SMARTS

SMARTS is a method for reconstructing condition-specific response networks in an unsupervised way by integrating static and time-series data from multiple individuals. It uses probabilistic graphical models to assign individuals to regulatory networks, taking into account varying individual start times and response rates. SMARTS was applied to human response to influenza and mouse brain development, improving baseline groupings while identifying relevant transcription factors that differentiate the observed responses between groups.

Topic

Systems biology;Pathology;Molecular interactions, pathways and networks

Detail

  • Operation: Metabolic network modelling

  • Software interface: Command-line user interface

  • Language: Shell;Java

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: National Institute of Health, the National Science Foundationand by the James S. McDonnell Foundation Scholars Award in Studying Complex Systems.

  • Input: -

  • Output: -

  • Contact: zivbj@cs.cmu.edu

  • Collection: -

  • Maturity: -

Publications

  • SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data.
  • Wise A and Bar-Joseph Z. SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data. SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data. 2015; 31:1250-7. doi: 10.1093/bioinformatics/btu800
  • https://doi.org/10.1093/bioinformatics/btu800
  • PMID: 25480376
  • PMC: PMC4393515

Download and documentation

    Currently not available or not maintained.

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