分子网络
The p53 protein is well-known for its tumour suppressor function. The p53-MDM2 negative feedback loop constitutes the core module of a network of regulatory interactions activated under cellular stress. In normal cells, the level of p53…
We study how the dynamic equilibrium of the reversible protein-protein binding network in yeast Saccharomyces cerevisiae responds to large changes in abundances of individual proteins. The magnitude of shifts between free and bound…
Recently, several studies have investigated the transcription process associated to specific genetic regulatory networks. In this work, we present a stochastic approach for analyzing the dynamics and effect of negative feedback loops (FBL)…
We propose a growing network model that consists of two tunable mechanisms: growth by merging modules which are represented as complete graphs and a fitness-driven preferential attachment. Our model exhibits the three prominent statistical…
The complexity of the cells can be described and understood by a number of networks such as protein-protein interaction, cytoskeletal, organelle, signalling, gene transcription and metabolic networks. All these networks are highly dynamic…
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.…
Wild animals, pets, zoo animals and mammals of veterinary importance heavily suffer from trypanosomiasis. Drugs with serious side effects are currently mainstay of therapies used by veterinarians. Trypanosomiasis is caused by Trypanosoma…
Recent studies have reported that T cells can integrate signals between interrupted encounters with Antigen Presenting Cells (APCs) in such a way that the process of signal integration exhibits a form of memory. Here, we carry out a…
The lac operon of Escherichia coli exhibits bistability. Early studies showed that bistability occurs during growth on TMG/succinate and lactose + glucose, but not during growth on lactose. More recent studies with lacGFP-transfected cells…
Sequence alignment forms the basis of many methods for functional annotation by phylogenetic comparison, but becomes unreliable in the `twilight' regions of high sequence divergence and short gene length. Here we perform a cross-species…
Cells store information in DNA and in stable programs of gene expression, which thereby implement forms of long-term cellular memory. Cells must also possess short-term forms of information storage, implemented post-translationally, to…
The important task of determining the connectivity of gene networks, and at a more detailed level even the kind of interaction existing between genes, can nowadays be tackled by microarraylike technologies. Yet, there is still a large…
Complex dynamical networks consisting of many components that interact and produce each other are difficult to understand, especially, when new components may appear. In this paper we outline a theory to deal with such systems. The theory…
Pathways are integral to systems biology. Their classical representation has proven useful but is inconsistent in the meaning assigned to each arrow (or edge) and inadvertently implies the isolation of one pathway from another. Conversely,…
It is the goal of systems biology to understand the behavior of the whole in terms of the knowledge of the parts. This is hard to achieve in many cases due to the difficulty of characterizing the many constituents and their complex web of…
In this Supporting Information, we provide background information on our model of the in vitro Kai system and the calculations that we have performed. We will closely follow the outline of the main text.
We analyze three simple genetic circuits which involve transcriptional regulation and feedback: the autorepressor, the switch and the repressilator, that consist of one, two and three genes, respectively. Such systems are commonly simulated…
Despite improved rational drug design and a remarkable progress in genomic, proteomic and high-throughput screening methods, the number of novel, single-target drugs fell much behind expectations during the past decade. Multi-target drugs…
The induction of the lac operon follows cooperative kinetics.The first mechanistic model of these kinetics is the de facto standard in the modeling literature (Yagil & Yagil, Biophys J, 11, 11-27, 1971). Yet, subsequent studies have shown…
The study of synchronization among genetic oscillators is essential for the understanding of the rhythmic phenomena of living organisms at both molecular and cellular levels. Genetic networks are intrinsically noisy due to natural random…