic analysis of plant protein kinases.

Professional Faculty Research

(Computational Systems Biology; Bioinformatics) Computational analysis of biological networks and the macromolecular components that they comprise.  My interests range from the relationship between patterns in macromolecular sequences and the evolution, structure and function of the corresponding molecules (RNA and protein), to the biological networks that control and integrate the information of that controls the development and function of the cell. In addition my work includes development of databases and computational tools for functional genomics, and the development of systems that federate knowledge across multiple electronic resources.

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