Publications related to Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

In silico tracing of the fate of single carbon atoms in different physiological states of E. coli

Jasmin Maria Hafner, Noushin Hadadi, Beatriz Lopes Pinto Basto Carreira

Many applications of systems biology such as the simulation of isotope labeling experiments and pathway inference in metabolic engineering rely on atom-level representation of metabolism. Because of its challenging complexity and the difficulty of obtainin ...

2018

Design of novel enzyme-catalyzed reactions linked to protein sequences for finding enzyme engineering targets

Vassily Hatzimanikatis, Jasmin Maria Hafner, Homa Mohammadi Peyhani, Noushin Hadadi

A key challenge in metabolic engineering is to find and to improve biosynthetic pathways that lead to the cellular production of a given industrial, pharmaceutical or specialty chemical compound. In many cases, the enzymatic reactions required for bio-prod ...

2017

Generation and Analysis of Large-Scale Dynamic Non-Linear Models of Metabolism

Vassily Hatzimanikatis, Ljubisa Miskovic, Georgios Fengos

Understanding complex responses of metabolic processes in biochemical systems requires the quantitative description of the dynamic interplay between metabolite levels, enzyme levels, and reaction rates. Generation and use of such models is hindered by the ...

2017

Fusing Individual-based Models with Genome-scale Metabolic Networks - a Novel Approach for Quantifying Emergent Microbial Community Spatiotemporal Dynamics

Vassily Hatzimanikatis, Meriç Ataman, Dani Or

Metabolic capabilities of organisms govern their growth characteristics and their capability to adapt to changing environmental conditions. In natural systems, substrates can change dynamically and spatially with multiple species competing for resources. G ...

2017

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

Vassily Hatzimanikatis, Jasmin Maria Hafner, Noushin Hadadi, Keng Cher Soh

Reaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely avai ...

Wiley-V C H Verlag Gmbh2017

One-Step Multigram-Scale Biomimetic Synthesis of Psiguadial B

Nicolai Cramer, Matthew Wodrich, Duc Tran Ngoc, Christopher Gordon Newton

A gram-scale synthesis of psiguadial B, a purported inhibitor of human hepatoma cell growth, has been achieved in one step by a biomimetic three-component coupling of caryophyllene, benzaldehyde, and diformylphloroglucinol. This cascade reaction is catalyz ...

2017

iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Vassily Hatzimanikatis, Ljubisa Miskovic, Stefano Andreozzi

Accurate determination of physiological states of cellular metabolism requires detailed information about metabolic fluxes, metabolite concentrations and distribution of enzyme states. Integration of fluxomics and metabolomics data, and thermodynamics-base ...

Academic Press Inc Elsevier Science2016

Identifying patterns in kinetic parameters that determine the impact of rate-limiting enzymes

Vassily Hatzimanikatis, Ljubisa Miskovic, Michaël Roger Germain Moret

Kinetic models are essential for studying complex behavior and properties of metabolism. However, a persistent hurdle for constructing these models is uncertainty in the kinetic properties of enzymes. Currently available methods for building kinetic models ...

2016

NRK1 controls nicotinamide mononucleotide and nicotinamide riboside metabolism in mammalian cells

Johan Auwerx, Carlos Canto Alvarez, Joanna Ratajczak

NAD(+) is a vital redox cofactor and a substrate required for activity of various enzyme families, including sirtuins and poly(ADP-ribose) polymerases. Supplementation with NAD(+) precursors, such as nicotinamide mononucleotide (NMN) or nicotinamide ribosi ...

Nature Publishing Group2016

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Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

In silico tracing of the fate of single carbon atoms in different physiological states of E. coli

Design of novel enzyme-catalyzed reactions linked to protein sequences for finding enzyme engineering targets

Computational methods and modeling of cellular function for the optimization of protein production and the study of cellular disease states

Generation and Analysis of Large-Scale Dynamic Non-Linear Models of Metabolism

Fusing Individual-based Models with Genome-scale Metabolic Networks - a Novel Approach for Quantifying Emergent Microbial Community Spatiotemporal Dynamics

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

One-Step Multigram-Scale Biomimetic Synthesis of Psiguadial B

iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Identifying patterns in kinetic parameters that determine the impact of rate-limiting enzymes

NRK1 controls nicotinamide mononucleotide and nicotinamide riboside metabolism in mammalian cells

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Chat with Graph Search

In silico tracing of the fate of single carbon atoms in different physiological states of E. coli

Computational methods and modeling of cellular function for the optimization of protein production and the study of cellular disease states

NRK1 controls nicotinamide mononucleotide and nicotinamide riboside metabolism in mammalian cells

One-Step Multigram-Scale Biomimetic Synthesis of Psiguadial B

iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Design of novel enzyme-catalyzed reactions linked to protein sequences for finding enzyme engineering targets

Generation and Analysis of Large-Scale Dynamic Non-Linear Models of Metabolism

Fusing Individual-based Models with Genome-scale Metabolic Networks - a Novel Approach for Quantifying Emergent Microbial Community Spatiotemporal Dynamics

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

Identifying patterns in kinetic parameters that determine the impact of rate-limiting enzymes