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Models and Algorithms in Biological Network Evolution with Modularity

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Towards an Understanding of Hydraulic Sensitivity: Graph Theory Contributions to Water Distribution Analysis

Jérôme Chenal

Water distribution systems (WDSs) are complex networks with numerous interconnected junctions and pipes. The robustness and reliability of these systems are critically dependent on their network structure, necessitating detailed analysis for proactive leak ...

Basel2024

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

Opinion Formation over Adaptive Networks

Virginia Bordignon

An adaptive network consists of multiple communicating agents, equipped with sensing and learning abilities that allow them to extract meaningful information from measurements. The objective of the network is to solve a global inference problem in a decent ...

EPFL2022

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

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We analyze about 200 naturally occurring networks with distinct dynamical origins to formally test whether the commonly assumed hypothesis of an underlying scale-free structure is generally viable. This has recently been questioned on the basis of statisti ...

NATL ACAD SCIENCES2021

Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of conserved network mot ...

IEEE COMPUTER SOC2020

Learning Neural Connectivity from Firing Activity: Scalable Algorithms with Provable Guarantees

Martin Vetterli, Amin Karbasi, Amir Hesam Salavati

The connectivity of a neuronal network has a major effect on its functionality and role. It is generally believed that the complex network structure of the brain provides a physiological basis for information processing. Therefore, identifying the network’ ...

Springer New York LLC2018

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Modeling the evolution of biological networks is a major challenge. Biological networks are usually represented as graphs; evolutionary events not only include addition and removal of vertices and edges but also duplication of vertices and their associated ...

IEEE Press2017

Alignment and Assembly

Lyudmila Yartseva

Over recent years, many large network datasets become available, giving rise to novel and valuable applications of data mining and machine learning techniques. These datasets include social networks, the structure of the Internet, and protein-interaction n ...

EPFL2017

Unlocking the full potential of kinetic metabolic models through characterization and reduction of uncertainty

Vassily Hatzimanikatis, Ljubisa Miskovic

Kinetic models are the most promising tool for comprehending the complex dynamic behavior of living cells. The primary goal of kinetic models is to capture the properties of the metabolic networks as a whole, and we need large-scale models for dependable i ...

2017