Concept

Metabolic network modelling

Related publications (106)

Coral photosymbiosis: Linking phylogenetic identity to single cell metabolic activity in mixed symbiont populations

Anders Meibom, Isabelle Domart-Coulon, Maoz Fine, Béatrice Gaume

Tropical reef-building corals live in symbiosis with a wide range of micro-organisms, including unicellular Symbiodinium dinoflagellates also called zooxanthellae. These photosynthetic endosymbionts live inside the coral gastroderm cells. Although corals c ...

2017

Navigating and Managing the Complexity of Genome Scale Metabolic Networks for Studies in Cellular Physiology and Industrial Biotechnology

Meriç Ataman

Metabolism is a network of biochemical reactions that converts carbon sources to cellu-lar fuels and building blocks. Metabolism of many organisms has been studied for many decades. These studies define metabolism as a very large and complex network. Stoic ...

EPFL2016

New technologies – new insights into the pathogenesis of hepatic encephalopathy

Bernard Lanz

Hepatic encephalopathy (HE) is a neuropsychiatric syndrome which frequently accompanies acute or chronic liver disease. It is characterized by a variety of symptoms of different severity such as cognitive deficits and impaired motor functions. Currently, H ...

Springer Verlag2016

Large Scale Dynamic Models of Metabolism as a Tool for Analysis and Design of Metabolic Engineering and Synthetic Biology Strategies

Vassily Hatzimanikatis, Ljubisa Miskovic, Georgios Fengos

Large-scale dynamic models of metabolism remain an overarching ambition of efforts that aim to analyze and explain complex behavior of living entities. However, intrinsic nonlinearity of dynamics of living organisms and structural and quantitative uncertai ...

2016

Refined Analysis of Brain Energy Metabolism Using In Vivo Dynamic Enrichment of 13C Multiplets

Rolf Gruetter, Bernard Lanz, João Miguel das Neves Duarte, Nicolas Kunz

Carbon-13 nuclear magnetic resonance spectroscopy in combination with the infusion of (13)C-labeled precursors is a unique approach to study in vivo brain energy metabolism. Incorporating the maximum information available from in vivo localized (13)C spect ...

Sage Publications Ltd2016

Computational studies on Escherichia coli metabolism

Stefano Andreozzi

Metabolic Engineering is fostered by an increasing effort and progress in the collection of large and accurate 'omics' datasets. The abundance of available measurements and advances in measurement techniques only alleviate to a certain extent the uncertai ...

EPFL2015

Integrating Transcriptomic Data with Thermodynamically Consistent Metabolic Models

Vikash Kumar Pandey, Daniel Federico Hernandez Gardiol

In metabolic modeling, experimental data is used to constrain the solution space of allowable flux distributions to biologically feasible phenotypes. This makes metabolic modeling a powerful tool for integrating information from different experimental sour ...

2015

Systematic Reduction of Genome Scale Metabolic Reconstructions - redGEM

Vassily Hatzimanikatis, Meriç Ataman, Georgios Fengos, Keng Cher Soh, Daniel Federico Hernandez Gardiol

Genome-scale metabolic reconstructions (GEMs) are valuable resources for understanding and redesigning cellular networks as they encapsulate all the known biochemistry of the organisms from genes to proteins to their functions. Complexity of these large me ...

2015

Systematic Reduction of Genome Scale Metabolic Reconstructions - redGEM

Vassily Hatzimanikatis, Meriç Ataman, Georgios Fengos, Keng Cher Soh, Daniel Federico Hernandez Gardiol

2015

In Silico Atom Labeling for the Reconstruction of Atom-mapped Metabolic Networks

Vassily Hatzimanikatis, Jasmin Maria Hafner, Noushin Hadadi

Field of atom mapping of metabolic networks is lacking an automated approach, which accounts for the information of reaction mechanism for atom mapping and is extendable from atom-mapped reactions to atom-mapped reaction networks. We developed “iAM.NICE” ( ...

2015

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