Similarity-Based Segmentation of Multi-Dimensional Signals

Machné, Rainer; Murray, Douglas B.; Stadler, Peter F.

doi:10.1038/s41598-017-12401-8

Cited by 21 publications

(39 citation statements)

References 52 publications

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“…Additionally, segmentation of multidimensional RNA-sequence time-series using Fourier and model-based clustering has been developed and integrated into all analyses. 112 The gas exchange kinetics in fermenters has been modeled with the help of Stephan Müller, thereby providing improved estimations of oxygen uptake dynamics and insights into the parameters necessary for efficient microbial growth. 57 11 State of the Art and Retrospective Over a Half-Century…”

Section: Further Analytical Refinements At the University Of Vienna Amentioning

confidence: 99%

Temporal metabolic partitioning of the yeast and protist cellular networks: the cell is a global scale-invariant (fractal or self-similar) multioscillator

et al. 2018

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Britton Chance, electronics expert when a teenager, became an enthusiastic student of biological oscillations, passing on this enthusiasm to many students and colleagues, including one of us (DL). This historical essay traces BC's influence through the accumulated work of DL to DL's many collaborators. The overall temporal organization of mass-energy, information, and signaling networks in yeast in self-synchronized continuous cultures represents, until now, the most characterized example of in vivo elucidation of time structure. Continuous online monitoring of dissolved gases by direct measurement (membrane-inlet mass spectrometry, together with NAD(P)H and flavin fluorescence) gives strain-specific dynamic information from timescales of minutes to hours as does two-photon imaging. The predominantly oscillatory behavior of network components becomes evident, with spontaneously synchronized cellular respiration cycles between discrete periods of increased oxygen consumption (oxidative phase) and decreased oxygen consumption (reductive phase). This temperature-compensated ultradian clock provides coordination, linking temporally partitioned functions by direct feedback loops between the energetic and redox state of the cell and its growing ultrastructure. Multioscillatory outputs in dissolved gases with 13 h, 40 min, and 4 min periods gave statistical self-similarity in power spectral and relative dispersional analyses: i.e., complex nonlinear (chaotic) behavior and a functional scale-free (fractal) network operating simultaneously over several timescales.

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Section: Further Analytical Refinements At the University Of Vienna Amentioning

confidence: 99%

Temporal metabolic partitioning of the yeast and protist cellular networks: the cell is a global scale-invariant (fractal or self-similar) multioscillator

et al. 2018

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“…In Sect. 3.4 we showed an example of how we can trivially extend our framework to the multi-dimensional case (Machné et al 2017 ). Here we test this ability with some formal experiments.…”

Section: Experimental Evaluationmentioning

confidence: 99%

Domain agnostic online semantic segmentation for multi-dimensional time series

Gharghabi

Yeh

Ding

et al. 2018

Data Min Knowl Disc

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Unsupervised semantic segmentation in the time series domain is a much studied problem due to its potential to detect unexpected regularities and regimes in poorly understood data. However, the current techniques have several shortcomings, which have limited the adoption of time series semantic segmentation beyond academic settings for four primary reasons. First, most methods require setting/learning many parameters and thus may have problems generalizing to novel situations. Second, most methods implicitly assume that all the data is segmentable and have difficulty when that assumption is unwarranted. Thirdly, many algorithms are only defined for the single dimensional case, despite the ubiquity of multi-dimensional data. Finally, most research efforts have been confined to the batch case, but online segmentation is clearly more useful and actionable. To address these issues, we present a multi-dimensional algorithm, which is domain agnostic, has only one, easily-determined parameter, and can handle data streaming at a high rate. In this context, we test the algorithm on the largest and most diverse collection of time series datasets ever considered for this task and demonstrate the algorithm’s superiority over current solutions.

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“…S8C). We previously developed a similarity-based segmentation algorithm ( Machné et al, 2017 ) to reduce read-count data to ca. 37,000 segments, each a putative individual transcript ( Figure 2 A, B and S8D).…”

Section: Resultsmentioning

confidence: 99%

Pulse-Width Modulation of Gene Expression in Budding Yeast

Machné

Sh²,

et al. 2021

Preprint

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Metabolic self-synchronization in yeast cultures highlights significant gaps in our understanding of fundamental cellular processes. The oscillation percolates throughout cellular physiology, and the transcriptome oscillates between expression of genes encoding for biosynthesis and growth, and for catabolism and stress-response. However, long protein half-lives dampen this oscillation of transcript abundances, and putative functions remain elusive. We analyze an RNA-seq time series over 2.5 cycles of a short period respiratory oscillation (≈36 min, strain IFO 0233), preceding a distinct bifurcation of system dynamics. An integrative analysis of metabolic dynamics and co-expression cohorts identifies CO2 and carbonic anhydrase as putative players in oscillation and culture synchronization via a feedforward from catabolic to anabolic metabolism. Differential modulation of the relative duration of biosynthetic and catabolic protein cohort transcription precedes the bifurcation, compatible with a causative role in growth rate-dependent cellular resource allocation. The temporal program of protein-coding transcripts encodes the spatial structure of the cell. We suggest a function of periodic transcription in subcellular pattern formation of the growing cell.

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Similarity-Based Segmentation of Multi-Dimensional Signals

Cited by 21 publications

References 52 publications

Temporal metabolic partitioning of the yeast and protist cellular networks: the cell is a global scale-invariant (fractal or self-similar) multioscillator

Temporal metabolic partitioning of the yeast and protist cellular networks: the cell is a global scale-invariant (fractal or self-similar) multioscillator

Domain agnostic online semantic segmentation for multi-dimensional time series

Pulse-Width Modulation of Gene Expression in Budding Yeast

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