ReviewFrontiers in microbiology2015
Data-driven integration of genome-scale regulatory and metabolic network models.
Review in Frontiers in microbiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed.
- The Evolution of Systems Biology and Systems Medicine: From Mechanistic Models to Uncertainty Quantification.Annual review of biomedical engineering · 2025Review
- Genetic epidemiology of resistance to M. tuberculosis Infection: importance of study design and recent findings.Genes and immunity · 2023Review
- Systems biology platform for efficient development and translation of multitargeted therapeutics.Frontiers in systems biology · 2023Article
- Exploring the expressiveness of abstract metabolic networks.PloS one · 2023Article
- Review
- Article
- SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.Bioinformatics (Oxford, England) · 2021Article
- Advances in flux balance analysis by integrating machine learning and mechanism-based models.Computational and structural biotechnology journal · 2021Review
- Article
- Metabolic modelling of chronic wound microbiota predicts mutualistic interactions that drive community composition.Journal of applied microbiology · 2019Article
- Perspective: Dimensions of the scientific method.PLoS computational biology · 2019Article
- Distribution of fitness effects of mutations obtained from a simple genetic regulatory network model.Scientific reports · 2019Article
- Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis.Bioinformatics (Oxford, England) · 2019Article
- A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli.PLoS computational biology · 2019Article
- OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling.PLoS computational biology · 2019Article
- Co-expression network analysis and cis-regulatory element enrichment determine putative functions and regulatory mechanisms of grapevine ATL E3 ubiquitin ligases.Scientific reports · 2018Article
- The Genome-Scale Integrated Networks in Microorganisms.Frontiers in microbiology · 2018Review
- redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models.PLoS computational biology · 2017Article
- SBMLmod: a Python-based web application and web service for efficient data integration and model simulation.BMC bioinformatics · 2017Article
- Inhibition of expression of the circadian clock gene Period causes metabolic abnormalities including repression of glycometabolism in Bombyx mori cells.Scientific reports · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription, and signaling) have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert-a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. In this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.