Automation is an open subject in DNA microarray image processing, aiming reliable gene expression estimation. The paper presents a novel shock filter based approach for automatic microarray grid alignment. The proposed method brings up significantly reduced computational complexity compared to state of the art approaches, while similar results in terms of accuracy are achieved. Based on this ap...

Singapore grouper iridovirus (SGIV), an iridovirus in the genus Ranavirus, is a major pathogen that results in significant economic losses in grouper aquaculture. To investigate further its infective mechanisms, for the first time, a viral DNA microarray was generated for the SGIV genome to measure the expression of its predicted open reading frames simultaneously in vitro. By using the viral D...

IntroductionPodocyte apoptosis is a common mechanism driving progression in Alport syndrome(AS). The aim of this study was to investigate the podocyte caused by COL4A3 mutations.MethodsWe recruited autosomal dominant AS(ADAS) patients. Patients with minimal change disease (MCD) were as controls. Microarray analysis carried out on isolated glomeruli from patients and validated. Then, correspondi...

The integration and evaluation of data from multiple DNA microarray datasets for a specific analysis is an important and yet challenging problem. In contrast to the majority of studies, which are focused on a particular biological problem, the present paper examines how the combination of several related microarray datasets affects different areas of preprocessing and analysis of gene expressio...

We construct a gene network based on expression data from DNA microarray experiments, by establishing a link between two genes whenever the Pearson’s correlation coefficient between their expression profiles is higher than a certain cutoff. The resulting connectivity distribution is compatible with a power-law decay with exponent γ ∼ 1, corrected by an exponential cutoff at large connectivity. ...

This paper presents a novel approach for the extraction of gene regulatory networks from DNA microarray data. The approach is characterized by the integration of data coming from static and dynamic experiments, exploiting also prior knowledge on the biological process under analysis. A strategy to learn a gene network from mutant static data has been integrated with a genetic algorithm approach...

Dynamic regulatory pathways, estimated using DNA microarray time-series information, provide predictions of dynamic interactions among genes. Even though several analysis methods have been studied, most of them fall short in analyzing or observing these interactions in detail. In contrast to other methods, we have developed a visual approach based on the gene regulatory pathway prediction metho...

Urbano França, Massimiliano Lattanzi, Julien Lesgourgues and Sergio Pastor Instituto de F́ısica Corpuscular (CSIC-Universitat de València), Ed. Institutos de Investigación, Apdo. 22085, 46071 Valencia, Spain ICRA & Dip. di Fisica, Universitá di Roma ”La Sapienza”, P.le A. Moro 2, 00185 Roma, Italy CERN, Theory Division, CH-1211 Geneva 23, Switzerland, and Institut de Théorie des Phénomènes Physi...