Journal of Computer Science & Systems Biology

Laboratory of Genomics and BioEnegria, Department of Genetics and Evolution, Microbiology and Immunology, São Paulo, Brazil

Publications

• Research Article   
  A Novel Method for the Integration of Stochastic Petri Net Simulation and Transcriptomic Data Applied to a Metabolic Pathway
  Author(s): Carvalho LM, Meirelles GV, Pereira GAG* and Carazzolle MF
  
  Over the years, methods capable of integrating data from omics, such as transcriptomics, proteomics and metabolomics have emerged in Systems Biology, principally the use of networks to integrate omics information. In particular, the role of each biological pathway aims to understand the intermolecular interactions. While there are theoretical and experimental strategies to investigate biological pathways involved in cellular metabolism, computational modeling methods allow for a better understanding of them. Here we propose a new method to connect transcriptomic data with simulation approach using stochastic Petri Net (PN) metabolic networks. This new approach was developed based on well-studied theoretical gene expression modeling while trying to assimilate dynamic ordinary systems to a stochastic model function. The developed method was used to perform st.. Read More»
  

  Abstract PDF