Florian Pein: Model free idealisation of patchclamp recordings
Channel: NorthWestBiomathsDataScienceSeminars
Date: 2021-03-03

North West Seminar Series of Mathematical Biology and Data Science 

Wednesday, 10th February 2021 (hosted by Ivo Siekmann) 

https://www.cms.livjm.ac.uk/APMSeminar/


Abstract:
The voltage patchclamp technique is a fundamental tool for the quantitative analysis of electrophysiological processes of transmembrane proteins, in particular of ion channels. Analysis of patchclamp recordings is often a challenging issue. In this talk we present a very general non-parametric model for such recordings. Based on this model we provide fully automatic model-free idealisation methods or in statistical words non-parametric estimation methods. Patchclamp recordings are typically lowpass filtered to suppress high-frequent noise components. Hence, a major point of our approaches is to take the filtering into account explicitly.
In a second step, we show how idealisations allowing us to obtain biochemical relevant information about the underlying gating dynamics. Finally, we discuss advantages and disadvantages of model-free approaches in comparison to hidden Markov model approaches and explain how they complement each other. Our methods are available as an R-package and as a graphical user interface.

Publications:

Analysis of Patchclamp Recordings: Model-Free Multiscale Methods and 
Software
F Pein, B Eltzner, A Munk; European Biophysics Journal, accepted
(2021) https://cran.uni-muenster.de/web/packages/clampSeg/vignettes/Vignette.pdf

Heterogeneous Idealization of Ion Channel Recordings – Open Channel 
Noise
F Pein, A Bartsch, C Steinem, A Munk; IEEE Transactions on 
NanoBioscience
(2021) 20, 57 (DOI: 10.1109/TNB.2020.3031202)

Fully Automatic Multiresolution Idealization for Filtered Ion Channel 
Recordings: Flickering Event Detection.
F Pein, I Tecuapetla-Gomez, OM Schutte, C Steinem, A Munk; IEEE 
Transactions on NanoBioscience
(2018) 17, 300 (DOI: 10.1109/TNB.2018.2845126