ArticlePLoS computational biology2015
Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 73 citations in OpenAlex.
- A Roadmap for the Future of Systems Biology in Cancer Research.Cancer research · 2025Review
- Technologies for whole-cell modeling: Genome-wide reconstruction of a cell in silico.Development, growth & differentiation · 2023Review
- The E. coli Whole-Cell Modeling Project.EcoSal Plus · 2021Article
- Multi-model and network inference based on ensemble estimates: avoiding the madness of crowds.Journal of the Royal Society, Interface · 2020Article
- A compiler for biological networks on silicon chips.PLoS computational biology · 2020Article
- Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology.Frontiers in bioengineering and biotechnology · 2020Article
- Metabolic Modeling of Microbial Community Interactions for Health, Environmental and Biotechnological Applications.Current genomics · 2018Review
- Defining informative priors for ensemble modeling in systems biology.Nature protocols · 2018Article
- Emerging whole-cell modeling principles and methods.Current opinion in biotechnology · 2018Review
- An integrative method to decode regulatory logics in gene transcription.Nature communications · 2017Article
- How to deal with parameters for whole-cell modelling.Journal of the Royal Society, Interface · 2017Review
- Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy.BMC bioinformatics · 2017Article
- Evolvix BEST Names for semantic reproducibility across code2brain interfaces.Annals of the New York Academy of Sciences · 2017Review
- Toward Community Standards and Software for Whole-Cell Modeling.IEEE transactions on bio-medical engineering · 2016Article
- Structural Identifiability of Dynamic Systems Biology Models.PLoS computational biology · 2016Article
- Quantifying differences in cell line population dynamics using CellPD.BMC systems biology · 2016Article
- Potentials of single-cell biology in identification and validation of disease biomarkers.Journal of cellular and molecular medicine · 2016Review
- A Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networks.PloS one · 2016Article
- DREAMTools: a Python package for scoring collaborative challenges.F1000Research · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 6 institutions in 2 countries.
Funding
Abstract
Whole-cell models that explicitly represent all cellular components at the molecular level have the potential to predict phenotype from genotype. However, even for simple bacteria, whole-cell models will contain thousands of parameters, many of which are poorly characterized or unknown. New algorithms are needed to estimate these parameters and enable researchers to build increasingly comprehensive models. We organized the Dialogue for Reverse Engineering Assessments and Methods (DREAM) 8 Whole-Cell Parameter Estimation Challenge to develop new parameter estimation algorithms for whole-cell models. We asked participants to identify a subset of parameters of a whole-cell model given the model's structure and in silico "experimental" data. Here we describe the challenge, the best performing methods, and new insights into the identifiability of whole-cell models. We also describe several valuable lessons we learned toward improving future challenges. Going forward, we believe that collaborative efforts supported by inexpensive cloud computing have the potential to solve whole-cell model parameter estimation.
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.