Computational identification of missing enzymes plays a significant role in reconstruction of metabolic network. For a metabolic reaction, given a set of candidate enzymes identified by certain biological evidences, there is a need to develop a powerful mathematical model to predict the actual enzyme(s) catalyzing the reaction. In this study, a regression model is proposed to solve the problem,...

Understanding of genotype-phenotype associations is important not only for furthering our knowledge on internal cellular processes, but also essential for providing the foundation necessary for genetic engineering of microorganisms for industrial use (e.g., production of bioenergy or biofuels). However, genotype-phenotype associations alone do not provide enough information to alter an organism...

Complex metabolic networks characterize the life of every cell. In this paper we review how such metabolic networks can emerge from a model that applies optimization pressure to artificial chemistries. This model can lead to metabolic networks that share many of the features of real networks, such as cycles and hierarchies. Notice: Cover figure reproduced from [1]. Metabolism is a collection of...

There is growing evidence that the metabolic network is an integral regulator of cellular physiology. Dynamic changes in metabolite concentrations, metabolic flux, or network topology act as reporters of biological or environmental signals, and are required for the cell to trigger an appropriate biological reaction. Changes in the metabolic network are recognized by specific sensory macromolecu...

The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. ...

In metabolic engineering, modification of metabolic networks is an important biotechnology and a challenging computational task. In the metabolic network modification, we should modify metabolic networks by newly adding enzymes or/and knocking-out genes to maximize the biomass production with minimum side-effect. In this mini-review, we briefly review constraint-based formalizations for Minimum...

Metabolism is the process of nutrient uptake and conversion, : Background and executed by the metabolic network. Its evolutionary precursors most likely originated in non-enzymatic chemistry. To be exploitable in a Darwinian process that forms a metabolic pathway, non-enzymatic reactions need to form a chemical network that produces advantage-providing metabolites in a single, life compatible c...

This article demonstrates, using simulations, the potential of the S-system formalism for the inference of unknown chemical reaction networks from simple experimental data, such as that typically obtained from laboratory scale reaction vessels. Virtually no prior knowledge of the products and reactants is assumed. S-systems are a power law formalism for the canonical approximate representation ...

Information on biological networks can greatly facilitate the function-orientated interpretation of high-throughput molecular data. Genome-wide metabolic network models of human cells, in particular, can be employed to contextualize gene expression profiles of patients with the goal of both, a better understanding of individual etiologies and an educated reclassification of (clinically defined)...

as an aromatic and colorful plant of substantive taste, saffron (crocus sativus l.) owes such properties of matter to growing class of the secondary metabolites derived from the carotenoids, apocarotenoids. regarding the critical role of micrornas in secondary metabolic synthesis and the limited number of identified mirnas in c. sativus, on the other hand, one may see the point how the characte...