Background: Epigenetic aberration such as DNA methylation and histone modifications appear to be involved in various diseases such as Endometriosis. Here, we investigated the epigenetic regulation of HOXA10 promoter, as a crucial gene, responsible for uterine organogenesis, functional endometrial differentiation and endometrial receptivity, and its correlation with mRNA expression of this gene ...

The aim of the current study was to identify gene signatures during the early proliferation stage of wound repair and the effect of TGF‑β on fibroblasts and reveal their potential mechanisms. The gene expression profiles of GSE79621 and GSE27165 were obtained from GEO database. Differentially expressed genes (DEGs) were identified using Morpheus and co‑expressed DEGs were selected using Venn Di...

The progress on gene expression profiling technology has allowed us to venture into the underlying regulatory rules and suggest many gene network models. Among them, the quantitative models are probably the most potent to achieve the highest precision and sensitivity. But the practical limitation of the approach is the requirement of lengthy data points and vulnerability to noise in the data. W...

In this paper we investigate how metabolic network structure affects any coordination between transcript and metabolite profiles. To achieve this goal we conduct two complementary analyses focused on the metabolic response to stress. First, we investigate the general size of any relationship between metabolic network gene expression and metabolite profiles. We find that strongly correlated tran...

The diversity of pigmentation patterns observed in plants occurs due to the spatial distribution and accumulation of colored compounds, which may also be associated with structural changes to the tissue. Anthocyanins are flavonoids that provide red/purple/blue coloration to plants, often forming complex patterns such as spots, stripes, and vein-associated pigmentation, particularly in flowers. ...

The evolution of development is an important ongoing question in developmental biology, and to study it, we examine evolution in the context of fundamental processes underlying development, gene expression and regulation. In this paper, we present the results of utilizing a biologicallymotivated model which implements gene expression and regulation to evolve genetic regulatory networks that exp...

BACKGROUND There are a wide range of phenotypes that are due to loss-of-function or null mutations. Previously, the functions of gene products that distinguish essential from nonessential genes were characterized. However, the functions of products of non-essential genes that contribute to fitness remain minimally understood. PRINCIPAL FINDINGS Using data from Saccharomyces cerevisiae, we inv...

The standard approach in evolutionary robotics is to evolve neural networks for control by encoding the parameters of the network in the genome. By contrast, we have evolved a neural controller based on biological principles from molecular and developmental biology. The key principles employed in our algorithms model the specific ligand-receptor interactions and gene regulation. These mechanism...

Introduction Comprehending gene regulation has been a major endeavour in the field of bioinformatics for many years and still poses a difficult problem with a lot of uncertainties. In spite of improvements in the technologies used, e.g. high-throughput methods like ChIP-sequencing, and progress in the analysis of the driving regulators, large parts of many gene regulatory networks still remain ...