DREAMS of metabolism

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Related publications (30)

Sensitivity and spectral control of network lasers

Recently, random lasing in complex networks has shown efficient lasing over more than 50 localised modes, promoted by multiple scattering over the underlying graph. If controlled, these network lasers can lead to fast-switching multifunctional light source ...

Nature Portfolio2022

Dissecting the role of the mitochondrial carrier SLC25A47

Nadia Bresciani

Transporters of the SLC25 mitochondrial carrier superfamily bridge cytoplasmic and mitochondrial metabolism by channeling metabolites across mitochondrial membranes and are pivotal for metabolic homeostasis. Despite their physiological relevance as gatekee ...

EPFL2022

Computational design of novel protein–protein interactions – An overview on methodological approaches and applications

Anthony Marchand, Bruno Emanuel Ferreira De Sousa Correia, Alexandra Krina Van Hall-Beauvais

Protein–protein interactions (PPIs) govern numerous cellular functions in terms of signaling, transport, defense and many others. Designing novel PPIs poses a fundamental challenge to our understanding of molecular interactions. The capability to robustly ...

2022

Primary data for EPFL thesis "Metabolic regulation of cytokinesis in Schizosaccharomyces pombe"

Özge Uysal Özdemir

All cells need to be able to sense their environment, and adapt their metabolism, growth and cell division appropriately. In this study, I examined the response of Schizosaccharomyces pombe to a change in the carbon source and how that affects cytokinesis. ...

EPFL Infoscience2022

Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression

Ming Yang, Vassily Hatzimanikatis, Maria Masid Barcon

Metabolic reprogramming is critical for tumor initiation and progression. However, the exact impact of specific metabolic changes on cancer progression is poorly understood. Here, we integrate multimodal analyses of primary and metastatic clonally-related ...

Nature Portfolio2022

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

Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

Vassily Hatzimanikatis, Pierre Guy Rémy Salvy

Diauxie, or the sequential consumption of carbohydrates in bacteria such as Escherichia coli, has been hypothesized to be an evolutionary strategy which allows the organism to maximize its instantaneous specific growth-giving the bacterium a competitive ad ...

National Academy of Sciences2021

The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli

Vassily Hatzimanikatis, Georgios Fengos, Tuure Eelis Hameri

Background Significant efforts have been made in building large-scale kinetic models of cellular metabolism in the past two decades. However, most kinetic models published to date, remain focused around central carbon pathways or are built around ad hoc re ...

BMC2021

Constraint-based metabolic control analysis for rational strain engineering

Ljubisa Miskovic, Vassily Hatzimanikatis, 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

The influence of the crowding assumptions in biofilm simulations

Vassily Hatzimanikatis, Liliana Angeles Martinez

Author summary In nature, many organisms grow in crowded biofilms that protect against stressful conditions, making their control/eradication a challenge. Modeling these microbial systems is a valuable tool for studying the interactions among cells and exp ...

2021

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