The principles of whole-cell modeling

Jonathan R. Karr, Koichi Takahashi, Akira Funahashi

Research output: Contribution to journalReview articlepeer-review

49 Citations (Scopus)


Whole-cell models which comprehensively predict how phenotypes emerge from genotype promise to enable rational bioengineering and precision medicine. Here, we outline the key principles of whole-cell modeling which have emerged from our work developing bacterial whole-cell models: single-cellularity; functional, genetic, molecular, and temporal completeness; biophysical realism including temporal dynamics and stochastic variation; species-specificity; and model integration and reproducibility. We also outline the whole-cell model construction process, highlighting existing resources. Numerous challenges remain to achieving fully complete models including developing new experimental tools to more completely characterize cells and developing a strong theoretical understanding of hybrid mathematics. Solving these challenges requires collaboration among computational and experimental biologists, biophysicists, biochemists, applied mathematicians, computer scientists, and software engineers.

Original languageEnglish
Pages (from-to)18-24
Number of pages7
JournalCurrent Opinion in Microbiology
Publication statusPublished - 2015 Oct 1

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)
  • Infectious Diseases


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