A comparison of mechanistic signaling pathway activity analysis methods

A Amadoz, MR Hidalgo, C Cubuk… - Briefings in …, 2019 - academic.oup.com
Understanding the aspects of cell functionality that account for disease mechanisms or drug
modes of action is a main challenge for precision medicine. Classical gene-based …

Babelomics 5.0: functional interpretation for new generations of genomic data

R Alonso, F Salavert, F Garcia-Garcia… - Nucleic acids …, 2015 - academic.oup.com
Babelomics has been running for more than one decade offering a user-friendly interface for
the functional analysis of gene expression and genomic data. Here we present its fifth …

High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes

MR Hidalgo, C Cubuk, A Amadoz, F Salavert… - …, 2016 - pmc.ncbi.nlm.nih.gov
Understanding the aspects of the cell functionality that account for disease or drug action
mechanisms is a main challenge for precision medicine. Here we propose a new method …

[HTML][HTML] Subpathway analysis of transcriptome profiles reveals new molecular mechanisms of acquired chemotherapy resistance in breast cancer

Y Huo, S Shao, E Liu, J Li, Z Tian, X Wu, S Zhang… - Cancers, 2022 - mdpi.com
Simple Summary The use of diverse omics platforms and small sample sizes in current
studies of cancer chemoresistance limits consensus regarding the molecular mechanisms …

Understanding disease mechanisms with models of signaling pathway activities

P Sebastian-Leon, E Vidal, P Minguez, A Conesa… - BMC systems …, 2014 - Springer
Background Understanding the aspects of the cell functionality that account for disease or
drug action mechanisms is one of the main challenges in the analysis of genomic data and …

Gene expression integration into pathway modules reveals a pan-cancer metabolic landscape

C Cubuk, MR Hidalgo, A Amadoz, MA Pujana… - Cancer …, 2018 - aacrjournals.org
Metabolic reprogramming plays an important role in cancer development and progression
and is a well-established hallmark of cancer. Despite its inherent complexity, cellular …

Using activation status of signaling pathways as mechanism-based biomarkers to predict drug sensitivity

A Amadoz, P Sebastian-Leon, E Vidal, F Salavert… - Scientific reports, 2015 - nature.com
Many complex traits, as drug response, are associated with changes in biological pathways
rather than being caused by single gene alterations. Here, a predictive framework is …

Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models

C Çubuk, MR Hidalgo, A Amadoz, K Rian… - NPJ systems biology …, 2019 - nature.com
In spite of the increasing availability of genomic and transcriptomic data, there is still a gap
between the detection of perturbations in gene expression and the understanding of their …

Using mechanistic models for the clinical interpretation of complex genomic variation

M Peña-Chilet, M Esteban-Medina, MM Falco, K Rian… - Scientific reports, 2019 - nature.com
The sustained generation of genomic data in the last decade has increased the knowledge
on the causal mutations of a large number of diseases, especially for highly penetrant …

Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models

F Salavert, MR Hidago, A Amadoz… - Nucleic acids …, 2016 - academic.oup.com
The discovery of actionable targets is crucial for targeted therapies and is also a constituent
part of the drug discovery process. The success of an intervention over a target depends …