Publications associées à Metabolic engineering

Computational tools and resources for designing new pathways to small molecules

Vassily Hatzimanikatis, Anastasia Sveshnikova

The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...

CURRENT BIOLOGY LTD2022

An optimized high throughput platform, from genetic transformation to fermentation, to screen for secreted laccases in Aspergillus niger

Laure Marie Colette Leynaud-Kieffer Curran

Many challenges are faced in the conversion of biomass into advanced biofuels, one of which is finding the correct organism for the job. The filamentous fungus Aspergillus niger has been chosen as a biocatalyst for cellulose, hemicellulose, and lignin degr ...

EPFL2022

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

Vassily Hatzimanikatis, Jasmin Maria Hafner, Anastasia Sveshnikova, Victor Luc Etienne Viterbo

Metabolic "dark matter" describes currently unknown metabolic processes, which form a blind spot in our general understanding of metabolism and slow down the development of biosynthetic cell factories and naturally derived pharmaceuticals. Mapping the dark ...

NATURE PORTFOLIO2022

Constraint-based metabolic control analysis for rational strain engineering

Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Tuure Eelis Hameri, Sofia Tsouka

The advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering ...

2021

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

Vassily Hatzimanikatis, Jasmin Maria Hafner

Motivation: Finding biosynthetic pathways is essential for metabolic engineering of organisms to produce chemicals, biodegradation prediction of pollutants and drugs, and for the elucidation of bioproduction pathways of secondary metabolites. A key step in ...

OXFORD UNIV PRESS2021

Modelling the Intracellular Environment under Uncertainty, from Post-translational Modification to Metabolic Networks

Robin Alexander Denhardt-Eriksson

Modelling and analysis of biological systems is crucial in order to quantitatively explain and predict their behaviour. The importance of modelling in systems biology becomes even more evident when tackling complex, large systems. Approaches that rely on ...

EPFL2021

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives

Vassily Hatzimanikatis, Jasmin Maria Hafner

Plant natural products (PNPs) and their derivatives are important but underexplored sources of pharmaceutical molecules. To access this untapped potential, the reconstitution of heterologous PNP biosynthesis pathways in engineered microbes provides a valua ...

NATURE RESEARCH2021

Mapping and Analysis of the Complexity of Lipid Metabolism for Applications in Health and Sustainability

Vassily Hatzimanikatis, Sofia Tsouka

Metabolism is a network of biotransformations that sustain life in cells. Over the past decades, metabolism has been studied in multiple contexts, ranging from medicine to industrial manufacturing. In particular, lipid metabolism has been linked to various ...

EPFL2020

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Metabolic engineering

Modeling, analysis, and design of complex biological networks

Expanding computational biochemistry towards complex and non-natural compounds

Computational tools and resources for designing new pathways to small molecules

An optimized high throughput platform, from genetic transformation to fermentation, to screen for secreted laccases in Aspergillus niger

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

Constraint-based metabolic control analysis for rational strain engineering

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

Modelling the Intracellular Environment under Uncertainty, from Post-translational Modification to Metabolic Networks

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives

Mapping and Analysis of the Complexity of Lipid Metabolism for Applications in Health and Sustainability

Graph Chatbot

Chattez avec Graph Search

Modeling, analysis, and design of complex biological networks

An optimized high throughput platform, from genetic transformation to fermentation, to screen for secreted laccases in Aspergillus niger

Computational tools and resources for designing new pathways to small molecules

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives

Constraint-based metabolic control analysis for rational strain engineering

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

Expanding computational biochemistry towards complex and non-natural compounds

Modelling the Intracellular Environment under Uncertainty, from Post-translational Modification to Metabolic Networks

Mapping and Analysis of the Complexity of Lipid Metabolism for Applications in Health and Sustainability