ReviewNPJ systems biology and applications2016
Synthetic and systems biology for microbial production of commodity chemicals.
Review in NPJ systems biology and applications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 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
72 citing papers in PubMed, 240 citations in OpenAlex.
- One-pot bioprocessing: dynamics and opportunities for integrated multiproduct recovery-a review.Bioprocess and biosystems engineering · 2026Review
- A standardized workflow for kinetic metabolic model curation and dissemination.PLoS computational biology · 2026Article
- Dynamics of genetic circuits in Pseudomonas protegens.Cell systems · 2026Article
- A highly active Burkholderia polyketoacyl-CoA thiolase for production of triacetic acid lactone.Nature communications · 2025Article
- Metabolic engineering ofBiodesign research · 2025Article
- Article
- Engineering biology applications for environmental solutions: potential and challenges.Nature communications · 2025Review
- Injectable microgels containing genetically engineered bacteria for colon cancer therapy through programmed Chemokine expression.Materials today. Bio · 2024Article
- Microbial Squalene: A Sustainable Alternative for the Cosmetics and Pharmaceutical Industry - A Review.Engineering in life sciences · 2024Review
- Data-driven learning of structure augments quantitative prediction of biological responses.PLoS computational biology · 2024Article
- State-of the-Art Constraint-Based Modeling of Microbial Metabolism: From Basics to Context-Specific Models with a Focus on Methanotrophs.Microorganisms · 2023Review
- Recent Challenges and Trends of Polyhydroxyalkanoate Production by Extremophilic Bacteria Using Renewable Feedstocks.Polymers · 2023Review
- BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale.PLoS computational biology · 2023Article
- A cellular platform for production of CChemical science · 2023Article
- Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch.Journal of molecular evolution · 2023Article
- Bridging the gap between mechanistic biological models and machine learning surrogates.PLoS computational biology · 2023Review
- Optimizing the strain engineering process for industrial-scale production of bio-based molecules.Journal of industrial microbiology & biotechnology · 2023Review
- Microbial Production of Human Milk Oligosaccharides.Molecules (Basel, Switzerland) · 2023Review
- Dynamic feedback regulation for efficient membrane protein production using a small RNA-based genetic circuit in Escherichia coli.Microbial cell factories · 2022Article
- Stabilization of antithetic control via molecular buffering.Journal of the Royal Society, Interface · 2022Article
12 more citing papers are in PubMed but not listed here.
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 at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.
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.