ReviewCurrent opinion in biotechnology2014
The future of whole-cell modeling.
Review in Current opinion in biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 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
41 citing papers in PubMed.
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- Development of specialized devices for microbial experimental evolution.Development, growth & differentiation · 2024Review
- A comprehensive review of computational cell cycle models in guiding cancer treatment strategies.NPJ systems biology and applications · 2024Review
- Technologies for whole-cell modeling: Genome-wide reconstruction of a cell in silico.Development, growth & differentiation · 2023Review
- Surveying membrane landscapes: a new look at the bacterial cell surface.Nature reviews. Microbiology · 2023Review
- Bridging the gap between mechanistic biological models and machine learning surrogates.PLoS computational biology · 2023Review
- Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format.Bioinformatics advances · 2023Article
- Molecular dynamics simulation of an entire cell.Frontiers in chemistry · 2023Article
- Integrative modeling of the cell.Acta biochimica et biophysica Sinica · 2022Review
- Genome-scale metabolic network models: from first-generation to next-generation.Applied microbiology and biotechnology · 2022Review
- Impact of Influenza A Virus Infection on Growth and Metabolism of Suspension MDCK Cells Using a Dynamic Model.Metabolites · 2022Article
- A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics.Nature communications · 2021Article
- A forecast for large-scale, predictive biology: Lessons from meteorology.Cell systems · 2021Review
- Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data.Frontiers in molecular biosciences · 2021Review
- Art and Science of the Cellular Mesoscale.Trends in biochemical sciences · 2020Review
- Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology.Frontiers in bioengineering and biotechnology · 2020Article
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- Scalable nonlinear programming framework for parameter estimation in dynamic biological system models.PLoS computational biology · 2019Article
- Perspective: The promise of multi-cellular engineered living systems.APL bioengineering · 2018Article
- Emerging whole-cell modeling principles and methods.Current opinion in biotechnology · 2018Review
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.
Funding
Abstract
Integrated whole-cell modeling is poised to make a dramatic impact on molecular and systems biology, bioengineering, and medicine--once certain obstacles are overcome. From our group's experience building a whole-cell model of Mycoplasma genitalium, we identified several significant challenges to building models of more complex cells. Here we review and discuss these challenges in seven areas: first, experimental interrogation; second, data curation; third, model building and integration; fourth, accelerated computation; fifth, analysis and visualization; sixth, model validation; and seventh, collaboration and community development. Surmounting these challenges will require the cooperation of an interdisciplinary group of researchers to create increasingly sophisticated whole-cell models and make data, models, and simulations more accessible to the wider community.
Indexed as
Identifiers
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.