Finding Maximal Common Subgraphs via Time-Space Efficient Reverse Search

International audienceFor any two given graphs, we study the problem of finding isomorphisms that correspond to inclusion-maximal common induced subgraphs that are connected. While common (induced or not) subgraphs can be easily listed using some well known reduction and state-of-the-art algorithms, they are not guaranteed to be connected. To meet the connectivity requirement, we propose an algorithm that revisits the paradigm of reverse search and guarantees polynomial time per solution (delay) and linear space, on top of showing good practical performance

Towards the reconstruction of integrated genome-scale models of metabolism and gene expression

The reconstruction of integrated genome-scale models of metabolism and gene expression has been a challenge for a while now. In fact, various methods that allow integrating reconstructions of Transcriptional Regulatory Networks, gene expression data or both into Genome-Scale Metabolic Models have been proposed. Several of these methods are surveyed in this article, which allowed identifying their strengths and weaknesses concerning the reconstruction of integrated models for multiple prokaryotic organisms. Additionally, the main resources of regulatory information were also surveyed, as the existence of novel sources of regulatory information and gene expression data may contribute for the improvement of methodologies referred herein.This study was supported by the Portuguese Foundation for Science andTechnology (FCT) under the scope of the strategic funding of UID/BIO/04469/2019 unit andBioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European RegionalDevelopment Fund under the scope of Norte2020-Programa Operacional Regional do Norte. Fernando Cruz holds a doctoral fellowship (SFRH/BD/139198/2018) funded by the FCT. The authors thank project SHIKIFACTORY100 - Modular cell factories for the production of 100 compounds from the shikimate pathway (814408) funded by the European Commission.info:eu-repo/semantics/publishedVersio

Computational Methods For Predicting Protein-Protein Interactions

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