ArticlePLoS computational biology2007
A numerical approach to ion channel modelling using whole-cell voltage-clamp recordings and a genetic algorithm.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 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
35 citing papers in PubMed.
- Neuronal excitability and parameter variability in the Hodgkin-Huxley model.PLoS computational biology · 2026Article
- IonBench: A benchmark of optimisation strategies for mathematical models of ion channel currents.PLoS computational biology · 2025Article
- Kinetic and thermodynamic modeling of a voltage-gated sodium channel.European biophysics journal : EBJ · 2022Article
- NeuroGPU: Accelerating multi-compartment, biophysically detailed neuron simulations on GPUs.Journal of neuroscience methods · 2022Article
- Article
- Identification of structures for ion channel kinetic models.PLoS computational biology · 2021Article
- A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms.PLoS computational biology · 2020Article
- Four Ways to Fit an Ion Channel Model.Biophysical journal · 2019Article
- Phenomenological models of NaScientific reports · 2019Article
- Article
- Inversion and computational maturation of drug response using human stem cell derived cardiomyocytes in microphysiological systems.Scientific reports · 2018Article
- OpenWorm: overview and recent advances in integrative biological simulation ofPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- Estimating kinetic mechanisms with prior knowledge I: Linear parameter constraints.The Journal of general physiology · 2018Article
- Estimating kinetic mechanisms with prior knowledge II: Behavioral constraints and numerical tests.The Journal of general physiology · 2018Article
- A Heart for Diversity: Simulating Variability in Cardiac Arrhythmia Research.Frontiers in physiology · 2018Review
- Determinants of Isoform-Specific Gating Kinetics of hERG1 Channel: Combined Experimental and Simulation Study.Frontiers in physiology · 2018Article
- Parameter Optimization Using Covariance Matrix Adaptation-Evolutionary Strategy (CMA-ES), an Approach to Investigate Differences in Channel Properties Between Neuron Subtypes.Frontiers in neuroinformatics · 2018Article
- Is realistic neuronal modeling realistic?Journal of neurophysiology · 2016Review
- BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience.Frontiers in neuroinformatics · 2016Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The activity of trans-membrane proteins such as ion channels is the essence of neuronal transmission. The currently most accurate method for determining ion channel kinetic mechanisms is single-channel recording and analysis. Yet, the limitations and complexities in interpreting single-channel recordings discourage many physiologists from using them. Here we show that a genetic search algorithm in combination with a gradient descent algorithm can be used to fit whole-cell voltage-clamp data to kinetic models with a high degree of accuracy. Previously, ion channel stimulation traces were analyzed one at a time, the results of these analyses being combined to produce a picture of channel kinetics. Here the entire set of traces from all stimulation protocols are analysed simultaneously. The algorithm was initially tested on simulated current traces produced by several Hodgkin-Huxley-like and Markov chain models of voltage-gated potassium and sodium channels. Currents were also produced by simulating levels of noise expected from actual patch recordings. Finally, the algorithm was used for finding the kinetic parameters of several voltage-gated sodium and potassium channels models by matching its results to data recorded from layer 5 pyramidal neurons of the rat cortex in the nucleated outside-out patch configuration. The minimization scheme gives electrophysiologists a tool for reproducing and simulating voltage-gated ion channel kinetics at the cellular level.
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.