ArticleProceedings of the National Academy of Sciences of the United States of America2005
Using independent open-to-closed transitions to simplify aggregated Markov models of ion channel gating kinetics.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 41 papers.
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41 citing papers in PubMed.
- Modelling ion channels with a view towards identifiability.Bulletin of mathematical biology · 2025Article
- Biological physics to uncover cell signaling.Biophysical reviews · 2025Review
- A deep learning approach to real-time Markov modeling of ion channel gating.Communications chemistry · 2024Article
- Identification of structures for ion channel kinetic models.PLoS computational biology · 2021Article
- Inferring phenomenological models of first passage processes.PLoS computational biology · 2021Article
- Article
- Bayesian-Estimated Hierarchical HMMs Enable Robust Analysis of Single-Molecule Kinetic Heterogeneity.Biophysical journal · 2019Article
- Stochastic shielding and edge importance for Markov chains with timescale separation.PLoS computational biology · 2018Article
- Efficient use of single molecule time traces to resolve kinetic rates, models and uncertainties.The Journal of chemical physics · 2018Article
- Estimating kinetic mechanisms with prior knowledge II: Behavioral constraints and numerical tests.The Journal of general physiology · 2018Article
- Estimating kinetic mechanisms with prior knowledge I: Linear parameter constraints.The Journal of general physiology · 2018Article
- Single-Molecule Analysis beyond Dwell Times: Demonstration and Assessment in and out of Equilibrium.Biophysical journal · 2016Article
- Modelling modal gating of ion channels with hierarchical Markov models.Proceedings. Mathematical, physical, and engineering sciences · 2016Article
- Bayesian Statistical Inference in Ion-Channel Models with Exact Missed Event Correction.Biophysical journal · 2016Article
- Analyzing and Quantifying the Gain-of-Function Enhancement of IP3 Receptor Gating by Familial Alzheimer's Disease-Causing Mutants in Presenilins.PLoS computational biology · 2015Article
- Analyzing single-molecule time series via nonparametric Bayesian inference.Biophysical journal · 2015Article
- Analyzing and Modeling the Kinetics of Amyloid Beta Pores Associated with Alzheimer's Disease Pathology.PloS one · 2015Article
- Dynamic disorder and the energetic costs of information transduction.The Journal of chemical physics · 2014Article
- Measuring edge importance: a quantitative analysis of the stochastic shielding approximation for random processes on graphs.Journal of mathematical neuroscience · 2014Article
- Determination of parameter identifiability in nonlinear biophysical models: A Bayesian approach.The Journal of general physiology · 2014Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
Deducing plausible reaction schemes from single-channel current traces is time-consuming and difficult. The goal is to find the simplest scheme that fits the data, but there are many ways to connect even a small number of states (>2 million schemes with four open and four closed states). Many schemes make identical predictions. An exhaustive search over model space does not address the many equivalent schemes that will result. We have found a canonical form that can express all reaction schemes for binary channels. This form has the minimal number of rate constants for any rank (number of independent open-closed transitions), unlike other canonical forms such as the well established "uncoupled" scheme. Because all of the interconductance transitions in the new form are independent, we refer to it as the manifest interconductance rank (MIR) form. In the case of four open and four closed states, there are four MIR form schemes, corresponding to ranks 1-4. For many models proposed in the literature for specific ion channels, the equivalent MIR form has dramatically fewer links than the uncoupled form. By using the MIR form we prove that all rank 1 topologies with a given number of open and closed states make identical predictions in steady state, thus narrowing the search space for simple models. Moreover, we prove that fitting to canonical form preserves detailed balance. We also propose an efficient hierarchical algorithm for searching for the simplest possible model consistent with a given data set.
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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 OpenQuestion graph.