The paper introduces METRIN-KG, a knowledge graph integrating plant metabolites, traits, and biotic interactions to facilitate biodiversity data analysis.

GigaScience · Jan 1, 2026Peer-reviewedBioinformatics

Exploring Disease Model Mouse Using Knowledge Graphs: Combining Gene Expression, Orthology, and Disease Datasets

Tatsuya Kushida, Tarcisio Mendes de Farias, Ana Claudia Sima, Christophe Dessimoz, Hirokazu Chiba, Frederic Bastian, Hiroshi Masuya

The paper integrates multiple biological datasets to explore disease-related genes and bioresources using SPARQL queries, identifying relevant genes and anatomical parts for Alzheimer's and melanoma research.

bioRxiv · Aug 30, 2023 · PreprintBioinformatics

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

Frederic Bastian, Julien Roux, Anne Niknejad, Aurélie Comte, Sara S Fonseca Costa, Tarcisio Mendes de Farias, Sébastien Moretti, Gilles Parmentier, Valentine Rech de Laval, Marta Rosikiewicz, Julien Wollbrett, Amina Echchiki, Angélique Escoriza, Walid H. Gharib, Mar Gonzàlez-Porta, , Marc Robinson‐Rechavi

Bgee provides an integrated expression atlas and comparative transcriptomics resource for multiple animal species using curated healthy wild-type expression data.

Nucleic Acids Research · Sep 15, 2020Peer-reviewedBioinformatics

Enabling Semantic Queries Across Federated Bioinformatics Databases

Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria O. Anisimova, Manuel Gil, Heinz Stockinger C, Kurt Stockinger, Marc Robinson‐Rechavi, Christophe Dessimoz

The paper introduces a semantic model and federated approach to integrate heterogeneous biological databases, enabling joint queries across gene expression, orthology, and protein data sources.

Database · Jan 1, 2019Peer-reviewedBioinformatics