Publications associées à Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

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

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 ...

EPFL2024

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

David Atienza Alonso, Marina Zapater Sancho, Luis Maria Costero Valero, Darong Huang, Qunyou Liu

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 ...

2024

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

Evangelia Vagena

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 ...

EPFL2024

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

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 ...

EPFL2023

Entrepreneurial Opportunities and Threats in the Era of Grand Societal Challenges

Enrico Bergamini

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 ...

EPFL2023

Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology

Felix Naef, Tomaz Martini

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 ...

ANNUAL REVIEWS2023

Expanding computational biochemistry towards complex and non-natural compounds

Anastasia Sveshnikova

In the beginning was the metabolism. The biochemical processes that make life possible transformed the soup of chemicals into the life on Earth we know today. Since then, living organisms have evolved, and life on Earth has become more complex. Living orga ...

EPFL2023

Rebooting Virtual Memory with Midgard

Siddharth Gupta

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 ...

EPFL2023

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

Daniel Probst

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 ...

2023

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

Dolaana Khovalyg, Mohamad Rida

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 ...

2023