Adaptation rules inducing synchronization of heterogeneous Kuramoto oscillator network with triadic couplings

A class of adaptation functions is found for which a synchronous oscillation mode exists in the network of phase oscillators with triadic couplings. It is shown that the destruction of the synchronous mode occurs differently for networks with pairwise couplings and with higher-order interactions. In the first case, a chimera state is realized. In the second case, the destruction of the synchronous state occurs more abruptly, and the chimera state is not formed. The patterns of formation of synchronization and desynchronization modes are determined

Shiny GATOM: Omics-based identification of regulated metabolic modules in atom transition networks

Multiple high-throughput omics techniques provide different angles on systematically quantifying and studying metabolic regulation of cellular processes. However, an unbiased analysis of such data and, in particular, integration of multiple types of data remains a challenge. Previously, for this purpose we developed GAM web-service for integrative metabolic network analysis. Here we describe an updated pipeline GATOM and the corresponding web-service Shiny GATOM, which takes as input transcriptional and/or metabolomic data and finds a metabolic subnetwork most regulated between the two conditions of interest. GATOM features a new metabolic network topology based on atom transition, which significantly improves interpretability of the analysis results. To address computational challenges arising with the new network topology, we introduce a new variant of the maximum weight connected subgraph problem and provide a corresponding exact solver. To make the used networks up-to-date we upgraded the KEGG-based network construction pipeline and developed one based on the Rhea database, which allows analysis of lipidomics data. Finally, we simplified local installation, providing R package mwcsr for solving relevant graph optimization problems and R package gatom, which implements the GATOM pipeline. The web-service is available at https://ctlab.itmo.ru/shiny/gatom and https://artyomovlab.wustl.edu/shiny/gatom