Microbial cell factories based on renewable carbon sources are fundamental to a sustainable bio-economy. The economic feasibility of producer cells requires robust performance balancing growth and production. However, the inherent competition between these two objectives often leads to instability and reduces productivity. While algorithms exist to design metabolic network reduction strategies ...

Basic ideas and recent developments in network analysis of metabolic systems and various applications of this analysis in bioengineering are reviewed. Central concepts are the null-space to the stoichiometry matrix and the elementary flux modes. The applicability of elementary-modes analysis in biotechnology is illustrated by the synthesis of the cyclooctadepsipeptides PF1022 in the fungus Myce...

Most diseases are the consequence of the breakdown of cellular processes, but the relationships among genetic/epigenetic defects, the molecular interaction networks underlying them, and the disease phenotypes remain poorly understood. To gain insights into such relationships, here we constructed a bipartite human disease association network in which nodes are diseases and two diseases are linke...

Cancer treatment is still of the greatest challenges that health care providers and patients are facing. One of the unsolved problems in cancer treatment is cells’ reaction to metabolic stress caused by harsh nutritional conditions around tumor. In order to be able to treat this disease properly, it is important to understand the true nature of the disease. In fact, the cells inside the central...

Many current and future applications of biological engineering hinge on our ability to measure, understand, and manipulate metabolism. Many diseases for which we seek cures are metabolic in nature. Small-molecule biomanufacturing almost always involves metabolic engineering. Biofuels, a current topic of great interest, is essentially a metabolic problem. Even bioprocesses that involve complex p...

Cancer treatment is still of the greatest challenges that health care providers and patients are facing. One of the unsolved problems in cancer treatment is cells’ reaction to metabolic stress caused by harsh nutritional conditions around tumor. In order to be able to treat this disease properly, it is important to understand the true nature of the disease. In fact, the cells inside the central...

Reliability on complex biological networks reconstructions remains a concern. Although observations are getting more and more precise, the data collection process is yet error prone and the proofs display uneven certitude. In the case of metabolic networks, the currently employed confidence scoring system rates reactions according to a discretized small set of labels denoting different levels o...

Biochemical networks – networks composed of the building blocks of the cell and their interactions are qualitative descriptions of the working of the cell. Such networks can be modeled as graphs. Metabolic networks are typical examples of such networks. They are composed of biochemical entities participating to reactions as substrates or products. Such a network can be modeled as a bipartite di...