wannesm/dtaidistance v2.0.0

Meert, Wannes; Hendrickx, Kilian; Craenendonck, Toon Van

doi:10.5281/zenodo.3981067

Cited by 10 publications

(5 citation statements)

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“…The mid-point of these maximas were defined as nucleosome dyads. The K -mean algorithm ( K = 2) based on dynamic time warping distances ( 23 ) was employed to clusterized the called dyads into well-positioned and poorly-positioned. Concretely, clustering used as input signals encompassing the 1 kb convolved profile upstream and downstream of each called dyad.…”

Section: Methodsmentioning

confidence: 99%

Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing

Leduque,

Edera,

Vitte

et al. 2024

Nucleic Acids Research

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Epigenetic regulations, including chromatin accessibility, nucleosome positioning and DNA methylation intricately shape genome function. However, current chromatin profiling techniques relying on short-read sequencing technologies fail to characterise highly repetitive genomic regions and cannot detect multiple chromatin features simultaneously. Here, we performed Simultaneous Accessibility and DNA Methylation Sequencing (SAM-seq) of purified plant nuclei. Thanks to the use of long-read nanopore sequencing, SAM-seq enables high-resolution profiling of m6A-tagged chromatin accessibility together with endogenous cytosine methylation in plants. Analysis of naked genomic DNA revealed significant sequence preference biases of m6A-MTases, controllable through a normalisation step. By applying SAM-seq to Arabidopsis and maize nuclei we obtained fine-grained accessibility and DNA methylation landscapes genome-wide. We uncovered crosstalk between chromatin accessibility and DNA methylation within nucleosomes of genes, TEs, and centromeric repeats. SAM-seq also detects DNA footprints over cis-regulatory regions. Furthermore, using the single-molecule information provided by SAM-seq we identified extensive cellular heterogeneity at chromatin domains with antagonistic chromatin marks, suggesting that bivalency reflects cell-specific regulations. SAM-seq is a powerful approach to simultaneously study multiple epigenetic features over unique and repetitive sequences, opening new opportunities for the investigation of epigenetic mechanisms.

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Section: Methodsmentioning

confidence: 99%

Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing

Leduque,

Edera,

Vitte

et al. 2024

Nucleic Acids Research

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“…IVESA provides configuration elements for all three parameter types of the motion retrieval algorithm (b). First, to account for different notions of similarity in the retrieval process, users can switch between two distance/similarity measures: Euclidean distance and dynamic time warping (implementation by Meert et al [72]). Second, a parameter to steer the kernel of the retrieval algorithm, i.e., the type of sliding windowing strategy applied to retrieve motifs.…”

Section: Motif Viewmentioning

confidence: 99%

IVESA - Visual Analysis of Time-Stamped Event Sequences

Bernard,

Barth,

Cuba

et al. 2024

IEEE Trans. Visual. Comput. Graphics

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Fig. 1. Overview of IVESA. On the left, the Sequence Overview and Details View primarily enable the analysis of the TSEQs content, i.e., events, event sequences, groups of event sequences, motifs, and features. On the right, the Metadata View supports the analysis of metadata attributes and the TSEQs contextualization, whereas the Summary View includes the entry point to auxiliary views for filtering, motif configuration, feature analysis, and clustering.

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“…This applies to this case, given that, sometimes, the rPPG and its ground truth are not aligned, so other metrics that match timestamps are less suitable. The Python package DTAIDistance (Meert et al, 2020) was used to implement the metric.…”

Section: Dtwmentioning

confidence: 99%

Evaluating RGB channels in remote photoplethysmography: a comparative study with contact-based PPG

Ontiveros,

Elgendi,

Missale

et al. 2023

Front. Physiol.

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Remote photoplethysmography (rPPG) provides a non-contact method for measuring blood volume changes. In this study, we compared rPPG signals obtained from video cameras with traditional contact-based photoplethysmography (cPPG) to assess the effectiveness of different RGB channels in cardiac signal extraction. Our objective was to determine the most effective RGB channel for detecting blood volume changes and estimating heart rate. We employed dynamic time warping, Pearson’s correlation coefficient, root-mean-square error, and Beats-per-minute Difference to evaluate the performance of each RGB channel relative to cPPG. The results revealed that the green channel was superior, outperforming the blue and red channels in detecting volumetric changes and accurately estimating heart rate across various activities. We also observed that the reliability of RGB signals varied based on recording conditions and subject activity. This finding underscores the importance of understanding the performance nuances of RGB inputs, crucial for constructing rPPG signals in algorithms. Our study is significant in advancing rPPG research, offering insights that could benefit clinical applications by improving non-contact methods for blood volume assessment.

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wannesm/dtaidistance v2.0.0

Cited by 10 publications

References 0 publications

Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing

Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing

IVESA - Visual Analysis of Time-Stamped Event Sequences

Evaluating RGB channels in remote photoplethysmography: a comparative study with contact-based PPG

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