scFBA

scFBA (single-cell Flux Balance Analysis) is a computational framework that translates single-cell transcriptome data into single-cell metabolic flux profiles (fluxomes). It integrates single-cell RNA-seq profiles of cancer cells into a multi-scale stoichiometric model of a cancer cell population. This integration helps to reduce the space of feasible single-cell fluxomes, identify clusters of cells with different growth rates within the population, and highlight possible metabolic interactions among cells via the exchange of metabolites.

Topic

Small molecules;Molecular interactions, pathways and networks;Endocrinology and metabolism

Detail

  • Operation: Metabolic network modelling;Natural product identification;Expression analysis

  • Software interface: Suite

  • Language: MATLAB

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: Italian Ministry of Education, Universities and Research, FLAG-ERA, EU, WOTRO.

  • Input: -

  • Output: -

  • Contact: Chiara Damiani chiara.damiani@unimib.it

  • Collection: -

  • Maturity: -

Publications

  • Integration of single-cell RNA-seq data into metabolic models to characterize tumour cell populations
  • Kaushik A, et al. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. 2015; 3:e1332. doi: 10.7717/peerj.1332
  • https://doi.org/10.1101/256644
  • PMID: -
  • PMC: -
  • Integration of single-cell RNA-seq data into population models to characterize cancer metabolism.
  • Damiani C, et al. Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. 2019; 15:e1006733. doi: 10.1371/journal.pcbi.1006733
  • https://doi.org/10.1371/journal.pcbi.1006733
  • PMID: 30818329
  • PMC: PMC6413955

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