Related papers: A comparative evolutionary study of transcription …
The E.coli transcription network has an essentially feedforward structure, with, however, abundant feedback at the level of self-regulations. Here, we investigate how these properties emerged during evolution. An assessment of the role of…
Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and…
Dynamical properties of the transcriptional regulatory network of {\it Escherichia coli} and {\it Saccharomyces cerevisiae} are studied within the framework of random Boolean functions. The dynamical response of these networks to a single…
The transcriptional regulation of gene expression is orchestrated by complex networks of interacting genes. Increasing evidence indicates that these transcriptional regulatory networks (TRNs) in bacteria have an inherently hierarchical…
We investigate the structural and dynamical properties of the transcriptional regulatory network of the yeast {\it Saccharomyces cerevisiae} and compare it with two unbiased ensembles: one obtained by reshuffling the edges and the other…
We investigate the dynamical properties of the transcriptional regulation of gene expression in the yeast Saccharomyces Cerevisiae within the framework of a synchronously and deterministically updated Boolean network model. By means of a…
MOTIVATION: A central goal of postgenomic biology is the elucidation of the regulatory relationships among all cellular constituents that together comprise the 'genetic network' of a cell or microorganism. Experimental manipulation of gene…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be restrictive in another. However, evolving Escherichia coli populations demonstrate remarkable flexibility in adaptation. The…
BACKGROUND. Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmental signals in the…
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…
We investigate the cycles in the transcription network of S. cerevisiae. Unlike a similar network of E. coli, it contains many cycles. We characterize properties of these cycles and their place in the regulatory mechanism of the cell.…
Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can…
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…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
Regulatory networks have evolved to allow gene expression to rapidly track changes in the environment as well as to buffer perturbations and maintain cellular homeostasis in the absence of change. Theoretical work and empirical…
The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data one can identify functional…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of…