{
  "abstract": "Whole-cell models serve as powerful tools to predict cellular phenotype from genotype by integrating genome-scale processes within a single computational framework. Single-gene knockout (KO) growth is a stringent benchmark, but comparisons to experimental resources require close alignment of assay conditions, especially temperature and growth medium. We benchmark an Escherichia coli (E. coli) whole-cell model by simulating multi-generation single-gene KOs in glucose minimal and amino-acid–supplemented media at 37 °C and by analyzing two independent eight-generation KO cohorts. For each KO we estimated generation-specific growth rates and harmonic-mean summaries across early generations. Experimental KO growth rates measured at 30°C were converted to s−1 and scaled to 37°C using an explicit Q10 correction Essential versus nonessential effects were tested using Welch’s t comparisons with 95% confidence intervals based on the Welch–Satterthwaite t approximation, and false discovery rate control across generations. Cross-medium generalization was evaluated using correlations and stratified regression for further prediction. Temperature adjustment shifted the experimental growth-rate distribution toward the simulated distribution. Essential KOs showed lower growth in the earliest generations, while the two eight-generation cohorts exhibited an overall decline in mean growth with substantial heterogeneity. Cross-medium correlations were weak, and in the held-out predictive comparison the global linear model achieved lower RMSE than the stratified SVR.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "case report",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "name": "Jiaqi Wei"
    },
    {
      "name": "Weiping Lin",
      "orcid": "0000-0002-8772-3919"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/5wyjthrh0jnex.bib",
  "cited_by": 0,
  "doi": "10.1093/bib/bbag344",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13712503/",
  "id": "5wyjthrh0jnex",
  "issns": [
    "1467-5463",
    "1477-4054"
  ],
  "landing_url": "https://doi.org/10.1093/bib/bbag344",
  "language": "en",
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "AcademicSubjects/SCI01060"
    ],
    [
      "heading",
      "Case Study"
    ],
    [
      "openalex",
      "1312|Microbial Metabolic Engineering and Bioproduction"
    ]
  ],
  "openalex": "W7223986000",
  "pdf_url": null,
  "pmcid": "PMC13712503",
  "pmid": "42946396",
  "published": "2026-10-27",
  "publisher": "Oxford University Press",
  "ris": "https://research.draconitic.com/paper/5wyjthrh0jnex.ris",
  "sources": [
    {
      "first_seen": "2026-10-31T12:23:04Z",
      "native_id": "PMC13712503",
      "source": "pmc",
      "url": "https://doi.org/10.1093/bib/bbag344"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Microbial Metabolic Engineering and Bioproduction",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Single-gene knockout analysis in an Escherichia coli whole-cell model reveals medium, temperature, and generational effects on growth",
  "title_text": "Single-gene knockout analysis in an Escherichia coli whole-cell model reveals medium, temperature, and generational effects on growth",
  "type": "peer-reviewed",
  "updated_at": "2026-10-31T12:23:04Z",
  "url": "https://research.draconitic.com/paper/5wyjthrh0jnex",
  "venue": "Briefings in Bioinformatics",
  "versions": []
}