Literature DB >> 23645997

Segmentation of time series with long-range fractal correlations.

P Bernaola-Galván1, J L Oliver, M Hackenberg, A V Coronado, P Ch Ivanov, P Carpena.   

Abstract

Segmentation is a standard method of data analysis to identify change-points dividing a nonstationary time series into homogeneous segments. However, for long-range fractal correlated series, most of the segmentation techniques detect spurious change-points which are simply due to the heterogeneities induced by the correlations and not to real nonstationarities. To avoid this oversegmentation, we present a segmentation algorithm which takes as a reference for homogeneity, instead of a random i.i.d. series, a correlated series modeled by a fractional noise with the same degree of correlations as the series to be segmented. We apply our algorithm to artificial series with long-range correlations and show that it systematically detects only the change-points produced by real nonstationarities and not those created by the correlations of the signal. Further, we apply the method to the sequence of the long arm of human chromosome 21, which is known to have long-range fractal correlations. We obtain only three segments that clearly correspond to the three regions of different G + C composition revealed by means of a multi-scale wavelet plot. Similar results have been obtained when segmenting all human chromosome sequences, showing the existence of previously unknown huge compositional superstructures in the human genome.

Entities:  

Year:  2012        PMID: 23645997      PMCID: PMC3643524          DOI: 10.1140/epjb/e2012-20969-5

Source DB:  PubMed          Journal:  Eur Phys J B        ISSN: 1434-6028            Impact factor:   1.500


  46 in total

1.  Sleep-wake differences in scaling behavior of the human heartbeat: analysis of terrestrial and long-term space flight data.

Authors:  A Bunde; L A Amaral; S Havlin; J Fritsch-Yelle; R M Baevsky; H E Stanley; A L Goldberger
Journal:  Europhys Lett       Date:  1999-12-01       Impact factor: 1.947

2.  IsoFinder: computational prediction of isochores in genome sequences.

Authors:  José L Oliver; Pedro Carpena; Michael Hackenberg; Pedro Bernaola-Galván
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

3.  Heuristic segmentation of a nonstationary time series.

Authors:  Kensuke Fukuda; H Eugene Stanley; Luís A Nunes Amaral
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2004-02-25

4.  Compositional searching of CpG islands in the human genome.

Authors:  Pedro Luis Luque-Escamilla; José Martínez-Aroza; José L Oliver; Juan Francisco Gómez-Lopera; Ramón Román-Roldán
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-06-29

5.  Markov models of genome segmentation.

Authors:  Vivek Thakur; Rajeev K Azad; Ram Ramaswamy
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2007-01-17

6.  Level statistics of words: finding keywords in literary texts and symbolic sequences.

Authors:  P Carpena; P Bernaola-Galván; M Hackenberg; A V Coronado; J L Oliver
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-03-10

7.  GC composition of the human genome: in search of isochores.

Authors:  Netta Cohen; Tal Dagan; Lewi Stone; Dan Graur
Journal:  Mol Biol Evol       Date:  2005-02-23       Impact factor: 16.240

8.  Scale invariance in the nonstationarity of human heart rate.

Authors:  P Bernaola-Galván; P C Ivanov; L A Nunes Amaral; H E Stanley
Journal:  Phys Rev Lett       Date:  2001-10-02       Impact factor: 9.161

9.  Cyclical variation of the heart rate in sleep apnoea syndrome. Mechanisms, and usefulness of 24 h electrocardiography as a screening technique.

Authors:  C Guilleminault; S Connolly; R Winkle; K Melvin; A Tilkian
Journal:  Lancet       Date:  1984-01-21       Impact factor: 79.321

10.  Isochores merit the prefix 'iso'.

Authors:  Wentian Li; Pedro Bernaola-Galván; Pedro Carpena; Jose L Oliver
Journal:  Comput Biol Chem       Date:  2003-02       Impact factor: 2.877

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  5 in total

1.  Magnitude and sign of long-range correlated time series: Decomposition and surrogate signal generation.

Authors:  Manuel Gómez-Extremera; Pedro Carpena; Plamen Ch Ivanov; Pedro A Bernaola-Galván
Journal:  Phys Rev E       Date:  2016-04-04       Impact factor: 2.529

2.  Mining the modular structure of protein interaction networks.

Authors:  Ariel José Berenstein; Janet Piñero; Laura Inés Furlong; Ariel Chernomoretz
Journal:  PLoS One       Date:  2015-04-09       Impact factor: 3.240

3.  NGSmethDB 2017: enhanced methylomes and differential methylation.

Authors:  Ricardo Lebrón; Cristina Gómez-Martín; Pedro Carpena; Pedro Bernaola-Galván; Guillermo Barturen; Michael Hackenberg; José L Oliver
Journal:  Nucleic Acids Res       Date:  2016-10-27       Impact factor: 16.971

4.  Driven progressive evolution of genome sequence complexity in Cyanobacteria.

Authors:  Andrés Moya; José L Oliver; Miguel Verdú; Luis Delaye; Vicente Arnau; Pedro Bernaola-Galván; Rebeca de la Fuente; Wladimiro Díaz; Cristina Gómez-Martín; Francisco M González; Amparo Latorre; Ricardo Lebrón; Ramón Román-Roldán
Journal:  Sci Rep       Date:  2020-11-04       Impact factor: 4.379

5.  On the Validity of Detrended Fluctuation Analysis at Short Scales.

Authors:  Pedro Carpena; Manuel Gómez-Extremera; Pedro A Bernaola-Galván
Journal:  Entropy (Basel)       Date:  2021-12-29       Impact factor: 2.524

  5 in total

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