ArticleNucleic acids research2014
Molecular mechanisms of system responses to novel stimuli are predictable from public data.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance.Cell reports · 2023Article
- A systems-level gene regulatory network model for Plasmodium falciparum.Nucleic acids research · 2021Article
- Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum.mSystems · 2020Article
- Peroxisome prognostications: Exploring the birth, life, and death of an organelle.The Journal of cell biology · 2020Review
- OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling.PLoS computational biology · 2019Article
- Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks.Cell reports · 2018Article
- Increased heme synthesis in yeast induces a metabolic switch from fermentation to respiration even under conditions of glucose repression.The Journal of biological chemistry · 2017Article
- Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast.PLoS computational biology · 2017Article
- The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria.Frontiers in microbiology · 2017Review
- Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions.eLife · 2015Article
- Signaling dynamics and peroxisomes.Current opinion in cell biology · 2015Review
- cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism.Nucleic acids research · 2015Article
- Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii.Biotechnology for biofuels · 2015Article
- Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.BMC systems biology · 2015Article
- Systems cell biology.The Journal of cell biology · 2014Review
- Network portal: a database for storage, analysis and visualization of biological networks.Nucleic acids research · 2014Article
- Peroxisomes take shape.Nature reviews. Molecular cell biology · 2013Review
Corrections and comments
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Authors and funding
13 authors.
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Abstract
Systems scale models provide the foundation for an effective iterative cycle between hypothesis generation, experiment and model refinement. Such models also enable predictions facilitating the understanding of biological complexity and the control of biological systems. Here, we demonstrate the reconstruction of a globally predictive gene regulatory model from public data: a model that can drive rational experiment design and reveal new regulatory mechanisms underlying responses to novel environments. Specifically, using ∼ 1500 publically available genome-wide transcriptome data sets from Saccharomyces cerevisiae, we have reconstructed an environment and gene regulatory influence network that accurately predicts regulatory mechanisms and gene expression changes on exposure of cells to completely novel environments. Focusing on transcriptional networks that induce peroxisomes biogenesis, the model-guided experiments allow us to expand a core regulatory network to include novel transcriptional influences and linkage across signaling and transcription. Thus, the approach and model provides a multi-scalar picture of gene dynamics and are powerful resources for exploiting extant data to rationally guide experimentation. The techniques outlined here are generally applicable to any biological system, which is especially important when experimental systems are challenging and samples are difficult and expensive to obtain-a common problem in laboratory animal and human studies.
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Registered trials
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