Publication
NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs
Publications associées (42)
Expanding computational biochemistry towards complex and non-natural compounds
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 ...
EPFL2023Computational tools and resources for designing new pathways to small molecules
Vassily Hatzimanikatis, Anastasia Sveshnikova
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 ...
CURRENT BIOLOGY LTD2022Supplementary datasets for "ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds"
Vassily Hatzimanikatis, Homa Mohammadi Peyhani, Anastasia Sveshnikova
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 ...
EPFL Infoscience2022Cluster-and-Conquer: When Randomness Meets Graph Locality
Anne-Marie Kermarrec, Olivier Ruas
K-Nearest-Neighbors (KNN) graphs are central to many emblematic data mining and machine-learning applications. Some of the most efficient KNN graph algorithms are incremental and local: they start from a random graph, which they incrementally improve by tr ...
IEEE COMPUTER SOC2021Phototransformation kinetics of cyanobacterial toxins and secondary metabolites in surface waters
Background Cyanobacteria and their toxins occur in high concentrations during the so-called bloom events in surface waters. To be able to assess the risks associated with cyanobacterial blooms, we need to understand the persistence and fate processes of th ...
SPRINGER2021Modeling, predicting and mining metabolism at atom-level resolution
Living organisms can catalyze many thousands of biochemical reactions that they use to convert energy and matter, which provides them with the essentials for life. The sum of these chemical reactions happening in an organism is called metabo-lism. Understa ...
EPFL2020Systematic model reduction captures the dynamics of extrinsic noise in biochemical subnetworks
We consider the general problem of describing the dynamics of subnetworks of larger biochemical reaction networks, e.g., protein interaction networks involving complex formation and dissociation reactions. We propose the use of model reduction strategies t ...
AMER INST PHYSICS2020Optimization methods and objective functions for analysis of metabolic network models
Computational studies of metabolism aim to systematically analyze the metabolic behaviour of biological systems in different conditions. Genome-scale metabolic network models (GEMs) capture the connection between elements of the network by applying stoichi ...
EPFL2020Local Tomography of Large Networks Under the Low-Observability Regime
Ali H. Sayed, Augusto José Rabelo Almeida Santos
This article studies the problem of reconstructing the topology of a network of interacting agents via observations of the state-evolution of the agents. We focus on the large-scale network setting with the additional constraint of partial observations, wh ...
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2020Extrapolating Paths with Graph Neural Networks
Andreas Loukas, Jean-Baptiste Francis Marie Juliette Cordonnier
We consider the problem of path inference: given a path prefix, i.e., a partially observed sequence of nodes in a graph, we want to predict which nodes are in the missing suffix. In particular, we focus on natural paths occurring as a by-product of the int ...
IJCAI, Inc.2019