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- Ivo Grosse, Pedro Bernaola-Galván, Pedro Carpena, Ramón Román-Roldán, Jose Oliver, H Eugene Stanley
- Physical review. E, Statistical, nonlinear, and…
- 2002

We study statistical properties of the Jensen-Shannon divergence D, which quantifies the difference between probability distributions, and which has been widely applied to analyses of symbolic sequences. We present three interpretations of D in the framework of statistical physics, information theory, and mathematical statistics, and obtain approximations… (More)

- Wentian Li, Pedro Bernaola-Galván, Fatameh Haghighi, Ivo Grosse
- Computers & Chemistry
- 2002

Recursive segmentation is a procedure that partitions a DNA sequence into domains with a homogeneous composition of the four nucleotides A, C, G and T. This procedure can also be applied to any sequence converted from a DNA sequence, such as to a binary strong(G + C)/weak(A + T) sequence, to a binary sequence indicating the presence or absence of the… (More)

- P Bernaola-Galván, I Grosse, P Carpena, J L Oliver, R Román-Roldán, H E Stanley
- Physical review letters
- 2000

We present a new computational approach to finding borders between coding and noncoding DNA. This approach has two features: (i) DNA sequences are described by a 12-letter alphabet that captures the differential base composition at each codon position, and (ii) the search for the borders is carried out by means of an entropic segmentation method which uses… (More)

- José L. Oliver, Pedro Carpena, Michael Hackenberg, Pedro Bernaola-Galván
- Nucleic Acids Research
- 2004

Isochores are long genome segments homogeneous in G+C. Here, we describe an algorithm (IsoFinder) running on the web (http://bioinfo2.ugr.es/IsoF/isofinder.html) able to predict isochores at the sequence level. We move a sliding pointer from left to right along the DNA sequence. At each position of the pointer, we compute the mean G+C values to the left and… (More)

A segmentation algorithm based on the Jensen-Shannon entropic divergence is used to decompose long-range correlated DNA sequences into statistically significant, compositionally homogeneous patches. By adequately setting the significance level for segmenting the sequence, the underlying power-law distribution of patch lengths can be revealed. Some of the… (More)

- Zhi Chen, Kun Hu, Pedro Carpena, Pedro Bernaola-Galvan, H Eugene Stanley, Plamen Ch Ivanov
- Physical review. E, Statistical, nonlinear, and…
- 2005

When investigating the dynamical properties of complex multiple-component physical and physiological systems, it is often the case that the measurable system's output does not directly represent the quantity we want to probe in order to understand the underlying mechanisms. Instead, the output signal is often a linear or nonlinear function of the quantity… (More)

- Michael Hackenberg, Pedro Bernaola-Galván, Pedro Carpena, José L Oliver
- Journal of molecular evolution
- 2005

Alu retrotransposons do not show a homogeneous distribution over the human genome but have a higher density in GC-rich (H) than in AT-rich (L) isochores. However, since they preferentially insert into the L isochores, the question arises: What is the evolutionary mechanism that shifts the Alu density maximum from L to H isochores? To disclose the role… (More)

According to Bloch's theorem, electronic wavefunctions in perfectly ordered crystals are extended, which implies that the probability of finding an electron is the same over the entire crystal. Such extended states can lead to metallic behaviour. But when disorder is introduced in the crystal, electron states can become localized, and the system can undergo… (More)

- W Li, G Stolovitzky, P Bernaola-Galván, J L Oliver
- Genome research
- 1998

The heterogeneity within, and similarities between, yeast chromosomes are studied. For the former, we show by the size distribution of domains, coding density, size distribution of open reading frames, spatial power spectra, and deviation from binomial distribution for C + G% in large moving windows that there is a strong deviation of the yeast sequences… (More)

- José L. Oliver, Ramón Román-Roldán, Javier Pérez, Pedro Bernaola-Galván
- Bioinformatics
- 1999

MOTIVATION
DNA sequences are formed by patches or domains of different nucleotide composition. In a few simple sequences, domains can simply be identified by eye; however, most DNA sequences show a complex compositional heterogeneity (fractal structure), which cannot be properly detected by current methods. Recently, a computationally efficient segmentation… (More)