分子网络
In many sensory systems, transmembrane receptors are spatially organized in large clusters. Such arrangement may facilitate signal amplification and the integration of multiple stimuli. However, this organization likely also affects the…
Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here…
Iron is essential for all known life due to its redox properties, however these same properties can also lead to its toxicity in overload through the production of reactive oxygen species. Robust systemic and cellular control are required…
We present a new experimental-computational technology of inferring network models that predict the response of cells to perturbations and that may be useful in the design of combinatorial therapy against cancer. The experiments are…
A major challenge in biology is to understand how molecular processes determine phenotypic features. We address this fundamental problem in a class of model systems by developing a general mathematical framework that allows the calculation…
Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context specific and dynamic in…
Mutations in proteins can have deleterious effects on a protein's stability and function, which ultimately causes particular diseases. Genetically inherited muscular dystrophies (MDs) include several genetic diseases, which cause increasing…
We study a system of dynamical units, each of which shows excitable or oscillatory behavior, depending on the choice of parameters. When we couple these units with repressive bonds, we can control the duration of collective oscillations for…
Cancer forms a robust system and progresses as stages over time typically with increasing aggressiveness and worsening prognosis. Characterizing these stages and identifying the genes driving transitions between them is critical to…
Cells often have tens of thousands of receptors, even though only a few activated receptors can trigger full cellular responses. Reasons for the overabundance of receptors remain unclear. We suggest that, in certain conditions, the large…
Living cells deploy many resources to sense their environments, including receptors, downstream signaling molecules, time and fuel. However, it is not known which resources fundamentally limit the precision of sensing, like weak links in a…
The DevRS two component system of Mycobacterium tuberculosis is responsible for its dormancy in host and becomes operative under hypoxic condition. It is experimentally known that phosphorylated DevR controls the expression of several…
A proof is presented that gene regulatory networks (GRNs) based solely on transcription factors cannot control the development of complex multicellular life. GRNs alone cannot explain the evolution of multicellular life in the Cambrian…
Model reduction is a central topic in systems biology and dynamical systems theory, for reducing the complexity of detailed models, finding important parameters, and developing multi-scale models for instance. While perturbation theory is a…
We calculate measures of hierarchy in gene and tissue networks of breast cancer patients. We find that the likelihood of metastasis in the future is correlated with increased values of network hierarchy for expression networks of…
Complex networks are intrinsically modular. Resolving small modules is particularly difficult when the network is densely connected; wide variation of link weights invites additional complexities. In this article we present an algorithm to…
Most sensory cells use surface receptors to detect environmental stimuli and initiate downstream signaling. Cooperative interactions among sensory receptors is known to play a crucial role in enhancing the sensitivity of biochemical…
We examine the modular structure of the metabolic network when combined with the regulatory network representing direct regulation of enzymes by small metabolites in E.coli. In order to identify the modular structure we introduce clustering…
Biological systems exhibit two structural features on many levels of organization: sparseness, in which only a small fraction of possible interactions between components actually occur; and modularity - the near decomposability of the…
Cells sense and predict their environment via energy-dissipating pathways. However, it is unclear whether dissipation helps or harms prediction. Here we study dissipation and prediction for a minimal sensory module of receptors that…