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4P-algorithm to segment single particle trajectories

Authors: Shukron, Ofir; Holcman, David;

4P-algorithm to segment single particle trajectories

Abstract

Introduction: We present here a new algorithm to classify single particle trajectoties into confined and unconfined. The algorithm uses live-cell 3D single-molecule tracking of NuRD complex at any temporal regimes, such as 20 ms and 500 ms. Method: The algorithm relies on machine learning method (a Gaussian mixture model) to segment the single molecule trajectories into different classes by studying their behaviour over a sliding window of several consecutive images. The algorthim was designed to analyse the nucleosome remodelling and deacetylase (NuRD) complex, a highly conserved 1 MDa multi-subunit protein complex which binds to all active enhancers. Results: The algorithm allows to estimate from each sub-trajectory the 1-apparent diffusion coefficient, 2-but also the anomalous exponent a, 3-the localisation length Lc, and 4-the drift magnitude V (fig.1a). The anomalous exponent a (from the mean squared displacement), is particularly informative. Reference: The algorithm is part of the publication,https://www.biorxiv.org/content/10.1101/2020.04.03.003178v2 Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics by S Basu et al. This article is with minor revisions in Nature structural and molecular biology 2022. The final reference will be added once the publication is accepted.

Keywords

SPTs, Gaussian Mixture model, diffusion, anomalous diffusion, segmentation, length of constrain, velocity, nucleus, NURD, chromatin

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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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