Published in BioRxiv, 2025
This study explores the use of open-source large language models (LLMs) for extracting molecular interaction data, specifically protein-protein and bene regulatory relations from scientific literature. The approach shows promising accuracy in relation extraction and offers a toolset for automating biological network curation.
Published in Database, 2024
Here we present a time-course multi-omics dataset from a mouse model of heart failure induced by transverse aortic constriction (TAC), analyzed using transcriptomics and proteomics to uncover molecular mechanisms of cardiac dysfunction. The data are integrated into TACOMA, a web application enabling interactive exploration of gene and protein expression, alternative splicing, and biological pathway enrichment across disease progression.
Published in RNA, 2023
Here we show how Adaptive Sampling for direct RNA sequencing with Oxford-Nanopore technology is feasible considering the specific technical and biological challenges.
Published in Bioinformatics, 2023
LINDA (Linear Integer programming for Network reconstruction using transcriptomics and Differential splicing data Analysis) is a method that integrates resources of protein–protein and domain–domain interactions, transcription factor targets, and differential splicing/transcript analysis to infer splicing-dependent effects on cellular pathways and regulatory networks.
Published in Journal of Proteome Research, 2021
PHONEMeS is a method that uses high-content shotgun phosphoproteomic data to build logical network models of signal perturbation flow through the implementation of an efficient Integer Linear Programming (ILP) formulation.
Published in Molecular Systems Biology, 2021
COSMOS combines extensive prior knowledge of signaling, metabolic, and gene regulatory networks with computational methods to estimate activities of transcription factors and kinases as well as network‐level causal reasoning.
Published in Bioinformatics, 2020
CellNOpt is a collection of Bioconductor R packages for building logic models from perturbation data and prior knowledge of signalling networks.
Published in npj Systems Biology and Applications, 2019
CARNIVAL - a causal network contextualization tool which derives network architectures from gene expression footprints.
Published in IFAC-PapersOnLine, 2019
This paper describes Dynamic-Feeder as a method which combines data-driven inference methods with general literature-based knowledge of proteins interaction networks.
Published in Molecular Systems Biology, 2019
A comprehensive logic model of endothelin signalling was constructed using phosphoproteomics data from melanoma cell lines, highlighting the role of specific kinases in Endothelin (EDN)-induced cell migration and supporting the strategic selection of kinase inhibitors for combined treatments with EDN receptor antagonists.