Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

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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 ...

The increasing demand for computing power and the emergence of heterogeneous computing architectures have driven the exploration of innovative techniques to address current limitations in both the compute and memory subsystems. One such solution is the use ...

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 ...

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 ...

We live in an era defined by attempts to grapple with an ever-expanding array of grand societal challenges (GCs). These challenges comprise transformational social and environmental issues, such as environmental degradation and global pandemics, and the cr ...

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 ...

Virtual Memory (VM) is a critical programming abstraction that is widely used in various modern computing platforms. With the rise of datacenter computing and birth of planet-scale online services, the semantic and capacity requirements from memory have ev ...

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 ...

Carbon dioxide generated by the human body and exhaled (VCO2) is commonly used for ventilation controls, while the metabolic rate (i.e., energy expenditure EE) is an important parameter defining human thermal comfort in buildings. These two parameters are ...

Glucose sensing in pancreatic D-cells depends on oxidative phosphorylation and mitochondria-derived signals that promote insulin secretion. Using mass spectrometry-based phosphoproteo-mics to search for downstream effectors of glucose-dependent signal tran ...

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 ...

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 ...

Objective The study was undertaken to show the magnitude of interindividual differences in energy expenditure (i.e., heat production) under normal living conditions with the aim of providing physiological evidence to support the advancement of a personaliz ...

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 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 ...

Approximately 2 billion people worldwide and a significant part of the domestic livestock are infected with soil-transmitted helminths, of which many establish chronic infections causing substantial eco-nomic and welfare burdens. Beside intensive research ...

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 ...

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 ...

Overweight and obesity are increasingly common public health issues worldwide, leading to a wide range of diseases from metabolic syndrome to steatohepatitis and cardiovascular diseases. While the increase in the prevalence of obesity is partly attributabl ...

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

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

Intermediate Address Space: virtual memory optimization of heterogeneous architectures for cache-resident workloads

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

Modeling, analysis, and design of complex biological networks

Entrepreneurial Opportunities and Threats in the Era of Grand Societal Challenges

Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology

Rebooting Virtual Memory with Midgard

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

Inter- and intra-individual variability in CO2 production and metabolic rate

SLC25A46 promotes mitochondrial fission and mediates resistance to lipotoxic stress in INS-1E insulin-secreting cells

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

Computational tools and resources for designing new pathways to small molecules

Interindividual variability of human thermoregulation: Toward personalized ergonomics of the indoor thermal environment

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

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

Dissecting the role of the mitochondrial carrier SLC25A47

Acetate, a metabolic product of Heligmosomoides polygyrus, facilitates intestinal epithelial barrier breakdown in a FFAR2-dependent manner

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

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

Genetic, metabolic, and molecular insights into the diverse outcomes of diet-induced obesity in mouse