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Interpretation of high-throughput biological data requires a knowledge of the design principles underlying the networks that sustain cellular functions. Of particular importance is the genetic network, a set of genes that interact through directed transcriptional regulation. Genes that exert a regulatory role encode dedicated transcription factors(More)
UNLABELLED We propose a simple algorithm to detect dominating synonymous codon usage bias in genomes. The algorithm is based on a precise mathematical formulation of the problem that lead us to use the Codon Adaptation Index (CAI) as a 'universal' measure of codon bias. This measure has been previously employed in the specific context of translational bias.(More)
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into discrete spatial foci called transcription factories. However, the mechanisms underlying the formation of these foci and(More)
A careful scrutiny of the dynamics of secretory compartments in the entire eukaryotic world reveals many common themes. The most fundamental theme is that the Golgi apparatus and related structures appear as compartments formed by the act of transporting cargo. The second common theme is the pivotal importance for endomembrane dynamics of shifting back and(More)
The principles underlying the architectural landscape of chromatin beyond the nucleosome level in living cells remains largely unknown despite its potential to play a role in mammalian gene regulation. We investigated the three-dimensional folding of a 1 Mbp region of human chromosome 11 containing the β-globin genes by integrating looping interactions of(More)
MOTIVATION The costs of head-on versus codirectional collisions between the replication complex and the much slower transcription complex on the circular bacterial chromosomes are much debated. Although it is established that the number of genes on the leading strand is higher than on the lagging strand of replication, the consequences of collisions on the(More)
BACKGROUND The specific position of functionally related genes along the DNA has been shown to reflect the interplay between chromosome structure and genetic regulation. By investigating the statistical properties of the distances separating such genes, several studies have highlighted various periodic trends. In many cases, however, groups built up from(More)
In the yeast Saccharomyces cerevisiae, the interplay between galactose, Gal3p, Gal80p and Gal4p determines the transcriptional status of the genes required for galactose utilization. After an increase in galactose concentration, galactose molecules bind onto Gal3p. This event leads via Gal80p to the activation of Gal4p, which then induces GAL3 and GAL80(More)
BACKGROUND An appropriate choice of the modeling formalism from the broad range of existing ones may be crucial for efficiently describing and analyzing biological systems. RESULTS We propose a new unifying and incremental formalism for the representation and modeling of biological interaction networks. This formalism allows automated translations into(More)
Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position-specific scoring matrices, which may(More)