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

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Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

Metabolic changes precede malignant histology. However, it remains unclear whether detectable characteristic metabolome exists in esophageal squamous cell carcinoma (ESCC) tissues and biofluids for early diagnosis. Here, we conduct NMR- and MS-based metabo ...

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

In my thesis, I present an investigation of the dissociation reactions of gas phase molecules on single crystal metal surfaces studied by a molecular beam in combination with Reflection Absorption Infrared Spectroscopy (RAIRS). Two gas/surface systems were ...

Assigning or proposing a catalysing enzyme given a chemical or biochemical reaction is of great interest to life sciences and chemistry alike. The exploration and design of metabolic pathways and the challenge of finding more sustainable enzyme-catalysed a ...

Hepatocytes are the main workers in the hepatic factory, managing metabolism of nutrients and xenobiotics, production and recycling of proteins, and glucose and lipid homeostasis. Division of labor between hepatocytes is critical to coordinate complex comp ...

Bromine radical (Br center dot) has been hypothesized to be a key intermediate of bromate formation during ozonation. Once formed, Br center dot further reacts with ozone to eventually form bromate. However, this reaction competes with the reaction of Br c ...

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 ...

AMP-activated Protein Kinase (AMPK) is a central regulator of energy homeostasis and a promising drug target for metabolic disorders. It exists as complexes of three subunits, a catalytic alpha, and two regulatory beta and gamma subunits. The regulation of ...

Disturbances in the brain's capacity to meet its energy demand increase the risk of synaptic loss, neurodegeneration, and cognitive decline. Nutritional and metabolic interventions that target metabolic pathways combined with diagnostics to identify defici ...

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 ...

Supplementary datasets accompanying the manuscript "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds" published in the Metabolic Engineering Journal (https://doi.org/10.1016/j.ymben.2022.03.013). In line w ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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

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

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

NMR and MS reveal characteristic metabolome atlas and optimize esophageal squamous cell carcinoma early detection

Modeling, analysis, and design of complex biological networks

Gas/Surface reactions probed by reflection absorption infrared spectroscopy

An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification

Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology

Reactivity of Bromine Radical with Dissolved Organic Matter Moieties and Monochloramine: Effect on Bromate Formation during Ozonation

Computational tools and resources for designing new pathways to small molecules

AMP-activated Protein Kinase (AMPK): New molecular insights and novel downstream targets

Nutritional metabolism and cerebral bioenergetics in Alzheimer's disease and related dementias

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

Supplementary datasets for "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds"

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

Dissecting the role of the mitochondrial carrier SLC25A47

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

Constraint-based metabolic control analysis for rational strain engineering

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

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

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