ReviewMetabolic engineering2012
Computational tools for metabolic engineering.
Review in Metabolic engineering, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
27 citing papers in PubMed.
- A constraint-based framework for exploring the impact of multireaction dependencies on metabolic functions.NPJ systems biology and applications · 2025Article
- Computational tools for nonnatural pathway design: Algorithms, applications, and challenges.Biodesign research · 2025Review
- Evolutionary engineering ofScience advances · 2024Article
- Shu: visualization of high-dimensional biological pathways.Bioinformatics (Oxford, England) · 2024Article
- Biomarker enrichment medium: A defined medium for metabolomic analysis of microbial pathogens.Frontiers in microbiology · 2022Article
- Biosynthesis and synthetic biology of psychoactive natural products.Chemical Society reviews · 2021Review
- Publishing reproducible dynamic kinetic models.Briefings in bioinformatics · 2021Article
- Lipid Traffic Analysis reveals the impact of high paternal carbohydrate intake on offsprings' lipid metabolism.Communications biology · 2021Article
- Design of a heme-binding peptide motif adopting a β-hairpin conformation.The Journal of biological chemistry · 2018Article
- Rewriting the Metabolic Blueprint: Advances in Pathway Diversification in Microorganisms.Frontiers in microbiology · 2018Review
- Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes.PloS one · 2018Article
- EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model.Scientific reports · 2017Article
- Mimoza: web-based semantic zooming and navigation in metabolic networks.BMC systems biology · 2015Article
- Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants.Frontiers in bioengineering and biotechnology · 2015Review
- Cell-free metabolic engineering: biomanufacturing beyond the cell.Biotechnology journal · 2015Review
- Simultaneous parameters identifiability and estimation of an E. coli metabolic network model.BioMed research international · 2015Article
- Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam.BMC evolutionary biology · 2014Article
- Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering.The Plant cell · 2014Review
- Enhancing microbial metabolite and enzyme production: current strategies and challenges.Frontiers in microbiology · 2014Article
- Predictive sulfur metabolism - a field in flux.Frontiers in plant science · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
A great variety of software applications are now employed in the metabolic engineering field. These applications have been created to support a wide range of experimental and analysis techniques. Computational tools are utilized throughout the metabolic engineering workflow to extract and interpret relevant information from large data sets, to present complex models in a more manageable form, and to propose efficient network design strategies. In this review, we present a number of tools that can assist in modifying and understanding cellular metabolic networks. The review covers seven areas of relevance to metabolic engineers. These include metabolic reconstruction efforts, network visualization, nucleic acid and protein engineering, metabolic flux analysis, pathway prospecting, post-structural network analysis and culture optimization. The list of available tools is extensive and we can only highlight a small, representative portion of the tools from each area.
Indexed as
Identifiers
What OpenQuestion holds
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.