Related papers: A computational approach to regulatory element dis…
Gene expression is a readily-observed quantification of transcriptional activity and cellular state that enables the recovery of the relationships between regulators and their target genes. Reconstructing transcriptional regulatory networks…
Transcription factor binding sites vary in their specificity, both within and between species. Binding specificity has a strong impact on the evolution of gene expression, because it determines how easily regulatory interactions are gained…
We model the transcription factor based regulation network of yeast using a content-based network model that mimicks the recognition of binding motifs on the regulatory regions of the genes. We are thereby able to faithfully reproduce many…
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need…
Transcriptional regulation of gene expression is one of the main processes that affect cell diversification from a single set of genes. Regulatory proteins often interact with DNA regions located distally from the transcription start sites…
The identification of motifs--subgraphs that appear significantly more often in a particular network than in an ensemble of randomized networks--has become a ubiquitous method for uncovering potentially important subunits within networks…
From a coarse-grained perspective the motif of a self-activating species, activating a second species which acts as its own repressor, is widely found in biological systems, in particular in genetic systems with inherent oscillatory…
Emerging evidence suggests that the introns and intergenic sequences of the genomes of higher eukaryotes (the ``junk'' DNA) codes for a vast, RNA-based, genetic regulatory network. It is believed that this network is responsible for the…
In the postgenome era many efforts have been dedicated to systematically elucidate the complex web of interacting genes and proteins. These efforts include experimental and computational methods. Microarray technology offers an opportunity…
By analyzing the spacing of genes on chromosomes, we find that transcriptional and RNA-processing regulatory sequences outside coding regions leave footprints on the distribution of intergenic distances. Using analogies between genes on…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
A substantial focus of research in molecular biology are gene regulatory networks: the set of transcription factors and target genes which control the involvement of different biological processes in living cells. Previous statistical…
Gene expression microarray technologies provide the simultaneous measurements of a large number of genes. Typical analyses of such data focus on the individual genes, but recent work has demonstrated that evaluating changes in expression…
Measuring natural selection on genomic elements involved in the cis-regulation of gene expression -- such as transcriptional enhancers and promoters -- is critical for understanding the evolution of genomes, yet it remains a major…
The number of studies dealing with RNA-Seq data analysis has experienced a fast increase in the past years making this type of gene expression a strong competitor to the DNA microarrays. This paper proposes a Bayesian model to detect down…
Identification of essential genes is one of the ultimate goals of drug designs. Here we introduce an {\it in silico} method to select essential genes through the microarray assay. We construct a graph of genes, called the gene transcription…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
A common problem in bioinformatics is related to identifying gene regulatory regions marked by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code for transcription and enhancer proteins. Predicting…
Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are…
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated…