Dynamic Constrained Allocation Flux Balance Analysis (dCAFBA).

Huili Yuan, Yang Bai, Xiongfei Fu

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

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.

2 · The registry

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3 · Its place in the literature

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0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

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PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Huili YuanState Key Laboratory for Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China. hl.yuan@siat.ac.cn.

Yang BaiState Key Laboratory for Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.

Xiongfei FuState Key Laboratory for Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China. xiongfei.fu@siat.ac.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The survival of bacteria in dynamic environments depends on their ability to coordinate metabolism and gene expression. This interplay is fundamental: metabolism provides the energy and building blocks for protein synthesis, while the proteome, in turn, catalyzes and constrains metabolic fluxes. Here, we present a practical guide to dynamic Constrained Allocation Flux Balance Analysis (dCAFBA), a computational framework that integrates proteome allocation constraints with metabolic models to simulate this coordination. We provide step-by-step instructions for model construction, simulation, and analysis. The utility of dCAFBA is demonstrated through case studies of bacterial adaptation to carbon and amino acid shifts.

Indexed as

BacteriaMetabolic Flux AnalysisProteomeAmino AcidsCarbonComputer SimulationMetabolic Networks and PathwaysModels, BiologicalAmino AcidsCarbonProteomeBacterial growth lawsChanging environmentConstraint-based modelingDynamic flux balance analysis (dFBA)Metabolic flux dynamicsProteome allocation

Identifiers

PMID42420740

DOI10.1038/s41564-022-01310-w

What Socratic holds

Textmetadata

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Registered trials

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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 Socratic graph.