ReviewFrontiers in molecular biosciences2016
Constraint Based Modeling Going Multicellular.
Review in Frontiers in molecular biosciences, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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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.
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Who cites it
23 citing papers in PubMed, 50 citations in OpenAlex.
- MEBOCOST maps metabolite-mediated intercellular communications using single-cell RNA-seq.Nucleic acids research · 2025Article
- Review
- Machine learning methods for predicting essential metabolic genes from Plasmodium falciparum genome-scale metabolic network.PloS one · 2024Article
- Development and applications of metabolic models in plant multi-omics research.Frontiers in plant science · 2024Review
- Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine.Metabolites · 2023Review
- Article
- The unraveling of balanced complexes in metabolic networks.Scientific reports · 2023Article
- A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale.PLoS computational biology · 2022Article
- Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer.Frontiers in oncology · 2022Review
- Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism.BMC bioinformatics · 2021Article
- Metabolic modelling approaches for describing and engineering microbial communities.Computational and structural biotechnology journal · 2021Review
- Advances in flux balance analysis by integrating machine learning and mechanism-based models.Computational and structural biotechnology journal · 2021Review
- FlySilico: Flux balance modeling of Drosophila larval growth and resource allocation.Scientific reports · 2019Article
- Metabolic modelling of chronic wound microbiota predicts mutualistic interactions that drive community composition.Journal of applied microbiology · 2019Article
- Homeostasis and systematic ageing as non-equilibrium phase transitions in computational multicellular organizations.Royal Society open science · 2019Article
- Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.Nature protocols · 2019Article
- Integration of single-cell RNA-seq data into population models to characterize cancer metabolism.PLoS computational biology · 2019Article
- Putting primary metabolism into perspective to obtain better fruits.Annals of botany · 2018Review
- Systems approaches in osteoarthritis: Identifying routes to novel diagnostic and therapeutic strategies.Journal of orthopaedic research : official publication of the Orthopaedic Research Society · 2017Article
- Advances on plant-pathogen interactions from molecular toward systems biology perspectives.The Plant journal : for cell and molecular biology · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Constraint based modeling has seen applications in many microorganisms. For example, there are now established methods to determine potential genetic modifications and external interventions to increase the efficiency of microbial strains in chemical production pipelines. In addition, multiple models of multicellular organisms have been created including plants and humans. While initially the focus here was on modeling individual cell types of the multicellular organism, this focus recently started to switch. Models of microbial communities, as well as multi-tissue models of higher organisms have been constructed. These models thereby can include different parts of a plant, like root, stem, or different tissue types in the same organ. Such models can elucidate details of the interplay between symbiotic organisms, as well as the concerted efforts of multiple tissues and can be applied to analyse the effects of drugs or mutations on a more systemic level. In this review we give an overview of the recent development of multi-tissue models using constraint based techniques and the methods employed when investigating these models. We further highlight advances in combining constraint based models with dynamic and regulatory information and give an overview of these types of hybrid or multi-level approaches.
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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.