A parametric signal processing approach for DNA sequence analysis based on autoregressive (AR) modeling is presented. AR model residual errors and AR model parameters are used as features. The AR residual erro...
Comparative genomics has been a valuable method for extracting and extrapolating genome information among closely related bacteria. The efficiency of the traditional methods is extremely influenced by the soft...
Heterogeneous DNA sequences can be partitioned into homogeneous domains that are comprised of the four nucleotides A, C, G, and T and the stop-codons. Recursively, we apply a new entropic segmentation method o...
This paper considers key issues in the emerging field of genomic signal processing and its relationship to functional genomics. It focuses on some of the biological mechanisms driving the development of genomi...
An unsupervised data clustering method, called the local maximum clustering (LMC) method, is proposed for identifying clusters in experiment data sets based on research interest. A magnitude property is define...
Complex representation of nucleotides is used to convert DNA sequences into complex digital genomic signals. The analysis of the cumulated phase and unwrapped phase of DNA genomic signals reveals large-scale f...
We performed frequency-domain analysis in the genomes of various organisms using tricolor spectrograms, identifying several types of distinct visual patterns characterizing specific DNA regions. We relate patt...
This paper introduces a statistical methodology for the identification of differentially expressed genes in DNA microarray experiments based on multiple criteria. These criteria are false discovery rate (FDR),...
A critical issue for the construction of genetic regulatory networks is the identification of network topology from data. In the context of deterministic and probabilistic Boolean networks, as well as their ex...
This paper focuses on the stability-based approach for estimating the number of clusters
in microarray data. The cluster stability appr...
This paper presents microarray BASICA: an integrated image processing tool for background adjustment, segmentation, image compression, and analysis of cDNA microarray images. BASICA uses a fast Mann-Whitney te...
Probabilistic Boolean networks (PBNs) comprise a model describing a directed graph with rule-based dependences between its nodes. The rules are selected, based on a given probability distribution which provide...
It has been observed that the protein-coding regions of DNA sequences exhibit period-three behaviour, which can be exploited to predict the location of coding regions within genes. Previously, discrete Fourier...
A novel approach to signal peptide identification is presented. We use an evolutionary algorithm for automatic evolution of classification programs, so-called programmatic motifs. The variant of evolutionary a...