Compositional structure of the genome: a review

P Bernaola-Galván, P Carpena, C Gómez-Martín… - Biology, 2023 - mdpi.com
Simple Summary DNA structural biology deals with the understanding of DNA and three-
dimensional chromatin structure, which can determine its function in the cell. The key …

On parameters of the human genome

W Li - Journal of theoretical biology, 2011 - Elsevier
There are mathematical constants that describe universal relationship between variables,
and physical/chemical constants that are invariant measurements of physical quantities. In a …

Generalization of entropy based divergence measures for symbolic sequence analysis

MA Ré, RK Azad - PloS one, 2014 - journals.plos.org
Entropy based measures have been frequently used in symbolic sequence analysis. A
symmetrized and smoothed form of Kullback-Leibler divergence or relative entropy, the …

Segmentation of time series with long-range fractal correlations

P Bernaola-Galván, JL Oliver, M Hackenberg… - The European Physical …, 2012 - Springer
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 …

Phase transitions in the first-passage time of scale-invariant correlated processes

C Carretero-Campos, P Bernaola-Galván… - Physical Review E …, 2012 - APS
A key quantity describing the dynamics of complex systems is the first-passage time (FPT).
The statistical properties of FPT depend on the specifics of the underlying system dynamics …

NGSmethDB 2017: enhanced methylomes and differential methylation

R Lebron, C Gómez-Martín, P Carpena… - Nucleic Acids …, 2016 - academic.oup.com
The 2017 update of NGSmethDB stores whole genome methylomes generated from short-
read data sets obtained by bisulfite sequencing (WGBS) technology. To generate high …

DNA viewed as an out-of-equilibrium structure

A Provata, C Nicolis, G Nicolis - Physical Review E, 2014 - APS
The complexity of the primary structure of human DNA is explored using methods from
nonequilibrium statistical mechanics, dynamical systems theory, and information theory. A …

Clustering of DNA words and biological function: a proof of principle

M Hackenberg, A Rueda, P Carpena… - Journal of theoretical …, 2012 - Elsevier
Relevant words in literary texts (key words) are known to be clustered, while common words
are randomly distributed. Given the clustered distribution of many functional genome …

Probability distribution of intersymbol distances in random symbolic sequences: Applications to improving detection of keywords in texts and of amino acid clustering …

P Carpena, PA Bernaola-Galván, C Carretero-Campos… - Physical Review E, 2016 - APS
Symbolic sequences have been extensively investigated in the past few years within the
framework of statistical physics. Paradigmatic examples of such sequences are written texts …

Algebraic segmentation of short nonstationary time series based on evolutionary prediction algorithms

R Palivonaite, K Lukoseviciute, M Ragulskis - Neurocomputing, 2013 - Elsevier
Algebraic segmentation of short nonstationary time series is presented in this paper. The
proposed algorithm is based on the algebraic one step-forward predictor which is used to …