Textual data compression in computational biology: a synopsis

R Giancarlo, D Scaturro, F Utro - Bioinformatics, 2009 - academic.oup.com
Motivation: Textual data compression, and the associated techniques coming from
information theory, are often perceived as being of interest for data communication and …

The evolution of isochore patterns in vertebrate genomes

M Costantini, R Cammarano, G Bernardi - BMC genomics, 2009 - Springer
Background Previous work from our laboratory showed that (i) vertebrate genomes are
mosaics of isochores, typically megabase-size DNA segments that are fairly homogeneous …

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 …

The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment

S De, BS Pedersen, K Kechris - Briefings in bioinformatics, 2014 - academic.oup.com
Integrative analyses of genomic, epigenomic and transcriptomic features for human and
various model organisms have revealed that many such features are nonrandomly …

Comparative testing of DNA segmentation algorithms using benchmark simulations

E Elhaik, D Graur, K Josić - Molecular biology and evolution, 2010 - academic.oup.com
Numerous segmentation methods for the detection of compositionally homogeneous
domains within genomic sequences have been proposed. Unfortunately, these methods …

Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm

E Elhaik, D Graur, K Josić, G Landan - Nucleic acids research, 2010 - academic.oup.com
It has been suggested that the mammalian genome is composed mainly of long
compositionally homogeneous domains. Such domains are frequently identified using …

Finding segmentations of sequences

E Bingham - Inductive databases and constraint-based data mining, 2010 - Springer
We describe a collection of approaches to inductive querying systems for data that contain
segmental structure. The main focus in this chapter is on work done in Helsinki area in 2004 …

Towards automated symptoms assessment in mental health

M Osipov - ar** methods agree on the
isochore classification of about two-thirds of the human DNA, they produce significantly …

A new method for splice site prediction based on the sequence patterns of splicing signals and regulatory elements

ZX Sun, LJ Sang, LN Ju, HQ Zhu - Chinese science bulletin, 2008 - Springer
It is of significance for splice site prediction to develop novel algorithms that combine the
sequence patterns of regulatory elements such as enhancers and silencers with the patterns …