Network Systems Science and Advanced Computing

Stefan Hoops

  • Research Associate Professor
Stefan Hoops headshot


Stefan Hoops is a research associate professor in the Network Systems Science and Advanced Computing division. Before joining the Biocomplexity Institute of Virginia Tech in 2000, Hoops served as a software developer for Schumann Consulting Corporation in Germany from 1995-2000. In 2006, Hoops was elected as one of the five editors of the Systems Biology Markup Language (SBML), where he served from 2007-2009.

At Virginia Tech, Hoops worked with Dr. Pedro Mendes in the Biochemical Networks Modeling Group. The research group was interested in understanding how cells work at the biochemical level and its approach can be labeled as Systems Biology, as they derive quantitative dynamic models from integrative functional genomic data. The research group had ongoing projects in development of methodologies and software for the complete process of going from functional genomic data to computational models: biochemical simulators (Gepasi and COPASI), database design (DOME and B-Net), data analysis, network inference, parameter estimation for nonlinear models, and theoretical aspects of biochemical regulation (such as Metabolic Control Analysis).

  • Modeling and simulation of biochemical systems, management and analysis of systems biology data sets, and reverse-engineering of biochemical networks

  • The Norwegian Institute of Technology, Trondheim, Norway, Mathematical Physics, Ph.D., 1993
    University of Alabama at Birmingham, AL, Mathematics, M.S., 1991
    Carolo-Wilhelmina Technical Uni. at Braunschweig, Germany, Physics, MS, 1990

  • 1995-2000 Software Designer/Developer, Schumann Unternehmensberatung AG (Schumann Consulting Corporation), Cologne, Germany

Selected Publications
Network Systems Science and Advanced Computing
PLOS ONE, 10(9):e0136139.: (2015) Alam M, Deng X, Philipson C, Bassaganya-Riera J, Bisset K, Carbo A, Eubank S, Hontecillas-Magarzo R, Hoops S, Mei Y, Abedi V, Marathe M.
Network Systems Science and Advanced Computing
PLOS ONE, 8(9):e73365.: (2013) Carbo A, Bassaganya-Riera J, Pedragosa M, Viladomiu M, Marathe M, Eubank S, Wendelsdorf K, Bisset K, Hoops S, Deng X, Alam M, Kronsteiner B, Mei Y, Hontecillas-Magarzo R.