ArticlePLoS computational biology2016
Reconstruction of Tissue-Specific Metabolic Networks Using CORDA.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers, 1 of them a synthesis that pooled it.
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Who cites it
78 citing papers in PubMed, 1 synthesis or guideline pooled it, 155 citations in OpenAlex.
- Preclinical techniques to investigate exercise training in vascular pathophysiology.American journal of physiology. Heart and circulatory physiology · 2021Pooled it
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- Flux sampling and context-specific genome-scale metabolic models for biotechnological applications.Trends in biotechnology · 2026Review
- Metabolic modeling and functional genomics reveal taxa and host gene interactions in colorectal cancer.bioRxiv : the preprint server for biology · 2026Article
- Modeling tissue-specific Drosophila metabolism identifies high sugar diet-induced metabolic dysregulation in muscle at reaction and pathway levels.Nature communications · 2026Article
- Modelling reliable metabolic phenotypes by analysing the context-specific transcriptomics data.NPJ systems biology and applications · 2025Article
- Metabolic network analysis of Crohn's disease reveals sex- and age-specific cellular phenotypes.Cell systems · 2025Article
- Neuronal subtype-specific metabolic changes in neurodegenerative and neuropsychiatric diseases predicted via a systems biology-based approach.bioRxiv : the preprint server for biology · 2025Article
- Gene-Embedded Multi-Modal Networks for Population-Scale Multi-Omics Discovery.bioRxiv : the preprint server for biology · 2025Article
- Understanding disease-associated metabolic changes in human colonic epithelial cells using the iColonEpithelium metabolic reconstruction.PLoS computational biology · 2025Article
- Temporal analysis of doxorubicin-induced cardiac toxicity and hypertrophy.NPJ systems biology and applications · 2025Article
- Genome-scale models in human metabologenomics.Nature reviews. Genetics · 2025Review
- Wheels turning: CHO cell modeling moves into a digital biomanufacturing era: Subtitle: CHO Metabolic Modeling.Computational and structural biotechnology journal · 2025Review
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- Modelling energy metabolism dysregulations in neuromuscular diseases: A case study of calpainopathy.Heliyon · 2024Article
- Intratumoral Heterogeneity and Metabolic Cross-Feeding in a Three-Dimensional Breast Cancer Culture: An In Silico Perspective.International journal of molecular sciences · 2024Article
- Driving towards digital biomanufacturing by CHO genome-scale models.Trends in biotechnology · 2024Review
- Identification of Anticancer Enzymes and Biomarkers for Hepatocellular Carcinoma through Constraint-Based Modeling.Molecules (Basel, Switzerland) · 2024Article
- "Energetics of the outer retina I: Estimates of nutrient exchange and ATP generation".PloS one · 2024Article
- State-of the-Art Constraint-Based Modeling of Microbial Metabolism: From Basics to Context-Specific Models with a Focus on Methanotrophs.Microorganisms · 2023Review
18 more citing papers are in PubMed but not listed here.
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2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Human metabolism involves thousands of reactions and metabolites. To interpret this complexity, computational modeling becomes an essential experimental tool. One of the most popular techniques to study human metabolism as a whole is genome scale modeling. A key challenge to applying genome scale modeling is identifying critical metabolic reactions across diverse human tissues. Here we introduce a novel algorithm called Cost Optimization Reaction Dependency Assessment (CORDA) to build genome scale models in a tissue-specific manner. CORDA performs more efficiently computationally, shows better agreement to experimental data, and displays better model functionality and capacity when compared to previous algorithms. CORDA also returns reaction associations that can greatly assist in any manual curation to be performed following the automated reconstruction process. Using CORDA, we developed a library of 76 healthy and 20 cancer tissue-specific reconstructions. These reconstructions identified which metabolic pathways are shared across diverse human tissues. Moreover, we identified changes in reactions and pathways that are differentially included and present different capacity profiles in cancer compared to healthy tissues, including up-regulation of folate metabolism, the down-regulation of thiamine metabolism, and tight regulation of oxidative phosphorylation.
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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.