ArticleBMC systems biology2011
Cell functional enviromics: unravelling the function of environmental factors.
Article in BMC systems biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- SBML2HYB: a Python interface for SBML compatible hybrid modeling.Bioinformatics (Oxford, England) · 2023Article
- Genome-scale modeling of Chinese hamster ovary cells by hybrid semi-parametric flux balance analysis.Bioprocess and biosystems engineering · 2022Article
- Review
- Enviromics in breeding: applications and perspectives on envirotypic-assisted selection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Towards a widespread adoption of metabolic modeling tools in biopharmaceutical industry: a process systems biology engineering perspective.NPJ systems biology and applications · 2020Review
- Hybrid semiparametric systems for quantitative sequence-activity modeling of synthetic biological parts.Synthetic biology (Oxford, England) · 2018Article
- A principal components method constrained by elementary flux modes: analysis of flux data sets.BMC bioinformatics · 2016Article
- Transgenerational latent early-life associated regulation unites environment and genetics across generations.Epigenomics · 2016Article
- Projection to latent pathways (PLP): a constrained projection to latent variables (PLS) method for elementary flux modes discrimination.BMC systems biology · 2011Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhile functional genomics, focused on gene functions and gene-gene interactions, has become a very active field of research in molecular biology, equivalent methodologies embracing the environment and gene-environment interactions are relatively less developed. Understanding the function of environmental factors is, however, of paramount importance given the complex, interactive nature of environmental and genetic factors across multiple time scales.
resultsHere, we propose a systems biology framework, where the function of environmental factors is set at its core. We set forth a "reverse" functional analysis approach, whereby cellular functions are reconstructed from the analysis of dynamic envirome data. Our results show these data sets can be mapped to less than 20 core cellular functions in a typical mammalian cell culture, while explaining over 90% of flux data variance. A functional enviromics map can be created, which provides a template for manipulating the environmental factors to induce a desired phenotypic trait.
conclusionOur results support the feasibility of cellular function reconstruction guided by the analysis and manipulation of dynamic envirome data.
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