ArticleNature communications2012
In silico method for modelling metabolism and gene product expression at genome scale.
Article in Nature communications, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 135 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
135 citing papers in PubMed, 291 citations in OpenAlex.
- Predictive Algal Systems Biology: Integrating Omics, Genome-Scale Metabolic Models, and Machine Learning.Bioengineering (Basel, Switzerland) · 2026Review
- Gut microbiota dysbiosis: Pathogenic drivers and emerging phage-based therapeutics.AIMS microbiology · 2026Review
- A voyage of reprogrammable metabolic bioengineering reshapes plant defense: from editing tools to synthetic systems.Frontiers in plant science · 2026Review
- Novel African American Colorectal CancerHuman mutation · 2026Article
- Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida.NPJ systems biology and applications · 2025Article
- New insights in metabolism modelling to decipher plant-microbe interactions.The New phytologist · 2025Review
- Integration of metatranscriptomics data improves the predictive capacity of microbial community metabolic models.The ISME journal · 2025Article
- Digital twins in healthcare: a comprehensive review and future directions.Frontiers in digital health · 2025Review
- Modelling energy metabolism dysregulations in neuromuscular diseases: A case study of calpainopathy.Heliyon · 2024Article
- Integration of proteomic data with genome-scale metabolic models: A methodological overview.Protein science : a publication of the Protein Society · 2024Review
- Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective.Metabolites · 2024Review
- Article
- Genome-scale metabolic modelling of extremophiles and its applications in astrobiological environments.Environmental microbiology reports · 2024Review
- Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states.Nature catalysis · 2024Article
- From observational to actionable: rethinking omics in biologics production.Trends in biotechnology · 2023Review
- The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions.PLoS computational biology · 2023Article
- Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution.Nature communications · 2023Article
- Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning.Nature communications · 2023Article
- Data integration across conditions improves turnover number estimates and metabolic predictions.Nature communications · 2023Article
- Systematizing Microbial Bioplastic Production for Developing Sustainable Bioeconomy: Metabolic Nexus Modeling, Economic and Environmental Technologies Assessment.Journal of polymers and the environment · 2023Review
75 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
11 authors at 2 institutions in 1 country.
Funding
Abstract
Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.
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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.