Related papers: Method for finding metabolic properties based on t…
The success of metabolomics studies depends upon the "fitness" of each biological sample used for analysis: it is critical that metabolite levels reported for a biological sample represent an accurate snapshot of the studied organism's…
We present a framework for modeling liver regrowth on the organ scale that is based on three components: (1) a multiscale perfusion model that combines synthetic vascular tree generation with a multi-compartment homogenized flow model,…
The growth and scaling of organs is a fundamental aspect of animal development. However, how organs grow to the right size and shape required by physiological demands, remains largely unknown. Here, we provide a framework combining theory…
Overweight and obesity remain a major global public health concern and identifying the individualized patterns that increase the risk of future weight gains has a crucial role in preventing obesity and numerous sub-sequent diseases…
Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic…
Branching in vascular networks and in overall organismic form is one of the most common and ancient features of multicellular plants, fungi, and animals. By combining machine-learning techniques with new theory that relates vascular form to…
Monod's law is a widely accepted phenomenology for bacterial growth. Since it has the same functional form as the Michaelis--Menten equation for enzyme kinetics, cell growth is often considered to be locally constrained by a single…
Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this…
Metabolic scaling is one of the most important patterns in biology. Theory explaining the 3/4-power size-scaling of biological metabolic rate does not predict the non-linear scaling observed for smaller life forms. Here we present a new…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
A central debate in biology has been the allometric scaling of metabolic rate. Kleiber's observation that animals' basal metabolic rate scales to the 3/4-power of body mass (Kleiber's rule) has been the prevailing hypothesis in the last…
The biomechanics of the human body allow humans a range of possible ways of executing movements to attain specific goals. Nevertheless, humans exhibit significant patterns in how they execute movements. We propose that the observed patterns…
An important question in biology is how the relative size of different organs is kept nearly constant during growth of an animal. This property, called proportionate growth, has received increased attention in recent years. We discuss our…
High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major…
The quarter power allometric scaling of mammalian metabolic rate is largely regarded as a universal law of biology. However, it is well known that cell cultures do not obey this law. The current thinking is that were in-vitro cultures to…
Metabolic pathways are fundamental maps in biochemistry that detail how molecules are transformed through various reactions. The complexity of metabolic network, where a single compound can play a part in multiple pathways, poses a…
The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…
Most organisms grow according to simple laws, which in principle can be derived from energy conservation and scaling arguments, critically dependent on the relation between the metabolic rate B of energy flow and the organism mass m.…
A longstanding problem in biology has been the origin of pervasive quarter-power allometric scaling laws that relate many characteristics of organisms to body mass (M) across the entire spectrum of life from molecules and microbes to…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…